issue-113 fixing if condition on flexibility & reference test cases

change umlauts to normal O's

Dockerfile

@@ -1,24 +0,0 @@
-FROM centos:7
-
-#RUN yum -y install epel-release && yum -y update && yum -y install gcc gcc-c++ make netcdf-devel; yum clean all
-RUN yum -y install gcc gcc-c++ make netcdf-devel; yum clean all
-
-# all of this mess is essentially to have a minimalistic build at the end
-COPY makefile /opt/fpocket/
-COPY src /opt/fpocket/src
-COPY man /opt/fpocket/man
-COPY headers /opt/fpocket/headers
-COPY obj /opt/fpocket/obj
-COPY scripts /opt/fpocket/scripts
-COPY bin /opt/fpocket/bin
-COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
-COPY plugins/include /opt/fpocket/plugins/include
-COPY plugins/noarch /opt/fpocket/plugins/noarch
-
-WORKDIR /opt/fpocket
-
-RUN make; make install; make clean
-
-WORKDIR /WORKDIR
-
-CMD ["fpocket"]

doc/GETTINGSTARTED.md

@@ -452,10 +452,11 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
     -b (none): (NOT USED BY DEFAULT) This option allows the user to choose a discrete algorithm  to calculate  the  volume of each pocket instead of the Monte Carlo method. This algorithm puts each pocket into a grid of dimension (1/N*X  ;  1/N*Y  ;  1/N*Z),  N being the value given using this option, and X, Y and Z being the box dimensions,  determined using coordinates of vertices. Then, a triple iteration on each dimensions is used to estimate the volume, checking if each points  given  by the iteration is in one of the pocket’s vertices. This parameter defines the grid discretization. If this parameter is used, this algorithm will be used instead of the Monte Carlo algorithm. 
     Warning: Although this algorithm could be more accurate, a high value might dramatically slow down the program, as this algorithm has a maximum complexity of N*N*N*nb_vertices, and a minimum of N*N*N !!!
 
-
     -d (none): Option allowing you to output pockets and properties in a condensed format. This will put to the stdout pocket properties in a tab separated string and write pocket files in a subfolder
     
     -r string: (None) This parameter allows you to run fpocket in a restricted mode. Let's suppose you have a very shallow or large pocket with a ligand inside and the automatic pocket prediction always splits up you pocket or you have only a part of the pocket found. Specifying your ligand residue with -r allows you to detect and characterize you ligand binding site explicitly. For instance for `1UYD.pdb` you can specify `-r 1224:PU8:A` (residue number of the ligand: residue name of the ligand: chain of the ligand)
+
+    -P string: (None) Binding site delimited by the user through the input. You can inidcate which amino-acids are part of the binding site you'd like to "identify" and calculate descriptors for. fpocket will run its usual alpha-sphere detection and clustering will be guided to collect all alpha spheres in contact with residues of interest. You should enter a string of residues with residue numbers, insertion codes & chain codes: 'residuenumber1:insertioncode1:chaincode1.residuenumber2:insertioncode2:chaincode2.residuenumber3:insertioncode3:chaincode3'. Insertion codes can be empty. `-P 107::A.138::A.51::A.98::A.55::A.93::A` for instance for part of the HSP90 binding site of 4cwr. NB: If you use an mmcif file as input, you need to use the automatically assigned residue number instead of author defined number for this to work.
     
     -y string: (filename) EXPERIMENTAL: here you can specify a topology filename in the Amber prmtop format. This can then be used by fpocket & mdpocket to calculate energy grids for your pockets. NB: you have to specify the -x flag to run energy calculations
     

doc/INSTALLATION.md

@@ -148,6 +148,5 @@ If you manage to build for other architectures and it works, I'd be happy to acc
 
 ## Read next
 
-* [Getting Started](GETTINGSTARTED.md)
+* [Getting Started & Advanced Features](GETTINGSTARTED.md)
 
-* [Advanced Features](ADVANCED.md)

doc/INTRODUCTION.md

@@ -40,6 +40,4 @@ We are happy about positive, negative, in any way constructive feedback.
 
 * [Installation](INSTALLATION.md)
 
-* [Getting Started](GETTINGSTARTED.md)
-
-* [Advanced Features](ADVANCED.md)
+* [Getting Started](GETTINGSTARTED.md)

headers/fparams.h

@@ -30,84 +30,88 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* Options of the pocket finder program */
 /* standard parameters */
 
+#define M_MIN_ASHAPE_SIZE_DEFAULT 3.4 /**< Use min alpha sphere radius of : 3.0 */ /*3.2, 2.6, */
 
-#define M_MIN_ASHAPE_SIZE_DEFAULT 3.4/**< Use min alpha sphere radius of : 3.0 */ /*3.2, 2.6, */
+#define M_MAX_ASHAPE_SIZE_DEFAULT 6.2 /**< Use max alpha sphere radius of : 6.0 */ /*7.0, 7.4, */
 
-#define M_MAX_ASHAPE_SIZE_DEFAULT 6.2/**< Use max alpha sphere radius of : 6.0 */ /*7.0, 7.4, */
+#define M_CLUST_MAX_DIST 2.4 /**< Use first connection distance (see report) : 2.0 */ /*1.8, 11.2, */
 
-#define M_CLUST_MAX_DIST 2.4/**< Use first connection distance (see report) : 2.0 */ /*1.8, 11.2, */
+#define M_REFINE_DIST 4.5 /**< use second connection distance (see report) : 4.5 */
 
-#define M_REFINE_DIST 4.5/**< use second connection distance (see report) : 4.5 */
+#define M_REFINE_MIN_PROP_APOL_AS 0.0 /**< At least a proportion of  M_REFINE_MIN_NAPOL_AS apolar alpha spheres in the pocket 0.0 */
 
-#define M_REFINE_MIN_PROP_APOL_AS 0.0/**< At least a proportion of  M_REFINE_MIN_NAPOL_AS apolar alpha spheres in the pocket 0.0 */
+#define M_MC_ITER 300 /**< Number of iterations for the Monte Carlo volume calculation 3000 */
 
-#define M_MC_ITER 300/**< Number of iterations for the Monte Carlo volume calculation 3000 */
+#define M_BASIC_VOL_DIVISION -1 /**< Precision for "exact" volume integration, set to -1 if not used -1 */
 
-#define M_BASIC_VOL_DIVISION -1/**< Precision for "exact" volume integration, set to -1 if not used -1 */
+#define M_MIN_POCK_NB_ASPH 15 /**< Minimum number of alpha spheres for a pocket to be kept */
 
-#define M_MIN_POCK_NB_ASPH 15/**< Minimum number of alpha spheres for a pocket to be kept */
-
-#define M_MIN_APOL_NEIGH_DEFAULT 3/**< Minimum number of atoms having a low electronegativity in order to declare an alpha sphere to be apolar 3 */
+#define M_MIN_APOL_NEIGH_DEFAULT 3 /**< Minimum number of atoms having a low electronegativity in order to declare an alpha sphere to be apolar 3 */
 
 #define M_DISTANCE_MEASURE 'e' /**< By default use euclidean distance measure for clustering*/
 
 #define M_CLUSTERING_METHOD 's' /**< Clustering method to be used for alpha sphere clustering*/ /*s*/
 
-#define M_DB_RUN 0  /**< default value for running fpocket for populating a database, 0 default*/
+#define M_DB_RUN 0 /**< default value for running fpocket for populating a database, 0 default*/
 
-#define M_MAX_CHAINS_DELETE 20 
+#define M_MAX_CHAINS_DELETE 20
 
 #define M_MIN_AS_DENSITY 0.7
 
-#define M_PAR_PDB_FILE 'f'          /**< flag to give a single pdb input file*/
-#define M_PAR_LONG_PDB_FILE "file"          /**< flag to give a single pdb input file*/
+#define M_MIN_N_EXPLICIT_POCKET 4 /**default value for minimum number of atoms part of the explicit pocket for an alpha sphere (between 0 and 4)*/
 
-#define M_PAR_PDB_LIST 'F'          /**< flag to give a txt file containing paths to multiple pdb files*/
-#define M_PAR_LONG_PDB_LIST "fileList"          /**< flag to give a txt file containing paths to multiple pdb files*/
+#define M_PAR_PDB_FILE 'f'		   /**< flag to give a single pdb input file*/
+#define M_PAR_LONG_PDB_FILE "file" /**< flag to give a single pdb input file*/
 
-#define M_PAR_MAX_ASHAPE_SIZE 'M'   /**< flag for the maximum alpha sphere size*/
-#define M_PAR_LONG_MAX_ASHAPE_SIZE "max_alpha_size"   /**< flag for the maximum alpha sphere size*/
+#define M_PAR_PDB_LIST 'F'			   /**< flag to give a txt file containing paths to multiple pdb files*/
+#define M_PAR_LONG_PDB_LIST "fileList" /**< flag to give a txt file containing paths to multiple pdb files*/
 
-#define M_PAR_MIN_ASHAPE_SIZE 'm'   /**< flag for the minimum alpha sphere size*/
-#define M_PAR_LONG_MIN_ASHAPE_SIZE "min_alpha_size"   /**< flag for the minimum alpha sphere size*/
+#define M_PAR_MAX_ASHAPE_SIZE 'M'					/**< flag for the maximum alpha sphere size*/
+#define M_PAR_LONG_MAX_ASHAPE_SIZE "max_alpha_size" /**< flag for the maximum alpha sphere size*/
 
-#define M_PAR_MIN_APOL_NEIGH 'A'    /**< flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar*/
-#define M_PAR_LONG_MIN_APOL_NEIGH "number_apol_asph_pocket"    /**< flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar*/
+#define M_PAR_MIN_ASHAPE_SIZE 'm'					/**< flag for the minimum alpha sphere size*/
+#define M_PAR_LONG_MIN_ASHAPE_SIZE "min_alpha_size" /**< flag for the minimum alpha sphere size*/
 
-#define M_PAR_CLUST_MAX_DIST 'D'    /**< flag for clustering distance*/
-#define M_PAR_LONG_CLUST_MAX_DIST "clustering_distance"    /**< flag for clustering distance*/
+#define M_PAR_MIN_APOL_NEIGH 'A'							/**< flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar*/
+#define M_PAR_LONG_MIN_APOL_NEIGH "number_apol_asph_pocket" /**< flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar*/
 
-#define M_PAR_MC_ITER 'v'           /**< flag for how many iterations for the monte carlo volume calculation algorithm*/
-#define M_PAR_LONG_MC_ITER "iterations_volume_mc"           /**< flag for how many iterations for the monte carlo volume calculation algorithm*/
+#define M_PAR_CLUST_MAX_DIST 'D'						/**< flag for clustering distance*/
+#define M_PAR_LONG_CLUST_MAX_DIST "clustering_distance" /**< flag for clustering distance*/
 
-#define M_PAR_BASIC_VOL_DIVISION 'b'/**< flag for the space approximation of the MC*/
-#define M_PAR_MIN_POCK_NB_ASPH 'i'  /**< flag for the min number of alpha spheres in the pocket*/
-#define M_PAR_LONG_MIN_POCK_NB_ASPH "min_spheres_per_pocket"  /**< flag for the min number of alpha spheres in the pocket*/
+#define M_PAR_MC_ITER 'v'						  /**< flag for how many iterations for the monte carlo volume calculation algorithm*/
+#define M_PAR_LONG_MC_ITER "iterations_volume_mc" /**< flag for how many iterations for the monte carlo volume calculation algorithm*/
 
-#define M_PAR_REFINE_MIN_NAPOL_AS 'p'/**< flag for minimum proportion of apolar alpha spheres*/
-#define M_PAR_LONG_REFINE_MIN_NAPOL_AS "ratio_apol_spheres_pocket"/**< flag for minimum proportion of apolar alpha spheres*/
+#define M_PAR_BASIC_VOL_DIVISION 'b'						 /**< flag for the space approximation of the MC*/
+#define M_PAR_MIN_POCK_NB_ASPH 'i'							 /**< flag for the min number of alpha spheres in the pocket*/
+#define M_PAR_LONG_MIN_POCK_NB_ASPH "min_spheres_per_pocket" /**< flag for the min number of alpha spheres in the pocket*/
 
-#define M_PAR_DB_RUN 'd'            /**<flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs*/
-#define M_PAR_LONG_DB_RUN "pocket_descr_stdout"            /**<flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs*/
+#define M_PAR_REFINE_MIN_NAPOL_AS 'p'							   /**< flag for minimum proportion of apolar alpha spheres*/
+#define M_PAR_LONG_REFINE_MIN_NAPOL_AS "ratio_apol_spheres_pocket" /**< flag for minimum proportion of apolar alpha spheres*/
 
-#define M_PAR_CLUSTERING_METHOD 'C'            /**<flag for specifying the clustering method to use for alpha sphere clustering*/
-#define M_PAR_LONG_CLUSTERING_METHOD "clustering_method"            /**<flag for specifying the clustering method to use for alpha sphere clustering*/
+#define M_PAR_DB_RUN 'd'						/**<flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs*/
+#define M_PAR_LONG_DB_RUN "pocket_descr_stdout" /**<flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs*/
 
-#define M_PAR_DISTANCE_MEASURE 'e' /**<flag for specifying the distance measure*/
+#define M_PAR_CLUSTERING_METHOD 'C'						 /**<flag for specifying the clustering method to use for alpha sphere clustering*/
+#define M_PAR_LONG_CLUSTERING_METHOD "clustering_method" /**<flag for specifying the clustering method to use for alpha sphere clustering*/
+
+#define M_PAR_DISTANCE_MEASURE 'e'						 /**<flag for specifying the distance measure*/
 #define M_PAR_LONG_DISTANCE_MEASURE "clustering_measure" /**<flag for specifying the distance measure*/
 
-#define M_PAR_GRID_CALCULATION 'x' /**<flag for specifying the distance measure*/
+#define M_PAR_GRID_CALCULATION 'x'								  /**<flag for specifying the distance measure*/
 #define M_PAR_LONG_GRID_CALCULATION "calculate_interaction_grids" /**<flag for specifying the distance measure*/
 
-#define M_PAR_TOPOLOGY 'y'         /**<flag for specifying a molecular topology suitable for FF calculations*/
+#define M_PAR_TOPOLOGY 'y'					/**<flag for specifying a molecular topology suitable for FF calculations*/
 #define M_PAR_LONG_TOPOLOGY "topology_file" /**<flag for specifying a molecular topology suitable for FF calculations*/
 
-#define M_PAR_MODEL_FLAG 'l'         /**<flag for analyzing a specific model in multimodel structures*/
+#define M_PAR_MODEL_FLAG 'l'				 /**<flag for analyzing a specific model in multimodel structures*/
 #define M_PAR_MODEL_FLAG_LONG "model_number" /**<flag for anamyzing a specific model in multimodel structures*/
 
 #define M_PAR_CUSTOM_LIGAND 'r' /**flag, to define detection of explicit pockets around the specified ligand*/
 #define M_PAR_CUSTOM_LIGAND_LONG "custom_ligand"
 
+#define M_PAR_CUSTOM_POCKET 'P' /** flag to define a specific location to calculate the binding site on*/
+#define M_PAR_CUSTOM_POCKET_LONG "custom_pocket"
+
 #define M_PAR_DROP_CHAINS 'c' /**flag, to define which chain are dropped before the pocket detection*/
 #define M_PAR_DROP_CHAINS_LONG "drop_chains"
 
@@ -120,8 +124,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_WRITE_MODE 'w' /**flag, to define which chains are defined as a ligand*/
 #define M_PAR_WRITE_MODE_LONG "write_mode"
 
-
-
+#define M_PAR_MIN_N_EXPLICIT_POCKET 'u'
+#define M_PAR_MIN_N_EXPLICIT_POCKET_LONG "min_n_explicit_pocket"
 
 #define M_FP_USAGE "\n\
 ***** USAGE (fpocket) *****\n\
@@ -164,78 +168,82 @@ Pocket finding on a pdb - list of pdb - file(s):             \n\
 \t              c : centroid linkage clustering\n\
 \nSee the manual (man fpocket), or the full documentation for\n\
 more information.\n\
-***************************\n",M_PAR_PDB_FILE,M_PAR_LONG_PDB_FILE,M_PAR_PDB_LIST,M_PAR_LONG_PDB_LIST /**< the usage print content*/
+***************************\n", \
+				   M_PAR_PDB_FILE, M_PAR_LONG_PDB_FILE, M_PAR_PDB_LIST, M_PAR_LONG_PDB_LIST /**< the usage print content*/
 
 /* --------------------------- PUBLIC STRUCTURES ---------------------------- */
 /**
 	Structure containing all necessary parameters that can be changed by the user.
-	This structure is commun to both programs (validation and pocket finding), 
+	This structure is commun to both programs (validation and pocket finding),
 	even if the pocked finding programm doesn't need some parameters.
 */
 typedef struct s_fparams
 {
-	char pdb_path[M_MAX_PDB_NAME_LEN] ;	/**< The pdb file */
-        char topology_path[M_MAX_PDB_NAME_LEN]; /**< a putative topology file*/
-        char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
-	char **pdb_lst ;
-        char xlig_chain_code[3];
-        char xlig_resname[3];
-        int xlig_resnumber;
-        char distance_measure;
-        char clustering_method;
-	int npdb ;      /**< number of pdb files*/
-        short fpocket_running;
-        int flag_do_asa_and_volume_calculations; /**<if 1, asa and volume calculations are performed(slower), if 0, not*/
-        int db_run;                 /**< flag for running fpocket for db population*/
-        int model_number;           /**<number of model to be analyzed>*/
-        unsigned short flag_do_grid_calculations; /**< if 1 do grid calculations and output these*/
-	int min_apol_neigh,		 /**< Min number of apolar neighbours for an a-sphere
-								to be an apolar a-sphere */
-		nb_mcv_iter,		 /**< Number of iteration for the Monte Carlo volume
-								calculation */
-		basic_volume_div,	 /**< Box division factor for basic volume calculation */
-		min_pock_nb_asph; 	 /**< Minimump number of alpha spheres per pocket */
-                
+	char pdb_path[M_MAX_PDB_NAME_LEN];		/**< The pdb file */
+	char topology_path[M_MAX_PDB_NAME_LEN]; /**< a putative topology file*/
+	char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
+	char custom_pocket_arg[M_MAX_CUSTOM_POCKET_LEN];
+	char **pdb_lst;
+	char xlig_chain_code[3];
+	char xlig_resname[3];
+	int xlig_resnumber;
+	int xpocket_n; /**number of residues defining the pocket to consider*/
+	char *xpocket_chain_code;
+	char *xpocket_insertion_code;
+	unsigned short *xpocket_residue_number;
+	char distance_measure;
+	char clustering_method;
+	int min_n_explicit_pocket_atoms; /**Minimum numer of atoms in contact with an alpha sphere part of the explicitly defined pocket in order to be considered as valid*/
+	int npdb;						 /**< number of pdb files*/
+	short fpocket_running;
+	int flag_do_asa_and_volume_calculations;  /**<if 1, asa and volume calculations are performed(slower), if 0, not*/
+	int db_run;								  /**< flag for running fpocket for db population*/
+	int model_number;						  /**<number of model to be analyzed>*/
+	unsigned short flag_do_grid_calculations; /**< if 1 do grid calculations and output these*/
+	int min_apol_neigh,						  /**< Min number of apolar neighbours for an a-sphere
+												 to be an apolar a-sphere */
+		nb_mcv_iter,						  /**< Number of iteration for the Monte Carlo volume
+												 calculation */
+		basic_volume_div,					  /**< Box division factor for basic volume calculation */
+		min_pock_nb_asph;					  /**< Minimump number of alpha spheres per pocket */
 
-	float clust_max_dist,					/**< First clustering distance criteria */
-		  refine_min_apolar_asphere_prop,	/**< Min proportion of apolar alpha
-											spheres for each pocket */
+	float clust_max_dist,				/**< First clustering distance criteria */
+		refine_min_apolar_asphere_prop, /**< Min proportion of apolar alpha
+										spheres for each pocket */
 
-		  asph_min_size,	 	/**< Minimum size of alpha spheres to keep */
-                min_as_density,                 /**<Minimum alpha sphere density for a pocket to be retained*/
-		  asph_max_size ;		/**< Maximum size of alpha spheres to keep */
+		asph_min_size,						/**< Minimum size of alpha spheres to keep */
+		min_as_density,						/**<Minimum alpha sphere density for a pocket to be retained*/
+		asph_max_size;						/**< Maximum size of alpha spheres to keep */
 	char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
 	char chain_as_ligand[M_MAX_CHAINS_DELETE];
-	int chain_is_kept;/* To choose if we keep the chains or not*/
+	int chain_is_kept;	/* To choose if we keep the chains or not*/
 	char write_par[10]; /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m  -> mmcif*/
 
-} s_fparams ;
-
-
+} s_fparams;
 
 /* ------------------------------- PROTOTYPES ------------------------------- */
 
-s_fparams* init_def_fparams(void) ;
-s_fparams* get_fpocket_args(int nargs, char **args) ;
+s_fparams *init_def_fparams(void);
+s_fparams *get_fpocket_args(int nargs, char **args);
 
-int parse_clust_max_dist(char *str, s_fparams *p) ;
+int parse_clust_max_dist(char *str, s_fparams *p);
 int parse_clustering_method(char *str, s_fparams *p);
 
-int parse_sclust_min_nneigh(char *str, s_fparams *p) ;
-int parse_min_apol_neigh(char *str, s_fparams *p) ;
-int parse_asph_min_size(char *str, s_fparams *p) ;
-int parse_asph_max_size(char *str, s_fparams *p) ;
-int parse_mc_niter(char *str, s_fparams *p) ;
-int parse_basic_vol_div(char *str, s_fparams *p)  ;
-int parse_refine_dist(char *str, s_fparams *p)  ;
+int parse_sclust_min_nneigh(char *str, s_fparams *p);
+int parse_min_apol_neigh(char *str, s_fparams *p);
+int parse_asph_min_size(char *str, s_fparams *p);
+int parse_asph_max_size(char *str, s_fparams *p);
+int parse_mc_niter(char *str, s_fparams *p);
+int parse_basic_vol_div(char *str, s_fparams *p);
+int parse_refine_dist(char *str, s_fparams *p);
 int parse_distance_measure(char *str, s_fparams *p);
-int parse_refine_minaap(char *str, s_fparams *p)  ;
-int parse_min_pock_nb_asph(char *str, s_fparams *p) ;
+int parse_refine_minaap(char *str, s_fparams *p);
+int parse_min_pock_nb_asph(char *str, s_fparams *p);
 
-int is_fpocket_opt(const char opt) ;
+int is_fpocket_opt(const char opt);
 
-void free_fparams(s_fparams *p) ;
-void print_pocket_usage(FILE *f) ;
-void print_fparams(s_fparams *p, FILE *f) ;
+void free_fparams(s_fparams *p);
+void print_pocket_usage(FILE *f);
+void print_fparams(s_fparams *p, FILE *f);
 
 #endif

headers/rpdb.h

@@ -90,6 +90,8 @@ typedef struct s_pdb
     char header[M_PDB_BUF_LEN] ; /**< Header container*/
     char fname[M_PDB_FILE_NAME_LEN];    /**< File name container*/
     float avg_bfactor;  /**<overall average B factor*/
+    float min_bfactor;  /**<overall minimum B factor*/
+    float max_bfactor;  /**<overall maximum B factor*/
     int model_flag; /**<flag set to 1 if a particular model / conformation was read*/
     int model_number; /**<number of the model read in*/
 

headers/utils.h

@@ -34,7 +34,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* ------------------------------- PUBLIC MACROS ---------------------------- */
 
 #define M_MAX_PDB_NAME_LEN 200  /**< maximum pdb filename length*/
-
+#define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
 #define M_SIGN 1
 #define M_NO_SIGN 0
 

headers/voronoi.h

@@ -8,7 +8,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
  */
 
-
 #ifndef DH_VORONOI
 #define DH_VORONOI
 
@@ -27,7 +26,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include "calc.h"
 #include "utils.h"
 
-
 #include "../src/qhull/src//qvoronoi/qvoronoi.h"
 #include "../src/qhull/src/qconvex/qconvex.h"
 
@@ -36,62 +34,61 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* ----------------------------------MACROS--------------------------------- */
 
 #define M_VORONOI_SUCCESS 0 /**< alpha sphere type - hydrophobic alpha sphere */
-#define M_APOLAR_AS 0 /**< alpha sphere type - hydrophilic alpha sphere */
-#define M_POLAR_AS 1 
+#define M_APOLAR_AS 0       /**< alpha sphere type - hydrophilic alpha sphere */
+#define M_POLAR_AS 1
 #define M_PREC_TOLERANCE 1e-3 /**< tolerance for coordinate imprecion during alpha sphere search*/
 
-#define M_BUFSIZE 1e6   /**< buffer size*/
-#define M_N_REPLICAS 1  /**< currently not used anymore : number of times we do the voronoi tesselation for translated coordinates to avoid precision problems with qhull */
+#define M_BUFSIZE 1e6  /**< buffer size*/
+#define M_N_REPLICAS 1 /**< currently not used anymore : number of times we do the voronoi tesselation for translated coordinates to avoid precision problems with qhull */
 
 /* --------------------------------STRUCTURES-------------------------------- */
 
 /**
  Container of the Voronoi vertice
  */
-typedef struct s_vvertice 
+typedef struct s_vvertice
 {
-	int resid ; /**< residue ID*/
-	int id, /**< vertice ID*/
-            seen,       /**< Say if we have seen this vertice during a neighbor search */
-            qhullId,    /**< ID of the vertice in qhull output*/
-            type ;	/**< 0 if apolar contacts, 1 if polar */
+        int resid;   /**< residue ID*/
+        int id,      /**< vertice ID*/
+            seen,    /**< Say if we have seen this vertice during a neighbor search */
+            qhullId, /**< ID of the vertice in qhull output*/
+            type;    /**< 0 if apolar contacts, 1 if polar */
 
-	float ray ;	/**< Ray of voronoi vertice */
-	float x,	/**< X coord */
-              y,	/**< Y coord */
-	      z ;	/**< Z coord */
-	
-	int sort_x;		/**< Index in the sorted tab by X coord */
-	int apol_neighbours;	/**< number of neighbouring apolar alpha spheres */
+        float ray; /**< Ray of voronoi vertice */
+        float x,   /**< X coord */
+            y,     /**< Y coord */
+            z;     /**< Z coord */
 
-	int vneigh[4] ;         /**< vertice neighbours (4 contact atoms)*/
- 	s_atm *neigh[4] ;	/**< The theorical 4 contacted atoms */
-	
-	float bary[3] ;         /**< Barycenter of the pocket */
-        float electrostatic_energy;     /**<estimate of electrostatic energy around the alpha sphere */
+        int sort_x;          /**< Index in the sorted tab by X coord */
+        int apol_neighbours; /**< number of neighbouring apolar alpha spheres */
 
-} s_vvertice ;
+        int vneigh[4];   /**< vertice neighbours (4 contact atoms)*/
+        s_atm *neigh[4]; /**< The theorical 4 contacted atoms */
+
+        float bary[3];              /**< Barycenter of the pocket */
+        float electrostatic_energy; /**<estimate of electrostatic energy around the alpha sphere */
+
+} s_vvertice;
 
 /**
  vertice list container
  */
 typedef struct s_lst_vvertice
 {
-	s_vvertice *vertices ;      /**< List of voronoi vertices */
-        s_vvertice **pvertices ;  /**< list of pointers to vertices*/
+        s_vvertice *vertices;   /**< List of voronoi vertices */
+        s_vvertice **pvertices; /**< list of pointers to vertices*/
 
         /* Indexes of heavy atoms used as input for qhull in the s_pdb list of atoms */
-	int *h_tr;
+        int *h_tr;
 
         /* Size of h_tr */
-	int n_h_tr;
+        int n_h_tr;
 
-	int *tr,    /**< translation of voronoi vertice indices*/
-            nvert,  /**< no of vertices*/
-	    qhullSize ; /**< number of vertices in qhull*/
-
-} s_lst_vvertice ;
+        int *tr,       /**< translation of voronoi vertice indices*/
+            nvert,     /**< no of vertices*/
+            qhullSize; /**< number of vertices in qhull*/
 
+} s_lst_vvertice;
 
 /**
  * clusterlib vertice info container
@@ -99,63 +96,57 @@ typedef struct s_lst_vvertice
 
 typedef struct s_clusterlib_vertices
 {
-        double ** pos;          /**< Positions (xyz) of Voronoi vertices*/
-        int ** mask;            /**< Mask for position array*/
-        double weight[3];       /**< column (coordinate weights for distance matrix calculation*/
-        int transpose;          /**< cluster by rows (transpose=0) or column(transpose=1)*/
-        char dist;              /**< char defining distance measure used*/
-        char method;            /**< char defining method used (clustering)*/
-        
+        double **pos;     /**< Positions (xyz) of Voronoi vertices*/
+        int **mask;       /**< Mask for position array*/
+        double weight[3]; /**< column (coordinate weights for distance matrix calculation*/
+        int transpose;    /**< cluster by rows (transpose=0) or column(transpose=1)*/
+        char dist;        /**< char defining distance measure used*/
+        char method;      /**< char defining method used (clustering)*/
 
-        
-} s_clusterlib_vertices ;
+} s_clusterlib_vertices;
 
 /* -----------------------------PROTOTYPES----------------------------------- */
 
-s_lst_vvertice* load_vvertices_DEPRECATED(s_pdb *pdb, int min_apol_neigh, 
-				float ashape_min_size, float ashape_max_size,
-                                float xshift,float yshift, float zshift) ;
-s_lst_vvertice* load_vvertices(s_pdb *pdb, int min_apol_neigh, float asph_min_size, float asph_max_size,float xshift,float yshift,float zshift);
-
+s_lst_vvertice *load_vvertices(s_pdb *pdb, s_fparams *params, float xshift, float yshift, float zshift);
 
 void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, int natoms,
-                           int min_apol_neigh, float asph_min_size, float asph_max_size,
-                           float xshift, float yshift, float zshift,float avg_bfactor,s_pdb *pdb) ;
+                    s_fparams *params,
+                    float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);
 
-
-void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, 
-                           int min_apol_neigh, float asph_min_size, float asph_max_size,
-                           float xshift, float yshift,float zshift, float avg_bfactor,s_pdb *pdb);
+void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms,
+                           s_fparams *params,
+                           float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);
 
 unsigned short check_if_similar_vertice_in_list(s_vvertice *v, s_lst_vvertice *lvvert);
-void add_vertice_to_vertice_list(s_lst_vvertice *lvvert,s_vvertice *v);
-void copy_vertice(s_vvertice *v1,s_vvertice *v2, int n);
+void add_vertice_to_vertice_list(s_lst_vvertice *lvvert, s_vvertice *v);
+void copy_vertice(s_vvertice *v1, s_vvertice *v2, int n);
 
-float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms, 
-				   float min_asph_size, float max_asph_size, 
-				   s_lst_vvertice *lvvert,
-                                   float xshift, float yshift, float zshift,float avg_bfactor,s_pdb *pdb);
+float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
+                   s_fparams *params,
+                   s_lst_vvertice *lvvert,
+                   float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);
+
+float atom_in_explicit_pocket(s_atm *cura, s_fparams *params);
 
 s_lst_vvertice *compare_vvertice_shifted_lists(s_lst_vvertice *lvvert,
-        s_lst_vvertice *list_shifted,float xshift,float yshift,float zshift);
-
+                                               s_lst_vvertice *list_shifted, float xshift, float yshift, float zshift);
 
 double **get_3d_array_from_vvertice_list(s_lst_vvertice *lvvert);
-s_clusterlib_vertices *prepare_vertices_for_cluster_lib(s_lst_vvertice *lvvert,char c_method,char d_method);
-void set_barycenter(s_vvertice *v) ;
-int is_in_lst_vert(s_vvertice **lst_vert, int nb_vert, int v_id) ;
+s_clusterlib_vertices *prepare_vertices_for_cluster_lib(s_lst_vvertice *lvvert, char c_method, char d_method);
+void set_barycenter(s_vvertice *v);
+int is_in_lst_vert(s_vvertice **lst_vert, int nb_vert, int v_id);
 int is_in_lst_vert_p(s_vvertice **lst_vert, int nb_vert, s_vvertice *vert);
 
-void write_pqr_vert(FILE *f, s_vvertice *v, int i) ;
-void write_pdb_vert(FILE *f, s_vvertice *v, int i) ;
+void write_pqr_vert(FILE *f, s_vvertice *v, int i);
+void write_pdb_vert(FILE *f, s_vvertice *v, int i);
 void write_mmcif_vert(FILE *f, s_vvertice *v, int i);
-float get_verts_volume_ptr(s_vvertice **verts, int nvert, int niter,float correct);
+float get_verts_volume_ptr(s_vvertice **verts, int nvert, int niter, float correct);
 float get_convex_hull_volume(s_vvertice **verts, int nvert);
 
-void print_vvertices(FILE *f, s_lst_vvertice *lvvert) ;
-void free_vert_lst(s_lst_vvertice *lvvert) ;
+void print_vvertices(FILE *f, s_lst_vvertice *lvvert);
+void free_vert_lst(s_lst_vvertice *lvvert);
 
-void transferClustersToVertices(int **clusterIds,s_lst_vvertice *lvert);
+void transferClustersToVertices(int **clusterIds, s_lst_vvertice *lvert);
 
 double frand_a_b(double a, double b);
 int free_cluster_lib_vertices(s_clusterlib_vertices *clusterlib_vertices, int nvert);

src/descriptors.c

@@ -423,7 +423,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
             /*fprintf(stdout,":%s:",desc->ligTag);*/
             desc->hydrophobicity_score = desc->hydrophobicity_score/ (float) nb_res_ids ;
             desc->volume_score = desc->volume_score / (float) nb_res_ids ;
-
+			
             desc->flex /= natoms ;
             desc->prop_polar_atm = ((float) nb_polar_atm) / ((float) natoms) * 100.0 ;
         }

src/fparams.c

@@ -35,7 +35,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 ##	27-11-08	(v)  PDB file check moved in fpmain + minor modif + relooking
 ##	01-04-08	(v)  Added comments and creation of history
 ##	01-01-08	(vp) Created (random date...)
-##	
+##
 ## TODO or SUGGESTIONS
 ##
 ##	(v) Check and update if necessary comments of each function!!
@@ -46,18 +46,18 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /**
    ## FUNCTION:
         init_def_fparams
-  
+
    ## SPECIFICATION:
         Initialisation of default parameters
-  
+
    ## PARAMETRES: void
-  
-   ## RETURN: 
+
+   ## RETURN:
         s_fparams*: Pointer to allocated paramers.
-  
+
  */
 
-char write_mode[10] = "d"; /*write mode : d -> default | b -> both pdb and mmcif | 
+char write_mode[10] = "d"; /*write mode : d -> default | b -> both pdb and mmcif |
                         p ->pdb | m  -> mmcif*/
 
 s_fparams *init_def_fparams(void)
@@ -87,34 +87,40 @@ s_fparams *init_def_fparams(void)
     par->xlig_resnumber = -1;
     par->chain_is_kept = 0;
     par->write_par[0] = 'd';
+    par->xpocket_n = 0;
+    par->min_n_explicit_pocket_atoms = M_MIN_N_EXPLICIT_POCKET;
     return par;
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         get_fpocket_args
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         This function analyse the user's command line and parse it to store parameters
         for the pocket finder programm.
-  
+
    ## PARAMETRES:
         @ int nargs   :  Number of arguments
         @ char **args : Arguments of main program
-  
-   ## RETURN: 
+
+   ## RETURN:
         s_params*: Pointer to parameters
-  
+
  */
 s_fparams *get_fpocket_args(int nargs, char **args)
 {
     int status = 0;
     s_fparams *par = init_def_fparams(); /*default param initialy*/
     int c = 0;
+    int apti = 0;
+    int pti = 0;
     short j = 0;
     short xflag;
     opterr = 0;
     char *pt;
+    char *apt;
+    char *residue_string[M_MAX_CUSTOM_POCKET_LEN];
     short custom_ligand_i = 0;
 
     static struct option fplong_options[] = {/*long options args located in fparams.h*/
@@ -133,6 +139,8 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                                              {"topology_file", required_argument, 0, M_PAR_TOPOLOGY},
                                              {"model_number", required_argument, 0, M_PAR_MODEL_FLAG},
                                              {"custom_ligand", required_argument, 0, M_PAR_CUSTOM_LIGAND},
+                                             {"custom_pocket", required_argument, 0, M_PAR_CUSTOM_POCKET},
+                                             {M_PAR_MIN_N_EXPLICIT_POCKET_LONG, required_argument, 0, M_PAR_MIN_N_EXPLICIT_POCKET},
                                              {M_PAR_DROP_CHAINS_LONG, required_argument, 0, M_PAR_DROP_CHAINS},         /*drop chains*/
                                              {M_PAR_CHAIN_AS_LIGAND_LONG, required_argument, 0, M_PAR_CHAIN_AS_LIGAND}, /*chain as ligand*/
                                              {M_PAR_KEEP_CHAINS_LONG, required_argument, 0, M_PAR_KEEP_CHAINS},         /*chain as ligand*/
@@ -145,7 +153,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
         /* getopt_long stores the option index here. */
         int option_index = 0;
         optarg = 0;
-        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:c:a:k:w:",
+        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:P:u:c:a:k:w:",
                         fplong_options, &option_index);
         //        printf("C: %d nargs : %d optindex:%d\n", c, nargs, option_index);
 
@@ -154,7 +162,6 @@ s_fparams *get_fpocket_args(int nargs, char **args)
         case 0:
             break;
 
-
         case M_PAR_WRITE_MODE: /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m  -> mmcif*/
             status++;
             if (optarg[0] != 'd' && optarg[0] != 'b' && optarg[0] != 'p' && optarg[0] != 'm' && strcmp(optarg, "both") && strcmp(optarg, "pdb") && strcmp(optarg, "cif") && strcmp(optarg, "mmcif"))
@@ -166,26 +173,20 @@ s_fparams *get_fpocket_args(int nargs, char **args)
             {
                 strcpy(par->write_par, "mmcif");
                 strcpy(write_mode, par->write_par);
-                
             }
             else
             {
                 strcpy(par->write_par, optarg);
                 strcpy(write_mode, par->write_par);
-               }
+            }
 
             break;
- 
-               
-                
-
-           
 
         case M_PAR_CHAIN_AS_LIGAND: /*option with -a "name of the chain" to be specified as a ligand*/
             /*select the chains as ligand*/
             status++;
             strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
-            const char *separatorss = ",";       /* defining separators*/
+            const char *separatorss = ",";        /* defining separators*/
             pt = strtok(par->chain_as_ligand, separatorss);
             int nn = 0;
             while (pt != NULL)
@@ -195,30 +196,26 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                 pt = strtok(NULL, separatorss);
             }
             par->xlig_resnumber = 0;
-            //printf("lig %s\n",par->chain_as_ligand);
-      break;
-           
-
-
-           
+            // printf("lig %s\n",par->chain_as_ligand);
+            break;
 
         case M_PAR_DROP_CHAINS:                /*option with -c "name of the chains"*/
                                                /*drop the selected chains from the pdb file*/
             strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            //printf("%s and %s",par->custom_ligand,optarg);
+            // printf("%s and %s",par->custom_ligand,optarg);
             const char *separators = ",:"; /* defining separators for drop chains args*/
             pt = strtok(par->chain_delete, separators);
             int n = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[n]), pt,1);
-                
+                strncpy(&(par->chain_delete[n]), pt, 1);
+
                 n++;
                 pt = strtok(NULL, separators);
             }
             par->chain_is_kept = 0;
-            
-            //printf("%s\n",par->chain_delete);
+
+            // printf("%s\n",par->chain_delete);
             status++;
             break;
 
@@ -226,7 +223,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                                 /*drop the selected chains from the pdb file*/
 
             strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            //printf("%s and %s",par->custom_ligand,optarg);
+            // printf("%s and %s",par->custom_ligand,optarg);
             const char *separator = ",:"; /* defining separators for drop chains args*/
             pt = strtok(par->chain_delete, separator);
             int nk = 0;
@@ -236,21 +233,21 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                 nk++;
                 pt = strtok(NULL, separator);
             }
-            //printf("%s\n",par->chain_delete);
+            // printf("%s\n",par->chain_delete);
             par->chain_is_kept = 1;
             status++;
             break;
 
         case M_PAR_CUSTOM_LIGAND:
 
-            //parse ligand specification that has to be given as
-            //residuenumber:residuename:chain_code
-            //for 1uyd for instance 1224:PU8:A
+            // parse ligand specification that has to be given as
+            // residuenumber:residuename:chain_code
+            // for 1uyd for instance 1224:PU8:A
 
             status++;
 
             strcpy(par->custom_ligand, optarg);
-            //printf("%s and %s",par->custom_ligand,optarg);
+            // printf("%s and %s",par->custom_ligand,optarg);
             pt = strtok(par->custom_ligand, ":");
 
             while (pt != NULL)
@@ -268,6 +265,55 @@ s_fparams *get_fpocket_args(int nargs, char **args)
             }
 
             break;
+
+        case M_PAR_CUSTOM_POCKET:
+
+            // parse pocket specification that has to be given as
+            // residuenumber1:insertion_code1:chain_code1.residuenumber2:insertion_code2:chain_code2& ....
+            // for 1uyd for instance 127::A.128::A
+
+            status++;
+
+            strcpy(par->custom_pocket_arg, optarg);
+            char *rest = par->custom_pocket_arg;
+            char *rest2;
+            /*count residues first*/
+            while ((pt = strtok_r(rest, ".", &rest)))
+                par->xpocket_n++;
+
+            par->xpocket_chain_code = (char *)my_malloc(par->xpocket_n * sizeof(char));
+            par->xpocket_insertion_code = (char *)my_malloc(par->xpocket_n * sizeof(char));
+            par->xpocket_residue_number = (unsigned short *)my_malloc(par->xpocket_n * sizeof(unsigned short));
+            pti = 0;
+            strcpy(par->custom_pocket_arg, optarg);
+            rest = par->custom_pocket_arg;
+            while ((pt = strtok_r(rest, ".", &rest)))
+            {
+                strcpy(&residue_string, pt);
+                rest2 = residue_string;
+                apti = 0;
+                while (apt = strtok_r(rest2, ":", &rest2))
+                {
+                    switch (apti)
+                    {
+                    case 0:
+                        par->xpocket_residue_number[pti] = (unsigned short)atoi(apt); // fprintf(stdout,"residuenumber: %d\n", atoi(apt));
+                    case 1:
+                        strncpy(&(par->xpocket_insertion_code[pti]), apt, 1);
+                    case 2:
+                        strncpy(&(par->xpocket_chain_code[pti]), apt, 1);
+                    }
+                    apti++;
+                }
+                pti++;
+            }
+            break;
+
+        case M_PAR_MIN_N_EXPLICIT_POCKET:
+            status++;
+            par->min_n_explicit_pocket_atoms = (int)atoi(optarg);
+            break;
+
         case M_PAR_PDB_FILE:
             //                printf("option -f with value `%s'\n", optarg);
             status++;
@@ -301,7 +347,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
             break;
         case M_PAR_DISTANCE_MEASURE:
             //                printf("option -e with value %s\n", optarg);
-            //strcpy(par->distance_measure,optarg);      /*might be problematic*/
+            // strcpy(par->distance_measure,optarg);      /*might be problematic*/
             strncpy(&(par->distance_measure), optarg, 1);
             status++;
 
@@ -335,7 +381,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
             status++;
             break;
         case M_PAR_MODEL_FLAG:
-            //printf("option -l with value %s", optarg);
+            // printf("option -l with value %s", optarg);
             par->model_number = (int)atoi(optarg);
             status++;
             break;
@@ -348,39 +394,45 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     {
         strcpy(par->write_par, "m");
         strcpy(write_mode, par->write_par);
-        //printf("%c", write_mode[0]);
+        // printf("%c", write_mode[0]);
     }
     else if (strstr(par->pdb_path, ".pdb") && par->write_par[0] == 'd')
     {
         strcpy(par->write_par, "p");
         strcpy(write_mode, par->write_par);
     }
+
+    if (par->xpocket_n > 0 && par->xlig_resnumber > -1)
+    {
+        fprintf(stderr, "\n\033[1mERROR:\033[0m you specified an explicit ligand (-r) AND an explicit pocke (-P) in the same fpocket run. This is currently not allowed, please use either the one or the other.\n\n");
+        return NULL;
+    }
     return (par);
     /*        if(status){
                 return(par);
             }
             else {
-            
-           
+
+
                 return(NULL);
             }*/
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         get_fpocket_args
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         This function analyse the user's command line and parse it to store parameters
         for the pocket finder programm.
-  
+
    ## PARAMETRES:
         @ int nargs   :  Number of arguments
         @ char **args : Arguments of main program
-  
-   ## RETURN: 
+
+   ## RETURN:
         s_params*: Pointer to parameters
-  
+
  */
 s_fparams *DEPR_get_fpocket_args(int nargs, char **args)
 {
@@ -391,7 +443,7 @@ s_fparams *DEPR_get_fpocket_args(int nargs, char **args)
     s_fparams *par = init_def_fparams();
     char *pdb_lst = NULL;
 
-    //read arguments by flags
+    // read arguments by flags
     for (i = 1; i < nargs; i++)
     {
         if (strlen(args[i]) == 2 && args[i][0] == '-' && i <= (nargs - 1))
@@ -520,19 +572,19 @@ s_fparams *DEPR_get_fpocket_args(int nargs, char **args)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_clust_max_dist
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the distance criteria first clustering algorithm.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid float), 1 if not
-  
+
  */
 int parse_clust_max_dist(char *str, s_fparams *p)
 {
@@ -550,19 +602,19 @@ int parse_clust_max_dist(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_sclust_max_dist
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the distance criteria in the single linkage clustering.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid float), 1 if not
-  
+
  */
 int parse_clustering_method(char *str, s_fparams *p)
 {
@@ -595,20 +647,20 @@ int parse_distance_measure(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_min_apol_neigh
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the minimum number of apolar contacted atom for an alpha
         sphere to be considered as apolar.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid int), 1 if not
-  
+
  */
 int parse_min_apol_neigh(char *str, s_fparams *p)
 {
@@ -630,19 +682,19 @@ int parse_min_apol_neigh(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_asph_min_size
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the minimum radius of each alpha shpere
-  
+
    ## PARAMETERS:
         @ char *str: The string to parse
         @ s_fparams *p: The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid float), 1 if not
-  
+
  */
 int parse_asph_min_size(char *str, s_fparams *p)
 {
@@ -660,19 +712,19 @@ int parse_asph_min_size(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_asph_max_size
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the maximum radius of each alpha shpere
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid float), 1 if not
-  
+
  */
 int parse_asph_max_size(char *str, s_fparams *p)
 {
@@ -690,20 +742,20 @@ int parse_asph_max_size(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_mc_niter
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the number of iteration for the Monte Carlo volume
         calculation.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid float), 1 if not
-  
+
  */
 int parse_mc_niter(char *str, s_fparams *p)
 {
@@ -721,19 +773,19 @@ int parse_mc_niter(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_basic_vol_div
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the number of iteration for the basic volume calculation.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid integer), 1 if not
-  
+
  */
 int parse_basic_vol_div(char *str, s_fparams *p)
 {
@@ -751,19 +803,19 @@ int parse_basic_vol_div(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_refine_min_apol
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the minimum number of apolar sphere per pocket.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid integer), 1 if not
-  
+
  */
 int parse_refine_minaap(char *str, s_fparams *p)
 {
@@ -781,19 +833,19 @@ int parse_refine_minaap(char *str, s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         parse_min_pock_nb_asph
-  
-   ## SPECIFICATION: 	
+
+   ## SPECIFICATION:
         Parsing function for the minimum number of alpha sphere per pocket.
-  
+
    ## PARAMETERS:
         @ char *str    : The string to parse
         @ s_fparams *p : The structure than will contain the parsed parameter
-  
-   ## RETURN: 
+
+   ## RETURN:
         int: 0 if the parameter is valid (here a valid integer), 1 if not
-  
+
  */
 int parse_min_pock_nb_asph(char *str, s_fparams *p)
 {
@@ -813,17 +865,17 @@ int parse_min_pock_nb_asph(char *str, s_fparams *p)
 /**
    ## FUNCTION:
         is_fpocket_opt
-  
+
    ## SPECIFICATION:
         Say either or not a single letter code is a fpocket option (excluding
         input file/list option.)
-  
+
    ## PARAMETRES:
         @ const char opt: The one letter code option.
-  
+
    ## RETURN:
         integer: 1 if it's a valid option parmeter, 0 if not.
-  
+
  */
 
 int is_fpocket_opt(const char opt)
@@ -846,18 +898,18 @@ int is_fpocket_opt(const char opt)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         free_fparams
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         Free parameters
-  
-   ## PARAMETRES: 
+
+   ## PARAMETRES:
         @ s_params *p: Pointer to the structure to free
-  
-   ## RETURN: 
+
+   ## RETURN:
         void
-  
+
  */
 void free_fparams(s_fparams *p)
 {
@@ -878,18 +930,18 @@ void free_fparams(s_fparams *p)
 }
 
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         print_pocket_usage
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         Displaying usage of the programm in the given buffer
-  
+
    ## PARAMETRES:
         @ FILE *f: buffer to print in
-  
+
    ## RETURN:
     void
-  
+
  */
 void print_pocket_usage(FILE *f)
 {
@@ -916,13 +968,21 @@ void print_pocket_usage(FILE *f)
     fprintf(f, "\n\n\033[1mOptional input parameters\033[0m\n");
     fprintf(f, "\t-%c --%s (int)\t\t\t: Number of Model to analyze.\t\n", M_PAR_MODEL_FLAG, M_PAR_MODEL_FLAG_LONG);
     fprintf(f, "\t-%c --%s (string)\t\t: File name of a topology file (Amber prmtop).\t\n", M_PAR_TOPOLOGY, M_PAR_LONG_TOPOLOGY);
-    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n", M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
+    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: \n\
+\t\t\t\t\t\t  residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n",
+            M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
+    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a pocket like: \n\ 
+\t\t\t\t\t\t  residuenumber1:insertion_code1('-' if empty):chain_code1.residuenumber2:insertion_code2:chain_code2 (ie. 138:-:A.139:-:A).\t\n",
+            M_PAR_CUSTOM_POCKET, M_PAR_CUSTOM_POCKET_LONG);
+    fprintf(f, "\t-%c --%s (int)\t: If explicit pocket provided, minimum number \n\ 
+\t\t\t\t\t\t  of atoms of an alpha sphere that have to be in the selected pocket.\t\n",
+            M_PAR_MIN_N_EXPLICIT_POCKET, M_PAR_MIN_N_EXPLICIT_POCKET_LONG);
     fprintf(f, "\t-%c --%s (char)\t\t: Character specifying a chain as a ligand\t\n", M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG);
 
     fprintf(f, "\n\n\033[1mOptional pocket detection parameters\033[0m (default parameters)           \n\
 \t-%c --%s (float)\t\t: Minimum radius of an alpha-sphere.\t(%.1f)\n",
-            M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
-    fprintf(f, "\t-%c --%s (float)\t\t: Maximum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MAX_ASHAPE_SIZE, M_PAR_LONG_MAX_ASHAPE_SIZE, M_MIN_ASHAPE_SIZE_DEFAULT);
+            M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MIN_ASHAPE_SIZE_DEFAULT);
+    fprintf(f, "\t-%c --%s (float)\t\t: Maximum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MAX_ASHAPE_SIZE, M_PAR_LONG_MAX_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
     fprintf(f, "\t-%c --%s (float)\t: Distance threshold for clustering algorithm\t(%.1f)\n", M_PAR_CLUST_MAX_DIST, M_PAR_LONG_CLUST_MAX_DIST, M_CLUST_MAX_DIST);
     fprintf(f, "\t-%c --%s (char)\t\t: Specify the clustering method wanted for     \n\
 \t\t\t\t\t\t  grouping voronoi vertices together (%c)\n\
@@ -952,7 +1012,7 @@ void print_pocket_usage(FILE *f)
 \t\t\t\t\t\t  able to keep up to (%d) chains (ie : -k A,B,C,E)\n",
             M_PAR_KEEP_CHAINS, M_PAR_KEEP_CHAINS_LONG, M_MAX_CHAINS_DELETE);
     fprintf(f, "\t-%c --%s (char)\t\t: consider this chain as a ligand explicitly (i.e. -%c D)\n",
-            M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG,M_PAR_CHAIN_AS_LIGAND);
+            M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG, M_PAR_CHAIN_AS_LIGAND);
     fprintf(f, "\t-%c --%s (char)\t\t\t: Writing mode to be used after pocket detection,      \n\
 \t\t\t\t\t\t  d -> default (same format outpout as input)\n\
 \t\t\t\t\t\t  b or both -> both pdb and mmcif | p or pdb ->pdb | m or cif or mmcif-> mmcif\n",
@@ -961,18 +1021,18 @@ void print_pocket_usage(FILE *f)
 }
 /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m  -> mmcif*/
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         print_fparams
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         Print function
-  
+
    ## PARAMETRES:
     @ s_fparams *p : Parameters to print
         @ FILE *f      : Buffer to write in
-  
-   ## RETURN: 
-  
+
+   ## RETURN:
+
  */
 void print_fparams(s_fparams *p, FILE *f)
 {

src/fpmain.c

@@ -30,7 +30,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 ##	27-11-08	(v)  PDB file check moved here instead of fparams
 ##	01-04-08	(v)  Added comments and creation of history
 ##	01-01-08	(vp) Created (random date...)
-##	
+##
 ## TODO or SUGGESTIONS
 ##
 
@@ -38,11 +38,11 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 /**
    ## FUNCTION:
-	int main(int argc, char *argv[])
-  
+        int main(int argc, char *argv[])
+
    ## SPECIFICATION:
-	Main program!
-  
+        Main program!
+
 */
 
 int main(int argc, char *argv[])
@@ -50,10 +50,10 @@ int main(int argc, char *argv[])
 
         s_fparams *params = get_fpocket_args(argc, argv);
 
-        params->fpocket_running = 1;
         /* If parameters parsing is ok */
         if (params)
         {
+                params->fpocket_running = 1;
                 if (!params->db_run)
                         fprintf(stdout, "***** POCKET HUNTING BEGINS ***** \n");
                 //                print_fparams(params,stdout);
@@ -103,20 +103,20 @@ int main(int argc, char *argv[])
         return 0;
 }
 /**
-   ## FUNCTION: 
-	process_pdb
-  
-   ## SPECIFICATION: 
-	Handle a single pdb: check the pdb name, load data, and launch fpocket if
-	the pdb file have been successfully read.
-  
+   ## FUNCTION:
+        process_pdb
+
+   ## SPECIFICATION:
+        Handle a single pdb: check the pdb name, load data, and launch fpocket if
+        the pdb file have been successfully read.
+
    ## PARAMETRES:
-	@ char *pdbname     : Name of the pdb
-	@ s_fparams *params : Parameters of the algorithm. See fparams.c/.h
-  
-   ## RETURN: 
-	void
-  
+        @ char *pdbname     : Name of the pdb
+        @ s_fparams *params : Parameters of the algorithm. See fparams.c/.h
+
+   ## RETURN:
+        void
+
 */
 void process_pdb(char *pdbname, s_fparams *params)
 {
@@ -140,15 +140,14 @@ void process_pdb(char *pdbname, s_fparams *params)
         if (DEBUG)
                 print_number_of_objects_in_memory();
 
-       
         s_pdb *pdb = open_file_format(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
-       s_pdb *pdb_w_lig = open_file_format(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
+        s_pdb *pdb_w_lig = open_file_format(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
 
-       // s_pdb *pdb = open_mmcif(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
-       // s_pdb *pdb_w_lig = open_mmcif(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
+        // s_pdb *pdb = open_mmcif(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+        // s_pdb *pdb_w_lig = open_mmcif(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
 
-        //s_pdb *pdb = rpdb_open(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
-        //s_pdb *pdb_w_lig = rpdb_open(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
+        // s_pdb *pdb = rpdb_open(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+        // s_pdb *pdb_w_lig = rpdb_open(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
         if (DEBUG)
                 print_number_of_objects_in_memory();
 
@@ -160,15 +159,15 @@ void process_pdb(char *pdbname, s_fparams *params)
         if (pdb)
         {
                 /* Actual reading of pdb data and then calculation */
-                
+
                 read_file_format(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
                 read_file_format(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
 
-                //read_mmcif(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
-                //read_mmcif(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
+                // read_mmcif(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+                // read_mmcif(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
 
-                //rpdb_read(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
-                //rpdb_read(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
+                // rpdb_read(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+                // rpdb_read(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
 
                 //                        fprintf(stdout,"Init coordinate grid\n");
                 create_coord_grid(pdb);
@@ -177,7 +176,7 @@ void process_pdb(char *pdbname, s_fparams *params)
                 /*free_pdb_atoms(pdb);
                         free_pdb_atoms(pdb_w_lig);
                         if(DEBUG)print_number_of_objects_in_memory();
-                        
+
                         return(NULL);*/
 
                 c_lst_pockets *pockets = search_pocket(pdb, params, pdb_w_lig);
@@ -230,23 +229,21 @@ void process_pdb(char *pdbname, s_fparams *params)
 s_pdb *open_file_format(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par)
 {
         s_pdb *pdb;
-        if (strstr(par->pdb_path, ".cif")) /*strstr finds the substring and here we search for the file extension we want */       
-                pdb =  open_mmcif(fpath, NULL, keep_lig, par->model_number, par);
+        if (strstr(par->pdb_path, ".cif")) /*strstr finds the substring and here we search for the file extension we want */
+                pdb = open_mmcif(fpath, NULL, keep_lig, par->model_number, par);
         else if (strstr(par->pdb_path, ".pdb"))
                 pdb = rpdb_open(fpath, NULL, keep_lig, par->model_number, par);
 
         return pdb;
 }
 
-
 void read_file_format(s_pdb *pdb, const char *ligan, const int keep_lig, int model_number, s_fparams *par)
 {
-        
-        if (strstr(par->pdb_path, ".cif")){ /*strstr finds the substring and here we search for the file extension we want */           
-                read_mmcif(pdb, NULL, keep_lig, par->model_number, par);    
+
+        if (strstr(par->pdb_path, ".cif"))
+        { /*strstr finds the substring and here we search for the file extension we want */
+                read_mmcif(pdb, NULL, keep_lig, par->model_number, par);
         }
         else if (strstr(par->pdb_path, ".pdb"))
                 rpdb_read(pdb, NULL, keep_lig, par->model_number, par);
-
-        
 }

src/fpocket.c

@@ -1,5 +1,5 @@
 
-#include "../headers/fpocket.h" 
+#include "../headers/fpocket.h"
 /*
  * Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
  * Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
@@ -32,31 +32,31 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 ##	28-11-08	(v)  Comments UTD
 ##	01-04-08	(v)  Added comments and creation of history
 ##	01-01-08	(vp) Created (random date...)
-##	
+##
 ## TODO or SUGGESTIONS
 ##
 
  */
 
-
 /**
-   ## FUNCTION: 
+   ## FUNCTION:
         pockets search_pocket
-  
-   ## SPECIFICATION: 
+
+   ## SPECIFICATION:
         This function will call all functions needed for the pocket finding algorith
         and will return the list of pockets found on the protein.
-  
+
    ## PARAMETRES:
         @ s_pdb *pdb : The pdb data of the protein to handle.
         @ s_fparams  : Parameters of the algorithm
-  
+
    ## RETURN:
         A chained list of pockets found, sorted according to the current critera
         (the default is a scoring function)
-  
+
  */
-c_lst_pockets* search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig) {
+c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
+{
 
     clock_t b, e;
     time_t bt, et;
@@ -66,21 +66,22 @@ c_lst_pockets* search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig) {
     s_clusterlib_vertices *clusterlib_vertices = NULL;
     Node *cluster_tree = NULL;
 
-
     /* Calculate and read voronoi vertices comming from qhull */
 
     //    fprintf(stdout, "========= fpocket algorithm begins =========\n");
 
-    if (DEBUG) {
+    if (DEBUG)
+    {
         fprintf(stdout, "> Calculating vertices ...\n");
     }
 
     bt = clock();
 
+    // s_lst_vvertice *lvert = load_vvertices(pdb, params->min_apol_neigh,
+    //                                        params->asph_min_size,
+    //                                        params->asph_max_size, 0.0, 0.0, 0.0);
 
-    s_lst_vvertice *lvert = load_vvertices(pdb, params->min_apol_neigh,
-            params->asph_min_size,
-            params->asph_max_size, 0.0, 0.0, 0.0);
+    s_lst_vvertice *lvert = load_vvertices(pdb, params, 0.0, 0.0, 0.0);
 
     /*if(lvert->nvert>8000){*/
     /*   params->asph_max_size=7.6;
@@ -96,112 +97,129 @@ c_lst_pockets* search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig) {
         params->min_pock_nb_asph=M_MIN_POCK_NB_ASPH;
     }*/
 
-
-    if (DEBUG) {
+    if (DEBUG)
+    {
         fprintf(stdout, "distance measure : %c\n", params->clustering_method);
         fprintf(stdout, "%d vertices\n", lvert->nvert);
-        fprintf(stdout, "needing %.5f s to read the vertices", (double) (clock() - b) / CLOCKS_PER_SEC);
+        fprintf(stdout, "needing %.5f s to read the vertices", (double)(clock() - b) / CLOCKS_PER_SEC);
     }
 
-
-
-    if (DEBUG) {
+    if (DEBUG)
+    {
         fprintf(stdout, "Preparing for clustering\n");
     }
 
-    if (DEBUG) print_number_of_objects_in_memory();
-    if (params->xlig_resnumber == -1) {
+    if (DEBUG)
+        print_number_of_objects_in_memory();
+    if (params->xlig_resnumber == -1 && params->xpocket_n == 0)
+    {
         clusterlib_vertices = prepare_vertices_for_cluster_lib(lvert, params->clustering_method, params->distance_measure);
-        if (DEBUG) fprintf(stdout, "Clustering\n");
+        if (DEBUG)
+            fprintf(stdout, "Clustering\n");
         //    fprintf(stdosut,"distance measure : %c\n",clusterlib_vertices->method);
 
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
 
         cluster_tree = treecluster(lvert->nvert,
-                3,
-                clusterlib_vertices->pos,
-                clusterlib_vertices->mask,
-                clusterlib_vertices->weight,
-                clusterlib_vertices->transpose,
-                clusterlib_vertices->dist,
-                clusterlib_vertices->method,
-                NULL);
-        if (DEBUG) print_number_of_objects_in_memory();
-        if (cluster_tree == NULL) {
+                                   3,
+                                   clusterlib_vertices->pos,
+                                   clusterlib_vertices->mask,
+                                   clusterlib_vertices->weight,
+                                   clusterlib_vertices->transpose,
+                                   clusterlib_vertices->dist,
+                                   clusterlib_vertices->method,
+                                   NULL);
+        if (DEBUG)
+            print_number_of_objects_in_memory();
+        if (cluster_tree == NULL)
+        {
             fprintf(stderr, "Error in creating clustering tree, return NULL pointer...breaking up");
             return (0);
         }
         int **clusterIds = cuttree_distance(lvert->nvert, cluster_tree, params->clust_max_dist);
-        //int i;
-        if (DEBUG) print_number_of_objects_in_memory();
+        // int i;
+        if (DEBUG)
+            print_number_of_objects_in_memory();
         transferClustersToVertices(clusterIds, lvert);
 
-        if (DEBUG) fprintf(DEBUG_STREAM, "freeing clusterlib vertices now\n");
+        if (DEBUG)
+            fprintf(DEBUG_STREAM, "freeing clusterlib vertices now\n");
         free_cluster_lib_vertices(clusterlib_vertices, lvert->nvert);
         free_cluster_tree(cluster_tree);
         free_cluster_ids(clusterIds, lvert->nvert);
     }
-    if (lvert == NULL) {
+    if (lvert == NULL)
+    {
         fprintf(stderr, "! Vertice calculation failed!\n");
         return NULL;
     }
 
     pockets = assign_pockets(lvert);
-    if (DEBUG) {
+    if (DEBUG)
+    {
         fprintf(DEBUG_STREAM, "After pocket assignment :\n");
         fflush(DEBUG_STREAM);
         print_number_of_objects_in_memory();
         fprintf(DEBUG_STREAM, "\tpocket : %p :\n\tpocket vertice list : %p\n", pockets, pockets->vertices);
         fflush(DEBUG_STREAM);
     }
-    
+
     apply_clustering(pockets, params);
-    if (DEBUG) {
+    if (DEBUG)
+    {
         fprintf(DEBUG_STREAM, "applied clustering to pockets");
         print_number_of_objects_in_memory();
     }
 
-    if (pockets) {
+    if (pockets)
+    {
         reIndexPockets(pockets);
 
         //        fprintf(stdout, "> Calculating descriptors and score...\n");
 
-        if (DEBUG)print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
         set_pockets_descriptors(pockets, pdb, params, pdb_w_lig);
-        if (DEBUG) print_number_of_objects_in_memory();
-
+        if (DEBUG)
+            print_number_of_objects_in_memory();
 
         /* Drop small and too polar binding pockets */
 
-        if (DEBUG) {
+        if (DEBUG)
+        {
             print_number_of_objects_in_memory();
             fprintf(DEBUG_STREAM, "drop small and polar clusters\n");
         }
 
         dropSmallNpolarPockets(pockets, params);
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
 
         reIndexPockets(pockets);
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
 
         /* Sorting pockets */
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
         sort_pockets(pockets, M_SCORE_SORT_FUNCT);
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
 
-        //sort_pockets(pockets, M_NASPH_SORT_FUNCT) ;
+        // sort_pockets(pockets, M_NASPH_SORT_FUNCT) ;
 
-
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
         reIndexPockets(pockets);
-        if (DEBUG) print_number_of_objects_in_memory();
+        if (DEBUG)
+            print_number_of_objects_in_memory();
         //        int i;
 
-        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path) calculate_pocket_energy_grids(pockets, params, pdb);
-        //params->fpocket_running && 
-
+        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path)
+            calculate_pocket_energy_grids(pockets, params, pdb);
+        // params->fpocket_running &&
     }
 
     return pockets;
 }
-

src/read_mmcif.c

@@ -115,10 +115,10 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                 if (par->xlig_resnumber > -1)
                 {
 
-                    if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
-                    {
-                        pdb->n_xlig_atoms++;
-                    }
+                    // if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                    // {
+                    //     pdb->n_xlig_atoms++;
+                    // }
 
                     if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
                     {
@@ -126,6 +126,14 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     }
                 }
             }
+            if (par->xlig_resnumber > -1)
+            {
+
+                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                {
+                    pdb->n_xlig_atoms++;
+                }
+            }
         }
         else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
         {
@@ -169,18 +177,19 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                         }
                     }
                 }
-                if (par->xlig_resnumber > -1)
-                {
-                    if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
-                    {
-                        pdb->n_xlig_atoms++;
-                    }
-                }
+
                 if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
                 {
                     pdb->n_xlig_atoms++;
                 }
             }
+            if (par->xlig_resnumber > -1)
+            {
+                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                {
+                    pdb->n_xlig_atoms++;
+                }
+            }
         }
     }
 
@@ -285,17 +294,6 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
             if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
             { /*if within first occurence*/
                 /* Enter this if when arg in command line is -r */
-                if (pdb->n_xlig_atoms)
-                {
-                    if (at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2])
-                    {
-
-                        *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
-                        *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
-                        *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
-                        i_explicit_ligand_atom++;
-                    }
-                }
 
                 /* Enter this if when arg in command line is -a */
                 if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
@@ -358,6 +356,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->res_name, at_in[i].resname);
                             strncpy(atom->chain, at_in[i].chain, 2);
                             atom->res_id = at_in[i].resid;
+                            // fprintf(stdout, " here : %c\n", at_in[i].insertion[0]);
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -434,25 +433,24 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
+            if (pdb->n_xlig_atoms)
+            {
+                if (at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2])
+                {
+
+                    *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
+                    *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
+                    *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
+                    i_explicit_ligand_atom++;
+                }
+            }
         }
         else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
         {
 
             if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
             { /*first occurence*/
-                if (pdb->n_xlig_atoms)
-                {
-                    if ((at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
-                    {
-                        // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
 
-                        *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
-                        *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
-                        *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
-
-                        i_explicit_ligand_atom++;
-                    }
-                }
                 if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
                 {
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
@@ -617,6 +615,19 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
+            if (pdb->n_xlig_atoms)
+            {
+                if ((at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                {
+                    // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
+
+                    *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
+                    *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
+                    *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
+
+                    i_explicit_ligand_atom++;
+                }
+            }
         }
         else if (strncmp(at_in[i].atom_type, "CRYST1", 6) == 0)
         {
@@ -628,6 +639,9 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     }
 
     pdb->avg_bfactor = 0.0;
+    pdb->min_bfactor = 0.0;
+    pdb->max_bfactor = 0.0;
+    
     for (i = 0; i < iatoms; i++)
     {
         atom = atoms + i;
@@ -641,6 +655,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
         atom->ff_radius = 0.0;
         atom->ff_well_depth = 0.0;
         atom->ff_well_depth_set = 0;
+        if(atom->bfactor<pdb->min_bfactor){
+            pdb->min_bfactor=atom->bfactor;
+        }
+        if(atom->bfactor>pdb->max_bfactor){
+            pdb->max_bfactor=atom->bfactor;
+        }
     }
     int num_h_atoms = get_number_of_h_atoms(pdb);
     pdb->avg_bfactor /= (iatoms - num_h_atoms);

src/rpdb.c

@@ -901,11 +901,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
                         // fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
 
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                        {
-                            pdb->n_xlig_atoms++;
-                            fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
-                        }
+                        // if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        // {
+                        //     pdb->n_xlig_atoms++;
+                        //     fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
+                        // }
 
                         if (is_ligand(par->chain_as_ligand, buf[21]))
                         {
@@ -914,7 +914,18 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         }
                     }
                 }
+                if (x < 9990 && y < 9990 && z < 9990)
+                {
+                    if (par->xlig_resnumber > -1)
+                    {
+                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        {
+                            pdb->n_xlig_atoms++;
+                        }
+                    }
+                }
             }
+
             else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, buf[21])))
             {
                 if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
@@ -969,25 +980,39 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
 
                     /*handle explicit ligand input here*/
 
-                    if (par->xlig_resnumber > -1)
-                    {
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                        {
-                            pdb->n_xlig_atoms++;
-                        }
-                    }
+                    // if (par->xlig_resnumber > -1)
+                    // {
+                    //     if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                    //     {
+                    //         pdb->n_xlig_atoms++;
+                    //     }
+                    // }
                     if (is_ligand(par->chain_as_ligand, buf[21]))
                     {
                         pdb->n_xlig_atoms++;
                         // fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
                     }
                 }
+                if (x < 9990 && y < 9990 && z < 9990)
+                {
+                    rpdb_extract_atm_resname(buf, resb);
+                    resnbuf = rpdb_extract_atm_resumber(buf);
+
+                    if (par->xlig_resnumber > -1)
+                    {
+                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        {
+
+                            pdb->n_xlig_atoms++;
+                        }
+                    }
+                }
             }
 
             /*
         else if (!strncmp(buf, "HEADER", 6))
             strncpy(pdb->header, buf, M_PDB_BUF_LEN) ;
-*/
+    */
 
             else if (model_read == 1 && !strncmp(buf, "ENDMDL", 6))
                 model_read = 0;
@@ -1023,7 +1048,6 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         pdb->latm_lig = (s_atm **)my_calloc(natm_lig, sizeof(s_atm *));
     else
         pdb->latm_lig = NULL;
-
     pdb->natoms = natoms;
     pdb->nhetatm = nhetatm;
     pdb->natm_lig = natm_lig;
@@ -1128,15 +1152,15 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
                     /* Enter this if when arg in command line is -r */
-                    if (pdb->n_xlig_atoms)
-                    {
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                        {
+                    // if (pdb->n_xlig_atoms)
+                    // {
+                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                    //     {
 
-                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-                            i_explicit_ligand_atom++;
-                        }
-                    }
+                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                    //         i_explicit_ligand_atom++;
+                    //     }
+                    // }
 
                     /* Enter this if when arg in command line is -a */
                     if (is_ligand(params->chain_as_ligand, pdb_line[21]))
@@ -1228,6 +1252,21 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                     }
                 }
+                if (tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
+                {
+                    if (pdb->n_xlig_atoms)
+                    {
+                        rpdb_extract_atm_resname(pdb_line, resb);
+                        resnbuf = rpdb_extract_atm_resumber(pdb_line);
+
+                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        {
+
+                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                            i_explicit_ligand_atom++;
+                        }
+                    }
+                }
             }
             else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, pdb_line[21])))
             {
@@ -1244,17 +1283,17 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
 
-                    if (pdb->n_xlig_atoms)
-                    {
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                        {
-                            // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
+                    // if (pdb->n_xlig_atoms)
+                    // {
+                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                    //     {
+                    //         // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
 
-                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
 
-                            i_explicit_ligand_atom++;
-                        }
-                    }
+                    //         i_explicit_ligand_atom++;
+                    //     }
+                    // }
                     if (is_ligand(params->chain_as_ligand, pdb_line[21]))
                     {
 
@@ -1375,6 +1414,23 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                     }
                 }
+
+                if (tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
+                {
+
+                    if (pdb->n_xlig_atoms)
+                    {
+                        resnbuf = rpdb_extract_atm_resumber(pdb_line);
+                        rpdb_extract_atm_resname(pdb_line, resb);
+                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        {
+
+                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+
+                            i_explicit_ligand_atom++;
+                        }
+                    }
+                }
             }
             else if (strncmp(pdb_line, "CRYST1", 6) == 0)
             {
@@ -1388,6 +1444,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         }
     }
     pdb->avg_bfactor = 0.0;
+    pdb->min_bfactor = 0.0;
+    pdb->max_bfactor = 0.0;
     for (i = 0; i < iatoms; i++)
     {
         atom = atoms + i;
@@ -1401,6 +1459,12 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         atom->ff_radius = 0.0;
         atom->ff_well_depth = 0.0;
         atom->ff_well_depth_set = 0;
+        if(atom->bfactor<pdb->min_bfactor){
+            pdb->min_bfactor=atom->bfactor;
+        }
+        if(atom->bfactor>pdb->max_bfactor){
+            pdb->max_bfactor=atom->bfactor;
+        }   
     }
     int num_h_atoms = get_number_of_h_atoms(pdb);
     pdb->natoms_h = num_h_atoms;

src/voronoi.c

@@ -44,115 +44,6 @@ double frand_a_b(double a, double b)
     return (rand() / (double)RAND_MAX) * (b - a) + a;
 }
 
-/**
-   ## FUNCTION:
-    s_lst_vvertice
-
-   ## SPECIFICATION:
-    Calculate voronoi vertices using an ensemble of atoms, and then load resulting
-    vertices into a s_lst_vvertice structure. The function call an external
-    programm qvoronoi, part of qhull programme which can be download at:
-        http://www.qhull.org/download/
-    or installed with apt-get install qhull-bin
-
-   ## PARAMETRES:
-    @ s_pdb *pdb          : PDB informations
-    @ int min_apol_neigh  : Number of apolar neighbor of a vertice to be
-                            considered as apolar
-    @ float asph_min_size : Minimum size of voronoi vertices to retain
-    @ float asph_max_size : Maximum size of voronoi vertices to retain
-
-   ## RETURN:
-    s_lst_vvertice * :The structure containing the list of vertices.
-
- */
-s_lst_vvertice *load_vvertices_DEPRECATED(s_pdb *pdb, int min_apol_neigh, float asph_min_size, float asph_max_size, float xshift, float yshift, float zshift)
-{
-    int i,
-        nb_h = 0;
-
-    s_atm *ca = NULL;
-    s_lst_vvertice *lvvert = NULL;
-
-    char tmpn1[250] = "";
-    char tmpn2[250] = "";
-    const char *env = getenv("TMPDIR");
-    pid_t pid = getpid();
-    if (!env)
-        env = "/tmp/";
-    sprintf(tmpn1, "%s/qvoro_in_fpocket_%d.dat", env, pid);
-    sprintf(tmpn2, "%s/qvoro_out_fpocket_%d.dat", env, pid);
-
-    srand(time(NULL));
-
-    FILE *fvoro = fopen(tmpn1, "w+");
-    FILE *ftmp = fopen(tmpn2, "w");
-
-    if (fvoro != NULL)
-    {
-        lvvert = (s_lst_vvertice *)my_malloc(sizeof(s_lst_vvertice));
-        lvvert->h_tr = NULL;
-        /* Loop a first time to get out how many heavy atoms are in the file */
-
-        for (i = 0; i < pdb->natoms; i++)
-        {
-            ca = (pdb->latoms) + i;
-            if (strcmp(ca->symbol, "H") != 0)
-            {
-                lvvert->h_tr = (int *)my_realloc(lvvert->h_tr, sizeof(int) * (i - nb_h + 1));
-                lvvert->h_tr[i - nb_h] = i;
-            }
-            else
-                nb_h++;
-        }
-        lvvert->n_h_tr = i - nb_h;
-
-        /* Write the header for qvoronoi */
-        fprintf(fvoro, "3 rbox D3\n%d\n", lvvert->n_h_tr);
-        /* Loop a second time for the qvoronoi input coordinates */
-
-        for (i = 0; i < pdb->natoms; i++)
-        {
-
-            ca = (pdb->latoms) + i;
-            if (strcmp(ca->symbol, "H") != 0)
-            {
-                fprintf(fvoro, "%.6f %.6f %.6f\n", ca->x + xshift, ca->y + yshift, ca->z + zshift);
-            }
-        }
-
-        fflush(fvoro);
-        rewind(fvoro);
-
-        // int status = system("qvoronoi p i Pp Fn < voro_tmp.dat > voro.tmp") ;
-        run_qvoronoi(fvoro, ftmp);
-        int status = M_VORONOI_SUCCESS;
-
-        if (status == M_VORONOI_SUCCESS)
-        {
-            fill_vvertices(lvvert, tmpn2, pdb->latoms, pdb->natoms,
-                           min_apol_neigh, asph_min_size, asph_max_size, xshift, yshift, zshift, pdb->avg_bfactor, pdb);
-        }
-        else
-        {
-            my_free(lvvert);
-            lvvert = NULL;
-            fprintf(stderr, "! Voronoi command failed with status %d...\n", status);
-        }
-    }
-    else
-    {
-        fprintf(stderr, "! File for Voronoi vertices calculation couldn't be opened...\n");
-    }
-    fclose(fvoro);
-    fclose(ftmp);
-
-    remove(tmpn1);
-    remove(tmpn2);
-
-    return lvvert;
-}
-
 /**
    ## FUNCTION:
 
@@ -175,7 +66,7 @@ s_lst_vvertice *load_vvertices_DEPRECATED(s_pdb *pdb, int min_apol_neigh, float
     s_lst_vvertice * :The structure containing the list of vertices.
 
  */
-s_lst_vvertice *load_vvertices(s_pdb *pdb, int min_apol_neigh, float asph_min_size, float asph_max_size, float xshift, float yshift, float zshift)
+s_lst_vvertice *load_vvertices(s_pdb *pdb, s_fparams *params, float xshift, float yshift, float zshift)
 {
     int i, j,
         nb_h = 0;
@@ -252,11 +143,11 @@ s_lst_vvertice *load_vvertices(s_pdb *pdb, int min_apol_neigh, float asph_min_si
             if (j == 0)
             {
                 fill_vvertices(lvvert, tmpn2, pdb->latoms, pdb->natoms,
-                               min_apol_neigh, asph_min_size, asph_max_size, xshift, yshift, zshift, pdb->avg_bfactor, pdb);
+                               params, xshift, yshift, zshift, pdb->avg_bfactor, pdb);
             }
             else
             {
-                add_missing_vvertices(lvvert, tmpn2, pdb->latoms, min_apol_neigh, asph_min_size, asph_max_size, xshift, yshift, zshift, pdb->avg_bfactor, pdb);
+                add_missing_vvertices(lvvert, tmpn2, pdb->latoms, params, xshift, yshift, zshift, pdb->avg_bfactor, pdb);
             }
         }
         //        printf("nverts : %d\n", lvvert->nvert);
@@ -476,7 +367,7 @@ int free_cluster_lib_vertices(s_clusterlib_vertices *clusterlib_vertices, int nv
 
  */
 void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, int natoms,
-                    int min_apol_neigh, float asph_min_size, float asph_max_size,
+                    s_fparams *params,
                     float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb)
 {
     FILE *f = NULL;   /* File handler for vertices coordinates */
@@ -484,7 +375,9 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
     /*FILE *fvNb = NULL ;  File handler for vertices vertice neighbours */
 
     s_vvertice *v = NULL;
-
+    int min_apol_neigh = params->min_apol_neigh;
+    float asph_min_size = params->asph_min_size;
+    float asph_max_size = params->asph_max_size;
     float tmpRadius; /* Temporary Ray of voronoi vertice (ray of alpha sphere) */
     float xyz[3] = {0, 0, 0};
 
@@ -522,7 +415,6 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
     lvvert->tr = (int *)my_malloc(lvvert->nvert * sizeof(int));
     for (i = 0; i < lvvert->nvert; i++)
         lvvert->tr[i] = -1;
-
     lvvert->vertices = (s_vvertice *)my_calloc(M_BUFSIZE, sizeof(s_vvertice));
     lvvert->pvertices = (s_vvertice **)my_calloc(M_BUFSIZE, sizeof(s_vvertice *));
 
@@ -557,8 +449,7 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
                 /* Test voro. vert. for alpha sphere cond. and returns radius if
                  * cond. are ok, -1 else */
 
-                tmpRadius = testVvertice(xyz, curNbIdx, atoms, asph_min_size,
-                                         asph_max_size, lvvert, xshift, yshift, zshift, avg_bfactor, pdb);
+                tmpRadius = testVvertice(xyz, curNbIdx, atoms, params, lvvert, xshift, yshift, zshift, avg_bfactor, pdb);
                 //                fprintf(stdout, "%f\n", tmpRadius);
                 if (tmpRadius > 0)
                 {
@@ -652,7 +543,7 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
 
  */
 void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms,
-                           int min_apol_neigh, float asph_min_size, float asph_max_size,
+                           s_fparams *params,
                            float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb)
 {
     FILE *f = NULL;    /* File handler for vertices coordinates */
@@ -742,8 +633,7 @@ void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *at
                     /* Test voro. vert. for alpha sphere cond. and returns radius if
                      * cond. are ok, -1 else */
 
-                    tmpRadius = testVvertice(xyz, curNbIdx, atoms, asph_min_size,
-                                             asph_max_size, lvvert, xshift, yshift, zshift, avg_bfactor, pdb);
+                    tmpRadius = testVvertice(xyz, curNbIdx, atoms, params, lvvert, xshift, yshift, zshift, avg_bfactor, pdb);
                     if (tmpRadius > 0)
                     {
                         tmpv->x = xyz[0] - xshift;
@@ -777,7 +667,7 @@ void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *at
                         //                        vInMem++ ; /* Vertices actually read
                         //                        v->id = natoms + i + 1 - vInMem ;
 
-                        if (tmpApolar >= min_apol_neigh)
+                        if (tmpApolar >= params->min_apol_neigh)
                             tmpv->type = M_APOLAR_AS;
                         else
                             tmpv->type = M_POLAR_AS;
@@ -1025,6 +915,38 @@ void set_barycenter(s_vvertice *v)
     v->bary[2] = zsum * 0.25;
 }
 
+/**
+ * ## FUNCTION:
+    atom_in_explicit_pocket
+
+   ## SPECIFICATION:
+    When specifying an explicit pocket, check if current atom is part of this explicit pocket
+
+   ## PARAMETERS:
+    @ s_atm *cura          : The current atom
+    @ s_fparams           : All fpocket parameters
+
+
+   ## RETURN:
+    short unsigned int : 0 if not part of the explicit pocket, 1 if it is part of the explicit pocket
+
+*/
+float atom_in_explicit_pocket(s_atm *cura, s_fparams *params)
+{
+    int current_residue_index;
+    for (current_residue_index = 0; current_residue_index < params->xpocket_n; current_residue_index++)
+    {
+
+        if (params->xpocket_residue_number[current_residue_index] == cura->res_id &&
+            params->xpocket_chain_code[current_residue_index] == cura->chain[0] &&
+            ((params->xpocket_insertion_code[current_residue_index] == cura->pdb_insert) || ((params->xpocket_insertion_code[current_residue_index] == '-' && cura->pdb_insert == ' ') || (params->xpocket_insertion_code[current_residue_index] == '-' && cura->pdb_insert == '\0'))))
+        {
+            return 1;
+        }
+    }
+    return 0;
+}
+
 /**
    ## FUNCTION:
     testVvertice
@@ -1045,17 +967,39 @@ void set_barycenter(s_vvertice *v)
 
  */
 float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
-                   float min_asph_size, float max_asph_size,
+                   s_fparams *params,
                    s_lst_vvertice *lvvert,
                    float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb)
 {
+    float min_asph_size = params->asph_min_size;
+    float max_asph_size = params->asph_max_size;
     float x = xyz[0] - xshift,
           y = xyz[1] - yshift,
           z = xyz[2] - zshift;
     float baryx = 0.0, baryy = 0.0, baryz = 0.0;
     float barybf = 0.0; /*temporary b factor for all atoms contacting the sphere*/
+    float sdbf=0.0;
     //    if(curNbIdx[0]!=lvvert->h_tr[curNbIdx[0]]) printf("%d vs %d : %s vs %s\n",curNbIdx[0],lvvert->h_tr[curNbIdx[0]],atoms[curNbIdx[0]].symbol,atoms[lvvert->h_tr[curNbIdx[0]]].symbol);
-    s_atm *cura = &(atoms[lvvert->h_tr[curNbIdx[0]]]);
+    s_atm *cura;
+
+    short unsigned int cur_atom_index = 0;
+    int n_explicit_atoms_ok = 0;
+    int vidx;
+
+    if (params->xpocket_n > 0)
+    {
+        for (cur_atom_index = 0; cur_atom_index < 4; cur_atom_index++)
+        {
+            cura = &(atoms[lvvert->h_tr[curNbIdx[cur_atom_index]]]);
+            if (atom_in_explicit_pocket(cura, params))
+                n_explicit_atoms_ok++;
+        }
+        if (n_explicit_atoms_ok < params->min_n_explicit_pocket_atoms)
+            return -3.0;
+    }
+
+    cura = &(atoms[lvvert->h_tr[curNbIdx[0]]]);
+
     baryx += cura->x;
     baryy += cura->y;
     baryz += cura->z;
@@ -1121,7 +1065,14 @@ float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
                 return (-1.0);
             }
 
-            if (avg_bfactor > 0.0 && barybf / avg_bfactor > 1.4)
+            //Compute local bfactor standard deviation (aims to avoid filtering out collective motions)
+            for(vidx=0;vidx<4;vidx++){
+                cura = &(atoms[lvvert->h_tr[curNbIdx[vidx]]]);
+                sdbf += (cura->bfactor-barybf)*(cura->bfactor-barybf);
+            }
+            sdbf=sqrt(sdbf/3);
+            if (((sdbf>avg_bfactor) || (sdbf>((pdb->max_bfactor-pdb->min_bfactor)/4))) && ((avg_bfactor > 0.0) && (barybf / avg_bfactor > 1.4)))
+            // if ((avg_bfactor > 0.0) && (barybf / avg_bfactor > 1.4))
                 return (-1.0);
             /*now test if the vertice is not too far away from the pocket*/
             if (dist(baryx, baryy, baryz, xyz[0], xyz[1], xyz[2]) > 1.0 && distVatom1 > (max_asph_size - 1.5))
@@ -1485,37 +1436,51 @@ void DEPR_write_pdb_vert(FILE *f, s_vvertice *v)
  */
 void write_pdb_vert(FILE *f, s_vvertice *v, int i)
 {
+    if(v->electrostatic_energy!=0.0){
+        if (v->electrostatic_energy <= -0.05)
+        {
+            write_pdb_atom_line(f, "HETATM", i, " POL",
+                                ' ', "ACC", "O", v->resid, ' ',
+                                v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);
+            /*write_mmcif_atom_line(f, "HETATM", i, " POL",
+                                ' ', "ACC", "O", v->resid, ' ',
+                                v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);*/
+        }
+        else if (v->electrostatic_energy >= 0.05)
+        {
+            write_pdb_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
+                                v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);
+            /*write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
+                                v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);*/
+        }
+        else
+        {
+            write_pdb_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
+                                v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);
+            /* write_mmcif_atom_line(f, "HETATM", i, " POL",
+                                ' ', "ACC", "O", v->resid, ' ',
+                                v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);*/
+        }
+    }
+    else {
+        if (v->type == M_APOLAR_AS)
+            write_pdb_atom_line(f, "HETATM", i, "APOL",
+                                ' ', "STP", "C", v->resid, ' ',
+                                v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);
 
-    if (v->electrostatic_energy <= -0.05)
-    {
-        write_pdb_atom_line(f, "HETATM", i, " POL",
-                            ' ', "ACC", "O", v->resid, ' ',
-                            v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);
-        /*write_mmcif_atom_line(f, "HETATM", i, " POL",
-                            ' ', "ACC", "O", v->resid, ' ',
-                            v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);*/
-    }
-    else if (v->electrostatic_energy >= 0.05)
-    {
-        write_pdb_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
-                            v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);
-        /*write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
-                            v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);*/
-    }
-    else
-    {
-        write_pdb_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
-                            v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);
-        /* write_mmcif_atom_line(f, "HETATM", i, " POL",
-                            ' ', "ACC", "O", v->resid, ' ',
-                            v->x, v->y, v->z, 0.0, 0.0, 0,
-                            "Ve", -1, 0.0);*/
+        else
+            write_pdb_atom_line(f, "HETATM", v->id, " POL", ' ', "STP", "C",
+                                v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+                                "Ve", -1, 0.0);
     }
+    
 }
 
 void write_mmcif_vert(FILE *f, s_vvertice *v, int i)

src/writepocket.c

@@ -524,6 +524,7 @@ void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
 void write_pocket_pqr(const char out[], s_pocket *pocket) {
     node_vertice *vcur = NULL;
     int i=0;
+
     FILE *f = fopen(out, "w");
     if (f && pocket) {
         fprintf(f, "HEADER\n");
@@ -607,7 +608,7 @@ void write_pocket_pdb(const char out[], s_pocket *pocket) {
         fprintf(f, "HEADER 7  - Polarity Score                    : %5d\n", pocket->pdesc->polarity_score);
         fprintf(f, "HEADER 8  - Amino Acid based volume Score     : %.4f\n", pocket->pdesc->volume_score);
         fprintf(f, "HEADER 9  - Pocket volume (Monte Carlo)       : %.4f\n", pocket->pdesc->volume);
-        fprintf(f, "HEADER 10  -Pocket volume (convex hull)       : %.4f\n", pocket->pdesc->convex_hull_volume);
+        fprintf(f, "HEADER 10 - Pocket volume (convex hull)       : %.4f\n", pocket->pdesc->convex_hull_volume);
         fprintf(f, "HEADER 11 - Charge Score                      : %5d\n", pocket->pdesc->charge_score);
         fprintf(f, "HEADER 12 - Local hydrophobic density Score   : %.4f\n", pocket->pdesc->mean_loc_hyd_dens);
         fprintf(f, "HEADER 13 - Number of apolar alpha sphere     : %5d\n", pocket->nAlphaApol);

tests/reference_output/1ATP_out/1ATP_info.txt

@@ -5,7 +5,7 @@ Pocket 1 :
 	Total SASA : 	8.888
 	Polar SASA : 	6.473
 	Apolar SASA : 	2.415
-	Volume : 	585.250
+	Volume : 	590.402
 	Mean local hydrophobic density : 	38.950
 	Mean alpha sphere radius :	3.904
 	Mean alp. sph. solvent access : 	0.457
@@ -17,37 +17,16 @@ Pocket 1 :
 	Proportion of polar atoms: 	43.636
 	Alpha sphere density : 	5.607
 	Cent. of mass - Alpha Sphere max dist: 	14.180
-	Flexibility : 	0.206
+	Flexibility : 	0.089
 
 Pocket 2 :
-	Score : 	0.140
-	Druggability Score : 	0.001
-	Number of Alpha Spheres : 	19
-	Total SASA : 	55.125
-	Polar SASA : 	23.727
-	Apolar SASA : 	31.398
-	Volume : 	262.323
-	Mean local hydrophobic density : 	4.000
-	Mean alpha sphere radius :	3.971
-	Mean alp. sph. solvent access : 	0.614
-	Apolar alpha sphere proportion : 	0.263
-	Hydrophobicity score:	12.167
-	Volume score: 	 4.250
-	Polarity score:	 7
-	Charge score :	 1
-	Proportion of polar atoms: 	56.522
-	Alpha sphere density : 	3.460
-	Cent. of mass - Alpha Sphere max dist: 	9.040
-	Flexibility : 	0.893
-
-Pocket 3 :
 	Score : 	0.127
 	Druggability Score : 	0.006
 	Number of Alpha Spheres : 	18
 	Total SASA : 	13.148
 	Polar SASA : 	1.071
 	Apolar SASA : 	12.076
-	Volume : 	77.200
+	Volume : 	78.453
 	Mean local hydrophobic density : 	17.000
 	Mean alpha sphere radius :	3.543
 	Mean alp. sph. solvent access : 	0.402
@@ -59,16 +38,16 @@ Pocket 3 :
 	Proportion of polar atoms: 	7.143
 	Alpha sphere density : 	1.532
 	Cent. of mass - Alpha Sphere max dist: 	3.109
-	Flexibility : 	0.632
+	Flexibility : 	0.273
 
-Pocket 4 :
+Pocket 3 :
 	Score : 	0.120
 	Druggability Score : 	0.001
 	Number of Alpha Spheres : 	37
 	Total SASA : 	72.975
 	Polar SASA : 	34.331
 	Apolar SASA : 	38.644
-	Volume : 	253.085
+	Volume : 	245.352
 	Mean local hydrophobic density : 	7.000
 	Mean alpha sphere radius :	3.703
 	Mean alp. sph. solvent access : 	0.441
@@ -80,7 +59,28 @@ Pocket 4 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	3.103
 	Cent. of mass - Alpha Sphere max dist: 	8.153
-	Flexibility : 	0.345
+	Flexibility : 	0.149
+
+Pocket 4 :
+	Score : 	0.109
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	22
+	Total SASA : 	68.866
+	Polar SASA : 	30.222
+	Apolar SASA : 	38.644
+	Volume : 	348.112
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	4.052
+	Mean alp. sph. solvent access : 	0.605
+	Apolar alpha sphere proportion : 	0.273
+	Hydrophobicity score:	8.846
+	Volume score: 	 4.231
+	Polarity score:	 8
+	Charge score :	 0
+	Proportion of polar atoms: 	57.692
+	Alpha sphere density : 	3.539
+	Cent. of mass - Alpha Sphere max dist: 	9.040
+	Flexibility : 	0.444
 
 Pocket 5 :
 	Score : 	0.099
@@ -89,7 +89,7 @@ Pocket 5 :
 	Total SASA : 	49.935
 	Polar SASA : 	36.651
 	Apolar SASA : 	13.284
-	Volume : 	192.686
+	Volume : 	191.749
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.800
 	Mean alp. sph. solvent access : 	0.414
@@ -101,7 +101,7 @@ Pocket 5 :
 	Proportion of polar atoms: 	66.667
 	Alpha sphere density : 	2.630
 	Cent. of mass - Alpha Sphere max dist: 	5.374
-	Flexibility : 	0.461
+	Flexibility : 	0.199
 
 Pocket 6 :
 	Score : 	0.082
@@ -110,7 +110,7 @@ Pocket 6 :
 	Total SASA : 	33.550
 	Polar SASA : 	21.473
 	Apolar SASA : 	12.076
-	Volume : 	117.318
+	Volume : 	113.865
 	Mean local hydrophobic density : 	4.000
 	Mean alpha sphere radius :	3.603
 	Mean alp. sph. solvent access : 	0.400
@@ -125,34 +125,13 @@ Pocket 6 :
 	Flexibility : 	0.000
 
 Pocket 7 :
-	Score : 	0.082
-	Druggability Score : 	0.005
-	Number of Alpha Spheres : 	31
-	Total SASA : 	82.474
-	Polar SASA : 	25.715
-	Apolar SASA : 	56.759
-	Volume : 	340.515
-	Mean local hydrophobic density : 	14.750
-	Mean alpha sphere radius :	4.083
-	Mean alp. sph. solvent access : 	0.590
-	Apolar alpha sphere proportion : 	0.516
-	Hydrophobicity score:	15.727
-	Volume score: 	 4.182
-	Polarity score:	 6
-	Charge score :	 0
-	Proportion of polar atoms: 	44.444
-	Alpha sphere density : 	3.292
-	Cent. of mass - Alpha Sphere max dist: 	8.916
-	Flexibility : 	0.730
-
-Pocket 8 :
 	Score : 	0.080
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	15
 	Total SASA : 	24.543
 	Polar SASA : 	6.429
 	Apolar SASA : 	18.114
-	Volume : 	110.939
+	Volume : 	111.778
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.630
 	Mean alp. sph. solvent access : 	0.358
@@ -164,16 +143,16 @@ Pocket 8 :
 	Proportion of polar atoms: 	42.857
 	Alpha sphere density : 	1.666
 	Cent. of mass - Alpha Sphere max dist: 	3.746
-	Flexibility : 	0.068
+	Flexibility : 	0.029
 
-Pocket 9 :
+Pocket 8 :
 	Score : 	0.043
 	Druggability Score : 	0.009
 	Number of Alpha Spheres : 	22
 	Total SASA : 	81.162
 	Polar SASA : 	10.803
 	Apolar SASA : 	70.359
-	Volume : 	257.653
+	Volume : 	254.082
 	Mean local hydrophobic density : 	15.000
 	Mean alpha sphere radius :	3.719
 	Mean alp. sph. solvent access : 	0.435
@@ -185,16 +164,16 @@ Pocket 9 :
 	Proportion of polar atoms: 	26.316
 	Alpha sphere density : 	3.360
 	Cent. of mass - Alpha Sphere max dist: 	6.916
-	Flexibility : 	0.655
+	Flexibility : 	0.282
 
-Pocket 10 :
+Pocket 9 :
 	Score : 	0.040
 	Druggability Score : 	0.001
 	Number of Alpha Spheres : 	16
 	Total SASA : 	74.931
 	Polar SASA : 	39.910
 	Apolar SASA : 	35.021
-	Volume : 	253.870
+	Volume : 	265.169
 	Mean local hydrophobic density : 	6.000
 	Mean alpha sphere radius :	3.866
 	Mean alp. sph. solvent access : 	0.612
@@ -206,16 +185,16 @@ Pocket 10 :
 	Proportion of polar atoms: 	42.105
 	Alpha sphere density : 	3.366
 	Cent. of mass - Alpha Sphere max dist: 	6.920
-	Flexibility : 	0.769
+	Flexibility : 	0.332
 
-Pocket 11 :
+Pocket 10 :
 	Score : 	0.033
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	16
 	Total SASA : 	59.946
 	Polar SASA : 	41.831
 	Apolar SASA : 	18.114
-	Volume : 	189.370
+	Volume : 	184.388
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.746
 	Mean alp. sph. solvent access : 	0.505
@@ -227,37 +206,37 @@ Pocket 11 :
 	Proportion of polar atoms: 	60.000
 	Alpha sphere density : 	2.650
 	Cent. of mass - Alpha Sphere max dist: 	6.451
-	Flexibility : 	0.948
+	Flexibility : 	0.408
+
+Pocket 11 :
+	Score : 	0.028
+	Druggability Score : 	0.004
+	Number of Alpha Spheres : 	33
+	Total SASA : 	107.153
+	Polar SASA : 	31.072
+	Apolar SASA : 	76.081
+	Volume : 	425.611
+	Mean local hydrophobic density : 	14.750
+	Mean alpha sphere radius :	4.088
+	Mean alp. sph. solvent access : 	0.593
+	Apolar alpha sphere proportion : 	0.485
+	Hydrophobicity score:	15.727
+	Volume score: 	 4.182
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	40.000
+	Alpha sphere density : 	3.609
+	Cent. of mass - Alpha Sphere max dist: 	10.761
+	Flexibility : 	0.370
 
 Pocket 12 :
-	Score : 	0.033
-	Druggability Score : 	0.295
-	Number of Alpha Spheres : 	35
-	Total SASA : 	99.895
-	Polar SASA : 	12.946
-	Apolar SASA : 	86.949
-	Volume : 	306.298
-	Mean local hydrophobic density : 	32.941
-	Mean alpha sphere radius :	3.827
-	Mean alp. sph. solvent access : 	0.450
-	Apolar alpha sphere proportion : 	0.971
-	Hydrophobicity score:	67.091
-	Volume score: 	 5.727
-	Polarity score:	 5
-	Charge score :	 0
-	Proportion of polar atoms: 	19.231
-	Alpha sphere density : 	3.327
-	Cent. of mass - Alpha Sphere max dist: 	6.862
-	Flexibility : 	0.625
-
-Pocket 13 :
 	Score : 	0.023
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	25
 	Total SASA : 	95.745
 	Polar SASA : 	55.893
 	Apolar SASA : 	39.852
-	Volume : 	418.062
+	Volume : 	417.352
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	4.066
 	Mean alp. sph. solvent access : 	0.569
@@ -269,16 +248,16 @@ Pocket 13 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	3.596
 	Cent. of mass - Alpha Sphere max dist: 	9.100
-	Flexibility : 	0.563
+	Flexibility : 	0.243
 
-Pocket 14 :
+Pocket 13 :
 	Score : 	0.014
 	Druggability Score : 	0.006
 	Number of Alpha Spheres : 	25
 	Total SASA : 	93.954
 	Polar SASA : 	32.365
 	Apolar SASA : 	61.589
-	Volume : 	370.607
+	Volume : 	369.771
 	Mean local hydrophobic density : 	11.000
 	Mean alpha sphere radius :	4.069
 	Mean alp. sph. solvent access : 	0.617
@@ -290,16 +269,16 @@ Pocket 14 :
 	Proportion of polar atoms: 	41.667
 	Alpha sphere density : 	3.378
 	Cent. of mass - Alpha Sphere max dist: 	9.735
-	Flexibility : 	0.574
+	Flexibility : 	0.248
 
-Pocket 15 :
+Pocket 14 :
 	Score : 	0.006
 	Druggability Score : 	0.009
 	Number of Alpha Spheres : 	29
 	Total SASA : 	113.512
 	Polar SASA : 	38.639
 	Apolar SASA : 	74.873
-	Volume : 	421.636
+	Volume : 	419.488
 	Mean local hydrophobic density : 	15.000
 	Mean alpha sphere radius :	4.236
 	Mean alp. sph. solvent access : 	0.683
@@ -311,7 +290,28 @@ Pocket 15 :
 	Proportion of polar atoms: 	37.037
 	Alpha sphere density : 	4.007
 	Cent. of mass - Alpha Sphere max dist: 	10.728
-	Flexibility : 	0.608
+	Flexibility : 	0.262
+
+Pocket 15 :
+	Score : 	0.005
+	Druggability Score : 	0.526
+	Number of Alpha Spheres : 	38
+	Total SASA : 	113.179
+	Polar SASA : 	12.946
+	Apolar SASA : 	100.233
+	Volume : 	359.526
+	Mean local hydrophobic density : 	35.838
+	Mean alpha sphere radius :	3.829
+	Mean alp. sph. solvent access : 	0.472
+	Apolar alpha sphere proportion : 	0.974
+	Hydrophobicity score:	67.091
+	Volume score: 	 5.727
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	16.667
+	Alpha sphere density : 	3.420
+	Cent. of mass - Alpha Sphere max dist: 	7.998
+	Flexibility : 	0.314
 
 Pocket 16 :
 	Score : 	-0.011
@@ -320,7 +320,7 @@ Pocket 16 :
 	Total SASA : 	78.643
 	Polar SASA : 	50.868
 	Apolar SASA : 	27.775
-	Volume : 	269.811
+	Volume : 	268.902
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.747
 	Mean alp. sph. solvent access : 	0.563
@@ -332,7 +332,7 @@ Pocket 16 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	2.899
 	Cent. of mass - Alpha Sphere max dist: 	7.698
-	Flexibility : 	0.313
+	Flexibility : 	0.135
 
 Pocket 17 :
 	Score : 	-0.021
@@ -341,7 +341,7 @@ Pocket 17 :
 	Total SASA : 	55.726
 	Polar SASA : 	37.612
 	Apolar SASA : 	18.114
-	Volume : 	169.833
+	Volume : 	171.872
 	Mean local hydrophobic density : 	10.000
 	Mean alpha sphere radius :	3.984
 	Mean alp. sph. solvent access : 	0.501
@@ -353,28 +353,28 @@ Pocket 17 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	1.832
 	Cent. of mass - Alpha Sphere max dist: 	3.476
-	Flexibility : 	0.595
+	Flexibility : 	0.257
 
 Pocket 18 :
-	Score : 	-0.086
+	Score : 	-0.072
 	Druggability Score : 	0.000
-	Number of Alpha Spheres : 	18
-	Total SASA : 	90.467
-	Polar SASA : 	32.343
-	Apolar SASA : 	58.124
-	Volume : 	257.485
-	Mean local hydrophobic density : 	0.000
-	Mean alpha sphere radius :	4.040
-	Mean alp. sph. solvent access : 	0.490
-	Apolar alpha sphere proportion : 	0.056
-	Hydrophobicity score:	33.300
-	Volume score: 	 4.600
-	Polarity score:	 6
-	Charge score :	 2
-	Proportion of polar atoms: 	47.368
-	Alpha sphere density : 	2.586
-	Cent. of mass - Alpha Sphere max dist: 	5.626
-	Flexibility : 	0.768
+	Number of Alpha Spheres : 	16
+	Total SASA : 	61.067
+	Polar SASA : 	15.177
+	Apolar SASA : 	45.890
+	Volume : 	164.296
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	3.903
+	Mean alp. sph. solvent access : 	0.516
+	Apolar alpha sphere proportion : 	0.375
+	Hydrophobicity score:	9.143
+	Volume score: 	 4.714
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	30.769
+	Alpha sphere density : 	1.575
+	Cent. of mass - Alpha Sphere max dist: 	3.520
+	Flexibility : 	0.419
 
 Pocket 19 :
 	Score : 	-0.086
@@ -383,7 +383,7 @@ Pocket 19 :
 	Total SASA : 	91.415
 	Polar SASA : 	51.563
 	Apolar SASA : 	39.852
-	Volume : 	201.650
+	Volume : 	208.742
 	Mean local hydrophobic density : 	2.000
 	Mean alpha sphere radius :	3.840
 	Mean alp. sph. solvent access : 	0.453
@@ -395,5 +395,26 @@ Pocket 19 :
 	Proportion of polar atoms: 	53.333
 	Alpha sphere density : 	2.483
 	Cent. of mass - Alpha Sphere max dist: 	6.556
-	Flexibility : 	0.556
+	Flexibility : 	0.240
+
+Pocket 20 :
+	Score : 	-0.094
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	21
+	Total SASA : 	94.090
+	Polar SASA : 	32.343
+	Apolar SASA : 	61.747
+	Volume : 	269.433
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	4.009
+	Mean alp. sph. solvent access : 	0.541
+	Apolar alpha sphere proportion : 	0.048
+	Hydrophobicity score:	33.300
+	Volume score: 	 4.600
+	Polarity score:	 6
+	Charge score :	 2
+	Proportion of polar atoms: 	45.000
+	Alpha sphere density : 	2.500
+	Cent. of mass - Alpha Sphere max dist: 	5.626
+	Flexibility : 	0.352
 

tests/reference_output/1ATP_out/1ATP_pockets.pqr

@@ -107,405 +107,432 @@ ATOM    103    C STP     1       8.025   9.593   3.157    0.00     4.18
 ATOM    104    C STP     1       9.377   9.170   3.567    0.00     4.51
 ATOM    105    O STP     1       9.399   8.934   3.561    0.00     4.38
 ATOM    106    O STP     1       9.649   9.131   3.392    0.00     4.48
-ATOM    107    O STP     2      17.904  16.846   2.034    0.00     4.00
-ATOM    108    C STP     2      13.212  24.010  -0.223    0.00     3.56
-ATOM    109    O STP     2      13.590  24.333  -0.124    0.00     3.66
-ATOM    110    C STP     2      16.767  18.684   1.078    0.00     4.22
-ATOM    111    C STP     2      16.715  18.704   1.057    0.00     4.20
-ATOM    112    O STP     2      17.342  17.855   1.830    0.00     4.24
-ATOM    113    O STP     2      17.041  17.846   1.980    0.00     4.08
-ATOM    114    O STP     2      16.580  19.060   0.747    0.00     4.27
-ATOM    115    O STP     2      17.635  17.024   1.403    0.00     3.80
-ATOM    116    O STP     2      17.395  17.419   1.401    0.00     3.89
-ATOM    117    C STP     2      16.900  18.376   1.091    0.00     4.07
-ATOM    118    O STP     2      17.782  16.444   1.256    0.00     3.57
-ATOM    119    O STP     2      14.632  22.244  -1.461    0.00     3.60
-ATOM    120    O STP     2      14.379  23.675  -0.187    0.00     4.18
-ATOM    121    O STP     2      14.950  20.959  -0.498    0.00     4.03
-ATOM    122    O STP     2      16.062  19.544  -0.072    0.00     4.25
-ATOM    123    O STP     2      16.188  19.842  -0.177    0.00     4.42
-ATOM    124    C STP     2      16.044  18.633   0.739    0.00     3.73
-ATOM    125    O STP     2      15.502  19.054  -0.011    0.00     3.68
-ATOM    126    C STP     3       5.666  -2.347   9.650    0.00     3.64
-ATOM    127    C STP     3       5.663  -2.342   9.659    0.00     3.64
-ATOM    128    C STP     3       4.857  -3.237  11.687    0.00     3.51
-ATOM    129    C STP     3       4.909  -3.421  12.179    0.00     3.52
-ATOM    130    C STP     3       4.463  -1.923  10.602    0.00     3.52
-ATOM    131    C STP     3       4.751  -3.640  11.929    0.00     3.49
-ATOM    132    C STP     3       4.816  -3.657  12.202    0.00     3.51
-ATOM    133    C STP     3       5.643  -2.334   9.598    0.00     3.62
-ATOM    134    C STP     3       5.573  -2.273   9.693    0.00     3.63
-ATOM    135    C STP     3       5.625  -2.300   9.658    0.00     3.64
-ATOM    136    C STP     3       5.618  -2.250   9.664    0.00     3.62
-ATOM    137    C STP     3       4.669  -1.977  10.488    0.00     3.53
-ATOM    138    C STP     3       4.819  -1.860  10.403    0.00     3.43
-ATOM    139    C STP     3       4.472  -1.924  10.605    0.00     3.53
-ATOM    140    C STP     3       4.423  -1.750  10.637    0.00     3.43
-ATOM    141    C STP     3       4.474  -1.928  10.609    0.00     3.53
-ATOM    142    C STP     3       4.552  -2.069  10.740    0.00     3.51
-ATOM    143    C STP     3       4.780  -3.687  12.261    0.00     3.48
-ATOM    144    O STP     4      10.707   8.465   9.562    0.00     3.56
-ATOM    145    O STP     4      11.897   7.600  10.387    0.00     3.53
-ATOM    146    O STP     4      11.713   7.651  10.429    0.00     3.61
-ATOM    147    O STP     4      11.722   7.673  10.440    0.00     3.59
-ATOM    148    O STP     4      11.706   7.635  10.442    0.00     3.60
-ATOM    149    O STP     4      13.057   5.577  11.209    0.00     3.45
-ATOM    150    C STP     4      13.599   4.782  12.622    0.00     3.56
-ATOM    151    O STP     4      12.926   5.521  11.298    0.00     3.49
-ATOM    152    O STP     4      11.593   6.620  11.138    0.00     3.56
-ATOM    153    O STP     4      11.150   6.837  11.229    0.00     3.58
-ATOM    154    O STP     4      11.203   6.847  11.061    0.00     3.66
-ATOM    155    O STP     4      10.100   6.854  10.639    0.00     3.72
-ATOM    156    O STP     4      10.043   6.829  10.609    0.00     3.72
-ATOM    157    O STP     4      10.008   6.832  11.002    0.00     3.55
-ATOM    158    O STP     4       9.996   6.814  10.721    0.00     3.65
-ATOM    159    O STP     4      14.136   3.921  15.176    0.00     4.64
-ATOM    160    O STP     4      13.450   4.065  15.198    0.00     4.27
-ATOM    161    O STP     4      14.349   4.009  14.805    0.00     4.61
-ATOM    162    O STP     4      13.844   4.358  14.153    0.00     4.07
-ATOM    163    C STP     4      14.400   4.002  14.664    0.00     4.57
-ATOM    164    C STP     4      13.873   4.433  13.491    0.00     3.88
-ATOM    165    C STP     4      13.578   4.355  12.749    0.00     3.43
-ATOM    166    O STP     4       9.524   6.563  10.325    0.00     3.47
-ATOM    167    C STP     4       9.327   7.050  10.077    0.00     3.46
-ATOM    168    O STP     4      10.903   8.245   9.723    0.00     3.55
-ATOM    169    O STP     4      11.424   7.798  10.169    0.00     3.58
-ATOM    170    O STP     4      10.102   6.908  10.584    0.00     3.71
-ATOM    171    O STP     4      10.425   8.337   9.557    0.00     3.58
-ATOM    172    O STP     4      10.324   8.322   9.469    0.00     3.54
-ATOM    173    O STP     4      10.351   8.314   9.560    0.00     3.59
-ATOM    174    C STP     4      10.082   7.855   9.856    0.00     3.56
-ATOM    175    C STP     4       9.763   7.428   9.952    0.00     3.52
-ATOM    176    C STP     4       9.808   6.869  10.405    0.00     3.64
-ATOM    177    O STP     4      10.016   6.824  10.586    0.00     3.71
-ATOM    178    O STP     4       9.960   6.815  10.553    0.00     3.70
-ATOM    179    O STP     4       9.895   6.462  10.350    0.00     3.45
-ATOM    180    O STP     4       9.826   6.743  10.451    0.00     3.64
-ATOM    181    O STP     5      -3.903   9.091  -8.804    0.00     4.57
-ATOM    182    O STP     5      -3.754   8.992  -8.593    0.00     4.51
-ATOM    183    O STP     5      -2.044   6.009  -7.092    0.00     3.61
-ATOM    184    O STP     5      -2.612   5.104  -6.282    0.00     3.41
-ATOM    185    O STP     5      -2.076   5.517  -6.742    0.00     3.61
-ATOM    186    O STP     5      -1.785   5.216  -7.035    0.00     3.65
-ATOM    187    O STP     5      -3.701   8.983  -8.573    0.00     4.49
-ATOM    188    O STP     5      -3.246   8.932  -8.467    0.00     4.30
-ATOM    189    O STP     5      -1.423   9.628  -8.928    0.00     3.47
-ATOM    190    O STP     5      -2.819   9.025  -8.670    0.00     4.13
-ATOM    191    O STP     5      -1.924   8.885  -8.753    0.00     3.78
-ATOM    192    O STP     5      -1.997   4.980  -6.859    0.00     3.52
-ATOM    193    O STP     5      -1.773   5.141  -7.052    0.00     3.64
-ATOM    194    O STP     5      -1.816   5.091  -7.152    0.00     3.55
-ATOM    195    O STP     5      -1.491   5.021  -7.121    0.00     3.59
-ATOM    196    O STP     5      -1.417   4.986  -7.145    0.00     3.57
-ATOM    197    O STP     5      -1.425   4.982  -7.131    0.00     3.57
-ATOM    198    O STP     5      -2.908   8.645  -8.261    0.00     4.08
-ATOM    199    O STP     5      -1.967   6.532  -7.237    0.00     3.55
-ATOM    200    C STP     5      -2.911   8.402  -8.137    0.00     3.98
-ATOM    201    O STP     5      -1.038   7.720  -7.892    0.00     3.49
-ATOM    202    O STP     5      -1.266   8.004  -8.024    0.00     3.55
-ATOM    203    C STP     6      17.284  -3.003  -7.392    0.00     3.79
-ATOM    204    C STP     6      17.140  -3.037  -7.495    0.00     3.70
-ATOM    205    C STP     6      17.287  -2.942  -7.558    0.00     3.71
-ATOM    206    O STP     6      15.862  -3.114  -6.582    0.00     3.49
-ATOM    207    O STP     6      18.410  -1.869  -6.831    0.00     3.46
-ATOM    208    O STP     6      18.093  -1.568  -4.665    0.00     3.47
-ATOM    209    O STP     6      18.176  -2.391  -6.545    0.00     3.68
-ATOM    210    O STP     6      18.178  -1.260  -4.556    0.00     3.40
-ATOM    211    O STP     6      18.146  -1.324  -4.503    0.00     3.45
-ATOM    212    O STP     6      17.446  -3.009  -6.936    0.00     3.90
-ATOM    213    O STP     6      17.338  -2.967  -7.164    0.00     3.86
-ATOM    214    O STP     6      16.971  -3.071  -6.456    0.00     3.78
-ATOM    215    O STP     6      16.372  -3.033  -6.540    0.00     3.63
-ATOM    216    O STP     6      16.616  -2.342  -4.591    0.00     3.50
-ATOM    217    O STP     6      16.735  -2.388  -4.679    0.00     3.51
-ATOM    218    C STP     6      16.003  -2.925  -6.361    0.00     3.50
-ATOM    219    C STP     6      15.537  -2.940  -6.326    0.00     3.41
-ATOM    220    O STP     7      -1.389 -15.808   4.608    0.00     3.81
-ATOM    221    O STP     7      -1.682 -16.022   4.590    0.00     3.66
-ATOM    222    O STP     7      -1.648 -15.823   4.692    0.00     3.85
-ATOM    223    C STP     7      -5.623 -13.895   2.816    0.00     3.42
-ATOM    224    C STP     7      -7.247 -14.004   3.331    0.00     3.65
-ATOM    225    C STP     7      -8.747 -13.072   4.181    0.00     3.82
-ATOM    226    C STP     7      -3.506 -14.247   3.643    0.00     3.79
-ATOM    227    O STP     7      -3.650 -14.469   3.805    0.00     3.84
-ATOM    228    O STP     7      -5.817 -14.938   3.693    0.00     3.87
-ATOM    229    C STP     7      -2.262 -14.253   4.649    0.00     4.35
-ATOM    230    O STP     7      -8.823 -12.829   5.969    0.00     3.78
-ATOM    231    C STP     7      -8.681 -12.900   4.221    0.00     3.68
-ATOM    232    O STP     7      -1.409 -15.542   5.914    0.00     4.33
-ATOM    233    O STP     7      -1.417 -15.715   4.699    0.00     3.91
-ATOM    234    O STP     7      -1.682 -15.399   5.074    0.00     4.31
-ATOM    235    C STP     7      -1.560 -13.587   5.226    0.00     4.51
-ATOM    236    C STP     7      -1.567 -13.472   5.345    0.00     4.45
-ATOM    237    O STP     7      -1.180 -15.075   6.105    0.00     4.34
-ATOM    238    O STP     7      -1.076 -15.289   7.116    0.00     4.14
-ATOM    239    O STP     7      -1.505 -13.532   5.394    0.00     4.46
-ATOM    240    O STP     7      -0.289 -13.357   5.212    0.00     3.55
-ATOM    241    C STP     7      -0.289 -13.067   3.400    0.00     3.46
-ATOM    242    O STP     7      -1.253 -14.770   5.826    0.00     4.37
-ATOM    243    C STP     7      -1.525 -13.665   5.202    0.00     4.54
-ATOM    244    O STP     7      -1.488 -13.667   5.270    0.00     4.52
-ATOM    245    C STP     7      -1.739 -14.231   4.832    0.00     4.53
-ATOM    246    C STP     7      -1.647 -14.742   4.977    0.00     4.44
-ATOM    247    C STP     7      -1.682 -14.732   5.030    0.00     4.49
-ATOM    248    C STP     7      -1.616 -13.199   5.185    0.00     4.27
-ATOM    249    C STP     7      -1.612 -13.209   5.227    0.00     4.28
-ATOM    250    C STP     7      -1.726 -13.041   5.798    0.00     4.17
-ATOM    251    O STP     8      15.640  11.395  -7.384    0.00     3.87
-ATOM    252    O STP     8      14.547  11.507  -5.506    0.00     3.47
-ATOM    253    C STP     8      15.133  11.716  -6.441    0.00     3.54
-ATOM    254    O STP     8      14.464  10.763  -5.571    0.00     3.51
-ATOM    255    O STP     8      14.467  10.370  -5.296    0.00     3.44
-ATOM    256    O STP     8      14.848  13.223  -6.639    0.00     3.50
-ATOM    257    O STP     8      15.418  12.203  -7.050    0.00     3.68
-ATOM    258    O STP     8      15.660  11.576  -7.445    0.00     3.87
-ATOM    259    O STP     8      16.047  11.948  -7.515    0.00     3.67
-ATOM    260    O STP     8      15.521  11.388  -7.841    0.00     3.75
-ATOM    261    O STP     8      15.570  11.317  -8.748    0.00     3.41
-ATOM    262    O STP     8      15.604  11.206  -7.376    0.00     3.86
-ATOM    263    O STP     8      15.544  11.122  -7.297    0.00     3.82
-ATOM    264    O STP     8      15.979  10.444  -7.233    0.00     3.55
-ATOM    265    C STP     8      15.792  10.270  -7.031    0.00     3.50
-ATOM    266    O STP     9       3.602  29.013   1.016    0.00     3.55
-ATOM    267    C STP     9       5.556  23.790   2.238    0.00     3.66
-ATOM    268    C STP     9       4.374  24.558   2.469    0.00     3.55
-ATOM    269    C STP     9       6.248  22.839   2.662    0.00     3.65
-ATOM    270    C STP     9       6.687  23.325   2.417    0.00     3.80
-ATOM    271    O STP     9       3.605  28.995   0.988    0.00     3.53
-ATOM    272    C STP     9       6.666  23.871   2.160    0.00     3.91
-ATOM    273    C STP     9       6.778  23.571   2.298    0.00     3.87
-ATOM    274    C STP     9       6.777  25.942   2.510    0.00     3.88
-ATOM    275    O STP     9       3.851  24.675   2.332    0.00     3.51
-ATOM    276    C STP     9       3.757  24.628   2.235    0.00     3.46
-ATOM    277    O STP     9       3.932  27.786   1.618    0.00     3.45
-ATOM    278    O STP     9       4.637  26.459   2.777    0.00     3.76
-ATOM    279    C STP     9       4.889  27.180   2.881    0.00     4.07
-ATOM    280    O STP     9       3.599  29.091   1.545    0.00     3.89
-ATOM    281    C STP     9       7.492  23.806   0.509    0.00     3.43
-ATOM    282    C STP     9       7.257  23.839   1.162    0.00     3.57
-ATOM    283    C STP     9       7.637  23.976   0.562    0.00     3.48
-ATOM    284    C STP     9       6.839  23.523   2.245    0.00     3.83
-ATOM    285    C STP     9       6.757  23.101   2.378    0.00     3.69
-ATOM    286    C STP     9       6.868  27.794   3.414    0.00     4.36
-ATOM    287    C STP     9       6.830  26.126   2.605    0.00     3.89
-ATOM    288    O STP    10      -7.764  15.242   7.103    0.00     3.96
-ATOM    289    C STP    10      -5.783  13.019   6.568    0.00     4.49
-ATOM    290    O STP    10      -5.788  12.752   6.449    0.00     4.69
-ATOM    291    O STP    10      -7.309  14.474   6.726    0.00     4.12
-ATOM    292    O STP    10      -7.432  15.466   6.755    0.00     3.70
-ATOM    293    O STP    10      -7.395  15.658   6.560    0.00     3.50
-ATOM    294    C STP    10      -4.485  12.252   8.033    0.00     3.97
-ATOM    295    C STP    10      -4.567  13.020   7.587    0.00     3.99
-ATOM    296    C STP    10      -4.565  12.978   7.571    0.00     4.02
-ATOM    297    O STP    10      -4.654  11.597   3.673    0.00     3.94
-ATOM    298    O STP    10      -3.791  12.064   4.278    0.00     3.43
-ATOM    299    O STP    10      -4.242  12.235   5.610    0.00     3.94
-ATOM    300    O STP    10      -3.273  10.191   7.558    0.00     3.44
-ATOM    301    C STP    10      -4.073  12.143   8.369    0.00     3.67
-ATOM    302    C STP    10      -3.693  10.881   8.123    0.00     3.54
-ATOM    303    C STP    10      -3.402  10.565   8.181    0.00     3.46
-ATOM    304    O STP    11      16.399  30.997  -2.408    0.00     3.51
-ATOM    305    O STP    11      16.378  31.564  -2.092    0.00     3.53
-ATOM    306    O STP    11      16.438  31.064  -2.387    0.00     3.53
-ATOM    307    O STP    11      17.895  28.085  -5.613    0.00     3.60
-ATOM    308    O STP    11      18.864  28.710  -3.265    0.00     4.57
-ATOM    309    O STP    11      17.852  28.163  -5.642    0.00     3.57
-ATOM    310    O STP    11      17.748  28.256  -3.638    0.00     3.99
-ATOM    311    O STP    11      18.340  28.694  -3.618    0.00     4.44
-ATOM    312    O STP    11      17.987  28.173  -5.180    0.00     3.72
-ATOM    313    O STP    11      18.227  28.380  -4.224    0.00     4.14
-ATOM    314    O STP    11      18.119  28.193  -4.507    0.00     3.99
-ATOM    315    O STP    11      16.692  30.260  -3.367    0.00     3.43
-ATOM    316    O STP    11      17.772  29.567  -4.909    0.00     3.47
-ATOM    317    C STP    11      17.710  27.065  -6.133    0.00     3.50
-ATOM    318    O STP    11      17.725  26.987  -6.025    0.00     3.51
-ATOM    319    O STP    11      17.545  26.715  -6.183    0.00     3.43
-ATOM    320    C STP    12      -3.012  -8.100  -8.760    0.00     3.99
-ATOM    321    C STP    12      -3.458  -8.552  -8.865    0.00     4.13
-ATOM    322    C STP    12      -2.959  -8.581 -10.924    0.00     3.60
-ATOM    323    C STP    12      -3.348 -12.034  -7.768    0.00     3.58
-ATOM    324    C STP    12      -4.265 -11.238  -7.349    0.00     3.85
-ATOM    325    C STP    12      -3.688  -6.964  -9.269    0.00     3.51
-ATOM    326    C STP    12      -2.701  -7.221 -10.008    0.00     3.68
-ATOM    327    C STP    12      -5.618  -8.473  -9.251    0.00     4.02
-ATOM    328    C STP    12      -3.297  -7.983  -9.300    0.00     4.15
-ATOM    329    C STP    12      -3.480  -8.204  -9.300    0.00     4.19
-ATOM    330    C STP    12      -2.711  -7.550  -9.906    0.00     3.88
-ATOM    331    C STP    12      -3.130  -8.353 -10.547    0.00     3.78
-ATOM    332    C STP    12      -6.416  -7.590  -9.212    0.00     3.65
-ATOM    333    C STP    12      -6.562  -8.616  -9.387    0.00     4.21
-ATOM    334    C STP    12      -3.584  -8.558 -11.489    0.00     3.41
-ATOM    335    C STP    12      -2.190  -7.904  -8.566    0.00     3.57
-ATOM    336    C STP    12      -2.781  -7.847  -8.009    0.00     3.57
-ATOM    337    C STP    12      -4.480 -10.505  -7.436    0.00     3.94
-ATOM    338    C STP    12      -4.026  -9.106  -8.251    0.00     4.00
-ATOM    339    C STP    12      -4.477  -9.071  -8.355    0.00     3.93
-ATOM    340    C STP    12      -6.605  -8.625  -9.403    0.00     4.22
-ATOM    341    C STP    12      -7.298  -9.850 -11.196    0.00     3.43
-ATOM    342    C STP    12      -6.455  -7.572  -9.223    0.00     3.65
-ATOM    343    C STP    12      -6.421  -7.573  -9.212    0.00     3.65
-ATOM    344    O STP    12      -1.367  -6.997 -10.176    0.00     3.51
-ATOM    345    C STP    12      -1.239  -6.770 -10.255    0.00     3.42
-ATOM    346    C STP    12      -4.616 -11.435  -7.345    0.00     3.83
-ATOM    347    C STP    12      -4.811 -11.636  -7.371    0.00     3.80
-ATOM    348    C STP    12      -4.913 -11.381  -7.364    0.00     3.83
-ATOM    349    C STP    12      -6.933  -9.877  -8.296    0.00     4.23
-ATOM    350    C STP    12      -6.950  -9.879  -8.185    0.00     4.17
-ATOM    351    C STP    12      -6.960  -7.202  -9.484    0.00     3.47
-ATOM    352    C STP    12      -6.846  -7.861  -9.393    0.00     3.82
-ATOM    353    C STP    12      -7.673  -8.310  -9.533    0.00     4.10
-ATOM    354    C STP    12      -6.670  -8.554  -9.417    0.00     4.18
-ATOM    355    O STP    13      10.769   4.600  17.144    0.00     4.66
-ATOM    356    O STP    13       8.918   7.040  15.105    0.00     3.53
-ATOM    357    O STP    13       8.811   6.910  15.467    0.00     3.75
-ATOM    358    O STP    13       8.654   7.049  15.351    0.00     3.57
-ATOM    359    O STP    13       7.009   4.684  15.839    0.00     4.13
-ATOM    360    O STP    13      10.267   4.709  16.884    0.00     4.61
-ATOM    361    O STP    13       9.090   4.045  16.233    0.00     4.02
-ATOM    362    O STP    13       8.866   5.705  16.024    0.00     4.41
-ATOM    363    O STP    13       8.485   4.984  16.506    0.00     4.67
-ATOM    364    O STP    13       7.933   4.703  15.769    0.00     4.23
-ATOM    365    O STP    13       8.124   4.913  16.122    0.00     4.48
-ATOM    366    O STP    13       5.406   4.327  17.670    0.00     4.50
-ATOM    367    O STP    13       6.841   4.575  15.663    0.00     4.04
-ATOM    368    C STP    13       6.255   4.603  14.860    0.00     3.42
-ATOM    369    C STP    13       5.811   4.553  15.542    0.00     3.60
-ATOM    370    O STP    13       6.320   4.537  16.081    0.00     4.07
-ATOM    371    O STP    13       5.988   4.465  16.323    0.00     4.09
-ATOM    372    O STP    13       6.008   4.524  16.167    0.00     4.03
-ATOM    373    O STP    13       7.257   4.342  15.204    0.00     3.86
-ATOM    374    O STP    13       4.688   3.338  16.867    0.00     3.82
-ATOM    375    O STP    13       4.288   3.032  16.894    0.00     3.79
-ATOM    376    O STP    13       2.992   2.180  16.473    0.00     3.71
-ATOM    377    O STP    13       2.016   2.191  16.513    0.00     3.71
-ATOM    378    O STP    13       2.230   2.170  17.329    0.00     4.23
-ATOM    379    O STP    13       2.219   2.587  18.277    0.00     4.70
-ATOM    380    O STP    14       2.506 -11.531 -14.753    0.00     3.67
-ATOM    381    O STP    14       3.068 -10.223 -15.746    0.00     4.35
-ATOM    382    O STP    14       2.399  -9.985 -15.545    0.00     4.02
-ATOM    383    O STP    14       2.404  -9.971 -15.570    0.00     4.02
-ATOM    384    C STP    14       5.125 -10.220 -14.880    0.00     4.59
-ATOM    385    O STP    14       6.885 -10.576 -13.808    0.00     4.29
-ATOM    386    C STP    14       5.976 -10.559 -14.490    0.00     4.50
-ATOM    387    O STP    14       6.965 -10.686 -13.636    0.00     4.15
-ATOM    388    C STP    14       6.745 -10.296 -13.292    0.00     4.06
-ATOM    389    C STP    14       6.779 -10.238 -13.247    0.00     4.00
-ATOM    390    O STP    14       6.903 -10.566 -13.771    0.00     4.28
-ATOM    391    O STP    14       7.436 -10.329 -13.922    0.00     4.04
-ATOM    392    C STP    14       5.178  -9.990 -14.394    0.00     4.28
-ATOM    393    C STP    14       6.257  -9.980 -12.969    0.00     3.90
-ATOM    394    C STP    14       5.645 -10.172 -13.886    0.00     4.19
-ATOM    395    C STP    14       5.308 -10.126 -14.302    0.00     4.32
-ATOM    396    C STP    14       6.375  -9.340 -12.443    0.00     3.44
-ATOM    397    C STP    14       8.583  -7.677 -16.792    0.00     3.57
-ATOM    398    O STP    14       9.881  -9.702 -14.137    0.00     3.47
-ATOM    399    C STP    14       8.914  -9.764 -16.244    0.00     4.57
-ATOM    400    C STP    14       9.059  -9.645 -15.171    0.00     4.05
-ATOM    401    O STP    14      12.065 -10.289 -14.422    0.00     3.41
-ATOM    402    O STP    14       5.610  -9.461 -16.514    0.00     4.49
-ATOM    403    O STP    14       5.607  -9.484 -16.523    0.00     4.51
-ATOM    404    O STP    14       4.200  -8.861 -15.470    0.00     3.55
-ATOM    405    O STP    15      20.762 -15.016  15.628    0.00     4.47
-ATOM    406    O STP    15      20.093 -13.782  15.160    0.00     3.81
-ATOM    407    O STP    15      21.482 -16.110  15.016    0.00     4.50
-ATOM    408    O STP    15      21.091 -14.702  15.246    0.00     4.03
-ATOM    409    C STP    15      18.817 -14.364  15.540    0.00     4.62
-ATOM    410    C STP    15      15.023 -10.073  17.441    0.00     4.26
-ATOM    411    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM    412    O STP    15      20.585 -16.489  14.223    0.00     4.09
-ATOM    413    O STP    15      19.415 -15.607  15.364    0.00     4.66
-ATOM    414    C STP    15      15.015 -10.071  17.451    0.00     4.26
-ATOM    415    C STP    15      14.777 -10.089  16.406    0.00     3.47
-ATOM    416    C STP    15      14.855 -10.051  17.251    0.00     4.06
-ATOM    417    O STP    15      13.277  -9.665  17.514    0.00     3.56
-ATOM    418    C STP    15      14.805 -10.108  17.922    0.00     4.49
-ATOM    419    O STP    15      18.495 -14.244  14.923    0.00     4.22
-ATOM    420    O STP    15      18.480 -14.689  14.307    0.00     3.84
-ATOM    421    C STP    15      18.270 -13.858  15.512    0.00     4.47
-ATOM    422    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM    423    C STP    15      15.742 -10.997  17.953    0.00     4.62
-ATOM    424    C STP    15      15.760 -10.982  17.951    0.00     4.60
-ATOM    425    C STP    15      16.138 -10.636  17.830    0.00     4.10
-ATOM    426    C STP    15      16.014 -10.748  17.869    0.00     4.26
-ATOM    427    O STP    15      17.979 -13.868  13.441    0.00     3.43
-ATOM    428    O STP    15      18.105 -13.657  15.491    0.00     4.41
-ATOM    429    O STP    15      17.165 -13.262  16.453    0.00     4.67
-ATOM    430    O STP    15      15.637 -10.294  15.930    0.00     3.65
-ATOM    431    C STP    15      16.936 -12.523  16.560    0.00     4.44
-ATOM    432    C STP    15      17.083 -12.356  16.365    0.00     4.23
-ATOM    433    C STP    15      16.850 -12.331  16.545    0.00     4.35
-ATOM    434    O STP    16      21.605   9.274   6.445    0.00     3.95
-ATOM    435    O STP    16      23.052   4.027   8.218    0.00     3.68
-ATOM    436    O STP    16      20.037  10.202   7.733    0.00     4.60
-ATOM    437    O STP    16      22.942   3.882   8.664    0.00     3.49
-ATOM    438    O STP    16      22.985   4.910   9.082    0.00     3.75
-ATOM    439    O STP    16      22.778   4.706   8.980    0.00     3.57
-ATOM    440    O STP    16      22.932   4.338   8.689    0.00     3.66
-ATOM    441    O STP    16      22.819   4.391   8.749    0.00     3.58
-ATOM    442    O STP    16      22.943   3.580   7.482    0.00     3.63
-ATOM    443    O STP    16      22.800   7.841   5.222    0.00     3.89
-ATOM    444    C STP    16      23.308   3.741   7.149    0.00     3.81
-ATOM    445    O STP    16      23.140   5.515   5.119    0.00     3.59
-ATOM    446    O STP    16      22.972   4.082   6.110    0.00     3.44
-ATOM    447    O STP    16      23.254   3.825   6.901    0.00     3.72
-ATOM    448    O STP    16      23.595   4.080   7.336    0.00     3.93
-ATOM    449    O STP    16      24.143   3.706   7.296    0.00     3.56
-ATOM    450    O STP    16      23.426   3.868   7.200    0.00     3.86
-ATOM    451    C STP    17      20.079 -17.759  -0.802    0.00     3.67
-ATOM    452    O STP    17      21.058 -19.186  -2.154    0.00     3.88
-ATOM    453    O STP    17      22.470 -19.926  -1.235    0.00     4.53
-ATOM    454    O STP    17      22.448 -20.166  -0.692    0.00     4.42
-ATOM    455    C STP    17      21.929 -20.012  -0.119    0.00     4.06
-ATOM    456    O STP    17      21.994 -20.327   0.005    0.00     4.04
-ATOM    457    C STP    17      22.152 -19.454  -1.681    0.00     4.50
-ATOM    458    O STP    17      22.110 -19.403  -1.774    0.00     4.50
-ATOM    459    C STP    17      20.135 -17.782  -0.862    0.00     3.68
-ATOM    460    C STP    17      20.333 -17.868  -1.159    0.00     3.71
-ATOM    461    O STP    17      22.730 -19.052  -1.278    0.00     3.92
-ATOM    462    C STP    17      21.017 -18.682  -1.343    0.00     4.01
-ATOM    463    C STP    17      21.042 -18.693  -1.380    0.00     4.03
-ATOM    464    C STP    17      20.540 -18.564  -0.766    0.00     3.77
-ATOM    465    C STP    17      21.084 -19.267  -0.227    0.00     3.70
-ATOM    466    C STP    17      20.059 -17.765  -0.768    0.00     3.67
-ATOM    467    C STP    17      20.019 -17.679  -0.714    0.00     3.63
-ATOM    468    O STP    18      23.290   7.625 -10.006    0.00     3.65
-ATOM    469    O STP    18      21.998   7.158  -8.997    0.00     3.42
-ATOM    470    O STP    18      21.767   7.080  -9.018    0.00     3.44
-ATOM    471    O STP    18      24.354   9.432 -11.111    0.00     3.89
-ATOM    472    O STP    18      24.924  10.086 -10.852    0.00     3.50
-ATOM    473    O STP    18      24.124   8.241 -11.073    0.00     4.17
-ATOM    474    O STP    18      23.599   7.744 -10.504    0.00     3.89
-ATOM    475    O STP    18      25.034   7.815 -11.334    0.00     4.30
-ATOM    476    O STP    18      24.595   7.493 -10.910    0.00     4.00
-ATOM    477    O STP    18      24.583   8.688 -11.745    0.00     4.51
-ATOM    478    O STP    18      24.433   8.715 -11.668    0.00     4.47
-ATOM    479    O STP    18      24.019   8.832 -11.950    0.00     4.30
-ATOM    480    O STP    18      22.801   8.729 -12.139    0.00     3.77
-ATOM    481    O STP    18      22.207   7.260 -10.194    0.00     3.50
-ATOM    482    C STP    18      24.752   8.793 -13.468    0.00     4.56
-ATOM    483    O STP    18      26.139   6.551 -11.712    0.00     4.46
-ATOM    484    O STP    18      26.177   6.535 -11.779    0.00     4.47
-ATOM    485    O STP    18      26.104   6.506 -11.714    0.00     4.41
-ATOM    486    O STP    19      23.996 -17.991  11.091    0.00     4.35
-ATOM    487    C STP    19      24.960 -14.038   8.738    0.00     3.95
-ATOM    488    O STP    19      22.931 -16.813  10.494    0.00     3.98
-ATOM    489    O STP    19      23.730 -14.416   9.050    0.00     3.79
-ATOM    490    O STP    19      23.534 -14.640   9.195    0.00     3.74
-ATOM    491    O STP    19      23.541 -14.438   9.194    0.00     3.71
-ATOM    492    O STP    19      23.319 -13.996   9.166    0.00     3.47
-ATOM    493    O STP    19      23.506 -14.658   9.215    0.00     3.73
-ATOM    494    O STP    19      22.772 -16.806  10.680    0.00     3.95
-ATOM    495    O STP    19      23.478 -14.756   9.266    0.00     3.71
-ATOM    496    O STP    19      22.867 -16.689  10.427    0.00     3.96
-ATOM    497    O STP    19      22.668 -16.487  10.105    0.00     3.79
-ATOM    498    O STP    19      22.623 -16.471  10.089    0.00     3.76
-ATOM    499    O STP    19      22.761 -16.808  10.687    0.00     3.94
-ATOM    500    O STP    19      24.040 -13.911   7.306    0.00     3.54
-ATOM    501    C STP    19      24.558 -13.610   8.244    0.00     4.08
-ATOM    502    O STP    19      24.402 -13.618   8.240    0.00     4.06
-ATOM    503    O STP    19      23.982 -13.022   8.288    0.00     3.77
-ATOM    504    C STP    19      24.023 -12.020   8.383    0.00     3.50
-ATOM    505    O STP    19      22.709 -16.865  10.854    0.00     3.94
-ATOM    506    O STP    19      22.701 -16.860  10.841    0.00     3.93
+ATOM    107    C STP     2       5.666  -2.347   9.650    0.00     3.64
+ATOM    108    C STP     2       5.663  -2.342   9.659    0.00     3.64
+ATOM    109    C STP     2       4.857  -3.237  11.687    0.00     3.51
+ATOM    110    C STP     2       4.909  -3.421  12.179    0.00     3.52
+ATOM    111    C STP     2       4.463  -1.923  10.602    0.00     3.52
+ATOM    112    C STP     2       4.751  -3.640  11.929    0.00     3.49
+ATOM    113    C STP     2       4.816  -3.657  12.202    0.00     3.51
+ATOM    114    C STP     2       5.643  -2.334   9.598    0.00     3.62
+ATOM    115    C STP     2       5.573  -2.273   9.693    0.00     3.63
+ATOM    116    C STP     2       5.625  -2.300   9.658    0.00     3.64
+ATOM    117    C STP     2       5.618  -2.250   9.664    0.00     3.62
+ATOM    118    C STP     2       4.669  -1.977  10.488    0.00     3.53
+ATOM    119    C STP     2       4.819  -1.860  10.403    0.00     3.43
+ATOM    120    C STP     2       4.472  -1.924  10.605    0.00     3.53
+ATOM    121    C STP     2       4.423  -1.750  10.637    0.00     3.43
+ATOM    122    C STP     2       4.474  -1.928  10.609    0.00     3.53
+ATOM    123    C STP     2       4.552  -2.069  10.740    0.00     3.51
+ATOM    124    C STP     2       4.780  -3.687  12.261    0.00     3.48
+ATOM    125    O STP     3      10.707   8.465   9.562    0.00     3.56
+ATOM    126    O STP     3      11.897   7.600  10.387    0.00     3.53
+ATOM    127    O STP     3      11.713   7.651  10.429    0.00     3.61
+ATOM    128    O STP     3      11.722   7.673  10.440    0.00     3.59
+ATOM    129    O STP     3      11.706   7.635  10.442    0.00     3.60
+ATOM    130    O STP     3      13.057   5.577  11.209    0.00     3.45
+ATOM    131    C STP     3      13.599   4.782  12.622    0.00     3.56
+ATOM    132    O STP     3      12.926   5.521  11.298    0.00     3.49
+ATOM    133    O STP     3      11.593   6.620  11.138    0.00     3.56
+ATOM    134    O STP     3      11.150   6.837  11.229    0.00     3.58
+ATOM    135    O STP     3      11.203   6.847  11.061    0.00     3.66
+ATOM    136    O STP     3      10.100   6.854  10.639    0.00     3.72
+ATOM    137    O STP     3      10.043   6.829  10.609    0.00     3.72
+ATOM    138    O STP     3      10.008   6.832  11.002    0.00     3.55
+ATOM    139    O STP     3       9.996   6.814  10.721    0.00     3.65
+ATOM    140    O STP     3      14.136   3.921  15.176    0.00     4.64
+ATOM    141    O STP     3      13.450   4.065  15.198    0.00     4.27
+ATOM    142    O STP     3      14.349   4.009  14.805    0.00     4.61
+ATOM    143    O STP     3      13.844   4.358  14.153    0.00     4.07
+ATOM    144    C STP     3      14.400   4.002  14.664    0.00     4.57
+ATOM    145    C STP     3      13.873   4.433  13.491    0.00     3.88
+ATOM    146    C STP     3      13.578   4.355  12.749    0.00     3.43
+ATOM    147    O STP     3       9.524   6.563  10.325    0.00     3.47
+ATOM    148    C STP     3       9.327   7.050  10.077    0.00     3.46
+ATOM    149    O STP     3      10.903   8.245   9.723    0.00     3.55
+ATOM    150    O STP     3      11.424   7.798  10.169    0.00     3.58
+ATOM    151    O STP     3      10.102   6.908  10.584    0.00     3.71
+ATOM    152    O STP     3      10.425   8.337   9.557    0.00     3.58
+ATOM    153    O STP     3      10.324   8.322   9.469    0.00     3.54
+ATOM    154    O STP     3      10.351   8.314   9.560    0.00     3.59
+ATOM    155    C STP     3      10.082   7.855   9.856    0.00     3.56
+ATOM    156    C STP     3       9.763   7.428   9.952    0.00     3.52
+ATOM    157    C STP     3       9.808   6.869  10.405    0.00     3.64
+ATOM    158    O STP     3      10.016   6.824  10.586    0.00     3.71
+ATOM    159    O STP     3       9.960   6.815  10.553    0.00     3.70
+ATOM    160    O STP     3       9.895   6.462  10.350    0.00     3.45
+ATOM    161    O STP     3       9.826   6.743  10.451    0.00     3.64
+ATOM    162    O STP     4      17.904  16.846   2.034    0.00     4.00
+ATOM    163    C STP     4      13.212  24.010  -0.223    0.00     3.56
+ATOM    164    O STP     4      13.590  24.333  -0.124    0.00     3.66
+ATOM    165    O STP     4      16.890  22.935   1.418    0.00     4.64
+ATOM    166    C STP     4      16.767  18.684   1.078    0.00     4.22
+ATOM    167    C STP     4      16.715  18.704   1.057    0.00     4.20
+ATOM    168    O STP     4      17.342  17.855   1.830    0.00     4.24
+ATOM    169    O STP     4      17.041  17.846   1.980    0.00     4.08
+ATOM    170    O STP     4      16.580  19.060   0.747    0.00     4.27
+ATOM    171    O STP     4      17.635  17.024   1.403    0.00     3.80
+ATOM    172    O STP     4      17.395  17.419   1.401    0.00     3.89
+ATOM    173    C STP     4      16.900  18.376   1.091    0.00     4.07
+ATOM    174    O STP     4      17.782  16.444   1.256    0.00     3.57
+ATOM    175    O STP     4      14.632  22.244  -1.461    0.00     3.60
+ATOM    176    O STP     4      14.379  23.675  -0.187    0.00     4.18
+ATOM    177    C STP     4      16.642  20.313   0.285    0.00     4.56
+ATOM    178    O STP     4      15.401  22.803   0.789    0.00     4.49
+ATOM    179    O STP     4      14.950  20.959  -0.498    0.00     4.03
+ATOM    180    O STP     4      16.062  19.544  -0.072    0.00     4.25
+ATOM    181    O STP     4      16.188  19.842  -0.177    0.00     4.42
+ATOM    182    C STP     4      16.044  18.633   0.739    0.00     3.73
+ATOM    183    O STP     4      15.502  19.054  -0.011    0.00     3.68
+ATOM    184    O STP     5      -3.903   9.091  -8.804    0.00     4.57
+ATOM    185    O STP     5      -3.754   8.992  -8.593    0.00     4.51
+ATOM    186    O STP     5      -2.044   6.009  -7.092    0.00     3.61
+ATOM    187    O STP     5      -2.612   5.104  -6.282    0.00     3.41
+ATOM    188    O STP     5      -2.076   5.517  -6.742    0.00     3.61
+ATOM    189    O STP     5      -1.785   5.216  -7.035    0.00     3.65
+ATOM    190    O STP     5      -3.701   8.983  -8.573    0.00     4.49
+ATOM    191    O STP     5      -3.246   8.932  -8.467    0.00     4.30
+ATOM    192    O STP     5      -1.423   9.628  -8.928    0.00     3.47
+ATOM    193    O STP     5      -2.819   9.025  -8.670    0.00     4.13
+ATOM    194    O STP     5      -1.924   8.885  -8.753    0.00     3.78
+ATOM    195    O STP     5      -1.997   4.980  -6.859    0.00     3.52
+ATOM    196    O STP     5      -1.773   5.141  -7.052    0.00     3.64
+ATOM    197    O STP     5      -1.816   5.091  -7.152    0.00     3.55
+ATOM    198    O STP     5      -1.491   5.021  -7.121    0.00     3.59
+ATOM    199    O STP     5      -1.417   4.986  -7.145    0.00     3.57
+ATOM    200    O STP     5      -1.425   4.982  -7.131    0.00     3.57
+ATOM    201    O STP     5      -2.908   8.645  -8.261    0.00     4.08
+ATOM    202    O STP     5      -1.967   6.532  -7.237    0.00     3.55
+ATOM    203    C STP     5      -2.911   8.402  -8.137    0.00     3.98
+ATOM    204    O STP     5      -1.038   7.720  -7.892    0.00     3.49
+ATOM    205    O STP     5      -1.266   8.004  -8.024    0.00     3.55
+ATOM    206    C STP     6      17.284  -3.003  -7.392    0.00     3.79
+ATOM    207    C STP     6      17.140  -3.037  -7.495    0.00     3.70
+ATOM    208    C STP     6      17.287  -2.942  -7.558    0.00     3.71
+ATOM    209    O STP     6      15.862  -3.114  -6.582    0.00     3.49
+ATOM    210    O STP     6      18.410  -1.869  -6.831    0.00     3.46
+ATOM    211    O STP     6      18.093  -1.568  -4.665    0.00     3.47
+ATOM    212    O STP     6      18.176  -2.391  -6.545    0.00     3.68
+ATOM    213    O STP     6      18.178  -1.260  -4.556    0.00     3.40
+ATOM    214    O STP     6      18.146  -1.324  -4.503    0.00     3.45
+ATOM    215    O STP     6      17.446  -3.009  -6.936    0.00     3.90
+ATOM    216    O STP     6      17.338  -2.967  -7.164    0.00     3.86
+ATOM    217    O STP     6      16.971  -3.071  -6.456    0.00     3.78
+ATOM    218    O STP     6      16.372  -3.033  -6.540    0.00     3.63
+ATOM    219    O STP     6      16.616  -2.342  -4.591    0.00     3.50
+ATOM    220    O STP     6      16.735  -2.388  -4.679    0.00     3.51
+ATOM    221    C STP     6      16.003  -2.925  -6.361    0.00     3.50
+ATOM    222    C STP     6      15.537  -2.940  -6.326    0.00     3.41
+ATOM    223    O STP     7      15.640  11.395  -7.384    0.00     3.87
+ATOM    224    O STP     7      14.547  11.507  -5.506    0.00     3.47
+ATOM    225    C STP     7      15.133  11.716  -6.441    0.00     3.54
+ATOM    226    O STP     7      14.464  10.763  -5.571    0.00     3.51
+ATOM    227    O STP     7      14.467  10.370  -5.296    0.00     3.44
+ATOM    228    O STP     7      14.848  13.223  -6.639    0.00     3.50
+ATOM    229    O STP     7      15.418  12.203  -7.050    0.00     3.68
+ATOM    230    O STP     7      15.660  11.576  -7.445    0.00     3.87
+ATOM    231    O STP     7      16.047  11.948  -7.515    0.00     3.67
+ATOM    232    O STP     7      15.521  11.388  -7.841    0.00     3.75
+ATOM    233    O STP     7      15.570  11.317  -8.748    0.00     3.41
+ATOM    234    O STP     7      15.604  11.206  -7.376    0.00     3.86
+ATOM    235    O STP     7      15.544  11.122  -7.297    0.00     3.82
+ATOM    236    O STP     7      15.979  10.444  -7.233    0.00     3.55
+ATOM    237    C STP     7      15.792  10.270  -7.031    0.00     3.50
+ATOM    238    O STP     8       3.602  29.013   1.016    0.00     3.55
+ATOM    239    C STP     8       5.556  23.790   2.238    0.00     3.66
+ATOM    240    C STP     8       4.374  24.558   2.469    0.00     3.55
+ATOM    241    C STP     8       6.248  22.839   2.662    0.00     3.65
+ATOM    242    C STP     8       6.687  23.325   2.417    0.00     3.80
+ATOM    243    O STP     8       3.605  28.995   0.988    0.00     3.53
+ATOM    244    C STP     8       6.666  23.871   2.160    0.00     3.91
+ATOM    245    C STP     8       6.778  23.571   2.298    0.00     3.87
+ATOM    246    C STP     8       6.777  25.942   2.510    0.00     3.88
+ATOM    247    O STP     8       3.851  24.675   2.332    0.00     3.51
+ATOM    248    C STP     8       3.757  24.628   2.235    0.00     3.46
+ATOM    249    O STP     8       3.932  27.786   1.618    0.00     3.45
+ATOM    250    O STP     8       4.637  26.459   2.777    0.00     3.76
+ATOM    251    C STP     8       4.889  27.180   2.881    0.00     4.07
+ATOM    252    O STP     8       3.599  29.091   1.545    0.00     3.89
+ATOM    253    C STP     8       7.492  23.806   0.509    0.00     3.43
+ATOM    254    C STP     8       7.257  23.839   1.162    0.00     3.57
+ATOM    255    C STP     8       7.637  23.976   0.562    0.00     3.48
+ATOM    256    C STP     8       6.839  23.523   2.245    0.00     3.83
+ATOM    257    C STP     8       6.757  23.101   2.378    0.00     3.69
+ATOM    258    C STP     8       6.868  27.794   3.414    0.00     4.36
+ATOM    259    C STP     8       6.830  26.126   2.605    0.00     3.89
+ATOM    260    O STP     9      -7.764  15.242   7.103    0.00     3.96
+ATOM    261    C STP     9      -5.783  13.019   6.568    0.00     4.49
+ATOM    262    O STP     9      -5.788  12.752   6.449    0.00     4.69
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+ATOM    498    O STP    19      23.319 -13.996   9.166    0.00     3.47
+ATOM    499    O STP    19      23.506 -14.658   9.215    0.00     3.73
+ATOM    500    O STP    19      22.772 -16.806  10.680    0.00     3.95
+ATOM    501    O STP    19      23.478 -14.756   9.266    0.00     3.71
+ATOM    502    O STP    19      22.867 -16.689  10.427    0.00     3.96
+ATOM    503    O STP    19      22.668 -16.487  10.105    0.00     3.79
+ATOM    504    O STP    19      22.623 -16.471  10.089    0.00     3.76
+ATOM    505    O STP    19      22.761 -16.808  10.687    0.00     3.94
+ATOM    506    O STP    19      24.040 -13.911   7.306    0.00     3.54
+ATOM    507    C STP    19      24.558 -13.610   8.244    0.00     4.08
+ATOM    508    O STP    19      24.402 -13.618   8.240    0.00     4.06
+ATOM    509    O STP    19      23.982 -13.022   8.288    0.00     3.77
+ATOM    510    C STP    19      24.023 -12.020   8.383    0.00     3.50
+ATOM    511    O STP    19      22.709 -16.865  10.854    0.00     3.94
+ATOM    512    O STP    19      22.701 -16.860  10.841    0.00     3.93
+ATOM    513    O STP    20      25.040   9.651 -11.168    0.00     3.75
+ATOM    514    O STP    20      25.268   9.534 -10.955    0.00     3.50
+ATOM    515    O STP    20      23.290   7.625 -10.006    0.00     3.65
+ATOM    516    O STP    20      21.998   7.158  -8.997    0.00     3.42
+ATOM    517    O STP    20      21.767   7.080  -9.018    0.00     3.44
+ATOM    518    O STP    20      24.354   9.432 -11.111    0.00     3.89
+ATOM    519    O STP    20      24.924  10.086 -10.852    0.00     3.50
+ATOM    520    O STP    20      25.153   7.836 -11.282    0.00     4.23
+ATOM    521    O STP    20      24.124   8.241 -11.073    0.00     4.17
+ATOM    522    O STP    20      23.599   7.744 -10.504    0.00     3.89
+ATOM    523    O STP    20      25.034   7.815 -11.334    0.00     4.30
+ATOM    524    O STP    20      24.595   7.493 -10.910    0.00     4.00
+ATOM    525    O STP    20      24.583   8.688 -11.745    0.00     4.51
+ATOM    526    O STP    20      24.433   8.715 -11.668    0.00     4.47
+ATOM    527    O STP    20      24.019   8.832 -11.950    0.00     4.30
+ATOM    528    O STP    20      22.801   8.729 -12.139    0.00     3.77
+ATOM    529    O STP    20      22.207   7.260 -10.194    0.00     3.50
+ATOM    530    C STP    20      24.752   8.793 -13.468    0.00     4.56
+ATOM    531    O STP    20      26.139   6.551 -11.712    0.00     4.46
+ATOM    532    O STP    20      26.177   6.535 -11.779    0.00     4.47
+ATOM    533    O STP    20      26.104   6.506 -11.714    0.00     4.41
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket10_atm.pdb

@@ -3,39 +3,35 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    10:
-HEADER 0  - Pocket Score                      : 0.0405
-HEADER 1  - Drug Score                        : 0.0006
+HEADER 0  - Pocket Score                      : 0.0334
+HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of alpha spheres           :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.8663
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6124
-HEADER 5  - Mean B-factor of pocket residues  : 0.7690
-HEADER 6  - Hydrophobicity Score              : 9.7000
-HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Amino Acid based volume Score     : 3.5000
-HEADER 9  - Pocket volume (Monte Carlo)       : 253.8700
-HEADER 10  -Pocket volume (convex hull)       : 12.1248
-HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 6.0000
-HEADER 13 - Number of apolar alpha sphere     :     7
-HEADER 14 - Proportion of apolar alpha sphere : 0.4375
-ATOM    434  CD2 HIS E  68      -4.370  16.956   8.208  0.00  0.00           C 0
-ATOM    418    O GLY E  66      -7.767  19.132   6.362  0.14  7.50           O 0
-ATOM    425  OD1 ASN E  67      -8.955  16.520   3.549  0.00  0.00           O 0
-ATOM   2530   CB PRO E 321      -6.517  14.426  10.771  0.00  0.00           C 0
-ATOM    427    N HIS E  68      -4.661  17.016   4.850  0.00  0.00           N 0
-ATOM    431   CB HIS E  68      -2.770  16.341   6.300  0.00  0.00           C 0
-ATOM    430    O HIS E  68      -3.452  15.333   3.304  0.00  0.00           O 0
-ATOM    420   CA ASN E  67      -6.657  18.056   4.121  0.00  0.00           C 0
-ATOM   2533    N GLY E 322      -3.195  14.519  11.020  0.00  0.00           N 0
-ATOM    891  CD2 TYR E 122      -0.618  12.346   7.159  0.00  0.00           C 0
-ATOM   2512   CZ PHE E 318      -4.685  10.281  11.468  0.00  0.00           C 0
-ATOM   2527   CA PRO E 321      -5.396  13.768  11.582  0.00  0.00           C 0
-ATOM    884    N TYR E 122      -0.887  11.623   2.511  0.00  0.00           N 0
-ATOM    887    O TYR E 122      -1.382   9.668   4.729  0.42  5.36           O 0
-ATOM    880   CG GLU E 121      -3.212   9.733   0.513  0.00  0.00           C 0
-ATOM    888   CB TYR E 122      -0.420  12.529   4.688  0.00  0.00           C 0
-ATOM   1344  NE2 GLN E 176      -5.655   7.996   8.723  0.00  0.00           N 0
-ATOM    907   CB ALA E 124      -0.748   8.672   9.338  0.00  0.00           C 0
-ATOM   2511  CE2 PHE E 318      -3.352  10.649  11.639  0.00  0.00           C 0
+HEADER 3  - Mean alpha-sphere radius          : 3.7458
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5051
+HEADER 5  - Mean B-factor of pocket residues  : 0.4085
+HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 184.3875
+HEADER 10 - Pocket volume (convex hull)       : 4.4609
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0625
+ATOM   2662    C VAL E 337      13.234  31.795  -3.685  0.00  0.00           C 0
+HETATM 2667    N SEP E 338      13.942  31.735  -4.796  0.00  0.00           N 0
+ATOM   2653   CB ARG E 336      14.890  29.572   0.417  0.00  0.00           C 0
+ATOM   2652    O ARG E 336      14.020  28.429  -2.226  0.67  4.29           O 0
+ATOM   2663    O VAL E 337      13.186  32.790  -2.978  0.25  9.64           O 0
+HETATM 2674  O1P SEP E 338      18.260  33.001  -4.713  0.00  0.00           O 0
+ATOM    511  OE1 GLN E  77      21.116  27.144  -6.918  0.74  4.29           O 0
+ATOM   2707   CG LYS E 342      18.487  28.736  -9.104  0.00  0.00           C 0
+ATOM    822   CB SER E 114      14.315  27.704  -5.595  0.00  0.00           C 0
+ATOM   2710   NZ LYS E 342      20.125  30.313  -7.353  0.64  2.19           N 0
+ATOM    494  OD2 ASP E  75      17.923  24.273  -3.807  0.00  0.00           O 0
+ATOM    823   OG SER E 114      14.411  29.102  -5.655  0.64  2.14           O 0
+HETATM 2669   CB SEP E 338      15.948  32.307  -6.020  0.00  0.00           C 0
+ATOM    509   CG GLN E  77      20.051  25.351  -8.083  0.00  0.00           C 0
+ATOM    821    O SER E 114      14.639  24.948  -6.617  0.00  0.00           O 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket10_vert.pqr

@@ -4,35 +4,35 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    10:
-HEADER 0  - Pocket Score                      : 0.0405
-HEADER 1  - Drug Score                        : 0.0006
+HEADER 0  - Pocket Score                      : 0.0334
+HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of V. Vertices             :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.8663
-HEADER 4  - Mean alpha-sphere SA              : 0.6124
-HEADER 5  - Mean B-factor                     : 0.7690
-HEADER 6  - Hydrophobicity Score              : 9.7000
-HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Volume Score                      : 3.5000
-HEADER 9  - Real volume (approximation)       : 253.8700
-HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 6.0000
-HEADER 12 - Number of apolar alpha sphere     :     7
-HEADER 13 - Proportion of apolar alpha sphere : 0.4375
-ATOM      1    O STP    10      -7.764  15.242   7.103    0.00     3.96
-ATOM      2    C STP    10      -5.783  13.019   6.568    0.00     4.49
-ATOM      3    O STP    10      -5.788  12.752   6.449    0.00     4.69
-ATOM      4    O STP    10      -7.309  14.474   6.726    0.00     4.12
-ATOM      5    O STP    10      -7.432  15.466   6.755    0.00     3.70
-ATOM      6    O STP    10      -7.395  15.658   6.560    0.00     3.50
-ATOM      7    C STP    10      -4.485  12.252   8.033    0.00     3.97
-ATOM      8    C STP    10      -4.567  13.020   7.587    0.00     3.99
-ATOM      9    C STP    10      -4.565  12.978   7.571    0.00     4.02
-ATOM     10    O STP    10      -4.654  11.597   3.673    0.00     3.94
-ATOM     11    O STP    10      -3.791  12.064   4.278    0.00     3.43
-ATOM     12    O STP    10      -4.242  12.235   5.610    0.00     3.94
-ATOM     13    O STP    10      -3.273  10.191   7.558    0.00     3.44
-ATOM     14    C STP    10      -4.073  12.143   8.369    0.00     3.67
-ATOM     15    C STP    10      -3.693  10.881   8.123    0.00     3.54
-ATOM     16    C STP    10      -3.402  10.565   8.181    0.00     3.46
+HEADER 3  - Mean alpha-sphere radius          : 3.7458
+HEADER 4  - Mean alpha-sphere SA              : 0.5051
+HEADER 5  - Mean B-factor                     : 0.4085
+HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 184.3875
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0625
+ATOM      1    O STP    10      16.399  30.997  -2.408    0.00     3.51
+ATOM      2    O STP    10      16.378  31.564  -2.092    0.00     3.53
+ATOM      3    O STP    10      16.438  31.064  -2.387    0.00     3.53
+ATOM      4    O STP    10      17.895  28.085  -5.613    0.00     3.60
+ATOM      5    O STP    10      18.864  28.710  -3.265    0.00     4.57
+ATOM      6    O STP    10      17.852  28.163  -5.642    0.00     3.57
+ATOM      7    O STP    10      17.748  28.256  -3.638    0.00     3.99
+ATOM      8    O STP    10      18.340  28.694  -3.618    0.00     4.44
+ATOM      9    O STP    10      17.987  28.173  -5.180    0.00     3.72
+ATOM     10    O STP    10      18.227  28.380  -4.224    0.00     4.14
+ATOM     11    O STP    10      18.119  28.193  -4.507    0.00     3.99
+ATOM     12    O STP    10      16.692  30.260  -3.367    0.00     3.43
+ATOM     13    O STP    10      17.772  29.567  -4.909    0.00     3.47
+ATOM     14    C STP    10      17.710  27.065  -6.133    0.00     3.50
+ATOM     15    O STP    10      17.725  26.987  -6.025    0.00     3.51
+ATOM     16    O STP    10      17.545  26.715  -6.183    0.00     3.43
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket11_atm.pdb

@@ -3,35 +3,50 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    11:
-HEADER 0  - Pocket Score                      : 0.0334
-HEADER 1  - Drug Score                        : 0.0002
-HEADER 2  - Number of alpha spheres           :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.7458
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5051
-HEADER 5  - Mean B-factor of pocket residues  : 0.9475
-HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 0  - Pocket Score                      : 0.0281
+HEADER 1  - Drug Score                        : 0.0043
+HEADER 2  - Number of alpha spheres           :    33
+HEADER 3  - Mean alpha-sphere radius          : 4.0876
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5931
+HEADER 5  - Mean B-factor of pocket residues  : 0.3702
+HEADER 6  - Hydrophobicity Score              : 15.7273
 HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.0000
-HEADER 9  - Pocket volume (Monte Carlo)       : 189.3697
-HEADER 10  -Pocket volume (convex hull)       : 4.4609
-HEADER 11 - Charge Score                      :     1
-HEADER 12 - Local hydrophobic density Score   : 0.0000
-HEADER 13 - Number of apolar alpha sphere     :     1
-HEADER 14 - Proportion of apolar alpha sphere : 0.0625
-ATOM   2662    C VAL E 337      13.234  31.795  -3.685  0.00  0.00           C 0
-HETATM 2667    N SEP E 338      13.942  31.735  -4.796  0.00  0.00           N 0
-ATOM   2653   CB ARG E 336      14.890  29.572   0.417  0.00  0.00           C 0
-ATOM   2652    O ARG E 336      14.020  28.429  -2.226  0.67  4.29           O 0
-ATOM   2663    O VAL E 337      13.186  32.790  -2.978  0.67  4.29           O 0
-HETATM 2674  O1P SEP E 338      18.260  33.001  -4.713  0.00  0.00           O 0
-ATOM    511  OE1 GLN E  77      21.116  27.144  -6.918  0.74  4.29           O 0
-ATOM   2707   CG LYS E 342      18.487  28.736  -9.104  0.00  0.00           C 0
-ATOM    822   CB SER E 114      14.315  27.704  -5.595  0.00  0.00           C 0
-ATOM   2710   NZ LYS E 342      20.125  30.313  -7.353  0.64  2.19           N 0
-ATOM    494  OD2 ASP E  75      17.923  24.273  -3.807  0.00  0.00           O 0
-ATOM    823   OG SER E 114      14.411  29.102  -5.655  0.64  2.14           O 0
-HETATM 2669   CB SEP E 338      15.948  32.307  -6.020  0.00  0.00           C 0
-ATOM    509   CG GLN E  77      20.051  25.351  -8.083  0.00  0.00           C 0
-ATOM    821    O SER E 114      14.639  24.948  -6.617  0.00  0.00           O 0
+HEADER 8  - Amino Acid based volume Score     : 4.1818
+HEADER 9  - Pocket volume (Monte Carlo)       : 425.6106
+HEADER 10 - Pocket volume (convex hull)       : 57.7753
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 14.7500
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.4848
+ATOM   2349   CA THR E 300      -2.136 -16.523   0.940  0.00  0.00           C 0
+ATOM   2348    N THR E 300      -1.897 -17.858   1.436  0.00  0.00           N 0
+ATOM   2353  OG1 THR E 300       0.238 -16.029   1.169  0.00  0.00           O 0
+ATOM   2346  OG1 THR E 299      -0.824 -19.572   4.432  0.43  5.36           O 0
+ATOM   2344    O THR E 299      -3.875 -18.070   2.502  0.36  6.43           O 0
+ATOM   2454  OE2 GLU E 311      -5.008 -14.364   8.021  0.28  8.57           O 0
+ATOM   2345   CB THR E 299      -2.145 -19.955   4.092  0.00  0.00           C 0
+ATOM   2343    C THR E 299      -2.779 -18.525   2.162  0.00  0.00           C 0
+ATOM   2444  CG1 VAL E 310      -5.465 -11.342   5.087  0.00  0.00           C 0
+ATOM   2359   CB ASP E 301      -6.814 -15.392  -0.021  0.00  0.00           C 0
+ATOM   2445  CG2 VAL E 310      -6.233 -10.529   2.840  0.00  0.00           C 0
+ATOM   2355    N ASP E 301      -4.279 -15.664   0.214  0.00  0.00           N 0
+ATOM   2389   CB ALA E 304      -8.532 -12.091   0.496  0.00  0.00           C 0
+ATOM   2433    O LYS E 309     -10.006  -9.496   4.644  0.00  0.00           O 0
+ATOM   2397  CD1 ILE E 305      -2.545 -11.291   1.475  0.00  0.00           C 0
+ATOM   2450   CB GLU E 311      -6.278 -11.111   9.158  0.00  0.00           C 0
+ATOM   2446    N GLU E 311      -6.776  -9.898   7.187  0.00  0.00           N 0
+ATOM   2451   CG GLU E 311      -5.748 -12.068   8.049  0.00  0.00           C 0
+ATOM   2440   CA VAL E 310      -7.234  -9.583   4.872  0.00  0.00           C 0
+ATOM   1067   CD ARG E 144       2.373 -16.320   3.946  0.00  0.00           C 0
+ATOM   1070  NH1 ARG E 144       2.427 -17.435   6.611  0.00  0.00           N 0
+ATOM   1073   CA PHE E 145       1.537 -10.378   4.578  0.00  0.00           C 0
+ATOM   1076   CB PHE E 145       0.971  -9.866   5.938  0.00  0.00           C 0
+ATOM   1042    O PRO E 141       2.365 -13.029   7.548  0.65  2.14           O 0
+ATOM   1043   CB PRO E 141       2.135 -15.510   9.719  0.00  0.00           C 0
+ATOM   1066   CG ARG E 144       2.651 -14.825   3.866  0.00  0.00           C 0
+ATOM   1072    N PHE E 145       2.605 -11.335   4.829  0.00  0.00           N 0
+ATOM   1064    O ARG E 144       2.912 -11.965   2.698  0.00  0.00           O 0
+ATOM   1078  CD1 PHE E 145      -1.292  -8.937   5.214  0.00  0.00           C 0
+ATOM   2452   CD GLU E 311      -4.896 -13.238   8.497  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket11_vert.pqr

@@ -4,35 +4,52 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    11:
-HEADER 0  - Pocket Score                      : 0.0334
-HEADER 1  - Drug Score                        : 0.0002
-HEADER 2  - Number of V. Vertices             :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.7458
-HEADER 4  - Mean alpha-sphere SA              : 0.5051
-HEADER 5  - Mean B-factor                     : 0.9475
-HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 0  - Pocket Score                      : 0.0281
+HEADER 1  - Drug Score                        : 0.0043
+HEADER 2  - Number of V. Vertices             :    33
+HEADER 3  - Mean alpha-sphere radius          : 4.0876
+HEADER 4  - Mean alpha-sphere SA              : 0.5931
+HEADER 5  - Mean B-factor                     : 0.3702
+HEADER 6  - Hydrophobicity Score              : 15.7273
 HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 189.3697
-HEADER 10 - Charge Score                      :     1
-HEADER 11 - Local hydrophobic density Score   : 0.0000
-HEADER 12 - Number of apolar alpha sphere     :     1
-HEADER 13 - Proportion of apolar alpha sphere : 0.0625
-ATOM      1    O STP    11      16.399  30.997  -2.408    0.00     3.51
-ATOM      2    O STP    11      16.378  31.564  -2.092    0.00     3.53
-ATOM      3    O STP    11      16.438  31.064  -2.387    0.00     3.53
-ATOM      4    O STP    11      17.895  28.085  -5.613    0.00     3.60
-ATOM      5    O STP    11      18.864  28.710  -3.265    0.00     4.57
-ATOM      6    O STP    11      17.852  28.163  -5.642    0.00     3.57
-ATOM      7    O STP    11      17.748  28.256  -3.638    0.00     3.99
-ATOM      8    O STP    11      18.340  28.694  -3.618    0.00     4.44
-ATOM      9    O STP    11      17.987  28.173  -5.180    0.00     3.72
-ATOM     10    O STP    11      18.227  28.380  -4.224    0.00     4.14
-ATOM     11    O STP    11      18.119  28.193  -4.507    0.00     3.99
-ATOM     12    O STP    11      16.692  30.260  -3.367    0.00     3.43
-ATOM     13    O STP    11      17.772  29.567  -4.909    0.00     3.47
-ATOM     14    C STP    11      17.710  27.065  -6.133    0.00     3.50
-ATOM     15    O STP    11      17.725  26.987  -6.025    0.00     3.51
-ATOM     16    O STP    11      17.545  26.715  -6.183    0.00     3.43
+HEADER 8  - Volume Score                      : 4.1818
+HEADER 9  - Real volume (approximation)       : 425.6106
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 14.7500
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.4848
+ATOM      1    O STP    11      -1.389 -15.808   4.608    0.00     3.81
+ATOM      2    O STP    11      -2.806 -16.644   5.884    0.00     3.82
+ATOM      3    O STP    11      -1.682 -16.022   4.590    0.00     3.66
+ATOM      4    O STP    11      -1.648 -15.823   4.692    0.00     3.85
+ATOM      5    C STP    11      -5.623 -13.895   2.816    0.00     3.42
+ATOM      6    C STP    11      -7.247 -14.004   3.331    0.00     3.65
+ATOM      7    C STP    11      -8.747 -13.072   4.181    0.00     3.82
+ATOM      8    C STP    11      -3.506 -14.247   3.643    0.00     3.79
+ATOM      9    O STP    11      -3.650 -14.469   3.805    0.00     3.84
+ATOM     10    O STP    11      -5.817 -14.938   3.693    0.00     3.87
+ATOM     11    C STP    11      -2.262 -14.253   4.649    0.00     4.35
+ATOM     12    O STP    11     -10.162 -12.809   7.673    0.00     4.49
+ATOM     13    O STP    11      -8.823 -12.829   5.969    0.00     3.78
+ATOM     14    C STP    11      -8.681 -12.900   4.221    0.00     3.68
+ATOM     15    O STP    11      -1.409 -15.542   5.914    0.00     4.33
+ATOM     16    O STP    11      -1.417 -15.715   4.699    0.00     3.91
+ATOM     17    O STP    11      -1.682 -15.399   5.074    0.00     4.31
+ATOM     18    C STP    11      -1.560 -13.587   5.226    0.00     4.51
+ATOM     19    C STP    11      -1.567 -13.472   5.345    0.00     4.45
+ATOM     20    O STP    11      -1.180 -15.075   6.105    0.00     4.34
+ATOM     21    O STP    11      -1.076 -15.289   7.116    0.00     4.14
+ATOM     22    O STP    11      -1.505 -13.532   5.394    0.00     4.46
+ATOM     23    O STP    11      -0.289 -13.357   5.212    0.00     3.55
+ATOM     24    C STP    11      -0.289 -13.067   3.400    0.00     3.46
+ATOM     25    O STP    11      -1.253 -14.770   5.826    0.00     4.37
+ATOM     26    C STP    11      -1.525 -13.665   5.202    0.00     4.54
+ATOM     27    O STP    11      -1.488 -13.667   5.270    0.00     4.52
+ATOM     28    C STP    11      -1.739 -14.231   4.832    0.00     4.53
+ATOM     29    C STP    11      -1.647 -14.742   4.977    0.00     4.44
+ATOM     30    C STP    11      -1.682 -14.732   5.030    0.00     4.49
+ATOM     31    C STP    11      -1.616 -13.199   5.185    0.00     4.27
+ATOM     32    C STP    11      -1.612 -13.209   5.227    0.00     4.28
+ATOM     33    C STP    11      -1.726 -13.041   5.798    0.00     4.17
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket12_atm.pdb

@@ -3,46 +3,42 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    12:
-HEADER 0  - Pocket Score                      : 0.0331
-HEADER 1  - Drug Score                        : 0.2947
-HEADER 2  - Number of alpha spheres           :    35
-HEADER 3  - Mean alpha-sphere radius          : 3.8268
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4500
-HEADER 5  - Mean B-factor of pocket residues  : 0.6250
-HEADER 6  - Hydrophobicity Score              : 67.0909
-HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Amino Acid based volume Score     : 5.7273
-HEADER 9  - Pocket volume (Monte Carlo)       : 306.2977
-HEADER 10  -Pocket volume (convex hull)       : 41.6134
-HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 32.9412
-HEADER 13 - Number of apolar alpha sphere     :    34
-HEADER 14 - Proportion of apolar alpha sphere : 0.9714
-ATOM    705   CZ PHE E 100      -1.744  -4.441  -7.799  0.00  0.00           C 0
-ATOM   1162  OE1 GLU E 155       0.157 -10.157 -10.045  0.84  5.36           O 0
-ATOM   1136  CD2 LEU E 152      -0.761 -10.147  -6.178  0.00  0.00           C 0
-ATOM   2405  CD2 TYR E 306      -5.142  -5.791  -6.300  0.00  0.00           C 0
-ATOM      7  CG2 VAL E  15      -4.494 -11.830 -11.149  0.00  0.00           C 0
-ATOM      6  CG1 VAL E  15      -2.823 -11.529 -12.987  0.00  0.00           C 0
-ATOM     43  CD1 LEU E  19      -2.165  -6.192 -13.498  0.00  0.00           C 0
-ATOM   2367   CB TRP E 302      -3.282 -13.838  -4.682  0.00  0.00           C 0
-ATOM   2283   NZ LYS E 292      -0.453 -12.979  -9.642  0.76  4.37           N 0
-ATOM   2366    O TRP E 302      -4.842 -11.031  -3.546  0.89  1.07           O 0
-ATOM     33  CD2 PHE E  18      -5.291  -5.668 -12.107  0.00  0.00           C 0
-ATOM    703  CE1 PHE E 100      -2.348  -3.750  -8.845  0.00  0.00           C 0
-ATOM   2403   CG TYR E 306      -6.064  -6.651  -5.700  0.00  0.00           C 0
-ATOM   2404  CD1 TYR E 306      -7.425  -6.424  -5.901  0.00  0.00           C 0
-ATOM   1133   CB LEU E 152      -0.075  -7.803  -5.686  0.00  0.00           C 0
-ATOM   2402   CB TYR E 306      -5.635  -7.781  -4.831  0.00  0.00           C 0
-ATOM     30   CB PHE E  18      -6.759  -7.267 -13.392  0.00  0.00           C 0
-ATOM      1    N VAL E  15      -6.512 -12.177 -13.595  0.00  0.00           N 0
-ATOM      2   CA VAL E  15      -5.276 -11.431 -13.476  0.00  0.00           C 0
-ATOM   2408   CZ TYR E 306      -6.937  -4.519  -7.289  0.00  0.00           C 0
-ATOM   2406  CE1 TYR E 306      -7.867  -5.363  -6.689  0.00  0.00           C 0
-ATOM   1132    O LEU E 152       1.330  -6.256  -8.054  0.66  2.14           O 0
-ATOM   1168   CB TYR E 156       0.836  -4.064 -10.536  0.00  0.00           C 0
-ATOM   2365    C TRP E 302      -5.058 -12.250  -3.632  0.00  0.00           C 0
-ATOM   2382  CG1 ILE E 303      -7.953 -13.342  -6.092  0.00  0.00           C 0
-ATOM     31   CG PHE E  18      -6.523  -5.962 -12.692  0.00  0.00           C 0
+HEADER 0  - Pocket Score                      : 0.0233
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0661
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5694
+HEADER 5  - Mean B-factor of pocket residues  : 0.2427
+HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 417.3524
+HEADER 10 - Pocket volume (convex hull)       : 21.6391
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.0800
+ATOM    983   CB ARG E 134      10.740  -0.052  17.353  0.00  0.00           C 0
+ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
+ATOM    985   CD ARG E 134       8.529   0.726  18.433  0.00  0.00           C 0
+ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
+ATOM   2569    O PHE E 327       8.517  10.413  14.152  0.62  3.21           O 0
+ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
+ATOM   2568    C PHE E 327       8.864   9.938  13.094  0.00  0.00           C 0
+ATOM   2555    O SER E 325       5.460   8.512  16.006  0.50  7.50           O 0
+ATOM   2560    C ASN E 326       6.141   7.798  12.923  0.00  0.00           C 0
+ATOM   2559   CA ASN E 326       4.870   7.517  13.722  0.00  0.00           C 0
+ATOM    988  NH1 ARG E 134       7.122   0.553  15.909  0.00  0.00           N 0
+ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
+ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
+ATOM   2564  OD1 ASN E 326       2.463   5.189  14.371  0.35  5.36           O 0
+ATOM    987   CZ ARG E 134       6.599   0.033  17.017  0.00  0.00           C 0
+ATOM    958  CE1 HIS E 131       5.030   1.759  13.404  0.00  0.00           C 0
+ATOM   2562   CB ASN E 326       3.999   6.458  13.078  0.00  0.00           C 0
+ATOM    989  NH2 ARG E 134       5.422  -0.582  16.939  0.00  0.00           N 0
+ATOM   2477   CZ PHE E 314       2.392  -0.719  14.240  0.00  0.00           C 0
+ATOM   2493    N LYS E 317      -1.434   2.889  15.336  0.00  0.00           N 0
+ATOM   2487   CA PRO E 316      -0.297   1.611  13.669  0.00  0.00           C 0
+ATOM   2496    O LYS E 317      -1.019   5.459  16.446  0.00  0.00           O 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket12_vert.pqr

@@ -4,54 +4,44 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    12:
-HEADER 0  - Pocket Score                      : 0.0331
-HEADER 1  - Drug Score                        : 0.2947
-HEADER 2  - Number of V. Vertices             :    35
-HEADER 3  - Mean alpha-sphere radius          : 3.8268
-HEADER 4  - Mean alpha-sphere SA              : 0.4500
-HEADER 5  - Mean B-factor                     : 0.6250
-HEADER 6  - Hydrophobicity Score              : 67.0909
-HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Volume Score                      : 5.7273
-HEADER 9  - Real volume (approximation)       : 306.2977
-HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 32.9412
-HEADER 12 - Number of apolar alpha sphere     :    34
-HEADER 13 - Proportion of apolar alpha sphere : 0.9714
-ATOM      1    C STP    12      -3.012  -8.100  -8.760    0.00     3.99
-ATOM      2    C STP    12      -3.458  -8.552  -8.865    0.00     4.13
-ATOM      3    C STP    12      -2.959  -8.581 -10.924    0.00     3.60
-ATOM      4    C STP    12      -3.348 -12.034  -7.768    0.00     3.58
-ATOM      5    C STP    12      -4.265 -11.238  -7.349    0.00     3.85
-ATOM      6    C STP    12      -3.688  -6.964  -9.269    0.00     3.51
-ATOM      7    C STP    12      -2.701  -7.221 -10.008    0.00     3.68
-ATOM      8    C STP    12      -5.618  -8.473  -9.251    0.00     4.02
-ATOM      9    C STP    12      -3.297  -7.983  -9.300    0.00     4.15
-ATOM     10    C STP    12      -3.480  -8.204  -9.300    0.00     4.19
-ATOM     11    C STP    12      -2.711  -7.550  -9.906    0.00     3.88
-ATOM     12    C STP    12      -3.130  -8.353 -10.547    0.00     3.78
-ATOM     13    C STP    12      -6.416  -7.590  -9.212    0.00     3.65
-ATOM     14    C STP    12      -6.562  -8.616  -9.387    0.00     4.21
-ATOM     15    C STP    12      -3.584  -8.558 -11.489    0.00     3.41
-ATOM     16    C STP    12      -2.190  -7.904  -8.566    0.00     3.57
-ATOM     17    C STP    12      -2.781  -7.847  -8.009    0.00     3.57
-ATOM     18    C STP    12      -4.480 -10.505  -7.436    0.00     3.94
-ATOM     19    C STP    12      -4.026  -9.106  -8.251    0.00     4.00
-ATOM     20    C STP    12      -4.477  -9.071  -8.355    0.00     3.93
-ATOM     21    C STP    12      -6.605  -8.625  -9.403    0.00     4.22
-ATOM     22    C STP    12      -7.298  -9.850 -11.196    0.00     3.43
-ATOM     23    C STP    12      -6.455  -7.572  -9.223    0.00     3.65
-ATOM     24    C STP    12      -6.421  -7.573  -9.212    0.00     3.65
-ATOM     25    O STP    12      -1.367  -6.997 -10.176    0.00     3.51
-ATOM     26    C STP    12      -1.239  -6.770 -10.255    0.00     3.42
-ATOM     27    C STP    12      -4.616 -11.435  -7.345    0.00     3.83
-ATOM     28    C STP    12      -4.811 -11.636  -7.371    0.00     3.80
-ATOM     29    C STP    12      -4.913 -11.381  -7.364    0.00     3.83
-ATOM     30    C STP    12      -6.933  -9.877  -8.296    0.00     4.23
-ATOM     31    C STP    12      -6.950  -9.879  -8.185    0.00     4.17
-ATOM     32    C STP    12      -6.960  -7.202  -9.484    0.00     3.47
-ATOM     33    C STP    12      -6.846  -7.861  -9.393    0.00     3.82
-ATOM     34    C STP    12      -7.673  -8.310  -9.533    0.00     4.10
-ATOM     35    C STP    12      -6.670  -8.554  -9.417    0.00     4.18
+HEADER 0  - Pocket Score                      : 0.0233
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0661
+HEADER 4  - Mean alpha-sphere SA              : 0.5694
+HEADER 5  - Mean B-factor                     : 0.2427
+HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.2000
+HEADER 9  - Real volume (approximation)       : 417.3524
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.0800
+ATOM      1    O STP    12      10.769   4.600  17.144    0.00     4.66
+ATOM      2    O STP    12       8.918   7.040  15.105    0.00     3.53
+ATOM      3    O STP    12       8.811   6.910  15.467    0.00     3.75
+ATOM      4    O STP    12       8.654   7.049  15.351    0.00     3.57
+ATOM      5    O STP    12       7.009   4.684  15.839    0.00     4.13
+ATOM      6    O STP    12      10.267   4.709  16.884    0.00     4.61
+ATOM      7    O STP    12       9.090   4.045  16.233    0.00     4.02
+ATOM      8    O STP    12       8.866   5.705  16.024    0.00     4.41
+ATOM      9    O STP    12       8.485   4.984  16.506    0.00     4.67
+ATOM     10    O STP    12       7.933   4.703  15.769    0.00     4.23
+ATOM     11    O STP    12       8.124   4.913  16.122    0.00     4.48
+ATOM     12    O STP    12       5.406   4.327  17.670    0.00     4.50
+ATOM     13    O STP    12       6.841   4.575  15.663    0.00     4.04
+ATOM     14    C STP    12       6.255   4.603  14.860    0.00     3.42
+ATOM     15    C STP    12       5.811   4.553  15.542    0.00     3.60
+ATOM     16    O STP    12       6.320   4.537  16.081    0.00     4.07
+ATOM     17    O STP    12       5.988   4.465  16.323    0.00     4.09
+ATOM     18    O STP    12       6.008   4.524  16.167    0.00     4.03
+ATOM     19    O STP    12       7.257   4.342  15.204    0.00     3.86
+ATOM     20    O STP    12       4.688   3.338  16.867    0.00     3.82
+ATOM     21    O STP    12       4.288   3.032  16.894    0.00     3.79
+ATOM     22    O STP    12       2.992   2.180  16.473    0.00     3.71
+ATOM     23    O STP    12       2.016   2.191  16.513    0.00     3.71
+ATOM     24    O STP    12       2.230   2.170  17.329    0.00     4.23
+ATOM     25    O STP    12       2.219   2.587  18.277    0.00     4.70
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket13_atm.pdb

@@ -3,42 +3,44 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    13:
-HEADER 0  - Pocket Score                      : 0.0233
-HEADER 1  - Drug Score                        : 0.0000
+HEADER 0  - Pocket Score                      : 0.0142
+HEADER 1  - Drug Score                        : 0.0061
 HEADER 2  - Number of alpha spheres           :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0661
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5694
-HEADER 5  - Mean B-factor of pocket residues  : 0.5629
-HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 3  - Mean alpha-sphere radius          : 4.0690
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6169
+HEADER 5  - Mean B-factor of pocket residues  : 0.2476
+HEADER 6  - Hydrophobicity Score              : 19.0000
 HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Amino Acid based volume Score     : 4.2000
-HEADER 9  - Pocket volume (Monte Carlo)       : 418.0618
-HEADER 10  -Pocket volume (convex hull)       : 21.6391
+HEADER 8  - Amino Acid based volume Score     : 4.0909
+HEADER 9  - Pocket volume (Monte Carlo)       : 369.7708
+HEADER 10 - Pocket volume (convex hull)       : 34.2649
 HEADER 11 - Charge Score                      :     2
-HEADER 12 - Local hydrophobic density Score   : 1.0000
-HEADER 13 - Number of apolar alpha sphere     :     2
-HEADER 14 - Proportion of apolar alpha sphere : 0.0800
-ATOM    983   CB ARG E 134      10.740  -0.052  17.353  0.00  0.00           C 0
-ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
-ATOM    985   CD ARG E 134       8.529   0.726  18.433  0.00  0.00           C 0
-ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
-ATOM   2569    O PHE E 327       8.517  10.413  14.152  0.62  3.21           O 0
-ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
-ATOM   2568    C PHE E 327       8.864   9.938  13.094  0.00  0.00           C 0
-ATOM   2555    O SER E 325       5.460   8.512  16.006  0.50  7.50           O 0
-ATOM   2560    C ASN E 326       6.141   7.798  12.923  0.00  0.00           C 0
-ATOM   2559   CA ASN E 326       4.870   7.517  13.722  0.00  0.00           C 0
-ATOM    988  NH1 ARG E 134       7.122   0.553  15.909  0.00  0.00           N 0
-ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
-ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
-ATOM   2564  OD1 ASN E 326       2.463   5.189  14.371  0.35  5.36           O 0
-ATOM    987   CZ ARG E 134       6.599   0.033  17.017  0.00  0.00           C 0
-ATOM    958  CE1 HIS E 131       5.030   1.759  13.404  0.00  0.00           C 0
-ATOM   2562   CB ASN E 326       3.999   6.458  13.078  0.00  0.00           C 0
-ATOM    989  NH2 ARG E 134       5.422  -0.582  16.939  0.00  0.00           N 0
-ATOM   2477   CZ PHE E 314       2.392  -0.719  14.240  0.00  0.00           C 0
-ATOM   2493    N LYS E 317      -1.434   2.889  15.336  0.00  0.00           N 0
-ATOM   2487   CA PRO E 316      -0.297   1.611  13.669  0.00  0.00           C 0
-ATOM   2496    O LYS E 317      -1.019   5.459  16.446  0.00  0.00           O 0
+HEADER 12 - Local hydrophobic density Score   : 11.0000
+HEADER 13 - Number of apolar alpha sphere     :    12
+HEADER 14 - Proportion of apolar alpha sphere : 0.4800
+ATOM   2249  CG1 VAL E 288       3.564 -12.956 -11.539  0.00  0.00           C 0
+ATOM   1160   CG GLU E 155       1.987  -9.808 -11.553  0.00  0.00           C 0
+ATOM     16   NZ LYS E  16      -0.505 -12.557 -16.586  0.00  0.00           N 0
+ATOM   1163  OE2 GLU E 155       0.538 -11.622 -11.655  0.59  1.07           O 0
+ATOM   1198   CB SER E 159       2.184  -5.965 -15.856  0.00  0.00           C 0
+ATOM   1158    O GLU E 155       2.592  -6.882 -13.001  0.00  0.00           O 0
+ATOM     44  CD2 LEU E  19      -0.942  -8.123 -14.318  0.00  0.00           C 0
+ATOM   1188   CB HIS E 158       7.249  -6.299 -13.781  0.00  0.00           C 0
+ATOM   2244    N VAL E 288       6.014 -14.516 -12.342  0.00  0.00           N 0
+ATOM   2206    O GLY E 282      10.358 -13.074 -13.450  0.45  9.64           O 0
+ATOM   2248   CB VAL E 288       4.901 -12.934 -10.819  0.00  0.00           C 0
+ATOM   1705  NE1 TRP E 221       9.870 -10.227 -10.703  0.63  2.19           N 0
+ATOM   1708  CZ2 TRP E 221       7.752 -10.019  -9.370  0.00  0.00           C 0
+ATOM   1191  CD2 HIS E 158       8.957  -7.116 -12.009  0.00  0.00           C 0
+ATOM   1156   CA GLU E 155       3.603  -7.906 -11.008  0.00  0.00           C 0
+ATOM   1675   CE LYS E 217       9.911  -4.369 -16.606  0.00  0.00           C 0
+ATOM   1187    O HIS E 158       6.222  -5.014 -16.513  0.63  6.43           O 0
+ATOM   1673   CG LYS E 217      11.555  -6.094 -15.608  0.00  0.00           C 0
+ATOM   1672   CB LYS E 217      11.906  -6.886 -14.343  0.00  0.00           C 0
+ATOM   1677    N ALA E 218      14.585  -8.461 -13.036  0.52  1.09           N 0
+ATOM   2213  OD1 ASN E 283      14.597 -12.174 -15.706  0.48  4.29           O 0
+ATOM   1194    N SER E 159       4.457  -5.333 -15.179  0.00  0.00           N 0
+ATOM   1186    C HIS E 158       5.736  -5.116 -15.393  0.00  0.00           C 0
+ATOM   1195   CA SER E 159       3.556  -5.471 -16.302  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket13_vert.pqr

@@ -4,44 +4,44 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    13:
-HEADER 0  - Pocket Score                      : 0.0233
-HEADER 1  - Drug Score                        : 0.0000
+HEADER 0  - Pocket Score                      : 0.0142
+HEADER 1  - Drug Score                        : 0.0061
 HEADER 2  - Number of V. Vertices             :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0661
-HEADER 4  - Mean alpha-sphere SA              : 0.5694
-HEADER 5  - Mean B-factor                     : 0.5629
-HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 3  - Mean alpha-sphere radius          : 4.0690
+HEADER 4  - Mean alpha-sphere SA              : 0.6169
+HEADER 5  - Mean B-factor                     : 0.2476
+HEADER 6  - Hydrophobicity Score              : 19.0000
 HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Volume Score                      : 4.2000
-HEADER 9  - Real volume (approximation)       : 418.0618
+HEADER 8  - Volume Score                      : 4.0909
+HEADER 9  - Real volume (approximation)       : 369.7708
 HEADER 10 - Charge Score                      :     2
-HEADER 11 - Local hydrophobic density Score   : 1.0000
-HEADER 12 - Number of apolar alpha sphere     :     2
-HEADER 13 - Proportion of apolar alpha sphere : 0.0800
-ATOM      1    O STP    13      10.769   4.600  17.144    0.00     4.66
-ATOM      2    O STP    13       8.918   7.040  15.105    0.00     3.53
-ATOM      3    O STP    13       8.811   6.910  15.467    0.00     3.75
-ATOM      4    O STP    13       8.654   7.049  15.351    0.00     3.57
-ATOM      5    O STP    13       7.009   4.684  15.839    0.00     4.13
-ATOM      6    O STP    13      10.267   4.709  16.884    0.00     4.61
-ATOM      7    O STP    13       9.090   4.045  16.233    0.00     4.02
-ATOM      8    O STP    13       8.866   5.705  16.024    0.00     4.41
-ATOM      9    O STP    13       8.485   4.984  16.506    0.00     4.67
-ATOM     10    O STP    13       7.933   4.703  15.769    0.00     4.23
-ATOM     11    O STP    13       8.124   4.913  16.122    0.00     4.48
-ATOM     12    O STP    13       5.406   4.327  17.670    0.00     4.50
-ATOM     13    O STP    13       6.841   4.575  15.663    0.00     4.04
-ATOM     14    C STP    13       6.255   4.603  14.860    0.00     3.42
-ATOM     15    C STP    13       5.811   4.553  15.542    0.00     3.60
-ATOM     16    O STP    13       6.320   4.537  16.081    0.00     4.07
-ATOM     17    O STP    13       5.988   4.465  16.323    0.00     4.09
-ATOM     18    O STP    13       6.008   4.524  16.167    0.00     4.03
-ATOM     19    O STP    13       7.257   4.342  15.204    0.00     3.86
-ATOM     20    O STP    13       4.688   3.338  16.867    0.00     3.82
-ATOM     21    O STP    13       4.288   3.032  16.894    0.00     3.79
-ATOM     22    O STP    13       2.992   2.180  16.473    0.00     3.71
-ATOM     23    O STP    13       2.016   2.191  16.513    0.00     3.71
-ATOM     24    O STP    13       2.230   2.170  17.329    0.00     4.23
-ATOM     25    O STP    13       2.219   2.587  18.277    0.00     4.70
+HEADER 11 - Local hydrophobic density Score   : 11.0000
+HEADER 12 - Number of apolar alpha sphere     :    12
+HEADER 13 - Proportion of apolar alpha sphere : 0.4800
+ATOM      1    O STP    13       2.506 -11.531 -14.753    0.00     3.67
+ATOM      2    O STP    13       3.068 -10.223 -15.746    0.00     4.35
+ATOM      3    O STP    13       2.399  -9.985 -15.545    0.00     4.02
+ATOM      4    O STP    13       2.404  -9.971 -15.570    0.00     4.02
+ATOM      5    C STP    13       5.125 -10.220 -14.880    0.00     4.59
+ATOM      6    O STP    13       6.885 -10.576 -13.808    0.00     4.29
+ATOM      7    C STP    13       5.976 -10.559 -14.490    0.00     4.50
+ATOM      8    O STP    13       6.965 -10.686 -13.636    0.00     4.15
+ATOM      9    C STP    13       6.745 -10.296 -13.292    0.00     4.06
+ATOM     10    C STP    13       6.779 -10.238 -13.247    0.00     4.00
+ATOM     11    O STP    13       6.903 -10.566 -13.771    0.00     4.28
+ATOM     12    O STP    13       7.436 -10.329 -13.922    0.00     4.04
+ATOM     13    C STP    13       5.178  -9.990 -14.394    0.00     4.28
+ATOM     14    C STP    13       6.257  -9.980 -12.969    0.00     3.90
+ATOM     15    C STP    13       5.645 -10.172 -13.886    0.00     4.19
+ATOM     16    C STP    13       5.308 -10.126 -14.302    0.00     4.32
+ATOM     17    C STP    13       6.375  -9.340 -12.443    0.00     3.44
+ATOM     18    C STP    13       8.583  -7.677 -16.792    0.00     3.57
+ATOM     19    O STP    13       9.881  -9.702 -14.137    0.00     3.47
+ATOM     20    C STP    13       8.914  -9.764 -16.244    0.00     4.57
+ATOM     21    C STP    13       9.059  -9.645 -15.171    0.00     4.05
+ATOM     22    O STP    13      12.065 -10.289 -14.422    0.00     3.41
+ATOM     23    O STP    13       5.610  -9.461 -16.514    0.00     4.49
+ATOM     24    O STP    13       5.607  -9.484 -16.523    0.00     4.51
+ATOM     25    O STP    13       4.200  -8.861 -15.470    0.00     3.55
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket14_atm.pdb

@@ -3,44 +3,47 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    14:
-HEADER 0  - Pocket Score                      : 0.0142
-HEADER 1  - Drug Score                        : 0.0061
-HEADER 2  - Number of alpha spheres           :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0690
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6169
-HEADER 5  - Mean B-factor of pocket residues  : 0.5743
-HEADER 6  - Hydrophobicity Score              : 19.0000
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0085
+HEADER 2  - Number of alpha spheres           :    29
+HEADER 3  - Mean alpha-sphere radius          : 4.2363
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6830
+HEADER 5  - Mean B-factor of pocket residues  : 0.2622
+HEADER 6  - Hydrophobicity Score              : 21.3636
 HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Amino Acid based volume Score     : 4.0909
-HEADER 9  - Pocket volume (Monte Carlo)       : 370.6070
-HEADER 10  -Pocket volume (convex hull)       : 34.2649
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 419.4885
+HEADER 10 - Pocket volume (convex hull)       : 21.9768
 HEADER 11 - Charge Score                      :     2
-HEADER 12 - Local hydrophobic density Score   : 11.0000
-HEADER 13 - Number of apolar alpha sphere     :    12
-HEADER 14 - Proportion of apolar alpha sphere : 0.4800
-ATOM   2249  CG1 VAL E 288       3.564 -12.956 -11.539  0.00  0.00           C 0
-ATOM   1160   CG GLU E 155       1.987  -9.808 -11.553  0.00  0.00           C 0
-ATOM     16   NZ LYS E  16      -0.505 -12.557 -16.586  0.00  0.00           N 0
-ATOM   1163  OE2 GLU E 155       0.538 -11.622 -11.655  0.59  1.07           O 0
-ATOM   1198   CB SER E 159       2.184  -5.965 -15.856  0.00  0.00           C 0
-ATOM   1158    O GLU E 155       2.592  -6.882 -13.001  0.00  0.00           O 0
-ATOM     44  CD2 LEU E  19      -0.942  -8.123 -14.318  0.00  0.00           C 0
-ATOM   1188   CB HIS E 158       7.249  -6.299 -13.781  0.00  0.00           C 0
-ATOM   2244    N VAL E 288       6.014 -14.516 -12.342  0.00  0.00           N 0
-ATOM   2206    O GLY E 282      10.358 -13.074 -13.450  0.45  9.64           O 0
-ATOM   2248   CB VAL E 288       4.901 -12.934 -10.819  0.00  0.00           C 0
-ATOM   1705  NE1 TRP E 221       9.870 -10.227 -10.703  0.63  2.19           N 0
-ATOM   1708  CZ2 TRP E 221       7.752 -10.019  -9.370  0.00  0.00           C 0
-ATOM   1191  CD2 HIS E 158       8.957  -7.116 -12.009  0.00  0.00           C 0
-ATOM   1156   CA GLU E 155       3.603  -7.906 -11.008  0.00  0.00           C 0
-ATOM   1675   CE LYS E 217       9.911  -4.369 -16.606  0.00  0.00           C 0
-ATOM   1187    O HIS E 158       6.222  -5.014 -16.513  0.63  6.43           O 0
-ATOM   1673   CG LYS E 217      11.555  -6.094 -15.608  0.00  0.00           C 0
-ATOM   1672   CB LYS E 217      11.906  -6.886 -14.343  0.00  0.00           C 0
-ATOM   1677    N ALA E 218      14.585  -8.461 -13.036  0.52  1.09           N 0
-ATOM   2213  OD1 ASN E 283      14.597 -12.174 -15.706  0.48  4.29           O 0
-ATOM   1194    N SER E 159       4.457  -5.333 -15.179  0.00  0.00           N 0
-ATOM   1186    C HIS E 158       5.736  -5.116 -15.393  0.00  0.00           C 0
-ATOM   1195   CA SER E 159       3.556  -5.471 -16.302  0.00  0.00           C 0
+HEADER 12 - Local hydrophobic density Score   : 15.0000
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.5517
+ATOM   1819   OH TYR E 235      20.722 -13.511  11.416  0.59  7.50           O 0
+ATOM   2786    N THR I   6      24.752 -13.023  15.286  0.00  0.00           N 0
+ATOM   2793    N TYR I   7      22.704 -11.012  15.175  0.73  1.09           N 0
+ATOM   2783   CB THR I   5      24.155 -13.603  18.177  0.00  0.00           C 0
+ATOM   1817  CE2 TYR E 235      19.985 -11.372  12.216  0.00  0.00           C 0
+ATOM   2797   CB TYR I   7      20.768 -10.287  16.509  0.00  0.00           C 0
+ATOM   2790   CB THR I   6      23.915 -12.886  13.021  0.00  0.00           C 0
+ATOM   2791  OG1 THR I   6      24.715 -14.012  12.684  0.46  6.43           O 0
+ATOM   2023  CD2 HIS E 260      15.149 -16.519  13.733  0.00  0.00           C 0
+ATOM   2803   CZ TYR I   7      17.998  -7.046  17.130  0.00  0.00           C 0
+ATOM   1008   CD ARG E 137      13.015 -12.390  14.489  0.00  0.00           C 0
+ATOM   1001    O GLY E 136      14.004  -7.535  14.180  0.55  1.07           O 0
+ATOM   2801  CE1 TYR I   7      18.129  -7.625  15.869  0.00  0.00           C 0
+ATOM   2802  CE2 TYR I   7      18.768  -7.509  18.203  0.00  0.00           C 0
+ATOM   2800  CD2 TYR I   7      19.671  -8.559  18.021  0.00  0.00           C 0
+ATOM   2007   CB PRO E 258      17.978 -16.703  11.072  0.00  0.00           C 0
+ATOM   2015   OG SER E 259      18.773 -20.147  14.551  0.00  0.00           O 0
+ATOM   2004   CA PRO E 258      18.907 -17.890  10.760  0.00  0.00           C 0
+ATOM   1000    C GLY E 136      13.099  -7.215  14.936  0.00  0.00           C 0
+ATOM   1007   CG ARG E 137      12.064 -11.168  14.522  0.00  0.00           C 0
+ATOM   1006   CB ARG E 137      12.547  -9.944  13.745  0.00  0.00           C 0
+ATOM   1002    N ARG E 137      11.897  -7.755  14.844  0.00  0.00           N 0
+ATOM    993    O ILE E 135      11.277  -6.737  17.844  0.39  8.57           O 0
+ATOM   2025  NE2 HIS E 260      14.962 -15.418  12.941  0.93  2.19           N 0
+ATOM   2798   CG TYR I   7      19.809  -9.148  16.762  0.00  0.00           C 0
+ATOM   2799  CD1 TYR I   7      19.040  -8.667  15.701  0.00  0.00           C 0
+ATOM   1802    O ALA E 233      16.247 -11.091  12.418  0.55  5.36           O 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket14_vert.pqr

@@ -4,44 +4,48 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    14:
-HEADER 0  - Pocket Score                      : 0.0142
-HEADER 1  - Drug Score                        : 0.0061
-HEADER 2  - Number of V. Vertices             :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0690
-HEADER 4  - Mean alpha-sphere SA              : 0.6169
-HEADER 5  - Mean B-factor                     : 0.5743
-HEADER 6  - Hydrophobicity Score              : 19.0000
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0085
+HEADER 2  - Number of V. Vertices             :    29
+HEADER 3  - Mean alpha-sphere radius          : 4.2363
+HEADER 4  - Mean alpha-sphere SA              : 0.6830
+HEADER 5  - Mean B-factor                     : 0.2622
+HEADER 6  - Hydrophobicity Score              : 21.3636
 HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Volume Score                      : 4.0909
-HEADER 9  - Real volume (approximation)       : 370.6070
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 419.4885
 HEADER 10 - Charge Score                      :     2
-HEADER 11 - Local hydrophobic density Score   : 11.0000
-HEADER 12 - Number of apolar alpha sphere     :    12
-HEADER 13 - Proportion of apolar alpha sphere : 0.4800
-ATOM      1    O STP    14       2.506 -11.531 -14.753    0.00     3.67
-ATOM      2    O STP    14       3.068 -10.223 -15.746    0.00     4.35
-ATOM      3    O STP    14       2.399  -9.985 -15.545    0.00     4.02
-ATOM      4    O STP    14       2.404  -9.971 -15.570    0.00     4.02
-ATOM      5    C STP    14       5.125 -10.220 -14.880    0.00     4.59
-ATOM      6    O STP    14       6.885 -10.576 -13.808    0.00     4.29
-ATOM      7    C STP    14       5.976 -10.559 -14.490    0.00     4.50
-ATOM      8    O STP    14       6.965 -10.686 -13.636    0.00     4.15
-ATOM      9    C STP    14       6.745 -10.296 -13.292    0.00     4.06
-ATOM     10    C STP    14       6.779 -10.238 -13.247    0.00     4.00
-ATOM     11    O STP    14       6.903 -10.566 -13.771    0.00     4.28
-ATOM     12    O STP    14       7.436 -10.329 -13.922    0.00     4.04
-ATOM     13    C STP    14       5.178  -9.990 -14.394    0.00     4.28
-ATOM     14    C STP    14       6.257  -9.980 -12.969    0.00     3.90
-ATOM     15    C STP    14       5.645 -10.172 -13.886    0.00     4.19
-ATOM     16    C STP    14       5.308 -10.126 -14.302    0.00     4.32
-ATOM     17    C STP    14       6.375  -9.340 -12.443    0.00     3.44
-ATOM     18    C STP    14       8.583  -7.677 -16.792    0.00     3.57
-ATOM     19    O STP    14       9.881  -9.702 -14.137    0.00     3.47
-ATOM     20    C STP    14       8.914  -9.764 -16.244    0.00     4.57
-ATOM     21    C STP    14       9.059  -9.645 -15.171    0.00     4.05
-ATOM     22    O STP    14      12.065 -10.289 -14.422    0.00     3.41
-ATOM     23    O STP    14       5.610  -9.461 -16.514    0.00     4.49
-ATOM     24    O STP    14       5.607  -9.484 -16.523    0.00     4.51
-ATOM     25    O STP    14       4.200  -8.861 -15.470    0.00     3.55
+HEADER 11 - Local hydrophobic density Score   : 15.0000
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.5517
+ATOM      1    O STP    14      20.762 -15.016  15.628    0.00     4.47
+ATOM      2    O STP    14      20.093 -13.782  15.160    0.00     3.81
+ATOM      3    O STP    14      21.482 -16.110  15.016    0.00     4.50
+ATOM      4    O STP    14      21.091 -14.702  15.246    0.00     4.03
+ATOM      5    C STP    14      18.817 -14.364  15.540    0.00     4.62
+ATOM      6    C STP    14      15.023 -10.073  17.441    0.00     4.26
+ATOM      7    C STP    14      15.741 -10.998  17.957    0.00     4.63
+ATOM      8    O STP    14      20.585 -16.489  14.223    0.00     4.09
+ATOM      9    O STP    14      19.415 -15.607  15.364    0.00     4.66
+ATOM     10    C STP    14      15.015 -10.071  17.451    0.00     4.26
+ATOM     11    C STP    14      14.777 -10.089  16.406    0.00     3.47
+ATOM     12    C STP    14      14.855 -10.051  17.251    0.00     4.06
+ATOM     13    O STP    14      13.277  -9.665  17.514    0.00     3.56
+ATOM     14    C STP    14      14.805 -10.108  17.922    0.00     4.49
+ATOM     15    O STP    14      18.495 -14.244  14.923    0.00     4.22
+ATOM     16    O STP    14      18.480 -14.689  14.307    0.00     3.84
+ATOM     17    C STP    14      18.270 -13.858  15.512    0.00     4.47
+ATOM     18    C STP    14      15.741 -10.998  17.957    0.00     4.63
+ATOM     19    C STP    14      15.742 -10.997  17.953    0.00     4.62
+ATOM     20    C STP    14      15.760 -10.982  17.951    0.00     4.60
+ATOM     21    C STP    14      16.138 -10.636  17.830    0.00     4.10
+ATOM     22    C STP    14      16.014 -10.748  17.869    0.00     4.26
+ATOM     23    O STP    14      17.979 -13.868  13.441    0.00     3.43
+ATOM     24    O STP    14      18.105 -13.657  15.491    0.00     4.41
+ATOM     25    O STP    14      17.165 -13.262  16.453    0.00     4.67
+ATOM     26    O STP    14      15.637 -10.294  15.930    0.00     3.65
+ATOM     27    C STP    14      16.936 -12.523  16.560    0.00     4.44
+ATOM     28    C STP    14      17.083 -12.356  16.365    0.00     4.23
+ATOM     29    C STP    14      16.850 -12.331  16.545    0.00     4.35
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket15_atm.pdb

@@ -3,47 +3,50 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    15:
-HEADER 0  - Pocket Score                      : 0.0056
-HEADER 1  - Drug Score                        : 0.0085
-HEADER 2  - Number of alpha spheres           :    29
-HEADER 3  - Mean alpha-sphere radius          : 4.2363
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6830
-HEADER 5  - Mean B-factor of pocket residues  : 0.6083
-HEADER 6  - Hydrophobicity Score              : 21.3636
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Amino Acid based volume Score     : 4.0000
-HEADER 9  - Pocket volume (Monte Carlo)       : 421.6359
-HEADER 10  -Pocket volume (convex hull)       : 21.9768
-HEADER 11 - Charge Score                      :     2
-HEADER 12 - Local hydrophobic density Score   : 15.0000
-HEADER 13 - Number of apolar alpha sphere     :    16
-HEADER 14 - Proportion of apolar alpha sphere : 0.5517
-ATOM   1819   OH TYR E 235      20.722 -13.511  11.416  0.59  7.50           O 0
-ATOM   2786    N THR I   6      24.752 -13.023  15.286  0.00  0.00           N 0
-ATOM   2793    N TYR I   7      22.704 -11.012  15.175  0.73  1.09           N 0
-ATOM   2783   CB THR I   5      24.155 -13.603  18.177  0.00  0.00           C 0
-ATOM   1817  CE2 TYR E 235      19.985 -11.372  12.216  0.00  0.00           C 0
-ATOM   2797   CB TYR I   7      20.768 -10.287  16.509  0.00  0.00           C 0
-ATOM   2790   CB THR I   6      23.915 -12.886  13.021  0.00  0.00           C 0
-ATOM   2791  OG1 THR I   6      24.715 -14.012  12.684  0.46  6.43           O 0
-ATOM   2023  CD2 HIS E 260      15.149 -16.519  13.733  0.00  0.00           C 0
-ATOM   2803   CZ TYR I   7      17.998  -7.046  17.130  0.00  0.00           C 0
-ATOM   1008   CD ARG E 137      13.015 -12.390  14.489  0.00  0.00           C 0
-ATOM   1001    O GLY E 136      14.004  -7.535  14.180  0.55  1.07           O 0
-ATOM   2801  CE1 TYR I   7      18.129  -7.625  15.869  0.00  0.00           C 0
-ATOM   2802  CE2 TYR I   7      18.768  -7.509  18.203  0.00  0.00           C 0
-ATOM   2800  CD2 TYR I   7      19.671  -8.559  18.021  0.00  0.00           C 0
-ATOM   2007   CB PRO E 258      17.978 -16.703  11.072  0.00  0.00           C 0
-ATOM   2015   OG SER E 259      18.773 -20.147  14.551  0.00  0.00           O 0
-ATOM   2004   CA PRO E 258      18.907 -17.890  10.760  0.00  0.00           C 0
-ATOM   1000    C GLY E 136      13.099  -7.215  14.936  0.00  0.00           C 0
-ATOM   1007   CG ARG E 137      12.064 -11.168  14.522  0.00  0.00           C 0
-ATOM   1006   CB ARG E 137      12.547  -9.944  13.745  0.00  0.00           C 0
-ATOM   1002    N ARG E 137      11.897  -7.755  14.844  0.00  0.00           N 0
-ATOM    993    O ILE E 135      11.277  -6.737  17.844  0.39  8.57           O 0
-ATOM   2025  NE2 HIS E 260      14.962 -15.418  12.941  0.93  2.19           N 0
-ATOM   2798   CG TYR I   7      19.809  -9.148  16.762  0.00  0.00           C 0
-ATOM   2799  CD1 TYR I   7      19.040  -8.667  15.701  0.00  0.00           C 0
-ATOM   1802    O ALA E 233      16.247 -11.091  12.418  0.55  5.36           O 0
+HEADER 0  - Pocket Score                      : 0.0047
+HEADER 1  - Drug Score                        : 0.5258
+HEADER 2  - Number of alpha spheres           :    38
+HEADER 3  - Mean alpha-sphere radius          : 3.8294
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4718
+HEADER 5  - Mean B-factor of pocket residues  : 0.3144
+HEADER 6  - Hydrophobicity Score              : 67.0909
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 5.7273
+HEADER 9  - Pocket volume (Monte Carlo)       : 359.5255
+HEADER 10 - Pocket volume (convex hull)       : 49.8527
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 35.8378
+HEADER 13 - Number of apolar alpha sphere     :    37
+HEADER 14 - Proportion of apolar alpha sphere : 0.9737
+ATOM    705   CZ PHE E 100      -1.744  -4.441  -7.799  0.00  0.00           C 0
+ATOM   1162  OE1 GLU E 155       0.157 -10.157 -10.045  0.84  5.36           O 0
+ATOM   1136  CD2 LEU E 152      -0.761 -10.147  -6.178  0.00  0.00           C 0
+ATOM   2405  CD2 TYR E 306      -5.142  -5.791  -6.300  0.00  0.00           C 0
+ATOM      7  CG2 VAL E  15      -4.494 -11.830 -11.149  0.00  0.00           C 0
+ATOM      6  CG1 VAL E  15      -2.823 -11.529 -12.987  0.00  0.00           C 0
+ATOM     43  CD1 LEU E  19      -2.165  -6.192 -13.498  0.00  0.00           C 0
+ATOM   2367   CB TRP E 302      -3.282 -13.838  -4.682  0.00  0.00           C 0
+ATOM   2283   NZ LYS E 292      -0.453 -12.979  -9.642  0.76  4.37           N 0
+ATOM   2366    O TRP E 302      -4.842 -11.031  -3.546  0.89  1.07           O 0
+ATOM     33  CD2 PHE E  18      -5.291  -5.668 -12.107  0.00  0.00           C 0
+ATOM    703  CE1 PHE E 100      -2.348  -3.750  -8.845  0.00  0.00           C 0
+ATOM   2403   CG TYR E 306      -6.064  -6.651  -5.700  0.00  0.00           C 0
+ATOM   2404  CD1 TYR E 306      -7.425  -6.424  -5.901  0.00  0.00           C 0
+ATOM   1133   CB LEU E 152      -0.075  -7.803  -5.686  0.00  0.00           C 0
+ATOM   2402   CB TYR E 306      -5.635  -7.781  -4.831  0.00  0.00           C 0
+ATOM     30   CB PHE E  18      -6.759  -7.267 -13.392  0.00  0.00           C 0
+ATOM      1    N VAL E  15      -6.512 -12.177 -13.595  0.00  0.00           N 0
+ATOM      2   CA VAL E  15      -5.276 -11.431 -13.476  0.00  0.00           C 0
+ATOM   2408   CZ TYR E 306      -6.937  -4.519  -7.289  0.00  0.00           C 0
+ATOM   2406  CE1 TYR E 306      -7.867  -5.363  -6.689  0.00  0.00           C 0
+ATOM   2407  CE2 TYR E 306      -5.569  -4.727  -7.097  0.00  0.00           C 0
+ATOM   1132    O LEU E 152       1.330  -6.256  -8.054  0.66  2.14           O 0
+ATOM   1168   CB TYR E 156       0.836  -4.064 -10.536  0.00  0.00           C 0
+ATOM   2365    C TRP E 302      -5.058 -12.250  -3.632  0.00  0.00           C 0
+ATOM   2382  CG1 ILE E 303      -7.953 -13.342  -6.092  0.00  0.00           C 0
+ATOM   2383  CG2 ILE E 303      -9.623 -11.703  -5.218  0.00  0.00           C 0
+ATOM   2378   CA ILE E 303      -7.378 -11.859  -4.194  0.00  0.00           C 0
+ATOM     31   CG PHE E  18      -6.523  -5.962 -12.692  0.00  0.00           C 0
+ATOM     32  CD1 PHE E  18      -7.536  -5.003 -12.655  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket15_vert.pqr

@@ -4,48 +4,57 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    15:
-HEADER 0  - Pocket Score                      : 0.0056
-HEADER 1  - Drug Score                        : 0.0085
-HEADER 2  - Number of V. Vertices             :    29
-HEADER 3  - Mean alpha-sphere radius          : 4.2363
-HEADER 4  - Mean alpha-sphere SA              : 0.6830
-HEADER 5  - Mean B-factor                     : 0.6083
-HEADER 6  - Hydrophobicity Score              : 21.3636
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 421.6359
-HEADER 10 - Charge Score                      :     2
-HEADER 11 - Local hydrophobic density Score   : 15.0000
-HEADER 12 - Number of apolar alpha sphere     :    16
-HEADER 13 - Proportion of apolar alpha sphere : 0.5517
-ATOM      1    O STP    15      20.762 -15.016  15.628    0.00     4.47
-ATOM      2    O STP    15      20.093 -13.782  15.160    0.00     3.81
-ATOM      3    O STP    15      21.482 -16.110  15.016    0.00     4.50
-ATOM      4    O STP    15      21.091 -14.702  15.246    0.00     4.03
-ATOM      5    C STP    15      18.817 -14.364  15.540    0.00     4.62
-ATOM      6    C STP    15      15.023 -10.073  17.441    0.00     4.26
-ATOM      7    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM      8    O STP    15      20.585 -16.489  14.223    0.00     4.09
-ATOM      9    O STP    15      19.415 -15.607  15.364    0.00     4.66
-ATOM     10    C STP    15      15.015 -10.071  17.451    0.00     4.26
-ATOM     11    C STP    15      14.777 -10.089  16.406    0.00     3.47
-ATOM     12    C STP    15      14.855 -10.051  17.251    0.00     4.06
-ATOM     13    O STP    15      13.277  -9.665  17.514    0.00     3.56
-ATOM     14    C STP    15      14.805 -10.108  17.922    0.00     4.49
-ATOM     15    O STP    15      18.495 -14.244  14.923    0.00     4.22
-ATOM     16    O STP    15      18.480 -14.689  14.307    0.00     3.84
-ATOM     17    C STP    15      18.270 -13.858  15.512    0.00     4.47
-ATOM     18    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM     19    C STP    15      15.742 -10.997  17.953    0.00     4.62
-ATOM     20    C STP    15      15.760 -10.982  17.951    0.00     4.60
-ATOM     21    C STP    15      16.138 -10.636  17.830    0.00     4.10
-ATOM     22    C STP    15      16.014 -10.748  17.869    0.00     4.26
-ATOM     23    O STP    15      17.979 -13.868  13.441    0.00     3.43
-ATOM     24    O STP    15      18.105 -13.657  15.491    0.00     4.41
-ATOM     25    O STP    15      17.165 -13.262  16.453    0.00     4.67
-ATOM     26    O STP    15      15.637 -10.294  15.930    0.00     3.65
-ATOM     27    C STP    15      16.936 -12.523  16.560    0.00     4.44
-ATOM     28    C STP    15      17.083 -12.356  16.365    0.00     4.23
-ATOM     29    C STP    15      16.850 -12.331  16.545    0.00     4.35
+HEADER 0  - Pocket Score                      : 0.0047
+HEADER 1  - Drug Score                        : 0.5258
+HEADER 2  - Number of V. Vertices             :    38
+HEADER 3  - Mean alpha-sphere radius          : 3.8294
+HEADER 4  - Mean alpha-sphere SA              : 0.4718
+HEADER 5  - Mean B-factor                     : 0.3144
+HEADER 6  - Hydrophobicity Score              : 67.0909
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 5.7273
+HEADER 9  - Real volume (approximation)       : 359.5255
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 35.8378
+HEADER 12 - Number of apolar alpha sphere     :    37
+HEADER 13 - Proportion of apolar alpha sphere : 0.9737
+ATOM      1    C STP    15      -3.012  -8.100  -8.760    0.00     3.99
+ATOM      2    C STP    15      -3.458  -8.552  -8.865    0.00     4.13
+ATOM      3    C STP    15      -2.959  -8.581 -10.924    0.00     3.60
+ATOM      4    C STP    15      -3.348 -12.034  -7.768    0.00     3.58
+ATOM      5    C STP    15      -4.265 -11.238  -7.349    0.00     3.85
+ATOM      6    C STP    15      -3.688  -6.964  -9.269    0.00     3.51
+ATOM      7    C STP    15      -2.701  -7.221 -10.008    0.00     3.68
+ATOM      8    C STP    15      -5.618  -8.473  -9.251    0.00     4.02
+ATOM      9    C STP    15      -3.297  -7.983  -9.300    0.00     4.15
+ATOM     10    C STP    15      -3.480  -8.204  -9.300    0.00     4.19
+ATOM     11    C STP    15      -2.711  -7.550  -9.906    0.00     3.88
+ATOM     12    C STP    15      -3.130  -8.353 -10.547    0.00     3.78
+ATOM     13    C STP    15      -6.416  -7.590  -9.212    0.00     3.65
+ATOM     14    C STP    15      -6.562  -8.616  -9.387    0.00     4.21
+ATOM     15    C STP    15      -3.584  -8.558 -11.489    0.00     3.41
+ATOM     16    C STP    15      -2.190  -7.904  -8.566    0.00     3.57
+ATOM     17    C STP    15      -2.781  -7.847  -8.009    0.00     3.57
+ATOM     18    C STP    15      -4.480 -10.505  -7.436    0.00     3.94
+ATOM     19    C STP    15      -4.026  -9.106  -8.251    0.00     4.00
+ATOM     20    C STP    15      -4.477  -9.071  -8.355    0.00     3.93
+ATOM     21    C STP    15      -6.605  -8.625  -9.403    0.00     4.22
+ATOM     22    C STP    15      -7.298  -9.850 -11.196    0.00     3.43
+ATOM     23    C STP    15      -6.455  -7.572  -9.223    0.00     3.65
+ATOM     24    C STP    15      -6.421  -7.573  -9.212    0.00     3.65
+ATOM     25    C STP    15      -6.417  -7.568  -9.212    0.00     3.64
+ATOM     26    O STP    15      -1.367  -6.997 -10.176    0.00     3.51
+ATOM     27    C STP    15      -1.239  -6.770 -10.255    0.00     3.42
+ATOM     28    C STP    15      -4.616 -11.435  -7.345    0.00     3.83
+ATOM     29    C STP    15      -4.811 -11.636  -7.371    0.00     3.80
+ATOM     30    C STP    15      -4.913 -11.381  -7.364    0.00     3.83
+ATOM     31    C STP    15      -6.933  -9.877  -8.296    0.00     4.23
+ATOM     32    C STP    15      -6.950  -9.879  -8.185    0.00     4.17
+ATOM     33    C STP    15      -7.173  -9.977  -7.342    0.00     3.67
+ATOM     34    C STP    15      -9.158  -7.838  -9.913    0.00     4.26
+ATOM     35    C STP    15      -6.960  -7.202  -9.484    0.00     3.47
+ATOM     36    C STP    15      -6.846  -7.861  -9.393    0.00     3.82
+ATOM     37    C STP    15      -7.673  -8.310  -9.533    0.00     4.10
+ATOM     38    C STP    15      -6.670  -8.554  -9.417    0.00     4.18
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket16_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of alpha spheres           :    17
 HEADER 3  - Mean alpha-sphere radius          : 3.7471
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5626
-HEADER 5  - Mean B-factor of pocket residues  : 0.3127
+HEADER 5  - Mean B-factor of pocket residues  : 0.1348
 HEADER 6  - Hydrophobicity Score              : -8.1429
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Amino Acid based volume Score     : 4.1429
-HEADER 9  - Pocket volume (Monte Carlo)       : 269.8107
-HEADER 10  -Pocket volume (convex hull)       : 12.6545
+HEADER 9  - Pocket volume (Monte Carlo)       : 268.9019
+HEADER 10 - Pocket volume (convex hull)       : 12.6545
 HEADER 11 - Charge Score                      :     3
 HEADER 12 - Local hydrophobic density Score   : 0.0000
 HEADER 13 - Number of apolar alpha sphere     :     1

tests/reference_output/1ATP_out/pockets/pocket16_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of V. Vertices             :    17
 HEADER 3  - Mean alpha-sphere radius          : 3.7471
 HEADER 4  - Mean alpha-sphere SA              : 0.5626
-HEADER 5  - Mean B-factor                     : 0.3127
+HEADER 5  - Mean B-factor                     : 0.1348
 HEADER 6  - Hydrophobicity Score              : -8.1429
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 4.1429
-HEADER 9  - Real volume (approximation)       : 269.8107
+HEADER 9  - Real volume (approximation)       : 268.9019
 HEADER 10 - Charge Score                      :     3
 HEADER 11 - Local hydrophobic density Score   : 0.0000
 HEADER 12 - Number of apolar alpha sphere     :     1

tests/reference_output/1ATP_out/pockets/pocket17_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of alpha spheres           :    17
 HEADER 3  - Mean alpha-sphere radius          : 3.9841
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5013
-HEADER 5  - Mean B-factor of pocket residues  : 0.5951
+HEADER 5  - Mean B-factor of pocket residues  : 0.2566
 HEADER 6  - Hydrophobicity Score              : 59.3333
 HEADER 7  - Polarity Score                    :     1
 HEADER 8  - Amino Acid based volume Score     : 4.6667
-HEADER 9  - Pocket volume (Monte Carlo)       : 169.8327
-HEADER 10  -Pocket volume (convex hull)       : 2.1844
+HEADER 9  - Pocket volume (Monte Carlo)       : 171.8715
+HEADER 10 - Pocket volume (convex hull)       : 2.1844
 HEADER 11 - Charge Score                      :     1
 HEADER 12 - Local hydrophobic density Score   : 10.0000
 HEADER 13 - Number of apolar alpha sphere     :    11

tests/reference_output/1ATP_out/pockets/pocket17_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of V. Vertices             :    17
 HEADER 3  - Mean alpha-sphere radius          : 3.9841
 HEADER 4  - Mean alpha-sphere SA              : 0.5013
-HEADER 5  - Mean B-factor                     : 0.5951
+HEADER 5  - Mean B-factor                     : 0.2566
 HEADER 6  - Hydrophobicity Score              : 59.3333
 HEADER 7  - Polarity Score                    :     1
 HEADER 8  - Volume Score                      : 4.6667
-HEADER 9  - Real volume (approximation)       : 169.8327
+HEADER 9  - Real volume (approximation)       : 171.8715
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 10.0000
 HEADER 12 - Number of apolar alpha sphere     :    11

tests/reference_output/1ATP_out/pockets/pocket18_atm.pdb

@@ -3,39 +3,33 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    18:
-HEADER 0  - Pocket Score                      : -0.0856
-HEADER 1  - Drug Score                        : 0.0002
-HEADER 2  - Number of alpha spheres           :    18
-HEADER 3  - Mean alpha-sphere radius          : 4.0398
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4898
-HEADER 5  - Mean B-factor of pocket residues  : 0.7684
-HEADER 6  - Hydrophobicity Score              : 33.3000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.6000
-HEADER 9  - Pocket volume (Monte Carlo)       : 257.4854
-HEADER 10  -Pocket volume (convex hull)       : 10.9194
-HEADER 11 - Charge Score                      :     2
-HEADER 12 - Local hydrophobic density Score   : 0.0000
-HEADER 13 - Number of apolar alpha sphere     :     1
-HEADER 14 - Proportion of apolar alpha sphere : 0.0556
-ATOM    570  NE2 GLN E  84      21.084  10.440  -9.253  0.35  5.47           N 0
-ATOM   1526    O LEU E 198      23.280   4.019  -9.415  0.52  3.21           O 0
-ATOM   2919    C HIS I  23      25.340   8.429  -7.089  0.00  0.00           C 0
-ATOM   2918   CA HIS I  23      23.968   8.408  -6.501  0.00  0.00           C 0
-ATOM   2912    O ILE I  22      22.002   6.740  -5.606  0.50  2.14           O 0
-ATOM   1536   SG CYS E 199      19.889   4.664 -10.584  0.00  0.00           S 0
-ATOM    548    O LEU E  82      23.088  12.682  -9.380  0.41  1.07           O 0
-ATOM    557   CB LYS E  83      23.916  13.115 -12.297  0.00  0.00           C 0
-ATOM   2927    N ASP I  24      25.770   9.592  -7.488  0.60  1.09           N 0
-ATOM   2931   CB ASP I  24      27.519  10.895  -8.641  0.00  0.00           C 0
-HETATM 1515  CG2 TPO E 197      22.109   5.117 -12.962  0.00  0.00           C 0
-ATOM   2920    O HIS I  23      26.014   7.407  -7.167  0.27  8.57           O 0
-ATOM   2933  OD1 ASP I  24      28.705   9.961 -10.427  0.00  0.00           O 0
-ATOM    556    O LYS E  83      21.390  12.223 -12.205  0.29  8.57           O 0
-ATOM    596  CE1 HIS E  87      19.137   7.871 -12.339  0.00  0.00           C 0
-ATOM    560   CE LYS E  83      27.475  12.261 -12.325  0.00  0.00           C 0
-ATOM    559   CD LYS E  83      26.370  13.031 -13.055  0.00  0.00           C 0
-ATOM   1527   CB LEU E 198      25.504   2.342 -10.392  0.00  0.00           C 0
-ATOM   1523    N LEU E 198      23.773   2.787 -12.142  0.00  0.00           N 0
+HEADER 0  - Pocket Score                      : -0.0721
+HEADER 1  - Drug Score                        : 0.0004
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.9030
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5159
+HEADER 5  - Mean B-factor of pocket residues  : 0.4194
+HEADER 6  - Hydrophobicity Score              : 9.1429
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.7143
+HEADER 9  - Pocket volume (Monte Carlo)       : 164.2957
+HEADER 10 - Pocket volume (convex hull)       : 1.8346
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 5.0000
+HEADER 13 - Number of apolar alpha sphere     :     6
+HEADER 14 - Proportion of apolar alpha sphere : 0.3750
+ATOM   1485   CG ARG E 194      19.690  -5.697 -20.692  0.00  0.00           C 0
+ATOM   2164  CD2 LEU E 277      19.542 -12.630 -15.688  0.00  0.00           C 0
+ATOM   1667  ND2 ASN E 216      15.794  -9.298 -17.169  0.59  8.75           N 0
+ATOM   1486   CD ARG E 194      20.788  -6.311 -21.588  0.00  0.00           C 0
+ATOM   1666  OD1 ASN E 216      16.657  -8.414 -15.277  0.75  1.07           O 0
+ATOM   1665   CG ASN E 216      16.108  -8.274 -16.385  0.00  0.00           C 0
+ATOM   1649   CA TYR E 215      19.992  -5.473 -16.064  0.00  0.00           C 0
+ATOM   1647    O GLY E 214      22.432  -6.449 -16.569  0.57  5.36           O 0
+ATOM   2163  CD1 LEU E 277      21.625 -12.347 -14.336  0.00  0.00           C 0
+ATOM   1642   CE LYS E 213      25.372 -10.559 -15.586  0.00  0.00           C 0
+ATOM   1603  OE1 GLU E 208      20.528  -8.065 -12.623  0.00  0.00           O 0
+ATOM   2162   CG LEU E 277      20.111 -12.180 -14.348  0.00  0.00           C 0
+ATOM   1650    C TYR E 215      18.537  -5.168 -16.455  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket18_vert.pqr

@@ -4,37 +4,35 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    18:
-HEADER 0  - Pocket Score                      : -0.0856
-HEADER 1  - Drug Score                        : 0.0002
-HEADER 2  - Number of V. Vertices             :    18
-HEADER 3  - Mean alpha-sphere radius          : 4.0398
-HEADER 4  - Mean alpha-sphere SA              : 0.4898
-HEADER 5  - Mean B-factor                     : 0.7684
-HEADER 6  - Hydrophobicity Score              : 33.3000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.6000
-HEADER 9  - Real volume (approximation)       : 257.4854
-HEADER 10 - Charge Score                      :     2
-HEADER 11 - Local hydrophobic density Score   : 0.0000
-HEADER 12 - Number of apolar alpha sphere     :     1
-HEADER 13 - Proportion of apolar alpha sphere : 0.0556
-ATOM      1    O STP    18      23.290   7.625 -10.006    0.00     3.65
-ATOM      2    O STP    18      21.998   7.158  -8.997    0.00     3.42
-ATOM      3    O STP    18      21.767   7.080  -9.018    0.00     3.44
-ATOM      4    O STP    18      24.354   9.432 -11.111    0.00     3.89
-ATOM      5    O STP    18      24.924  10.086 -10.852    0.00     3.50
-ATOM      6    O STP    18      24.124   8.241 -11.073    0.00     4.17
-ATOM      7    O STP    18      23.599   7.744 -10.504    0.00     3.89
-ATOM      8    O STP    18      25.034   7.815 -11.334    0.00     4.30
-ATOM      9    O STP    18      24.595   7.493 -10.910    0.00     4.00
-ATOM     10    O STP    18      24.583   8.688 -11.745    0.00     4.51
-ATOM     11    O STP    18      24.433   8.715 -11.668    0.00     4.47
-ATOM     12    O STP    18      24.019   8.832 -11.950    0.00     4.30
-ATOM     13    O STP    18      22.801   8.729 -12.139    0.00     3.77
-ATOM     14    O STP    18      22.207   7.260 -10.194    0.00     3.50
-ATOM     15    C STP    18      24.752   8.793 -13.468    0.00     4.56
-ATOM     16    O STP    18      26.139   6.551 -11.712    0.00     4.46
-ATOM     17    O STP    18      26.177   6.535 -11.779    0.00     4.47
-ATOM     18    O STP    18      26.104   6.506 -11.714    0.00     4.41
+HEADER 0  - Pocket Score                      : -0.0721
+HEADER 1  - Drug Score                        : 0.0004
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.9030
+HEADER 4  - Mean alpha-sphere SA              : 0.5159
+HEADER 5  - Mean B-factor                     : 0.4194
+HEADER 6  - Hydrophobicity Score              : 9.1429
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.7143
+HEADER 9  - Real volume (approximation)       : 164.2957
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 5.0000
+HEADER 12 - Number of apolar alpha sphere     :     6
+HEADER 13 - Proportion of apolar alpha sphere : 0.3750
+ATOM      1    C STP    18      19.731  -9.845 -19.131    0.00     4.43
+ATOM      2    O STP    18      19.569  -9.317 -17.533    0.00     3.79
+ATOM      3    C STP    18      19.614  -8.814 -18.207    0.00     3.99
+ATOM      4    C STP    18      20.232  -9.555 -18.715    0.00     4.37
+ATOM      5    O STP    18      19.894  -9.360 -18.454    0.00     4.30
+ATOM      6    O STP    18      19.659  -8.864 -18.207    0.00     4.03
+ATOM      7    C STP    18      22.012 -10.240 -17.683    0.00     3.97
+ATOM      8    O STP    18      19.763  -9.200 -17.763    0.00     4.01
+ATOM      9    O STP    18      19.665  -8.895 -18.122    0.00     4.01
+ATOM     10    O STP    18      19.761  -9.178 -17.610    0.00     3.96
+ATOM     11    O STP    18      19.722  -9.037 -17.573    0.00     3.88
+ATOM     12    O STP    18      20.063  -9.001 -15.994    0.00     3.53
+ATOM     13    C STP    18      21.170  -9.679 -16.504    0.00     3.47
+ATOM     14    O STP    18      20.051  -9.115 -16.218    0.00     3.59
+ATOM     15    O STP    18      20.074  -9.041 -16.005    0.00     3.55
+ATOM     16    C STP    18      19.181  -8.215 -18.208    0.00     3.57
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket19_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of alpha spheres           :    21
 HEADER 3  - Mean alpha-sphere radius          : 3.8400
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4526
-HEADER 5  - Mean B-factor of pocket residues  : 0.5558
+HEADER 5  - Mean B-factor of pocket residues  : 0.2396
 HEADER 6  - Hydrophobicity Score              : 29.1250
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Amino Acid based volume Score     : 5.2500
-HEADER 9  - Pocket volume (Monte Carlo)       : 201.6497
-HEADER 10  -Pocket volume (convex hull)       : 5.4189
+HEADER 9  - Pocket volume (Monte Carlo)       : 208.7422
+HEADER 10 - Pocket volume (convex hull)       : 5.4189
 HEADER 11 - Charge Score                      :     1
 HEADER 12 - Local hydrophobic density Score   : 2.0000
 HEADER 13 - Number of apolar alpha sphere     :     3

tests/reference_output/1ATP_out/pockets/pocket19_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of V. Vertices             :    21
 HEADER 3  - Mean alpha-sphere radius          : 3.8400
 HEADER 4  - Mean alpha-sphere SA              : 0.4526
-HEADER 5  - Mean B-factor                     : 0.5558
+HEADER 5  - Mean B-factor                     : 0.2396
 HEADER 6  - Hydrophobicity Score              : 29.1250
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 5.2500
-HEADER 9  - Real volume (approximation)       : 201.6497
+HEADER 9  - Real volume (approximation)       : 208.7422
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 2.0000
 HEADER 12 - Number of apolar alpha sphere     :     3

tests/reference_output/1ATP_out/pockets/pocket1_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.9590
 HEADER 2  - Number of alpha spheres           :   106
 HEADER 3  - Mean alpha-sphere radius          : 3.9041
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4571
-HEADER 5  - Mean B-factor of pocket residues  : 0.2063
+HEADER 5  - Mean B-factor of pocket residues  : 0.0889
 HEADER 6  - Hydrophobicity Score              : 21.6296
 HEADER 7  - Polarity Score                    :    14
 HEADER 8  - Amino Acid based volume Score     : 4.0000
-HEADER 9  - Pocket volume (Monte Carlo)       : 585.2505
-HEADER 10  -Pocket volume (convex hull)       : 134.8042
+HEADER 9  - Pocket volume (Monte Carlo)       : 590.4016
+HEADER 10 - Pocket volume (convex hull)       : 134.8042
 HEADER 11 - Charge Score                      :     0
 HEADER 12 - Local hydrophobic density Score   : 38.9500
 HEADER 13 - Number of apolar alpha sphere     :    40

tests/reference_output/1ATP_out/pockets/pocket1_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.9590
 HEADER 2  - Number of V. Vertices             :   106
 HEADER 3  - Mean alpha-sphere radius          : 3.9041
 HEADER 4  - Mean alpha-sphere SA              : 0.4571
-HEADER 5  - Mean B-factor                     : 0.2063
+HEADER 5  - Mean B-factor                     : 0.0889
 HEADER 6  - Hydrophobicity Score              : 21.6296
 HEADER 7  - Polarity Score                    :    14
 HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 585.2505
+HEADER 9  - Real volume (approximation)       : 590.4016
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 38.9500
 HEADER 12 - Number of apolar alpha sphere     :    40

tests/reference_output/1ATP_out/pockets/pocket20_atm.pdb

@@ -0,0 +1,42 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    20:
+HEADER 0  - Pocket Score                      : -0.0941
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    21
+HEADER 3  - Mean alpha-sphere radius          : 4.0095
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5411
+HEADER 5  - Mean B-factor of pocket residues  : 0.3519
+HEADER 6  - Hydrophobicity Score              : 33.3000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.6000
+HEADER 9  - Pocket volume (Monte Carlo)       : 269.4327
+HEADER 10 - Pocket volume (convex hull)       : 11.4160
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0476
+ATOM   2927    N ASP I  24      25.770   9.592  -7.488  0.60  1.09           N 0
+ATOM   2931   CB ASP I  24      27.519  10.895  -8.641  0.00  0.00           C 0
+ATOM   2933  OD1 ASP I  24      28.705   9.961 -10.427  0.00  0.00           O 0
+ATOM    560   CE LYS E  83      27.475  12.261 -12.325  0.00  0.00           C 0
+ATOM   2928   CA ASP I  24      27.093   9.595  -7.965  0.00  0.00           C 0
+ATOM    570  NE2 GLN E  84      21.084  10.440  -9.253  0.35  5.47           N 0
+ATOM   1526    O LEU E 198      23.280   4.019  -9.415  0.52  3.21           O 0
+ATOM   2919    C HIS I  23      25.340   8.429  -7.089  0.00  0.00           C 0
+ATOM   2918   CA HIS I  23      23.968   8.408  -6.501  0.00  0.00           C 0
+ATOM   2912    O ILE I  22      22.002   6.740  -5.606  0.50  2.14           O 0
+ATOM   1536   SG CYS E 199      19.889   4.664 -10.584  0.00  0.00           S 0
+ATOM    548    O LEU E  82      23.088  12.682  -9.380  0.41  1.07           O 0
+ATOM    557   CB LYS E  83      23.916  13.115 -12.297  0.00  0.00           C 0
+ATOM   2920    O HIS I  23      26.014   7.407  -7.167  0.27  8.57           O 0
+HETATM 1515  CG2 TPO E 197      22.109   5.117 -12.962  0.00  0.00           C 0
+ATOM    556    O LYS E  83      21.390  12.223 -12.205  0.29  8.57           O 0
+ATOM    596  CE1 HIS E  87      19.137   7.871 -12.339  0.00  0.00           C 0
+ATOM    559   CD LYS E  83      26.370  13.031 -13.055  0.00  0.00           C 0
+ATOM   1527   CB LEU E 198      25.504   2.342 -10.392  0.00  0.00           C 0
+ATOM   1523    N LEU E 198      23.773   2.787 -12.142  0.00  0.00           N 0
+TER
+END

tests/reference_output/1ATP_out/pockets/pocket20_vert.pqr

@@ -0,0 +1,43 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    20:
+HEADER 0  - Pocket Score                      : -0.0941
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    21
+HEADER 3  - Mean alpha-sphere radius          : 4.0095
+HEADER 4  - Mean alpha-sphere SA              : 0.5411
+HEADER 5  - Mean B-factor                     : 0.3519
+HEADER 6  - Hydrophobicity Score              : 33.3000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.6000
+HEADER 9  - Real volume (approximation)       : 269.4327
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0476
+ATOM      1    O STP    20      25.040   9.651 -11.168    0.00     3.75
+ATOM      2    O STP    20      25.268   9.534 -10.955    0.00     3.50
+ATOM      3    O STP    20      23.290   7.625 -10.006    0.00     3.65
+ATOM      4    O STP    20      21.998   7.158  -8.997    0.00     3.42
+ATOM      5    O STP    20      21.767   7.080  -9.018    0.00     3.44
+ATOM      6    O STP    20      24.354   9.432 -11.111    0.00     3.89
+ATOM      7    O STP    20      24.924  10.086 -10.852    0.00     3.50
+ATOM      8    O STP    20      25.153   7.836 -11.282    0.00     4.23
+ATOM      9    O STP    20      24.124   8.241 -11.073    0.00     4.17
+ATOM     10    O STP    20      23.599   7.744 -10.504    0.00     3.89
+ATOM     11    O STP    20      25.034   7.815 -11.334    0.00     4.30
+ATOM     12    O STP    20      24.595   7.493 -10.910    0.00     4.00
+ATOM     13    O STP    20      24.583   8.688 -11.745    0.00     4.51
+ATOM     14    O STP    20      24.433   8.715 -11.668    0.00     4.47
+ATOM     15    O STP    20      24.019   8.832 -11.950    0.00     4.30
+ATOM     16    O STP    20      22.801   8.729 -12.139    0.00     3.77
+ATOM     17    O STP    20      22.207   7.260 -10.194    0.00     3.50
+ATOM     18    C STP    20      24.752   8.793 -13.468    0.00     4.56
+ATOM     19    O STP    20      26.139   6.551 -11.712    0.00     4.46
+ATOM     20    O STP    20      26.177   6.535 -11.779    0.00     4.47
+ATOM     21    O STP    20      26.104   6.506 -11.714    0.00     4.41
+TER
+END

tests/reference_output/1ATP_out/pockets/pocket2_atm.pdb

@@ -3,43 +3,34 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     2:
-HEADER 0  - Pocket Score                      : 0.1402
-HEADER 1  - Drug Score                        : 0.0010
-HEADER 2  - Number of alpha spheres           :    19
-HEADER 3  - Mean alpha-sphere radius          : 3.9712
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6139
-HEADER 5  - Mean B-factor of pocket residues  : 0.8934
-HEADER 6  - Hydrophobicity Score              : 12.1667
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Amino Acid based volume Score     : 4.2500
-HEADER 9  - Pocket volume (Monte Carlo)       : 262.3233
-HEADER 10  -Pocket volume (convex hull)       : 7.2454
-HEADER 11 - Charge Score                      :     1
-HEADER 12 - Local hydrophobic density Score   : 4.0000
-HEADER 13 - Number of apolar alpha sphere     :     5
-HEADER 14 - Proportion of apolar alpha sphere : 0.2632
-ATOM    309    O GLY E  52      18.223  12.904   1.426  0.00  0.00           O 0
-ATOM    330    O GLY E  55      14.729  14.598   1.098  0.00  0.00           O 0
-ATOM    304  OG1 THR E  51      15.944  14.681   4.769  0.00  0.00           O 0
-ATOM    521   NZ LYS E  78      20.649  16.599  -0.867  0.21  4.37           N 0
-ATOM   2648  CD1 ILE E 335      11.727  24.114   3.014  0.00  0.00           C 0
-ATOM   2647  CG2 ILE E 335      10.550  26.263   0.508  0.00  0.00           C 0
-ATOM    831  ND2 ASN E 115      12.293  25.406  -3.370  0.55  1.09           N 0
-ATOM    477  CG2 ILE E  73      11.117  21.494  -1.628  0.00  0.00           C 0
-ATOM   2649    N ARG E 336      13.118  27.889   0.582  0.00  0.00           N 0
-ATOM    340  NH1 ARG E  56      14.550  20.184   4.336  0.00  0.00           N 0
-ATOM    329    C GLY E  55      14.286  15.376   0.253  0.00  0.00           C 0
-ATOM    328   CA GLY E  55      14.897  15.583  -1.082  0.00  0.00           C 0
-ATOM    520   CE LYS E  78      19.997  17.773  -1.474  0.00  0.00           C 0
-ATOM    335   CB ARG E  56      13.027  17.288   2.478  0.00  0.00           C 0
-ATOM   2631  OE2 GLU E 333      16.987  19.040   5.884  0.00  0.00           O 0
-ATOM    319    O PHE E  54      17.192  16.071  -2.246  0.00  0.00           O 0
-ATOM    830  OD1 ASN E 115      14.070  24.389  -4.295  0.00  0.00           O 0
-ATOM    487    N ASP E  75      15.327  20.402  -4.473  0.00  0.00           N 0
-ATOM    491   CB ASP E  75      17.237  21.958  -3.927  0.00  0.00           C 0
-ATOM    337   CD ARG E  56      12.800  19.652   2.652  0.00  0.00           C 0
-ATOM    474    O ILE E  73      12.604  18.077  -2.062  0.72  2.14           O 0
-ATOM    331    N ARG E  56      13.263  16.163   0.423  0.00  0.00           N 0
-ATOM    336   CG ARG E  56      12.385  18.520   1.875  0.00  0.00           C 0
+HEADER 0  - Pocket Score                      : 0.1266
+HEADER 1  - Drug Score                        : 0.0057
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.5428
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4022
+HEADER 5  - Mean B-factor of pocket residues  : 0.2726
+HEADER 6  - Hydrophobicity Score              : 68.8750
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 5.2500
+HEADER 9  - Pocket volume (Monte Carlo)       : 78.4534
+HEADER 10 - Pocket volume (convex hull)       : 0.4010
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 17.0000
+HEADER 13 - Number of apolar alpha sphere     :    18
+HEADER 14 - Proportion of apolar alpha sphere : 1.0000
+ATOM    930   CG MET E 128       8.403  -2.687   7.280  0.00  0.00           C 0
+ATOM    926   CA MET E 128       8.115  -0.207   8.023  0.00  0.00           C 0
+ATOM   1094   OH TYR E 146       3.007  -4.773   9.128  0.69  1.07           O 0
+ATOM   1023   CZ PHE E 138       7.842  -4.944  10.972  0.00  0.00           C 0
+ATOM    954   CB HIS E 131       7.301  -0.869  12.556  0.00  0.00           C 0
+ATOM   2473  CD1 PHE E 314       1.599  -2.313  12.616  0.00  0.00           C 0
+ATOM    997  CD1 ILE E 135       6.961  -4.213  14.925  0.00  0.00           C 0
+ATOM   1325  CG1 ILE E 174       3.748   0.392   8.044  0.00  0.00           C 0
+ATOM   2475  CE1 PHE E 314       1.989  -1.013  12.939  0.00  0.00           C 0
+ATOM   1054  CE1 HIS E 142       4.019  -7.046  11.747  0.00  0.00           C 0
+ATOM   1327  CD1 ILE E 174       3.664  -0.736   7.020  0.00  0.00           C 0
+ATOM    955   CG HIS E 131       6.397   0.292  12.561  0.00  0.00           C 0
+ATOM    957  CD2 HIS E 131       6.036   1.134  11.558  0.00  0.00           C 0
+ATOM   2472   CG PHE E 314       1.571  -3.331  13.568  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket2_vert.pqr

@@ -4,38 +4,37 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     2:
-HEADER 0  - Pocket Score                      : 0.1402
-HEADER 1  - Drug Score                        : 0.0010
-HEADER 2  - Number of V. Vertices             :    19
-HEADER 3  - Mean alpha-sphere radius          : 3.9712
-HEADER 4  - Mean alpha-sphere SA              : 0.6139
-HEADER 5  - Mean B-factor                     : 0.8934
-HEADER 6  - Hydrophobicity Score              : 12.1667
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Volume Score                      : 4.2500
-HEADER 9  - Real volume (approximation)       : 262.3233
-HEADER 10 - Charge Score                      :     1
-HEADER 11 - Local hydrophobic density Score   : 4.0000
-HEADER 12 - Number of apolar alpha sphere     :     5
-HEADER 13 - Proportion of apolar alpha sphere : 0.2632
-ATOM      1    O STP     2      17.904  16.846   2.034    0.00     4.00
-ATOM      2    C STP     2      13.212  24.010  -0.223    0.00     3.56
-ATOM      3    O STP     2      13.590  24.333  -0.124    0.00     3.66
-ATOM      4    C STP     2      16.767  18.684   1.078    0.00     4.22
-ATOM      5    C STP     2      16.715  18.704   1.057    0.00     4.20
-ATOM      6    O STP     2      17.342  17.855   1.830    0.00     4.24
-ATOM      7    O STP     2      17.041  17.846   1.980    0.00     4.08
-ATOM      8    O STP     2      16.580  19.060   0.747    0.00     4.27
-ATOM      9    O STP     2      17.635  17.024   1.403    0.00     3.80
-ATOM     10    O STP     2      17.395  17.419   1.401    0.00     3.89
-ATOM     11    C STP     2      16.900  18.376   1.091    0.00     4.07
-ATOM     12    O STP     2      17.782  16.444   1.256    0.00     3.57
-ATOM     13    O STP     2      14.632  22.244  -1.461    0.00     3.60
-ATOM     14    O STP     2      14.379  23.675  -0.187    0.00     4.18
-ATOM     15    O STP     2      14.950  20.959  -0.498    0.00     4.03
-ATOM     16    O STP     2      16.062  19.544  -0.072    0.00     4.25
-ATOM     17    O STP     2      16.188  19.842  -0.177    0.00     4.42
-ATOM     18    C STP     2      16.044  18.633   0.739    0.00     3.73
-ATOM     19    O STP     2      15.502  19.054  -0.011    0.00     3.68
+HEADER 0  - Pocket Score                      : 0.1266
+HEADER 1  - Drug Score                        : 0.0057
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.5428
+HEADER 4  - Mean alpha-sphere SA              : 0.4022
+HEADER 5  - Mean B-factor                     : 0.2726
+HEADER 6  - Hydrophobicity Score              : 68.8750
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 5.2500
+HEADER 9  - Real volume (approximation)       : 78.4534
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 17.0000
+HEADER 12 - Number of apolar alpha sphere     :    18
+HEADER 13 - Proportion of apolar alpha sphere : 1.0000
+ATOM      1    C STP     2       5.666  -2.347   9.650    0.00     3.64
+ATOM      2    C STP     2       5.663  -2.342   9.659    0.00     3.64
+ATOM      3    C STP     2       4.857  -3.237  11.687    0.00     3.51
+ATOM      4    C STP     2       4.909  -3.421  12.179    0.00     3.52
+ATOM      5    C STP     2       4.463  -1.923  10.602    0.00     3.52
+ATOM      6    C STP     2       4.751  -3.640  11.929    0.00     3.49
+ATOM      7    C STP     2       4.816  -3.657  12.202    0.00     3.51
+ATOM      8    C STP     2       5.643  -2.334   9.598    0.00     3.62
+ATOM      9    C STP     2       5.573  -2.273   9.693    0.00     3.63
+ATOM     10    C STP     2       5.625  -2.300   9.658    0.00     3.64
+ATOM     11    C STP     2       5.618  -2.250   9.664    0.00     3.62
+ATOM     12    C STP     2       4.669  -1.977  10.488    0.00     3.53
+ATOM     13    C STP     2       4.819  -1.860  10.403    0.00     3.43
+ATOM     14    C STP     2       4.472  -1.924  10.605    0.00     3.53
+ATOM     15    C STP     2       4.423  -1.750  10.637    0.00     3.43
+ATOM     16    C STP     2       4.474  -1.928  10.609    0.00     3.53
+ATOM     17    C STP     2       4.552  -2.069  10.740    0.00     3.51
+ATOM     18    C STP     2       4.780  -3.687  12.261    0.00     3.48
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket3_atm.pdb

@@ -3,34 +3,42 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     3:
-HEADER 0  - Pocket Score                      : 0.1266
-HEADER 1  - Drug Score                        : 0.0057
-HEADER 2  - Number of alpha spheres           :    18
-HEADER 3  - Mean alpha-sphere radius          : 3.5428
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4022
-HEADER 5  - Mean B-factor of pocket residues  : 0.6322
-HEADER 6  - Hydrophobicity Score              : 68.8750
-HEADER 7  - Polarity Score                    :     3
-HEADER 8  - Amino Acid based volume Score     : 5.2500
-HEADER 9  - Pocket volume (Monte Carlo)       : 77.2004
-HEADER 10  -Pocket volume (convex hull)       : 0.4010
-HEADER 11 - Charge Score                      :     2
-HEADER 12 - Local hydrophobic density Score   : 17.0000
-HEADER 13 - Number of apolar alpha sphere     :    18
-HEADER 14 - Proportion of apolar alpha sphere : 1.0000
-ATOM    930   CG MET E 128       8.403  -2.687   7.280  0.00  0.00           C 0
-ATOM    926   CA MET E 128       8.115  -0.207   8.023  0.00  0.00           C 0
-ATOM   1094   OH TYR E 146       3.007  -4.773   9.128  0.69  1.07           O 0
-ATOM   1023   CZ PHE E 138       7.842  -4.944  10.972  0.00  0.00           C 0
-ATOM    954   CB HIS E 131       7.301  -0.869  12.556  0.00  0.00           C 0
-ATOM   2473  CD1 PHE E 314       1.599  -2.313  12.616  0.00  0.00           C 0
-ATOM    997  CD1 ILE E 135       6.961  -4.213  14.925  0.00  0.00           C 0
-ATOM   1325  CG1 ILE E 174       3.748   0.392   8.044  0.00  0.00           C 0
-ATOM   2475  CE1 PHE E 314       1.989  -1.013  12.939  0.00  0.00           C 0
-ATOM   1054  CE1 HIS E 142       4.019  -7.046  11.747  0.00  0.00           C 0
-ATOM   1327  CD1 ILE E 174       3.664  -0.736   7.020  0.00  0.00           C 0
-ATOM    955   CG HIS E 131       6.397   0.292  12.561  0.00  0.00           C 0
-ATOM    957  CD2 HIS E 131       6.036   1.134  11.558  0.00  0.00           C 0
-ATOM   2472   CG PHE E 314       1.571  -3.331  13.568  0.00  0.00           C 0
+HEADER 0  - Pocket Score                      : 0.1199
+HEADER 1  - Drug Score                        : 0.0012
+HEADER 2  - Number of alpha spheres           :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.7030
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4414
+HEADER 5  - Mean B-factor of pocket residues  : 0.1487
+HEADER 6  - Hydrophobicity Score              : 21.3000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 5.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 245.3520
+HEADER 10 - Pocket volume (convex hull)       : 9.3769
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 7.0000
+HEADER 13 - Number of apolar alpha sphere     :     8
+HEADER 14 - Proportion of apolar alpha sphere : 0.2162
+ATOM   2604   OH TYR E 330      13.684  10.354   9.085  0.00  0.00           O 0
+ATOM   2577    N ASP E 328      10.151   9.909  12.765  0.43  2.19           N 0
+ATOM    290    O LEU E  49       9.471  11.567   8.335  0.39  1.07           O 0
+ATOM    924  OE2 GLU E 127      11.685   6.755   6.599  0.00  0.00           O 0
+ATOM    923  OE1 GLU E 127      11.951   5.007   7.989  0.60  1.07           O 0
+ATOM   2584  OD2 ASP E 328      14.041   8.286  13.108  0.00  0.00           O 0
+ATOM   2880   CD ARG I  18      14.991   7.067   8.769  0.00  0.00           C 0
+ATOM   2582   CG ASP E 328      13.020   8.743  13.609  0.00  0.00           C 0
+ATOM    940  CD2 PHE E 129      14.226   2.625   9.854  0.00  0.00           C 0
+ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
+ATOM    942  CE2 PHE E 129      15.500   2.729  10.413  0.00  0.00           C 0
+ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
+ATOM   2567   CA PHE E 327       7.809   9.376  12.138  0.00  0.00           C 0
+ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
+ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
+ATOM    972   CB ARG E 133      14.518  -0.467  13.709  0.00  0.00           C 0
+ATOM    945   CA SER E 130      10.922   2.228  12.285  0.00  0.00           C 0
+ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
+ATOM    921   CG GLU E 127       9.791   5.422   7.060  0.00  0.00           C 0
+ATOM    916    N GLU E 127       7.291   4.505   8.648  0.00  0.00           N 0
+ATOM   2572  CD1 PHE E 327       6.963   9.283   8.898  0.00  0.00           C 0
+ATOM    922   CD GLU E 127      11.253   5.708   7.267  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket3_vert.pqr

@@ -4,37 +4,56 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     3:
-HEADER 0  - Pocket Score                      : 0.1266
-HEADER 1  - Drug Score                        : 0.0057
-HEADER 2  - Number of V. Vertices             :    18
-HEADER 3  - Mean alpha-sphere radius          : 3.5428
-HEADER 4  - Mean alpha-sphere SA              : 0.4022
-HEADER 5  - Mean B-factor                     : 0.6322
-HEADER 6  - Hydrophobicity Score              : 68.8750
-HEADER 7  - Polarity Score                    :     3
-HEADER 8  - Volume Score                      : 5.2500
-HEADER 9  - Real volume (approximation)       : 77.2004
-HEADER 10 - Charge Score                      :     2
-HEADER 11 - Local hydrophobic density Score   : 17.0000
-HEADER 12 - Number of apolar alpha sphere     :    18
-HEADER 13 - Proportion of apolar alpha sphere : 1.0000
-ATOM      1    C STP     3       5.666  -2.347   9.650    0.00     3.64
-ATOM      2    C STP     3       5.663  -2.342   9.659    0.00     3.64
-ATOM      3    C STP     3       4.857  -3.237  11.687    0.00     3.51
-ATOM      4    C STP     3       4.909  -3.421  12.179    0.00     3.52
-ATOM      5    C STP     3       4.463  -1.923  10.602    0.00     3.52
-ATOM      6    C STP     3       4.751  -3.640  11.929    0.00     3.49
-ATOM      7    C STP     3       4.816  -3.657  12.202    0.00     3.51
-ATOM      8    C STP     3       5.643  -2.334   9.598    0.00     3.62
-ATOM      9    C STP     3       5.573  -2.273   9.693    0.00     3.63
-ATOM     10    C STP     3       5.625  -2.300   9.658    0.00     3.64
-ATOM     11    C STP     3       5.618  -2.250   9.664    0.00     3.62
-ATOM     12    C STP     3       4.669  -1.977  10.488    0.00     3.53
-ATOM     13    C STP     3       4.819  -1.860  10.403    0.00     3.43
-ATOM     14    C STP     3       4.472  -1.924  10.605    0.00     3.53
-ATOM     15    C STP     3       4.423  -1.750  10.637    0.00     3.43
-ATOM     16    C STP     3       4.474  -1.928  10.609    0.00     3.53
-ATOM     17    C STP     3       4.552  -2.069  10.740    0.00     3.51
-ATOM     18    C STP     3       4.780  -3.687  12.261    0.00     3.48
+HEADER 0  - Pocket Score                      : 0.1199
+HEADER 1  - Drug Score                        : 0.0012
+HEADER 2  - Number of V. Vertices             :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.7030
+HEADER 4  - Mean alpha-sphere SA              : 0.4414
+HEADER 5  - Mean B-factor                     : 0.1487
+HEADER 6  - Hydrophobicity Score              : 21.3000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 5.0000
+HEADER 9  - Real volume (approximation)       : 245.3520
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 7.0000
+HEADER 12 - Number of apolar alpha sphere     :     8
+HEADER 13 - Proportion of apolar alpha sphere : 0.2162
+ATOM      1    O STP     3      10.707   8.465   9.562    0.00     3.56
+ATOM      2    O STP     3      11.897   7.600  10.387    0.00     3.53
+ATOM      3    O STP     3      11.713   7.651  10.429    0.00     3.61
+ATOM      4    O STP     3      11.722   7.673  10.440    0.00     3.59
+ATOM      5    O STP     3      11.706   7.635  10.442    0.00     3.60
+ATOM      6    O STP     3      13.057   5.577  11.209    0.00     3.45
+ATOM      7    C STP     3      13.599   4.782  12.622    0.00     3.56
+ATOM      8    O STP     3      12.926   5.521  11.298    0.00     3.49
+ATOM      9    O STP     3      11.593   6.620  11.138    0.00     3.56
+ATOM     10    O STP     3      11.150   6.837  11.229    0.00     3.58
+ATOM     11    O STP     3      11.203   6.847  11.061    0.00     3.66
+ATOM     12    O STP     3      10.100   6.854  10.639    0.00     3.72
+ATOM     13    O STP     3      10.043   6.829  10.609    0.00     3.72
+ATOM     14    O STP     3      10.008   6.832  11.002    0.00     3.55
+ATOM     15    O STP     3       9.996   6.814  10.721    0.00     3.65
+ATOM     16    O STP     3      14.136   3.921  15.176    0.00     4.64
+ATOM     17    O STP     3      13.450   4.065  15.198    0.00     4.27
+ATOM     18    O STP     3      14.349   4.009  14.805    0.00     4.61
+ATOM     19    O STP     3      13.844   4.358  14.153    0.00     4.07
+ATOM     20    C STP     3      14.400   4.002  14.664    0.00     4.57
+ATOM     21    C STP     3      13.873   4.433  13.491    0.00     3.88
+ATOM     22    C STP     3      13.578   4.355  12.749    0.00     3.43
+ATOM     23    O STP     3       9.524   6.563  10.325    0.00     3.47
+ATOM     24    C STP     3       9.327   7.050  10.077    0.00     3.46
+ATOM     25    O STP     3      10.903   8.245   9.723    0.00     3.55
+ATOM     26    O STP     3      11.424   7.798  10.169    0.00     3.58
+ATOM     27    O STP     3      10.102   6.908  10.584    0.00     3.71
+ATOM     28    O STP     3      10.425   8.337   9.557    0.00     3.58
+ATOM     29    O STP     3      10.324   8.322   9.469    0.00     3.54
+ATOM     30    O STP     3      10.351   8.314   9.560    0.00     3.59
+ATOM     31    C STP     3      10.082   7.855   9.856    0.00     3.56
+ATOM     32    C STP     3       9.763   7.428   9.952    0.00     3.52
+ATOM     33    C STP     3       9.808   6.869  10.405    0.00     3.64
+ATOM     34    O STP     3      10.016   6.824  10.586    0.00     3.71
+ATOM     35    O STP     3       9.960   6.815  10.553    0.00     3.70
+ATOM     36    O STP     3       9.895   6.462  10.350    0.00     3.45
+ATOM     37    O STP     3       9.826   6.743  10.451    0.00     3.64
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket4_atm.pdb

@@ -3,42 +3,46 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     4:
-HEADER 0  - Pocket Score                      : 0.1199
-HEADER 1  - Drug Score                        : 0.0012
-HEADER 2  - Number of alpha spheres           :    37
-HEADER 3  - Mean alpha-sphere radius          : 3.7030
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4414
-HEADER 5  - Mean B-factor of pocket residues  : 0.3449
-HEADER 6  - Hydrophobicity Score              : 21.3000
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Amino Acid based volume Score     : 5.0000
-HEADER 9  - Pocket volume (Monte Carlo)       : 253.0846
-HEADER 10  -Pocket volume (convex hull)       : 9.3769
+HEADER 0  - Pocket Score                      : 0.1091
+HEADER 1  - Drug Score                        : 0.0011
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 4.0522
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6054
+HEADER 5  - Mean B-factor of pocket residues  : 0.4438
+HEADER 6  - Hydrophobicity Score              : 8.8462
+HEADER 7  - Polarity Score                    :     8
+HEADER 8  - Amino Acid based volume Score     : 4.2308
+HEADER 9  - Pocket volume (Monte Carlo)       : 348.1119
+HEADER 10 - Pocket volume (convex hull)       : 14.9748
 HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 7.0000
-HEADER 13 - Number of apolar alpha sphere     :     8
-HEADER 14 - Proportion of apolar alpha sphere : 0.2162
-ATOM   2604   OH TYR E 330      13.684  10.354   9.085  0.00  0.00           O 0
-ATOM   2577    N ASP E 328      10.151   9.909  12.765  0.43  2.19           N 0
-ATOM    290    O LEU E  49       9.471  11.567   8.335  0.39  1.07           O 0
-ATOM    924  OE2 GLU E 127      11.685   6.755   6.599  0.00  0.00           O 0
-ATOM    923  OE1 GLU E 127      11.951   5.007   7.989  0.60  1.07           O 0
-ATOM   2584  OD2 ASP E 328      14.041   8.286  13.108  0.00  0.00           O 0
-ATOM   2880   CD ARG I  18      14.991   7.067   8.769  0.00  0.00           C 0
-ATOM   2582   CG ASP E 328      13.020   8.743  13.609  0.00  0.00           C 0
-ATOM    940  CD2 PHE E 129      14.226   2.625   9.854  0.00  0.00           C 0
-ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
-ATOM    942  CE2 PHE E 129      15.500   2.729  10.413  0.00  0.00           C 0
-ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
-ATOM   2567   CA PHE E 327       7.809   9.376  12.138  0.00  0.00           C 0
-ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
-ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
-ATOM    972   CB ARG E 133      14.518  -0.467  13.709  0.00  0.00           C 0
-ATOM    945   CA SER E 130      10.922   2.228  12.285  0.00  0.00           C 0
-ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
-ATOM    921   CG GLU E 127       9.791   5.422   7.060  0.00  0.00           C 0
-ATOM    916    N GLU E 127       7.291   4.505   8.648  0.00  0.00           N 0
-ATOM   2572  CD1 PHE E 327       6.963   9.283   8.898  0.00  0.00           C 0
-ATOM    922   CD GLU E 127      11.253   5.708   7.267  0.00  0.00           C 0
+HEADER 12 - Local hydrophobic density Score   : 5.0000
+HEADER 13 - Number of apolar alpha sphere     :     6
+HEADER 14 - Proportion of apolar alpha sphere : 0.2727
+ATOM    309    O GLY E  52      18.223  12.904   1.426  0.00  0.00           O 0
+ATOM    330    O GLY E  55      14.729  14.598   1.098  0.00  0.00           O 0
+ATOM    304  OG1 THR E  51      15.944  14.681   4.769  0.00  0.00           O 0
+ATOM    521   NZ LYS E  78      20.649  16.599  -0.867  0.21  4.37           N 0
+ATOM   2648  CD1 ILE E 335      11.727  24.114   3.014  0.00  0.00           C 0
+ATOM   2647  CG2 ILE E 335      10.550  26.263   0.508  0.00  0.00           C 0
+ATOM    831  ND2 ASN E 115      12.293  25.406  -3.370  0.55  1.09           N 0
+ATOM    477  CG2 ILE E  73      11.117  21.494  -1.628  0.00  0.00           C 0
+ATOM   2649    N ARG E 336      13.118  27.889   0.582  0.00  0.00           N 0
+ATOM    340  NH1 ARG E  56      14.550  20.184   4.336  0.00  0.00           N 0
+ATOM   2635    O GLU E 334      14.331  26.131   3.608  0.51  3.21           O 0
+ATOM   2627   CB GLU E 333      15.915  22.401   5.926  0.00  0.00           C 0
+ATOM   2659  NH2 ARG E 336      17.338  26.295   4.591  0.52  3.28           N 0
+ATOM    329    C GLY E  55      14.286  15.376   0.253  0.00  0.00           C 0
+ATOM    328   CA GLY E  55      14.897  15.583  -1.082  0.00  0.00           C 0
+ATOM    520   CE LYS E  78      19.997  17.773  -1.474  0.00  0.00           C 0
+ATOM    335   CB ARG E  56      13.027  17.288   2.478  0.00  0.00           C 0
+ATOM   2631  OE2 GLU E 333      16.987  19.040   5.884  0.00  0.00           O 0
+ATOM    319    O PHE E  54      17.192  16.071  -2.246  0.00  0.00           O 0
+ATOM    830  OD1 ASN E 115      14.070  24.389  -4.295  0.00  0.00           O 0
+ATOM    487    N ASP E  75      15.327  20.402  -4.473  0.00  0.00           N 0
+ATOM    491   CB ASP E  75      17.237  21.958  -3.927  0.00  0.00           C 0
+ATOM    337   CD ARG E  56      12.800  19.652   2.652  0.00  0.00           C 0
+ATOM    474    O ILE E  73      12.604  18.077  -2.062  0.72  2.14           O 0
+ATOM    331    N ARG E  56      13.263  16.163   0.423  0.00  0.00           N 0
+ATOM    336   CG ARG E  56      12.385  18.520   1.875  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket4_vert.pqr

@@ -4,56 +4,41 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     4:
-HEADER 0  - Pocket Score                      : 0.1199
-HEADER 1  - Drug Score                        : 0.0012
-HEADER 2  - Number of V. Vertices             :    37
-HEADER 3  - Mean alpha-sphere radius          : 3.7030
-HEADER 4  - Mean alpha-sphere SA              : 0.4414
-HEADER 5  - Mean B-factor                     : 0.3449
-HEADER 6  - Hydrophobicity Score              : 21.3000
-HEADER 7  - Polarity Score                    :     7
-HEADER 8  - Volume Score                      : 5.0000
-HEADER 9  - Real volume (approximation)       : 253.0846
+HEADER 0  - Pocket Score                      : 0.1091
+HEADER 1  - Drug Score                        : 0.0011
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 4.0522
+HEADER 4  - Mean alpha-sphere SA              : 0.6054
+HEADER 5  - Mean B-factor                     : 0.4438
+HEADER 6  - Hydrophobicity Score              : 8.8462
+HEADER 7  - Polarity Score                    :     8
+HEADER 8  - Volume Score                      : 4.2308
+HEADER 9  - Real volume (approximation)       : 348.1119
 HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 7.0000
-HEADER 12 - Number of apolar alpha sphere     :     8
-HEADER 13 - Proportion of apolar alpha sphere : 0.2162
-ATOM      1    O STP     4      10.707   8.465   9.562    0.00     3.56
-ATOM      2    O STP     4      11.897   7.600  10.387    0.00     3.53
-ATOM      3    O STP     4      11.713   7.651  10.429    0.00     3.61
-ATOM      4    O STP     4      11.722   7.673  10.440    0.00     3.59
-ATOM      5    O STP     4      11.706   7.635  10.442    0.00     3.60
-ATOM      6    O STP     4      13.057   5.577  11.209    0.00     3.45
-ATOM      7    C STP     4      13.599   4.782  12.622    0.00     3.56
-ATOM      8    O STP     4      12.926   5.521  11.298    0.00     3.49
-ATOM      9    O STP     4      11.593   6.620  11.138    0.00     3.56
-ATOM     10    O STP     4      11.150   6.837  11.229    0.00     3.58
-ATOM     11    O STP     4      11.203   6.847  11.061    0.00     3.66
-ATOM     12    O STP     4      10.100   6.854  10.639    0.00     3.72
-ATOM     13    O STP     4      10.043   6.829  10.609    0.00     3.72
-ATOM     14    O STP     4      10.008   6.832  11.002    0.00     3.55
-ATOM     15    O STP     4       9.996   6.814  10.721    0.00     3.65
-ATOM     16    O STP     4      14.136   3.921  15.176    0.00     4.64
-ATOM     17    O STP     4      13.450   4.065  15.198    0.00     4.27
-ATOM     18    O STP     4      14.349   4.009  14.805    0.00     4.61
-ATOM     19    O STP     4      13.844   4.358  14.153    0.00     4.07
-ATOM     20    C STP     4      14.400   4.002  14.664    0.00     4.57
-ATOM     21    C STP     4      13.873   4.433  13.491    0.00     3.88
-ATOM     22    C STP     4      13.578   4.355  12.749    0.00     3.43
-ATOM     23    O STP     4       9.524   6.563  10.325    0.00     3.47
-ATOM     24    C STP     4       9.327   7.050  10.077    0.00     3.46
-ATOM     25    O STP     4      10.903   8.245   9.723    0.00     3.55
-ATOM     26    O STP     4      11.424   7.798  10.169    0.00     3.58
-ATOM     27    O STP     4      10.102   6.908  10.584    0.00     3.71
-ATOM     28    O STP     4      10.425   8.337   9.557    0.00     3.58
-ATOM     29    O STP     4      10.324   8.322   9.469    0.00     3.54
-ATOM     30    O STP     4      10.351   8.314   9.560    0.00     3.59
-ATOM     31    C STP     4      10.082   7.855   9.856    0.00     3.56
-ATOM     32    C STP     4       9.763   7.428   9.952    0.00     3.52
-ATOM     33    C STP     4       9.808   6.869  10.405    0.00     3.64
-ATOM     34    O STP     4      10.016   6.824  10.586    0.00     3.71
-ATOM     35    O STP     4       9.960   6.815  10.553    0.00     3.70
-ATOM     36    O STP     4       9.895   6.462  10.350    0.00     3.45
-ATOM     37    O STP     4       9.826   6.743  10.451    0.00     3.64
+HEADER 11 - Local hydrophobic density Score   : 5.0000
+HEADER 12 - Number of apolar alpha sphere     :     6
+HEADER 13 - Proportion of apolar alpha sphere : 0.2727
+ATOM      1    O STP     4      17.904  16.846   2.034    0.00     4.00
+ATOM      2    C STP     4      13.212  24.010  -0.223    0.00     3.56
+ATOM      3    O STP     4      13.590  24.333  -0.124    0.00     3.66
+ATOM      4    O STP     4      16.890  22.935   1.418    0.00     4.64
+ATOM      5    C STP     4      16.767  18.684   1.078    0.00     4.22
+ATOM      6    C STP     4      16.715  18.704   1.057    0.00     4.20
+ATOM      7    O STP     4      17.342  17.855   1.830    0.00     4.24
+ATOM      8    O STP     4      17.041  17.846   1.980    0.00     4.08
+ATOM      9    O STP     4      16.580  19.060   0.747    0.00     4.27
+ATOM     10    O STP     4      17.635  17.024   1.403    0.00     3.80
+ATOM     11    O STP     4      17.395  17.419   1.401    0.00     3.89
+ATOM     12    C STP     4      16.900  18.376   1.091    0.00     4.07
+ATOM     13    O STP     4      17.782  16.444   1.256    0.00     3.57
+ATOM     14    O STP     4      14.632  22.244  -1.461    0.00     3.60
+ATOM     15    O STP     4      14.379  23.675  -0.187    0.00     4.18
+ATOM     16    C STP     4      16.642  20.313   0.285    0.00     4.56
+ATOM     17    O STP     4      15.401  22.803   0.789    0.00     4.49
+ATOM     18    O STP     4      14.950  20.959  -0.498    0.00     4.03
+ATOM     19    O STP     4      16.062  19.544  -0.072    0.00     4.25
+ATOM     20    O STP     4      16.188  19.842  -0.177    0.00     4.42
+ATOM     21    C STP     4      16.044  18.633   0.739    0.00     3.73
+ATOM     22    O STP     4      15.502  19.054  -0.011    0.00     3.68
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket5_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of alpha spheres           :    22
 HEADER 3  - Mean alpha-sphere radius          : 3.8005
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4136
-HEADER 5  - Mean B-factor of pocket residues  : 0.4612
+HEADER 5  - Mean B-factor of pocket residues  : 0.1988
 HEADER 6  - Hydrophobicity Score              : 53.5556
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Amino Acid based volume Score     : 4.6667
-HEADER 9  - Pocket volume (Monte Carlo)       : 192.6857
-HEADER 10  -Pocket volume (convex hull)       : 3.2029
+HEADER 9  - Pocket volume (Monte Carlo)       : 191.7486
+HEADER 10 - Pocket volume (convex hull)       : 3.2029
 HEADER 11 - Charge Score                      :     1
 HEADER 12 - Local hydrophobic density Score   : 0.0000
 HEADER 13 - Number of apolar alpha sphere     :     1

tests/reference_output/1ATP_out/pockets/pocket5_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0002
 HEADER 2  - Number of V. Vertices             :    22
 HEADER 3  - Mean alpha-sphere radius          : 3.8005
 HEADER 4  - Mean alpha-sphere SA              : 0.4136
-HEADER 5  - Mean B-factor                     : 0.4612
+HEADER 5  - Mean B-factor                     : 0.1988
 HEADER 6  - Hydrophobicity Score              : 53.5556
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 4.6667
-HEADER 9  - Real volume (approximation)       : 192.6857
+HEADER 9  - Real volume (approximation)       : 191.7486
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 0.0000
 HEADER 12 - Number of apolar alpha sphere     :     1

tests/reference_output/1ATP_out/pockets/pocket6_atm.pdb

@@ -12,8 +12,8 @@ HEADER 5  - Mean B-factor of pocket residues  : 0.0000
 HEADER 6  - Hydrophobicity Score              : 42.3636
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Amino Acid based volume Score     : 4.0909
-HEADER 9  - Pocket volume (Monte Carlo)       : 117.3184
-HEADER 10  -Pocket volume (convex hull)       : 2.2427
+HEADER 9  - Pocket volume (Monte Carlo)       : 113.8652
+HEADER 10 - Pocket volume (convex hull)       : 2.2427
 HEADER 11 - Charge Score                      :     0
 HEADER 12 - Local hydrophobic density Score   : 4.0000
 HEADER 13 - Number of apolar alpha sphere     :     5

tests/reference_output/1ATP_out/pockets/pocket6_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0000
 HEADER 6  - Hydrophobicity Score              : 42.3636
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 4.0909
-HEADER 9  - Real volume (approximation)       : 117.3184
+HEADER 9  - Real volume (approximation)       : 113.8652
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 4.0000
 HEADER 12 - Number of apolar alpha sphere     :     5

tests/reference_output/1ATP_out/pockets/pocket7_atm.pdb

@@ -3,47 +3,34 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     7:
-HEADER 0  - Pocket Score                      : 0.0816
-HEADER 1  - Drug Score                        : 0.0045
-HEADER 2  - Number of alpha spheres           :    31
-HEADER 3  - Mean alpha-sphere radius          : 4.0832
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5901
-HEADER 5  - Mean B-factor of pocket residues  : 0.7298
-HEADER 6  - Hydrophobicity Score              : 15.7273
+HEADER 0  - Pocket Score                      : 0.0798
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.6298
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.3583
+HEADER 5  - Mean B-factor of pocket residues  : 0.0294
+HEADER 6  - Hydrophobicity Score              : 19.9000
 HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.1818
-HEADER 9  - Pocket volume (Monte Carlo)       : 340.5146
-HEADER 10  -Pocket volume (convex hull)       : 37.2504
+HEADER 8  - Amino Acid based volume Score     : 4.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 111.7776
+HEADER 10 - Pocket volume (convex hull)       : 2.3995
 HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 14.7500
-HEADER 13 - Number of apolar alpha sphere     :    16
-HEADER 14 - Proportion of apolar alpha sphere : 0.5161
-ATOM   2349   CA THR E 300      -2.136 -16.523   0.940  0.00  0.00           C 0
-ATOM   2348    N THR E 300      -1.897 -17.858   1.436  0.00  0.00           N 0
-ATOM   2353  OG1 THR E 300       0.238 -16.029   1.169  0.00  0.00           O 0
-ATOM   2346  OG1 THR E 299      -0.824 -19.572   4.432  0.76  3.21           O 0
-ATOM   2344    O THR E 299      -3.875 -18.070   2.502  0.36  6.43           O 0
-ATOM   2343    C THR E 299      -2.779 -18.525   2.162  0.00  0.00           C 0
-ATOM   2444  CG1 VAL E 310      -5.465 -11.342   5.087  0.00  0.00           C 0
-ATOM   2359   CB ASP E 301      -6.814 -15.392  -0.021  0.00  0.00           C 0
-ATOM   2445  CG2 VAL E 310      -6.233 -10.529   2.840  0.00  0.00           C 0
-ATOM   2355    N ASP E 301      -4.279 -15.664   0.214  0.00  0.00           N 0
-ATOM   2389   CB ALA E 304      -8.532 -12.091   0.496  0.00  0.00           C 0
-ATOM   2433    O LYS E 309     -10.006  -9.496   4.644  0.00  0.00           O 0
-ATOM   2397  CD1 ILE E 305      -2.545 -11.291   1.475  0.00  0.00           C 0
-ATOM   2454  OE2 GLU E 311      -5.008 -14.364   8.021  0.00  0.00           O 0
-ATOM   2446    N GLU E 311      -6.776  -9.898   7.187  0.00  0.00           N 0
-ATOM   2440   CA VAL E 310      -7.234  -9.583   4.872  0.00  0.00           C 0
-ATOM   1067   CD ARG E 144       2.373 -16.320   3.946  0.00  0.00           C 0
-ATOM   1070  NH1 ARG E 144       2.427 -17.435   6.611  0.00  0.00           N 0
-ATOM   1073   CA PHE E 145       1.537 -10.378   4.578  0.00  0.00           C 0
-ATOM   1076   CB PHE E 145       0.971  -9.866   5.938  0.00  0.00           C 0
-ATOM   1042    O PRO E 141       2.365 -13.029   7.548  0.65  2.14           O 0
-ATOM   1043   CB PRO E 141       2.135 -15.510   9.719  0.00  0.00           C 0
-ATOM   1066   CG ARG E 144       2.651 -14.825   3.866  0.00  0.00           C 0
-ATOM   1072    N PHE E 145       2.605 -11.335   4.829  0.00  0.00           N 0
-ATOM   1064    O ARG E 144       2.912 -11.965   2.698  0.00  0.00           O 0
-ATOM   1078  CD1 PHE E 145      -1.292  -8.937   5.214  0.00  0.00           C 0
-ATOM   2452   CD GLU E 311      -4.896 -13.238   8.497  0.00  0.00           C 0
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.1333
+ATOM    321   CG PHE E  54      17.995  12.178  -4.417  0.00  0.00           C 0
+ATOM    569  OE1 GLN E  84      18.789  10.413  -9.405  0.00  0.00           O 0
+ATOM    323  CD2 PHE E  54      17.672  10.850  -4.138  0.00  0.00           C 0
+ATOM    628  OE1 GLU E  91      11.799  11.798  -7.613  0.61  4.29           O 0
+ATOM    320   CB PHE E  54      17.100  13.280  -3.954  0.00  0.00           C 0
+ATOM    470   NZ LYS E  72      11.886  11.415  -3.274  0.62  1.09           N 0
+ATOM   1421   CA GLY E 186      12.913   8.374  -7.628  0.00  0.00           C 0
+ATOM   1407  OD1 ASP E 184      12.373   7.897  -4.139  0.00  0.00           O 0
+ATOM    603  OG1 THR E  88      14.838  14.429  -9.929  0.79  2.14           O 0
+ATOM    485  CD1 LEU E  74      13.945  15.900  -4.565  0.00  0.00           C 0
+ATOM    566   CB GLN E  84      18.752  13.052  -9.731  0.00  0.00           C 0
+ATOM   1423    O GLY E 186      14.353   8.217  -9.471  0.00  0.00           O 0
+ATOM    592   CB HIS E  87      16.234   9.885 -11.768  0.00  0.00           C 0
+ATOM   1432  CE1 PHE E 187      17.677   7.326  -7.166  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket7_vert.pqr

@@ -4,50 +4,34 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     7:
-HEADER 0  - Pocket Score                      : 0.0816
-HEADER 1  - Drug Score                        : 0.0045
-HEADER 2  - Number of V. Vertices             :    31
-HEADER 3  - Mean alpha-sphere radius          : 4.0832
-HEADER 4  - Mean alpha-sphere SA              : 0.5901
-HEADER 5  - Mean B-factor                     : 0.7298
-HEADER 6  - Hydrophobicity Score              : 15.7273
+HEADER 0  - Pocket Score                      : 0.0798
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.6298
+HEADER 4  - Mean alpha-sphere SA              : 0.3583
+HEADER 5  - Mean B-factor                     : 0.0294
+HEADER 6  - Hydrophobicity Score              : 19.9000
 HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.1818
-HEADER 9  - Real volume (approximation)       : 340.5146
+HEADER 8  - Volume Score                      : 4.2000
+HEADER 9  - Real volume (approximation)       : 111.7776
 HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 14.7500
-HEADER 12 - Number of apolar alpha sphere     :    16
-HEADER 13 - Proportion of apolar alpha sphere : 0.5161
-ATOM      1    O STP     7      -1.389 -15.808   4.608    0.00     3.81
-ATOM      2    O STP     7      -1.682 -16.022   4.590    0.00     3.66
-ATOM      3    O STP     7      -1.648 -15.823   4.692    0.00     3.85
-ATOM      4    C STP     7      -5.623 -13.895   2.816    0.00     3.42
-ATOM      5    C STP     7      -7.247 -14.004   3.331    0.00     3.65
-ATOM      6    C STP     7      -8.747 -13.072   4.181    0.00     3.82
-ATOM      7    C STP     7      -3.506 -14.247   3.643    0.00     3.79
-ATOM      8    O STP     7      -3.650 -14.469   3.805    0.00     3.84
-ATOM      9    O STP     7      -5.817 -14.938   3.693    0.00     3.87
-ATOM     10    C STP     7      -2.262 -14.253   4.649    0.00     4.35
-ATOM     11    O STP     7      -8.823 -12.829   5.969    0.00     3.78
-ATOM     12    C STP     7      -8.681 -12.900   4.221    0.00     3.68
-ATOM     13    O STP     7      -1.409 -15.542   5.914    0.00     4.33
-ATOM     14    O STP     7      -1.417 -15.715   4.699    0.00     3.91
-ATOM     15    O STP     7      -1.682 -15.399   5.074    0.00     4.31
-ATOM     16    C STP     7      -1.560 -13.587   5.226    0.00     4.51
-ATOM     17    C STP     7      -1.567 -13.472   5.345    0.00     4.45
-ATOM     18    O STP     7      -1.180 -15.075   6.105    0.00     4.34
-ATOM     19    O STP     7      -1.076 -15.289   7.116    0.00     4.14
-ATOM     20    O STP     7      -1.505 -13.532   5.394    0.00     4.46
-ATOM     21    O STP     7      -0.289 -13.357   5.212    0.00     3.55
-ATOM     22    C STP     7      -0.289 -13.067   3.400    0.00     3.46
-ATOM     23    O STP     7      -1.253 -14.770   5.826    0.00     4.37
-ATOM     24    C STP     7      -1.525 -13.665   5.202    0.00     4.54
-ATOM     25    O STP     7      -1.488 -13.667   5.270    0.00     4.52
-ATOM     26    C STP     7      -1.739 -14.231   4.832    0.00     4.53
-ATOM     27    C STP     7      -1.647 -14.742   4.977    0.00     4.44
-ATOM     28    C STP     7      -1.682 -14.732   5.030    0.00     4.49
-ATOM     29    C STP     7      -1.616 -13.199   5.185    0.00     4.27
-ATOM     30    C STP     7      -1.612 -13.209   5.227    0.00     4.28
-ATOM     31    C STP     7      -1.726 -13.041   5.798    0.00     4.17
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.1333
+ATOM      1    O STP     7      15.640  11.395  -7.384    0.00     3.87
+ATOM      2    O STP     7      14.547  11.507  -5.506    0.00     3.47
+ATOM      3    C STP     7      15.133  11.716  -6.441    0.00     3.54
+ATOM      4    O STP     7      14.464  10.763  -5.571    0.00     3.51
+ATOM      5    O STP     7      14.467  10.370  -5.296    0.00     3.44
+ATOM      6    O STP     7      14.848  13.223  -6.639    0.00     3.50
+ATOM      7    O STP     7      15.418  12.203  -7.050    0.00     3.68
+ATOM      8    O STP     7      15.660  11.576  -7.445    0.00     3.87
+ATOM      9    O STP     7      16.047  11.948  -7.515    0.00     3.67
+ATOM     10    O STP     7      15.521  11.388  -7.841    0.00     3.75
+ATOM     11    O STP     7      15.570  11.317  -8.748    0.00     3.41
+ATOM     12    O STP     7      15.604  11.206  -7.376    0.00     3.86
+ATOM     13    O STP     7      15.544  11.122  -7.297    0.00     3.82
+ATOM     14    O STP     7      15.979  10.444  -7.233    0.00     3.55
+ATOM     15    C STP     7      15.792  10.270  -7.031    0.00     3.50
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket8_atm.pdb

@@ -3,34 +3,39 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     8:
-HEADER 0  - Pocket Score                      : 0.0798
-HEADER 1  - Drug Score                        : 0.0003
-HEADER 2  - Number of alpha spheres           :    15
-HEADER 3  - Mean alpha-sphere radius          : 3.6298
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.3583
-HEADER 5  - Mean B-factor of pocket residues  : 0.0681
-HEADER 6  - Hydrophobicity Score              : 19.9000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.2000
-HEADER 9  - Pocket volume (Monte Carlo)       : 110.9388
-HEADER 10  -Pocket volume (convex hull)       : 2.3995
+HEADER 0  - Pocket Score                      : 0.0433
+HEADER 1  - Drug Score                        : 0.0090
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.7189
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4354
+HEADER 5  - Mean B-factor of pocket residues  : 0.2823
+HEADER 6  - Hydrophobicity Score              : 61.3000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 5.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 254.0818
+HEADER 10 - Pocket volume (convex hull)       : 20.1196
 HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 1.0000
-HEADER 13 - Number of apolar alpha sphere     :     2
-HEADER 14 - Proportion of apolar alpha sphere : 0.1333
-ATOM    321   CG PHE E  54      17.995  12.178  -4.417  0.00  0.00           C 0
-ATOM    569  OE1 GLN E  84      18.789  10.413  -9.405  0.00  0.00           O 0
-ATOM    323  CD2 PHE E  54      17.672  10.850  -4.138  0.00  0.00           C 0
-ATOM    628  OE1 GLU E  91      11.799  11.798  -7.613  0.61  4.29           O 0
-ATOM    320   CB PHE E  54      17.100  13.280  -3.954  0.00  0.00           C 0
-ATOM    470   NZ LYS E  72      11.886  11.415  -3.274  0.62  1.09           N 0
-ATOM   1421   CA GLY E 186      12.913   8.374  -7.628  0.00  0.00           C 0
-ATOM   1407  OD1 ASP E 184      12.373   7.897  -4.139  0.00  0.00           O 0
-ATOM    603  OG1 THR E  88      14.838  14.429  -9.929  0.79  2.14           O 0
-ATOM    485  CD1 LEU E  74      13.945  15.900  -4.565  0.00  0.00           C 0
-ATOM    566   CB GLN E  84      18.752  13.052  -9.731  0.00  0.00           C 0
-ATOM   1423    O GLY E 186      14.353   8.217  -9.471  0.00  0.00           O 0
-ATOM    592   CB HIS E  87      16.234   9.885 -11.768  0.00  0.00           C 0
-ATOM   1432  CE1 PHE E 187      17.677   7.326  -7.166  0.00  0.00           C 0
+HEADER 12 - Local hydrophobic density Score   : 15.0000
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.7273
+ATOM    211    O LEU E  40       1.756  26.553  -0.763  0.56  1.07           O 0
+ATOM    216    N ASP E  41       1.737  28.499  -1.964  0.00  0.00           N 0
+ATOM    217   CA ASP E  41       0.826  29.328  -1.179  0.00  0.00           C 0
+ATOM    214  CD1 LEU E  40       6.287  27.704  -0.907  0.00  0.00           C 0
+ATOM    371  CG2 VAL E  60       2.938  21.371   3.082  0.00  0.00           C 0
+ATOM    215  CD2 LEU E  40       4.920  25.611  -0.876  0.00  0.00           C 0
+ATOM    256   CB ARG E  45       5.477  24.448   5.841  0.00  0.00           C 0
+ATOM    460   SD MET E  71       5.246  21.433  -0.548  0.00  0.00           S 0
+ATOM    252    N ARG E  45       3.004  24.807   5.734  0.36  2.19           N 0
+ATOM    355   SD MET E  58       8.463  21.425   5.189  0.00  0.00           S 0
+ATOM    356   CE MET E  58       9.807  22.030   4.159  0.00  0.00           C 0
+ATOM    210    C LEU E  40       2.136  27.238  -1.696  0.00  0.00           C 0
+ATOM   2646  CG1 ILE E 335      10.465  24.754   2.439  0.00  0.00           C 0
+ATOM    236    O PHE E  43       0.880  26.519   2.621  0.59  5.36           O 0
+ATOM    237   CB PHE E  43       0.553  23.837   1.182  0.00  0.00           C 0
+ATOM    478  CD1 ILE E  73       9.538  21.094   1.013  0.00  0.00           C 0
+ATOM    849  CE2 TYR E 117       8.106  23.530  -2.859  0.00  0.00           C 0
+ATOM   2645   CB ILE E 335      10.671  26.195   2.001  0.00  0.00           C 0
+ATOM    261  NH1 ARG E  45       9.719  25.580   5.861  0.00  0.00           N 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket8_vert.pqr

@@ -4,34 +4,41 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     8:
-HEADER 0  - Pocket Score                      : 0.0798
-HEADER 1  - Drug Score                        : 0.0003
-HEADER 2  - Number of V. Vertices             :    15
-HEADER 3  - Mean alpha-sphere radius          : 3.6298
-HEADER 4  - Mean alpha-sphere SA              : 0.3583
-HEADER 5  - Mean B-factor                     : 0.0681
-HEADER 6  - Hydrophobicity Score              : 19.9000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.2000
-HEADER 9  - Real volume (approximation)       : 110.9388
+HEADER 0  - Pocket Score                      : 0.0433
+HEADER 1  - Drug Score                        : 0.0090
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.7189
+HEADER 4  - Mean alpha-sphere SA              : 0.4354
+HEADER 5  - Mean B-factor                     : 0.2823
+HEADER 6  - Hydrophobicity Score              : 61.3000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 5.2000
+HEADER 9  - Real volume (approximation)       : 254.0818
 HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 1.0000
-HEADER 12 - Number of apolar alpha sphere     :     2
-HEADER 13 - Proportion of apolar alpha sphere : 0.1333
-ATOM      1    O STP     8      15.640  11.395  -7.384    0.00     3.87
-ATOM      2    O STP     8      14.547  11.507  -5.506    0.00     3.47
-ATOM      3    C STP     8      15.133  11.716  -6.441    0.00     3.54
-ATOM      4    O STP     8      14.464  10.763  -5.571    0.00     3.51
-ATOM      5    O STP     8      14.467  10.370  -5.296    0.00     3.44
-ATOM      6    O STP     8      14.848  13.223  -6.639    0.00     3.50
-ATOM      7    O STP     8      15.418  12.203  -7.050    0.00     3.68
-ATOM      8    O STP     8      15.660  11.576  -7.445    0.00     3.87
-ATOM      9    O STP     8      16.047  11.948  -7.515    0.00     3.67
-ATOM     10    O STP     8      15.521  11.388  -7.841    0.00     3.75
-ATOM     11    O STP     8      15.570  11.317  -8.748    0.00     3.41
-ATOM     12    O STP     8      15.604  11.206  -7.376    0.00     3.86
-ATOM     13    O STP     8      15.544  11.122  -7.297    0.00     3.82
-ATOM     14    O STP     8      15.979  10.444  -7.233    0.00     3.55
-ATOM     15    C STP     8      15.792  10.270  -7.031    0.00     3.50
+HEADER 11 - Local hydrophobic density Score   : 15.0000
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.7273
+ATOM      1    O STP     8       3.602  29.013   1.016    0.00     3.55
+ATOM      2    C STP     8       5.556  23.790   2.238    0.00     3.66
+ATOM      3    C STP     8       4.374  24.558   2.469    0.00     3.55
+ATOM      4    C STP     8       6.248  22.839   2.662    0.00     3.65
+ATOM      5    C STP     8       6.687  23.325   2.417    0.00     3.80
+ATOM      6    O STP     8       3.605  28.995   0.988    0.00     3.53
+ATOM      7    C STP     8       6.666  23.871   2.160    0.00     3.91
+ATOM      8    C STP     8       6.778  23.571   2.298    0.00     3.87
+ATOM      9    C STP     8       6.777  25.942   2.510    0.00     3.88
+ATOM     10    O STP     8       3.851  24.675   2.332    0.00     3.51
+ATOM     11    C STP     8       3.757  24.628   2.235    0.00     3.46
+ATOM     12    O STP     8       3.932  27.786   1.618    0.00     3.45
+ATOM     13    O STP     8       4.637  26.459   2.777    0.00     3.76
+ATOM     14    C STP     8       4.889  27.180   2.881    0.00     4.07
+ATOM     15    O STP     8       3.599  29.091   1.545    0.00     3.89
+ATOM     16    C STP     8       7.492  23.806   0.509    0.00     3.43
+ATOM     17    C STP     8       7.257  23.839   1.162    0.00     3.57
+ATOM     18    C STP     8       7.637  23.976   0.562    0.00     3.48
+ATOM     19    C STP     8       6.839  23.523   2.245    0.00     3.83
+ATOM     20    C STP     8       6.757  23.101   2.378    0.00     3.69
+ATOM     21    C STP     8       6.868  27.794   3.414    0.00     4.36
+ATOM     22    C STP     8       6.830  26.126   2.605    0.00     3.89
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket9_atm.pdb

@@ -3,39 +3,39 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     9:
-HEADER 0  - Pocket Score                      : 0.0433
-HEADER 1  - Drug Score                        : 0.0090
-HEADER 2  - Number of alpha spheres           :    22
-HEADER 3  - Mean alpha-sphere radius          : 3.7189
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4354
-HEADER 5  - Mean B-factor of pocket residues  : 0.6548
-HEADER 6  - Hydrophobicity Score              : 61.3000
-HEADER 7  - Polarity Score                    :     3
-HEADER 8  - Amino Acid based volume Score     : 5.2000
-HEADER 9  - Pocket volume (Monte Carlo)       : 257.6532
-HEADER 10  -Pocket volume (convex hull)       : 20.1196
+HEADER 0  - Pocket Score                      : 0.0405
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8663
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6124
+HEADER 5  - Mean B-factor of pocket residues  : 0.3315
+HEADER 6  - Hydrophobicity Score              : 9.7000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.5000
+HEADER 9  - Pocket volume (Monte Carlo)       : 265.1693
+HEADER 10 - Pocket volume (convex hull)       : 12.1248
 HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 15.0000
-HEADER 13 - Number of apolar alpha sphere     :    16
-HEADER 14 - Proportion of apolar alpha sphere : 0.7273
-ATOM    211    O LEU E  40       1.756  26.553  -0.763  0.56  1.07           O 0
-ATOM    216    N ASP E  41       1.737  28.499  -1.964  0.00  0.00           N 0
-ATOM    217   CA ASP E  41       0.826  29.328  -1.179  0.00  0.00           C 0
-ATOM    214  CD1 LEU E  40       6.287  27.704  -0.907  0.00  0.00           C 0
-ATOM    371  CG2 VAL E  60       2.938  21.371   3.082  0.00  0.00           C 0
-ATOM    215  CD2 LEU E  40       4.920  25.611  -0.876  0.00  0.00           C 0
-ATOM    256   CB ARG E  45       5.477  24.448   5.841  0.00  0.00           C 0
-ATOM    460   SD MET E  71       5.246  21.433  -0.548  0.00  0.00           S 0
-ATOM    252    N ARG E  45       3.004  24.807   5.734  0.36  2.19           N 0
-ATOM    355   SD MET E  58       8.463  21.425   5.189  0.00  0.00           S 0
-ATOM    356   CE MET E  58       9.807  22.030   4.159  0.00  0.00           C 0
-ATOM    210    C LEU E  40       2.136  27.238  -1.696  0.00  0.00           C 0
-ATOM   2646  CG1 ILE E 335      10.465  24.754   2.439  0.00  0.00           C 0
-ATOM    236    O PHE E  43       0.880  26.519   2.621  0.59  5.36           O 0
-ATOM    237   CB PHE E  43       0.553  23.837   1.182  0.00  0.00           C 0
-ATOM    478  CD1 ILE E  73       9.538  21.094   1.013  0.00  0.00           C 0
-ATOM    849  CE2 TYR E 117       8.106  23.530  -2.859  0.00  0.00           C 0
-ATOM   2645   CB ILE E 335      10.671  26.195   2.001  0.00  0.00           C 0
-ATOM    261  NH1 ARG E  45       9.719  25.580   5.861  0.00  0.00           N 0
+HEADER 12 - Local hydrophobic density Score   : 6.0000
+HEADER 13 - Number of apolar alpha sphere     :     7
+HEADER 14 - Proportion of apolar alpha sphere : 0.4375
+ATOM    434  CD2 HIS E  68      -4.370  16.956   8.208  0.00  0.00           C 0
+ATOM    418    O GLY E  66      -7.767  19.132   6.362  0.14  7.50           O 0
+ATOM    425  OD1 ASN E  67      -8.955  16.520   3.549  0.00  0.00           O 0
+ATOM   2530   CB PRO E 321      -6.517  14.426  10.771  0.00  0.00           C 0
+ATOM    427    N HIS E  68      -4.661  17.016   4.850  0.00  0.00           N 0
+ATOM    431   CB HIS E  68      -2.770  16.341   6.300  0.00  0.00           C 0
+ATOM    430    O HIS E  68      -3.452  15.333   3.304  0.00  0.00           O 0
+ATOM    420   CA ASN E  67      -6.657  18.056   4.121  0.00  0.00           C 0
+ATOM   2533    N GLY E 322      -3.195  14.519  11.020  0.00  0.00           N 0
+ATOM    891  CD2 TYR E 122      -0.618  12.346   7.159  0.00  0.00           C 0
+ATOM   2512   CZ PHE E 318      -4.685  10.281  11.468  0.00  0.00           C 0
+ATOM   2527   CA PRO E 321      -5.396  13.768  11.582  0.00  0.00           C 0
+ATOM    884    N TYR E 122      -0.887  11.623   2.511  0.00  0.00           N 0
+ATOM    887    O TYR E 122      -1.382   9.668   4.729  0.42  5.36           O 0
+ATOM    880   CG GLU E 121      -3.212   9.733   0.513  0.00  0.00           C 0
+ATOM    888   CB TYR E 122      -0.420  12.529   4.688  0.00  0.00           C 0
+ATOM   1344  NE2 GLN E 176      -5.655   7.996   8.723  0.00  0.00           N 0
+ATOM    907   CB ALA E 124      -0.748   8.672   9.338  0.00  0.00           C 0
+ATOM   2511  CE2 PHE E 318      -3.352  10.649  11.639  0.00  0.00           C 0
 TER
 END

tests/reference_output/1ATP_out/pockets/pocket9_vert.pqr

@@ -4,41 +4,35 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     9:
-HEADER 0  - Pocket Score                      : 0.0433
-HEADER 1  - Drug Score                        : 0.0090
-HEADER 2  - Number of V. Vertices             :    22
-HEADER 3  - Mean alpha-sphere radius          : 3.7189
-HEADER 4  - Mean alpha-sphere SA              : 0.4354
-HEADER 5  - Mean B-factor                     : 0.6548
-HEADER 6  - Hydrophobicity Score              : 61.3000
-HEADER 7  - Polarity Score                    :     3
-HEADER 8  - Volume Score                      : 5.2000
-HEADER 9  - Real volume (approximation)       : 257.6532
+HEADER 0  - Pocket Score                      : 0.0405
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8663
+HEADER 4  - Mean alpha-sphere SA              : 0.6124
+HEADER 5  - Mean B-factor                     : 0.3315
+HEADER 6  - Hydrophobicity Score              : 9.7000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.5000
+HEADER 9  - Real volume (approximation)       : 265.1693
 HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 15.0000
-HEADER 12 - Number of apolar alpha sphere     :    16
-HEADER 13 - Proportion of apolar alpha sphere : 0.7273
-ATOM      1    O STP     9       3.602  29.013   1.016    0.00     3.55
-ATOM      2    C STP     9       5.556  23.790   2.238    0.00     3.66
-ATOM      3    C STP     9       4.374  24.558   2.469    0.00     3.55
-ATOM      4    C STP     9       6.248  22.839   2.662    0.00     3.65
-ATOM      5    C STP     9       6.687  23.325   2.417    0.00     3.80
-ATOM      6    O STP     9       3.605  28.995   0.988    0.00     3.53
-ATOM      7    C STP     9       6.666  23.871   2.160    0.00     3.91
-ATOM      8    C STP     9       6.778  23.571   2.298    0.00     3.87
-ATOM      9    C STP     9       6.777  25.942   2.510    0.00     3.88
-ATOM     10    O STP     9       3.851  24.675   2.332    0.00     3.51
-ATOM     11    C STP     9       3.757  24.628   2.235    0.00     3.46
-ATOM     12    O STP     9       3.932  27.786   1.618    0.00     3.45
-ATOM     13    O STP     9       4.637  26.459   2.777    0.00     3.76
-ATOM     14    C STP     9       4.889  27.180   2.881    0.00     4.07
-ATOM     15    O STP     9       3.599  29.091   1.545    0.00     3.89
-ATOM     16    C STP     9       7.492  23.806   0.509    0.00     3.43
-ATOM     17    C STP     9       7.257  23.839   1.162    0.00     3.57
-ATOM     18    C STP     9       7.637  23.976   0.562    0.00     3.48
-ATOM     19    C STP     9       6.839  23.523   2.245    0.00     3.83
-ATOM     20    C STP     9       6.757  23.101   2.378    0.00     3.69
-ATOM     21    C STP     9       6.868  27.794   3.414    0.00     4.36
-ATOM     22    C STP     9       6.830  26.126   2.605    0.00     3.89
+HEADER 11 - Local hydrophobic density Score   : 6.0000
+HEADER 12 - Number of apolar alpha sphere     :     7
+HEADER 13 - Proportion of apolar alpha sphere : 0.4375
+ATOM      1    O STP     9      -7.764  15.242   7.103    0.00     3.96
+ATOM      2    C STP     9      -5.783  13.019   6.568    0.00     4.49
+ATOM      3    O STP     9      -5.788  12.752   6.449    0.00     4.69
+ATOM      4    O STP     9      -7.309  14.474   6.726    0.00     4.12
+ATOM      5    O STP     9      -7.432  15.466   6.755    0.00     3.70
+ATOM      6    O STP     9      -7.395  15.658   6.560    0.00     3.50
+ATOM      7    C STP     9      -4.485  12.252   8.033    0.00     3.97
+ATOM      8    C STP     9      -4.567  13.020   7.587    0.00     3.99
+ATOM      9    C STP     9      -4.565  12.978   7.571    0.00     4.02
+ATOM     10    O STP     9      -4.654  11.597   3.673    0.00     3.94
+ATOM     11    O STP     9      -3.791  12.064   4.278    0.00     3.43
+ATOM     12    O STP     9      -4.242  12.235   5.610    0.00     3.94
+ATOM     13    O STP     9      -3.273  10.191   7.558    0.00     3.44
+ATOM     14    C STP     9      -4.073  12.143   8.369    0.00     3.67
+ATOM     15    C STP     9      -3.693  10.881   8.123    0.00     3.54
+ATOM     16    C STP     9      -3.402  10.565   8.181    0.00     3.46
 TER
 END

tests/reference_output/1QNH_out/1QNH_info.txt

@@ -5,7 +5,7 @@ Pocket 1 :
 	Total SASA : 	319.981
 	Polar SASA : 	172.651
 	Apolar SASA : 	147.331
-	Volume : 	5091.737
+	Volume : 	4956.883
 	Mean local hydrophobic density : 	13.444
 	Mean alpha sphere radius :	4.302
 	Mean alp. sph. solvent access : 	0.583

tests/reference_output/1QNH_out/pockets/pocket1_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket     1:
 6  - Hydrophobicity Score              : 16.8148
 7  - Polarity Score                    :    16
 8  - Amino Acid based volume Score     : 3.8889
-9  - Pocket volume (Monte Carlo)       : 5091.7368
+9  - Pocket volume (Monte Carlo)       : 4956.8828
 10  -Pocket volume (convex hull)       : 10904.4561
 11 - Charge Score                      :     6
 12 - Local hydrophobic density Score   : 13.4444

tests/reference_output/1QNH_out/pockets/pocket1_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0000
 HEADER 6  - Hydrophobicity Score              : 16.8148
 HEADER 7  - Polarity Score                    :    16
 HEADER 8  - Volume Score                      : 3.8889
-HEADER 9  - Real volume (approximation)       : 5091.7368
+HEADER 9  - Real volume (approximation)       : 4956.8828
 HEADER 10 - Charge Score                      :     6
 HEADER 11 - Local hydrophobic density Score   : 13.4444
 HEADER 12 - Number of apolar alpha sphere     :    54

tests/reference_output/1UYD_out/1UYD_info.txt

@@ -5,7 +5,7 @@ Pocket 1 :
 	Total SASA : 	214.924
 	Polar SASA : 	111.068
 	Apolar SASA : 	103.856
-	Volume : 	1437.686
+	Volume : 	1455.507
 	Mean local hydrophobic density : 	53.083
 	Mean alpha sphere radius :	3.977
 	Mean alp. sph. solvent access : 	0.451
@@ -17,7 +17,7 @@ Pocket 1 :
 	Proportion of polar atoms: 	36.905
 	Alpha sphere density : 	8.233
 	Cent. of mass - Alpha Sphere max dist: 	21.512
-	Flexibility : 	0.227
+	Flexibility : 	0.136
 
 Pocket 2 :
 	Score : 	0.122
@@ -26,7 +26,7 @@ Pocket 2 :
 	Total SASA : 	94.066
 	Polar SASA : 	68.706
 	Apolar SASA : 	25.360
-	Volume : 	425.424
+	Volume : 	419.048
 	Mean local hydrophobic density : 	2.000
 	Mean alpha sphere radius :	4.011
 	Mean alp. sph. solvent access : 	0.544
@@ -38,16 +38,37 @@ Pocket 2 :
 	Proportion of polar atoms: 	52.174
 	Alpha sphere density : 	4.862
 	Cent. of mass - Alpha Sphere max dist: 	10.651
-	Flexibility : 	0.601
+	Flexibility : 	0.361
 
 Pocket 3 :
+	Score : 	0.087
+	Druggability Score : 	0.116
+	Number of Alpha Spheres : 	70
+	Total SASA : 	228.410
+	Polar SASA : 	71.181
+	Apolar SASA : 	157.229
+	Volume : 	748.955
+	Mean local hydrophobic density : 	27.481
+	Mean alpha sphere radius :	3.929
+	Mean alp. sph. solvent access : 	0.530
+	Apolar alpha sphere proportion : 	0.771
+	Hydrophobicity score:	20.933
+	Volume score: 	 4.400
+	Polarity score:	 10
+	Charge score :	 -1
+	Proportion of polar atoms: 	34.043
+	Alpha sphere density : 	8.104
+	Cent. of mass - Alpha Sphere max dist: 	21.409
+	Flexibility : 	0.484
+
+Pocket 4 :
 	Score : 	0.050
 	Druggability Score : 	0.014
 	Number of Alpha Spheres : 	31
 	Total SASA : 	124.126
 	Polar SASA : 	31.139
 	Apolar SASA : 	92.987
-	Volume : 	438.371
+	Volume : 	434.580
 	Mean local hydrophobic density : 	19.455
 	Mean alpha sphere radius :	3.914
 	Mean alp. sph. solvent access : 	0.605
@@ -59,16 +80,16 @@ Pocket 3 :
 	Proportion of polar atoms: 	34.483
 	Alpha sphere density : 	5.097
 	Cent. of mass - Alpha Sphere max dist: 	11.542
-	Flexibility : 	0.285
+	Flexibility : 	0.171
 
-Pocket 4 :
+Pocket 5 :
 	Score : 	0.042
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	19
 	Total SASA : 	75.497
 	Polar SASA : 	24.776
 	Apolar SASA : 	50.720
-	Volume : 	275.129
+	Volume : 	275.331
 	Mean local hydrophobic density : 	3.000
 	Mean alpha sphere radius :	3.801
 	Mean alp. sph. solvent access : 	0.490
@@ -80,37 +101,37 @@ Pocket 4 :
 	Proportion of polar atoms: 	35.294
 	Alpha sphere density : 	3.508
 	Cent. of mass - Alpha Sphere max dist: 	6.460
-	Flexibility : 	0.230
-
-Pocket 5 :
-	Score : 	-0.012
-	Druggability Score : 	0.011
-	Number of Alpha Spheres : 	28
-	Total SASA : 	92.394
-	Polar SASA : 	25.737
-	Apolar SASA : 	66.657
-	Volume : 	314.367
-	Mean local hydrophobic density : 	23.000
-	Mean alpha sphere radius :	3.858
-	Mean alp. sph. solvent access : 	0.522
-	Apolar alpha sphere proportion : 	0.857
-	Hydrophobicity score:	-4.429
-	Volume score: 	 4.571
-	Polarity score:	 6
-	Charge score :	 0
-	Proportion of polar atoms: 	38.095
-	Alpha sphere density : 	3.282
-	Cent. of mass - Alpha Sphere max dist: 	7.261
-	Flexibility : 	0.748
+	Flexibility : 	0.138
 
 Pocket 6 :
+	Score : 	-0.014
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	61.760
+	Polar SASA : 	27.946
+	Apolar SASA : 	33.814
+	Volume : 	243.448
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	3.892
+	Mean alp. sph. solvent access : 	0.675
+	Apolar alpha sphere proportion : 	0.235
+	Hydrophobicity score:	-22.500
+	Volume score: 	 5.500
+	Polarity score:	 4
+	Charge score :	 0
+	Proportion of polar atoms: 	44.444
+	Alpha sphere density : 	2.373
+	Cent. of mass - Alpha Sphere max dist: 	5.520
+	Flexibility : 	0.383
+
+Pocket 7 :
 	Score : 	-0.021
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	16
 	Total SASA : 	82.319
 	Polar SASA : 	70.242
 	Apolar SASA : 	12.076
-	Volume : 	256.757
+	Volume : 	252.088
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.889
 	Mean alp. sph. solvent access : 	0.547
@@ -122,70 +143,49 @@ Pocket 6 :
 	Proportion of polar atoms: 	71.429
 	Alpha sphere density : 	3.223
 	Cent. of mass - Alpha Sphere max dist: 	7.463
-	Flexibility : 	0.620
+	Flexibility : 	0.372
 
-Pocket 7 :
-	Score : 	-0.034
+Pocket 8 :
+	Score : 	-0.038
 	Druggability Score : 	0.001
-	Number of Alpha Spheres : 	15
-	Total SASA : 	76.174
+	Number of Alpha Spheres : 	18
+	Total SASA : 	82.035
+	Polar SASA : 	20.446
+	Apolar SASA : 	61.589
+	Volume : 	284.503
+	Mean local hydrophobic density : 	7.556
+	Mean alpha sphere radius :	3.942
+	Mean alp. sph. solvent access : 	0.485
+	Apolar alpha sphere proportion : 	0.500
+	Hydrophobicity score:	14.875
+	Volume score: 	 4.750
+	Polarity score:	 4
+	Charge score :	 0
+	Proportion of polar atoms: 	41.176
+	Alpha sphere density : 	2.949
+	Cent. of mass - Alpha Sphere max dist: 	8.135
+	Flexibility : 	0.511
+
+Pocket 9 :
+	Score : 	-0.042
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	17
+	Total SASA : 	78.589
 	Polar SASA : 	20.623
-	Apolar SASA : 	55.551
-	Volume : 	262.364
-	Mean local hydrophobic density : 	5.000
-	Mean alpha sphere radius :	3.728
-	Mean alp. sph. solvent access : 	0.402
-	Apolar alpha sphere proportion : 	0.400
+	Apolar SASA : 	57.966
+	Volume : 	259.304
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.716
+	Mean alp. sph. solvent access : 	0.420
+	Apolar alpha sphere proportion : 	0.412
 	Hydrophobicity score:	7.714
 	Volume score: 	 4.000
 	Polarity score:	 4
 	Charge score :	 -1
 	Proportion of polar atoms: 	37.500
-	Alpha sphere density : 	2.882
+	Alpha sphere density : 	2.817
 	Cent. of mass - Alpha Sphere max dist: 	6.933
-	Flexibility : 	0.716
-
-Pocket 8 :
-	Score : 	-0.039
-	Druggability Score : 	0.009
-	Number of Alpha Spheres : 	25
-	Total SASA : 	97.119
-	Polar SASA : 	15.000
-	Apolar SASA : 	82.119
-	Volume : 	292.064
-	Mean local hydrophobic density : 	18.500
-	Mean alpha sphere radius :	4.046
-	Mean alp. sph. solvent access : 	0.563
-	Apolar alpha sphere proportion : 	0.800
-	Hydrophobicity score:	46.556
-	Volume score: 	 4.333
-	Polarity score:	 4
-	Charge score :	 -1
-	Proportion of polar atoms: 	25.000
-	Alpha sphere density : 	3.371
-	Cent. of mass - Alpha Sphere max dist: 	8.654
-	Flexibility : 	0.688
-
-Pocket 9 :
-	Score : 	-0.060
-	Druggability Score : 	0.001
-	Number of Alpha Spheres : 	17
-	Total SASA : 	85.530
-	Polar SASA : 	40.848
-	Apolar SASA : 	44.682
-	Volume : 	280.765
-	Mean local hydrophobic density : 	6.000
-	Mean alpha sphere radius :	3.890
-	Mean alp. sph. solvent access : 	0.593
-	Apolar alpha sphere proportion : 	0.412
-	Hydrophobicity score:	-11.375
-	Volume score: 	 3.375
-	Polarity score:	 4
-	Charge score :	 -1
-	Proportion of polar atoms: 	50.000
-	Alpha sphere density : 	2.895
-	Cent. of mass - Alpha Sphere max dist: 	6.688
-	Flexibility : 	0.637
+	Flexibility : 	0.430
 
 Pocket 10 :
 	Score : 	-0.063
@@ -194,7 +194,7 @@ Pocket 10 :
 	Total SASA : 	66.665
 	Polar SASA : 	36.474
 	Apolar SASA : 	30.191
-	Volume : 	188.758
+	Volume : 	190.262
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.982
 	Mean alp. sph. solvent access : 	0.596
@@ -206,16 +206,37 @@ Pocket 10 :
 	Proportion of polar atoms: 	57.143
 	Alpha sphere density : 	1.979
 	Cent. of mass - Alpha Sphere max dist: 	4.058
-	Flexibility : 	0.138
+	Flexibility : 	0.083
 
 Pocket 11 :
+	Score : 	-0.071
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	19
+	Total SASA : 	92.504
+	Polar SASA : 	42.991
+	Apolar SASA : 	49.513
+	Volume : 	327.288
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.953
+	Mean alp. sph. solvent access : 	0.584
+	Apolar alpha sphere proportion : 	0.368
+	Hydrophobicity score:	-8.667
+	Volume score: 	 3.333
+	Polarity score:	 5
+	Charge score :	 -1
+	Proportion of polar atoms: 	52.941
+	Alpha sphere density : 	2.982
+	Cent. of mass - Alpha Sphere max dist: 	7.474
+	Flexibility : 	0.404
+
+Pocket 12 :
 	Score : 	-0.085
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	24
 	Total SASA : 	104.600
 	Polar SASA : 	55.087
 	Apolar SASA : 	49.513
-	Volume : 	314.715
+	Volume : 	318.522
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.941
 	Mean alp. sph. solvent access : 	0.631
@@ -227,26 +248,26 @@ Pocket 11 :
 	Proportion of polar atoms: 	60.870
 	Alpha sphere density : 	3.147
 	Cent. of mass - Alpha Sphere max dist: 	7.973
-	Flexibility : 	0.419
+	Flexibility : 	0.252
 
-Pocket 12 :
-	Score : 	-0.094
+Pocket 13 :
+	Score : 	-0.096
 	Druggability Score : 	0.000
-	Number of Alpha Spheres : 	17
+	Number of Alpha Spheres : 	19
 	Total SASA : 	93.149
 	Polar SASA : 	56.920
 	Apolar SASA : 	36.229
-	Volume : 	258.996
-	Mean local hydrophobic density : 	0.000
-	Mean alpha sphere radius :	3.969
-	Mean alp. sph. solvent access : 	0.469
-	Apolar alpha sphere proportion : 	0.059
+	Volume : 	255.791
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.951
+	Mean alp. sph. solvent access : 	0.497
+	Apolar alpha sphere proportion : 	0.105
 	Hydrophobicity score:	17.125
 	Volume score: 	 4.375
 	Polarity score:	 4
 	Charge score :	 0
 	Proportion of polar atoms: 	46.667
-	Alpha sphere density : 	2.873
+	Alpha sphere density : 	2.780
 	Cent. of mass - Alpha Sphere max dist: 	7.632
-	Flexibility : 	0.681
+	Flexibility : 	0.409
 

tests/reference_output/1UYD_out/1UYD_out.pdb

@@ -1,7 +1,7 @@
 ATOM      1    N GLU A  16       6.484  28.442  39.441  0.00  0.00           N 0
 ATOM      2   CA GLU A  16       7.718  28.546  38.611  0.00  0.00           C 0
 ATOM      3    C GLU A  16       7.625  27.706  37.277  0.00  0.00           C 0
-ATOM      4    O GLU A  16       7.333  26.478  37.304  0.32  2.14           O 0
+ATOM      4    O GLU A  16       7.333  26.478  37.304  0.27  3.21           O 0
 ATOM      5   CB GLU A  16       8.951  28.140  39.474  0.00  0.00           C 0
 ATOM      6   CG GLU A  16       9.355  26.647  39.367  0.00  0.00           C 0
 ATOM      7   CD GLU A  16      10.138  26.088  40.562  0.00  0.00           C 0
@@ -10,7 +10,7 @@ ATOM      9  OE2 GLU A  16       9.875  24.900  40.943  0.00  0.00           O 0
 ATOM     10    N VAL A  17       7.856  28.355  36.137  0.65  4.37           N 0
 ATOM     11   CA VAL A  17       8.110  27.634  34.889  0.00  0.00           C 0
 ATOM     12    C VAL A  17       9.523  27.050  34.954  0.00  0.00           C 0
-ATOM     13    O VAL A  17      10.499  27.794  35.209  0.00  0.00           O 0
+ATOM     13    O VAL A  17      10.499  27.794  35.209  0.46  9.64           O 0
 ATOM     14   CB VAL A  17       7.967  28.556  33.636  0.00  0.00           C 0
 ATOM     15  CG1 VAL A  17       8.234  27.763  32.310  0.00  0.00           C 0
 ATOM     16  CG2 VAL A  17       6.598  29.245  33.609  0.00  0.00           C 0
@@ -553,7 +553,7 @@ ATOM    552   CB LYS A  84      -9.155  30.393  11.757  0.00  0.00           C 0
 ATOM    553   CG LYS A  84      -9.184  29.350  10.611  0.00  0.00           C 0
 ATOM    554   CD LYS A  84     -10.564  29.203   9.966  0.00  0.00           C 0
 ATOM    555   CE LYS A  84     -10.617  28.047   8.968  0.00  0.00           C 0
-ATOM    556   NZ LYS A  84     -10.127  28.466   7.603  0.37  5.47           N 0
+ATOM    556   NZ LYS A  84     -10.127  28.466   7.603  0.00  5.47           N 0
 ATOM    557    N GLN A  85      -8.405  31.761  14.594  0.00  0.00           N 0
 ATOM    558   CA GLN A  85      -8.030  32.999  15.250  0.00  0.00           C 0
 ATOM    559    C GLN A  85      -6.741  32.870  16.076  0.00  0.00           C 0
@@ -580,8 +580,8 @@ ATOM    579   CG ARG A  87      -2.439  29.588  12.535  0.00  0.00           C 0
 ATOM    580   CD ARG A  87      -1.024  29.781  12.216  0.00  0.00           C 0
 ATOM    581   NE ARG A  87      -0.749  31.111  11.680  0.24  2.19           N 0
 ATOM    582   CZ ARG A  87       0.454  31.713  11.756  0.00  0.00           C 0
-ATOM    583  NH1 ARG A  87       1.503  31.117  12.350  0.41  2.19           N 0
-ATOM    584  NH2 ARG A  87       0.614  32.921  11.229  0.09  5.47           N 0
+ATOM    583  NH1 ARG A  87       1.503  31.117  12.350  0.00  0.00           N 0
+ATOM    584  NH2 ARG A  87       0.614  32.921  11.229  0.09  7.66           N 0
 ATOM    585    N THR A  88      -4.532  27.404  15.850  0.00  0.00           N 0
 ATOM    586   CA THR A  88      -4.198  26.208  16.584  0.00  0.00           C 0
 ATOM    587    C THR A  88      -5.071  25.080  16.134  0.00  0.00           C 0
@@ -763,7 +763,7 @@ ATOM    762   NZ LYS A 112      21.607   8.008  25.890  0.00  0.00           N 0
 ATOM    763    N SER A 113      15.789   5.150  22.428  0.44  1.09           N 0
 ATOM    764   CA SER A 113      16.055   4.025  21.526  0.00  0.00           C 0
 ATOM    765    C SER A 113      15.215   4.001  20.212  0.00  0.00           C 0
-ATOM    766    O SER A 113      15.737   3.621  19.139  0.39  1.07           O 0
+ATOM    766    O SER A 113      15.737   3.621  19.139  0.73  1.07           O 0
 ATOM    767   CB SER A 113      15.982   2.688  22.265  0.00  0.00           C 0
 ATOM    768   OG SER A 113      14.665   2.361  22.677  0.00  0.00           O 0
 ATOM    769    N GLY A 114      13.930   4.387  20.291  0.41  2.19           N 0
@@ -805,7 +805,7 @@ ATOM    804   CZ PHE A 118      11.073   9.173  11.107  0.00  0.00           C 0
 ATOM    805    N MET A 119      16.183   6.823  13.145  0.00  0.00           N 0
 ATOM    806   CA MET A 119      17.225   7.512  12.401  0.00  0.00           C 0
 ATOM    807    C MET A 119      18.017   6.580  11.507  0.00  0.00           C 0
-ATOM    808    O MET A 119      18.239   6.888  10.339  0.59  1.07           O 0
+ATOM    808    O MET A 119      18.239   6.888  10.339  0.60  1.07           O 0
 ATOM    809   CB MET A 119      18.047   8.438  13.304  0.00  0.00           C 0
 ATOM    810   CG MET A 119      17.406   9.804  13.159  0.00  0.00           C 0
 ATOM    811   SD MET A 119      17.851  11.068  14.259  0.00  0.00           S 0
@@ -813,11 +813,11 @@ ATOM    812   CE MET A 119      18.896  12.204  13.031  0.00  0.00           C 0
 ATOM    813    N GLU A 120      18.338   5.404  12.039  0.00  0.00           N 0
 ATOM    814   CA GLU A 120      18.941   4.316  11.259  0.00  0.00           C 0
 ATOM    815    C GLU A 120      18.115   3.858  10.068  0.00  0.00           C 0
-ATOM    816    O GLU A 120      18.674   3.618   8.994  0.58  3.21           O 0
+ATOM    816    O GLU A 120      18.674   3.618   8.994  0.53  5.36           O 0
 ATOM    817   CB GLU A 120      19.237   3.104  12.146  0.00  0.00           C 0
 ATOM    818   CG GLU A 120      20.403   3.337  13.075  0.00  0.00           C 0
 ATOM    819   CD GLU A 120      20.806   2.092  13.835  0.00  0.00           C 0
-ATOM    820  OE1 GLU A 120      19.956   1.164  14.024  0.56  9.64           O 0
+ATOM    820  OE1 GLU A 120      19.956   1.164  14.024  0.00  0.00           O 0
 ATOM    821  OE2 GLU A 120      21.989   2.052  14.246  0.00  0.00           O 0
 ATOM    822    N ALA A 121      16.806   3.683  10.268  0.00  0.00           N 0
 ATOM    823   CA ALA A 121      15.901   3.220   9.202  0.00  0.00           C 0
@@ -839,7 +839,7 @@ ATOM    838    O GLN A 123      19.704   3.496   6.666  0.00  0.00           O 0
 ATOM    839   CB GLN A 123      20.591   6.207   6.709  0.00  0.00           C 0
 ATOM    840   CG GLN A 123      20.411   7.331   7.673  0.00  0.00           C 0
 ATOM    841   CD GLN A 123      21.740   7.846   8.175  0.00  0.00           C 0
-ATOM    842  OE1 GLN A 123      22.317   7.267   9.116  0.00  0.00           O 0
+ATOM    842  OE1 GLN A 123      22.317   7.267   9.116  0.48  8.57           O 0
 ATOM    843  NE2 GLN A 123      22.244   8.929   7.550  0.00  0.00           N 0
 ATOM    844    N ALA A 124      18.627   3.896   4.740  0.00  0.00           N 0
 ATOM    845   CA ALA A 124      18.224   2.536   4.426  0.00  0.00           C 0
@@ -1205,7 +1205,7 @@ ATOM   1204  CG2 THR A 171       9.908  26.194  29.049  0.00  0.00           C 0
 ATOM   1205    N VAL A 172       8.206  22.828  31.540  0.00  0.00           N 0
 ATOM   1206   CA VAL A 172       7.108  22.253  32.321  0.00  0.00           C 0
 ATOM   1207    C VAL A 172       6.724  23.222  33.485  0.00  0.00           C 0
-ATOM   1208    O VAL A 172       7.596  23.750  34.183  0.62  1.07           O 0
+ATOM   1208    O VAL A 172       7.596  23.750  34.183  0.76  1.07           O 0
 ATOM   1209   CB VAL A 172       7.529  20.864  32.925  0.00  0.00           C 0
 ATOM   1210  CG1 VAL A 172       6.460  20.343  33.886  0.00  0.00           C 0
 ATOM   1211  CG2 VAL A 172       7.852  19.835  31.806  0.00  0.00           C 0
@@ -1220,17 +1220,17 @@ ATOM   1219   NE ARG A 173       2.147  27.127  31.807  0.63  6.56           N 0
 ATOM   1220   CZ ARG A 173       0.805  27.006  31.932  0.00  0.00           C 0
 ATOM   1221  NH1 ARG A 173       0.238  26.926  33.135  0.44  2.19           N 0
 ATOM   1222  NH2 ARG A 173       0.041  26.956  30.843  0.53  4.37           N 0
-ATOM   1223    N THR A 174       3.248  23.560  36.507  0.56  1.09           N 0
+ATOM   1223    N THR A 174       3.248  23.560  36.507  0.00  0.00           N 0
 ATOM   1224   CA THR A 174       1.898  23.154  36.879  0.00  0.00           C 0
 ATOM   1225    C THR A 174       0.864  24.110  36.206  0.00  0.00           C 0
 ATOM   1226    O THR A 174       1.042  25.347  36.169  0.63  4.29           O 0
 ATOM   1227   CB THR A 174       1.701  23.100  38.398  0.00  0.00           C 0
-ATOM   1228  OG1 THR A 174       1.757  24.429  38.888  0.35  8.57           O 0
+ATOM   1228  OG1 THR A 174       1.757  24.429  38.888  0.61  8.57           O 0
 ATOM   1229  CG2 THR A 174       2.847  22.388  39.106  0.00  0.00           C 0
 ATOM   1230    N ASP A 175      -0.195  23.529  35.643  0.00  0.00           N 0
 ATOM   1231   CA ASP A 175      -1.191  24.317  34.919  0.00  0.00           C 0
 ATOM   1232    C ASP A 175      -2.283  24.776  35.893  0.00  0.00           C 0
-ATOM   1233    O ASP A 175      -2.967  23.964  36.554  0.34  7.50           O 0
+ATOM   1233    O ASP A 175      -2.967  23.964  36.554  0.52  6.43           O 0
 ATOM   1234   CB ASP A 175      -1.776  23.521  33.748  0.00  0.00           C 0
 ATOM   1235   CG ASP A 175      -2.626  24.378  32.797  0.00  0.00           C 0
 ATOM   1236  OD1 ASP A 175      -2.222  25.511  32.451  0.50  2.14           O 0
@@ -1238,18 +1238,18 @@ ATOM   1237  OD2 ASP A 175      -3.713  23.987  32.328  0.00  0.00           O 0
 ATOM   1238    N THR A 176      -2.425  26.091  35.987  0.00  0.00           N 0
 ATOM   1239   CA THR A 176      -3.520  26.665  36.759  0.00  0.00           C 0
 ATOM   1240    C THR A 176      -4.727  27.064  35.861  0.00  0.00           C 0
-ATOM   1241    O THR A 176      -5.738  27.556  36.386  0.00  0.00           O 0
+ATOM   1241    O THR A 176      -5.738  27.556  36.386  0.54  9.64           O 0
 ATOM   1242   CB THR A 176      -3.032  27.850  37.667  0.00  0.00           C 0
 ATOM   1243  OG1 THR A 176      -2.494  28.900  36.846  0.31  7.50           O 0
 ATOM   1244  CG2 THR A 176      -1.862  27.427  38.592  0.00  0.00           C 0
 ATOM   1245    N GLY A 177      -4.628  26.837  34.541  0.28  1.09           N 0
 ATOM   1246   CA GLY A 177      -5.755  26.984  33.627  0.00  0.00           C 0
 ATOM   1247    C GLY A 177      -6.997  26.168  34.002  0.00  0.00           C 0
-ATOM   1248    O GLY A 177      -7.087  25.609  35.109  0.40  4.29           O 0
+ATOM   1248    O GLY A 177      -7.087  25.609  35.109  0.58  3.21           O 0
 ATOM   1249    N GLU A 178      -7.967  26.111  33.085  0.00  0.00           N 0
 ATOM   1250   CA GLU A 178      -9.157  25.265  33.255  0.00  0.00           C 0
 ATOM   1251    C GLU A 178      -8.771  23.873  33.873  0.00  0.00           C 0
-ATOM   1252    O GLU A 178      -7.954  23.140  33.285  0.64  2.14           O 0
+ATOM   1252    O GLU A 178      -7.954  23.140  33.285  0.66  2.14           O 0
 ATOM   1253   CB GLU A 178      -9.877  25.079  31.919  0.00  0.00           C 0
 ATOM   1254   CG GLU A 178     -11.190  24.323  32.022  0.00  0.00           C 0
 ATOM   1255   CD GLU A 178     -12.297  25.159  32.633  0.00  0.00           C 0
@@ -1424,7 +1424,7 @@ ATOM   1423    O GLU A 199     -10.133  21.257   7.662  0.00  0.00           O 0
 ATOM   1424   CB GLU A 199      -9.608  23.763   5.933  0.00  0.00           C 0
 ATOM   1425   CG GLU A 199      -9.537  25.154   5.323  0.00  0.00           C 0
 ATOM   1426   CD GLU A 199      -8.730  25.094   4.024  0.00  0.00           C 0
-ATOM   1427  OE1 GLU A 199      -9.058  24.242   3.117  0.35  5.36           O 0
+ATOM   1427  OE1 GLU A 199      -9.058  24.242   3.117  0.00  0.00           O 0
 ATOM   1428  OE2 GLU A 199      -7.732  25.865   3.915  0.00  0.00           O 0
 ATOM   1429    N GLU A 200     -12.069  22.448   7.649  0.00  0.00           N 0
 ATOM   1430   CA GLU A 200     -12.880  21.303   8.052  0.00  0.00           C 0
@@ -1631,7 +1631,7 @@ ATOM   1631    O GLU A 223     -17.365  27.664  12.274  0.00  0.00           O 0
 ATOM   1632   CB GLU A 223     -14.450  27.765  13.143  0.00  0.00           C 0
 ATOM   1633   CG GLU A 223     -13.156  27.273  13.733  0.00  0.00           C 0
 ATOM   1634   CD GLU A 223     -12.051  28.292  13.569  0.00  0.00           C 0
-ATOM   1635  OE1 GLU A 223     -12.191  29.432  14.068  0.69  6.43           O 0
+ATOM   1635  OE1 GLU A 223     -12.191  29.432  14.068  0.68  7.50           O 0
 ATOM   1636  OE2 GLU A 223     -11.062  27.934  12.915  0.00  0.00           O 0
 ATOM   1637    N LYS A 224     -17.505  28.648  14.271  0.00  0.00           N 0
 ATOM   1638   CA LYS A 224     -16.885  29.440  15.328  0.00  0.00           C 0
@@ -1645,55 +1645,55 @@ ATOM   1645   NZ LYS A 224     -17.737  32.741  10.567  0.00  0.00           N 0
 HETATM    1 APOL STP C   1       7.785   6.838  24.439  0.00  0.00          Ve  
 HETATM    2 APOL STP C   1       5.774   9.979  23.751  0.00  0.00          Ve  
 HETATM    3 APOL STP C   1       4.349   9.667  23.812  0.00  0.00          Ve  
-HETATM    4 APOL STP C   1      -1.508  10.969  24.938  0.00  0.00          Ve  
-HETATM    5 APOL STP C   1       6.817   8.930  24.068  0.00  0.00          Ve  
+HETATM 2203  POL STP C   1      -1.508  10.969  24.938  0.00  0.00          Ve  
+HETATM 2695  POL STP C   1       6.817   8.930  24.068  0.00  0.00          Ve  
 HETATM    6 APOL STP C   1       5.854   9.885  23.690  0.00  0.00          Ve  
-HETATM    7 APOL STP C   1       4.623   9.304  23.580  0.00  0.00          Ve  
-HETATM    8 APOL STP C   1       7.615   6.878  24.306  0.00  0.00          Ve  
-HETATM    9 APOL STP C   1       7.083   7.215  24.474  0.00  0.00          Ve  
-HETATM   10 APOL STP C   1       3.114   6.284  29.706  0.00  0.00          Ve  
+HETATM 2695  POL STP C   1       4.623   9.304  23.580  0.00  0.00          Ve  
+HETATM 2695  POL STP C   1       7.615   6.878  24.306  0.00  0.00          Ve  
+HETATM 2695  POL STP C   1       7.083   7.215  24.474  0.00  0.00          Ve  
+HETATM 2721  POL STP C   1       3.114   6.284  29.706  0.00  0.00          Ve  
 HETATM   11 APOL STP C   1       6.727   6.176  30.320  0.00  0.00          Ve  
-HETATM   12 APOL STP C   1       6.590   4.208  31.665  0.00  0.00          Ve  
-HETATM   13 APOL STP C   1       4.754   4.946  29.971  0.00  0.00          Ve  
-HETATM   14 APOL STP C   1      13.912  14.330  27.259  0.00  0.00          Ve  
-HETATM   15 APOL STP C   1      16.020  12.287  30.152  0.00  0.00          Ve  
-HETATM   16 APOL STP C   1      16.084  11.656  30.325  0.00  0.00          Ve  
-HETATM   17 APOL STP C   1       8.887  11.600  24.709  0.00  0.00          Ve  
+HETATM 2721  POL STP C   1       6.590   4.208  31.665  0.00  0.00          Ve  
+HETATM 2723  POL STP C   1       4.754   4.946  29.971  0.00  0.00          Ve  
+HETATM 2738  POL STP C   1      13.912  14.330  27.259  0.00  0.00          Ve  
+HETATM 2738  POL STP C   1      16.020  12.287  30.152  0.00  0.00          Ve  
+HETATM 2738  POL STP C   1      16.084  11.656  30.325  0.00  0.00          Ve  
+HETATM 2790  POL STP C   1       8.887  11.600  24.709  0.00  0.00          Ve  
 HETATM   18 APOL STP C   1      -0.732  13.051  21.091  0.00  0.00          Ve  
 HETATM   19 APOL STP C   1      -0.386  13.047  21.225  0.00  0.00          Ve  
-HETATM   20 APOL STP C   1      -1.558  11.234  24.081  0.00  0.00          Ve  
-HETATM   21 APOL STP C   1      -1.802  11.344  23.665  0.00  0.00          Ve  
-HETATM   22 APOL STP C   1      -1.699  12.544  22.872  0.00  0.00          Ve  
-HETATM   23 APOL STP C   1      -1.739  12.698  22.218  0.00  0.00          Ve  
-HETATM   24 APOL STP C   1      -1.975  11.852  23.036  0.00  0.00          Ve  
+HETATM 2839  POL STP C   1      -1.558  11.234  24.081  0.00  0.00          Ve  
+HETATM 2841  POL STP C   1      -1.802  11.344  23.665  0.00  0.00          Ve  
+HETATM 3007  POL STP C   1      -1.699  12.544  22.872  0.00  0.00          Ve  
+HETATM 3007  POL STP C   1      -1.739  12.698  22.218  0.00  0.00          Ve  
+HETATM 3007  POL STP C   1      -1.975  11.852  23.036  0.00  0.00          Ve  
 HETATM   25 APOL STP C   1       0.563  12.588  23.454  0.00  0.00          Ve  
-HETATM   26 APOL STP C   1      -0.950  10.812  25.145  0.00  0.00          Ve  
+HETATM 3783  POL STP C   1      -0.950  10.812  25.145  0.00  0.00          Ve  
 HETATM   27 APOL STP C   1       0.277  13.297  21.360  0.00  0.00          Ve  
 HETATM   28 APOL STP C   1       0.736  12.678  23.430  0.00  0.00          Ve  
-HETATM   29 APOL STP C   1       0.753   6.534  22.979  0.00  0.00          Ve  
-HETATM   30 APOL STP C   1       0.730   6.506  22.916  0.00  0.00          Ve  
-HETATM   31 APOL STP C   1       1.477   7.589  24.040  0.00  0.00          Ve  
-HETATM   32 APOL STP C   1       0.889   7.396  23.257  0.00  0.00          Ve  
+HETATM 3822  POL STP C   1       0.753   6.534  22.979  0.00  0.00          Ve  
+HETATM 3822  POL STP C   1       0.730   6.506  22.916  0.00  0.00          Ve  
+HETATM 3822  POL STP C   1       1.477   7.589  24.040  0.00  0.00          Ve  
+HETATM 3822  POL STP C   1       0.889   7.396  23.257  0.00  0.00          Ve  
 HETATM   33 APOL STP C   1      11.631  14.628  26.606  0.00  0.00          Ve  
 HETATM   34 APOL STP C   1      12.945  13.969  25.376  0.00  0.00          Ve  
 HETATM   35 APOL STP C   1      13.913  14.874  26.698  0.00  0.00          Ve  
 HETATM   36 APOL STP C   1      13.708  14.441  26.773  0.00  0.00          Ve  
-HETATM   37 APOL STP C   1      13.827  14.182  26.170  0.00  0.00          Ve  
+HETATM 4283  POL STP C   1      13.827  14.182  26.170  0.00  0.00          Ve  
 HETATM   38 APOL STP C   1      13.822  14.141  26.067  0.00  0.00          Ve  
-HETATM   39 APOL STP C   1      13.857  14.157  26.064  0.00  0.00          Ve  
+HETATM 4283  POL STP C   1      13.857  14.157  26.064  0.00  0.00          Ve  
 HETATM   40 APOL STP C   1       7.381  10.470  21.326  0.00  0.00          Ve  
-HETATM   41 APOL STP C   1       7.972  11.066  23.806  0.00  0.00          Ve  
-HETATM   42 APOL STP C   1       8.295  11.024  23.750  0.00  0.00          Ve  
-HETATM   43 APOL STP C   1       7.478  10.337  23.282  0.00  0.00          Ve  
-HETATM   44 APOL STP C   1       7.280  10.418  23.358  0.00  0.00          Ve  
+HETATM 4872  POL STP C   1       7.972  11.066  23.806  0.00  0.00          Ve  
+HETATM 4872  POL STP C   1       8.295  11.024  23.750  0.00  0.00          Ve  
+HETATM 4872  POL STP C   1       7.478  10.337  23.282  0.00  0.00          Ve  
+HETATM 4872  POL STP C   1       7.280  10.418  23.358  0.00  0.00          Ve  
 HETATM   45 APOL STP C   1       7.156  10.473  23.341  0.00  0.00          Ve  
-HETATM   46 APOL STP C   1       8.724   6.926  23.719  0.00  0.00          Ve  
-HETATM   47 APOL STP C   1      16.251  10.521  30.258  0.00  0.00          Ve  
-HETATM   48 APOL STP C   1      16.016  10.444  30.032  0.00  0.00          Ve  
-HETATM   49 APOL STP C   1      16.674  10.615  30.805  0.00  0.00          Ve  
-HETATM   50 APOL STP C   1      16.395   8.912  33.152  0.00  0.00          Ve  
-HETATM   51 APOL STP C   1      15.810   9.633  32.174  0.00  0.00          Ve  
-HETATM   52 APOL STP C   1      17.109  10.453  31.017  0.00  0.00          Ve  
+HETATM 4886  POL STP C   1       8.724   6.926  23.719  0.00  0.00          Ve  
+HETATM 5071  POL STP C   1      16.251  10.521  30.258  0.00  0.00          Ve  
+HETATM 5071  POL STP C   1      16.016  10.444  30.032  0.00  0.00          Ve  
+HETATM 5071  POL STP C   1      16.674  10.615  30.805  0.00  0.00          Ve  
+HETATM 5071  POL STP C   1      16.395   8.912  33.152  0.00  0.00          Ve  
+HETATM 5071  POL STP C   1      15.810   9.633  32.174  0.00  0.00          Ve  
+HETATM 5072  POL STP C   1      17.109  10.453  31.017  0.00  0.00          Ve  
 HETATM   53 APOL STP C   1       1.424  11.066  24.202  0.00  0.00          Ve  
 HETATM   54 APOL STP C   1       2.034   9.777  24.491  0.00  0.00          Ve  
 HETATM   55 APOL STP C   1       3.535  10.777  24.109  0.00  0.00          Ve  
@@ -1705,31 +1705,31 @@ HETATM   60 APOL STP C   1       1.463  14.193  23.946  0.00  0.00          Ve
 HETATM   61 APOL STP C   1       3.864  14.031  24.821  0.00  0.00          Ve  
 HETATM   62 APOL STP C   1       0.172  12.525  23.583  0.00  0.00          Ve  
 HETATM   63 APOL STP C   1      -1.579  12.507  23.063  0.00  0.00          Ve  
-HETATM   64 APOL STP C   1      -1.912  11.626  24.998  0.00  0.00          Ve  
-HETATM   65 APOL STP C   1      -0.989  11.052  24.874  0.00  0.00          Ve  
+HETATM 5253  POL STP C   1      -1.912  11.626  24.998  0.00  0.00          Ve  
+HETATM 5253  POL STP C   1      -0.989  11.052  24.874  0.00  0.00          Ve  
 HETATM   66 APOL STP C   1      -0.879  11.128  24.694  0.00  0.00          Ve  
-HETATM   67 APOL STP C   1      -1.354  11.116  24.781  0.00  0.00          Ve  
-HETATM   68 APOL STP C   1      -1.288  11.285  24.407  0.00  0.00          Ve  
-HETATM   69 APOL STP C   1      -1.482  10.096  27.670  0.00  0.00          Ve  
-HETATM   70 APOL STP C   1       1.783   6.931  28.759  0.00  0.00          Ve  
-HETATM   71 APOL STP C   1       1.714   6.908  28.614  0.00  0.00          Ve  
-HETATM   72 APOL STP C   1      15.581  12.421  30.019  0.00  0.00          Ve  
-HETATM   73 APOL STP C   1      15.750  12.621  30.007  0.00  0.00          Ve  
-HETATM   74 APOL STP C   1      16.662  14.424  30.372  0.00  0.00          Ve  
-HETATM   75 APOL STP C   1      14.219  12.652  28.837  0.00  0.00          Ve  
-HETATM   76 APOL STP C   1      14.087  14.330  27.578  0.00  0.00          Ve  
-HETATM   77 APOL STP C   1      14.631  14.244  28.046  0.00  0.00          Ve  
-HETATM   78 APOL STP C   1      13.939  14.281  27.501  0.00  0.00          Ve  
-HETATM   79 APOL STP C   1      14.756  14.840  28.269  0.00  0.00          Ve  
-HETATM   80 APOL STP C   1      15.299  14.577  28.703  0.00  0.00          Ve  
-HETATM   81 APOL STP C   1      16.054  10.122  29.656  0.00  0.00          Ve  
-HETATM   82 APOL STP C   1      16.456   9.802  29.471  0.00  0.00          Ve  
+HETATM 5253  POL STP C   1      -1.354  11.116  24.781  0.00  0.00          Ve  
+HETATM 5253  POL STP C   1      -1.288  11.285  24.407  0.00  0.00          Ve  
+HETATM 5731  POL STP C   1      -1.482  10.096  27.670  0.00  0.00          Ve  
+HETATM 5734  POL STP C   1       1.783   6.931  28.759  0.00  0.00          Ve  
+HETATM 5734  POL STP C   1       1.714   6.908  28.614  0.00  0.00          Ve  
+HETATM 6139  POL STP C   1      15.581  12.421  30.019  0.00  0.00          Ve  
+HETATM 6139  POL STP C   1      15.750  12.621  30.007  0.00  0.00          Ve  
+HETATM 6139  POL STP C   1      16.662  14.424  30.372  0.00  0.00          Ve  
+HETATM 6140  POL STP C   1      14.219  12.652  28.837  0.00  0.00          Ve  
+HETATM 6141  POL STP C   1      14.087  14.330  27.578  0.00  0.00          Ve  
+HETATM 6141  POL STP C   1      14.631  14.244  28.046  0.00  0.00          Ve  
+HETATM 6141  POL STP C   1      13.939  14.281  27.501  0.00  0.00          Ve  
+HETATM 6145  POL STP C   1      14.756  14.840  28.269  0.00  0.00          Ve  
+HETATM 6145  POL STP C   1      15.299  14.577  28.703  0.00  0.00          Ve  
+HETATM 6388  POL STP C   1      16.054  10.122  29.656  0.00  0.00          Ve  
+HETATM 6390  POL STP C   1      16.456   9.802  29.471  0.00  0.00          Ve  
 HETATM   83 APOL STP C   1      16.445   9.833  29.519  0.00  0.00          Ve  
 HETATM   84 APOL STP C   1      16.465   9.812  29.510  0.00  0.00          Ve  
 HETATM   85 APOL STP C   1       1.618   7.073  28.344  0.00  0.00          Ve  
 HETATM   86 APOL STP C   1      -0.008   8.421  27.485  0.00  0.00          Ve  
-HETATM   87 APOL STP C   1       1.812   7.179  28.734  0.00  0.00          Ve  
-HETATM   88 APOL STP C   1      -1.242  10.098  27.540  0.00  0.00          Ve  
+HETATM 6500  POL STP C   1       1.812   7.179  28.734  0.00  0.00          Ve  
+HETATM 6500  POL STP C   1      -1.242  10.098  27.540  0.00  0.00          Ve  
 HETATM   89 APOL STP C   1      -0.795  10.331  26.577  0.00  0.00          Ve  
 HETATM   90 APOL STP C   1      -0.351  10.061  26.183  0.00  0.00          Ve  
 HETATM   91 APOL STP C   1       5.216  14.534  25.639  0.00  0.00          Ve  
@@ -1760,263 +1760,321 @@ HETATM  115 APOL STP C   1       1.551  14.776  24.130  0.00  0.00          Ve
 HETATM  116 APOL STP C   1       1.848  14.707  24.298  0.00  0.00          Ve  
 HETATM  117 APOL STP C   1       4.926  15.350  25.662  0.00  0.00          Ve  
 HETATM  118 APOL STP C   1       6.620  14.280  27.401  0.00  0.00          Ve  
-HETATM  119 APOL STP C   1      10.896  15.156  26.541  0.00  0.00          Ve  
-HETATM  120 APOL STP C   1      10.721  14.194  26.674  0.00  0.00          Ve  
-HETATM  121 APOL STP C   1      11.490  13.931  27.857  0.00  0.00          Ve  
-HETATM  122 APOL STP C   1      11.366  14.623  26.733  0.00  0.00          Ve  
-HETATM  123 APOL STP C   1       9.184  13.635  26.450  0.00  0.00          Ve  
-HETATM  124 APOL STP C   1      11.789  14.458  27.414  0.00  0.00          Ve  
-HETATM  125 APOL STP C   1      11.772  14.543  27.511  0.00  0.00          Ve  
-HETATM  126 APOL STP C   1      10.363  15.394  26.388  0.00  0.00          Ve  
-HETATM  127 APOL STP C   1      10.557  15.655  26.584  0.00  0.00          Ve  
-HETATM  128 APOL STP C   1       6.897  14.234  25.492  0.00  0.00          Ve  
-HETATM  129 APOL STP C   1       7.349  14.139  25.864  0.00  0.00          Ve  
-HETATM  130 APOL STP C   1       7.403  14.166  26.142  0.00  0.00          Ve  
-HETATM  131 APOL STP C   1       7.664  14.151  26.041  0.00  0.00          Ve  
-HETATM  132 APOL STP C   1       6.658  14.520  26.744  0.00  0.00          Ve  
+HETATM10334  POL STP C   1      10.896  15.156  26.541  0.00  0.00          Ve  
+HETATM10334  POL STP C   1      10.721  14.194  26.674  0.00  0.00          Ve  
+HETATM10334  POL STP C   1      11.490  13.931  27.857  0.00  0.00          Ve  
+HETATM10336  POL STP C   1      11.366  14.623  26.733  0.00  0.00          Ve  
+HETATM10336  POL STP C   1       9.184  13.635  26.450  0.00  0.00          Ve  
+HETATM10337  POL STP C   1      11.789  14.458  27.414  0.00  0.00          Ve  
+HETATM10337  POL STP C   1      11.772  14.543  27.511  0.00  0.00          Ve  
+HETATM10657  POL STP C   1      10.363  15.394  26.388  0.00  0.00          Ve  
+HETATM10658  POL STP C   1      10.557  15.655  26.584  0.00  0.00          Ve  
+HETATM10659  POL STP C   1       6.897  14.234  25.492  0.00  0.00          Ve  
+HETATM10659  POL STP C   1       7.349  14.139  25.864  0.00  0.00          Ve  
+HETATM10659  POL STP C   1       7.403  14.166  26.142  0.00  0.00          Ve  
+HETATM10659  POL STP C   1       7.664  14.151  26.041  0.00  0.00          Ve  
+HETATM10659  POL STP C   1       6.658  14.520  26.744  0.00  0.00          Ve  
 HETATM  133 APOL STP C   1       5.424  15.941  26.511  0.00  0.00          Ve  
 HETATM  134 APOL STP C   1       5.487  15.835  26.436  0.00  0.00          Ve  
 HETATM  135 APOL STP C   1       7.227  14.775  25.129  0.00  0.00          Ve  
-HETATM  136 APOL STP C   1       7.217  14.760  25.143  0.00  0.00          Ve  
-HETATM  137 APOL STP C   1       7.249  14.785  25.136  0.00  0.00          Ve  
+HETATM11169  POL STP C   1       7.217  14.760  25.143  0.00  0.00          Ve  
+HETATM11169  POL STP C   1       7.249  14.785  25.136  0.00  0.00          Ve  
 HETATM  138 APOL STP C   1       5.482  15.772  26.370  0.00  0.00          Ve  
 HETATM  139 APOL STP C   1       5.091  15.244  25.653  0.00  0.00          Ve  
 HETATM  140 APOL STP C   1       5.067  15.273  25.656  0.00  0.00          Ve  
 HETATM  141 APOL STP C   1       5.814  14.647  25.758  0.00  0.00          Ve  
 HETATM  142 APOL STP C   1       5.861  14.632  25.749  0.00  0.00          Ve  
 HETATM  143 APOL STP C   1       5.829  14.647  25.770  0.00  0.00          Ve  
-HETATM    1 APOL STP C   2      -3.991   5.938  38.283  0.00  0.00          Ve  
-HETATM    2 APOL STP C   2      -3.568   5.524  37.917  0.00  0.00          Ve  
+HETATM 2141  POL STP C   2      -3.991   5.938  38.283  0.00  0.00          Ve  
+HETATM 2690  POL STP C   2      -3.568   5.524  37.917  0.00  0.00          Ve  
 HETATM    3 APOL STP C   2      -3.931   5.923  38.105  0.00  0.00          Ve  
 HETATM    4 APOL STP C   2      -4.180   5.886  37.623  0.00  0.00          Ve  
-HETATM    5 APOL STP C   2      -4.420   5.879  37.503  0.00  0.00          Ve  
-HETATM    6 APOL STP C   2      -4.377   6.059  37.115  0.00  0.00          Ve  
-HETATM    7 APOL STP C   2      -7.842   6.647  41.105  0.00  0.00          Ve  
-HETATM    8 APOL STP C   2      -7.652   7.448  41.790  0.00  0.00          Ve  
-HETATM    9 APOL STP C   2      -4.666   6.404  35.706  0.00  0.00          Ve  
+HETATM 2692  POL STP C   2      -4.420   5.879  37.503  0.00  0.00          Ve  
+HETATM 2692  POL STP C   2      -4.377   6.059  37.115  0.00  0.00          Ve  
+HETATM 2692  POL STP C   2      -7.842   6.647  41.105  0.00  0.00          Ve  
+HETATM 2692  POL STP C   2      -7.652   7.448  41.790  0.00  0.00          Ve  
+HETATM 3550  POL STP C   2      -4.666   6.404  35.706  0.00  0.00          Ve  
 HETATM   10 APOL STP C   2      -5.556   6.104  39.988  0.00  0.00          Ve  
-HETATM   11 APOL STP C   2      -6.919   6.642  41.684  0.00  0.00          Ve  
-HETATM   12 APOL STP C   2      -6.980   6.668  41.645  0.00  0.00          Ve  
-HETATM   13 APOL STP C   2      -6.526   5.836  41.929  0.00  0.00          Ve  
-HETATM   14 APOL STP C   2      -6.378   5.700  41.831  0.00  0.00          Ve  
-HETATM   15 APOL STP C   2      -7.822   6.625  41.102  0.00  0.00          Ve  
-HETATM   16 APOL STP C   2      -7.825   7.749  41.660  0.00  0.00          Ve  
-HETATM   17 APOL STP C   2      -8.100   8.674  42.098  0.00  0.00          Ve  
-HETATM   18 APOL STP C   2      -8.659   9.530  41.927  0.00  0.00          Ve  
-HETATM   19 APOL STP C   2      -8.737  12.631  40.804  0.00  0.00          Ve  
-HETATM   20 APOL STP C   2     -11.049  12.429  41.049  0.00  0.00          Ve  
-HETATM   21 APOL STP C   2     -11.267  12.028  41.036  0.00  0.00          Ve  
-HETATM   22 APOL STP C   2     -10.890  12.386  41.380  0.00  0.00          Ve  
-HETATM   23 APOL STP C   2      -9.951  10.626  40.848  0.00  0.00          Ve  
-HETATM   24 APOL STP C   2     -10.041   9.901  40.431  0.00  0.00          Ve  
-HETATM    1 APOL STP C   3     -13.394   8.035  11.699  0.00  0.00          Ve  
-HETATM    2 APOL STP C   3     -13.866   8.149  12.756  0.00  0.00          Ve  
-HETATM    3 APOL STP C   3     -13.235   6.985  13.878  0.00  0.00          Ve  
-HETATM    4 APOL STP C   3     -13.396  13.376  12.554  0.00  0.00          Ve  
-HETATM    5 APOL STP C   3     -14.773   7.681  13.727  0.00  0.00          Ve  
-HETATM    6 APOL STP C   3     -14.552   8.323  12.854  0.00  0.00          Ve  
-HETATM    7 APOL STP C   3     -14.690   7.717  13.852  0.00  0.00          Ve  
-HETATM    8 APOL STP C   3     -13.947  10.342   9.126  0.00  0.00          Ve  
-HETATM    9 APOL STP C   3     -12.889   8.488   9.768  0.00  0.00          Ve  
-HETATM   10 APOL STP C   3     -14.059  10.991   9.026  0.00  0.00          Ve  
-HETATM   11 APOL STP C   3     -12.850  13.648  12.578  0.00  0.00          Ve  
-HETATM   12 APOL STP C   3     -12.635  13.830  12.726  0.00  0.00          Ve  
-HETATM   13 APOL STP C   3     -15.321  12.050   6.421  0.00  0.00          Ve  
-HETATM   14 APOL STP C   3     -15.149  12.299   5.990  0.00  0.00          Ve  
-HETATM   15 APOL STP C   3     -14.138  13.128   4.148  0.00  0.00          Ve  
-HETATM   16 APOL STP C   3     -13.842  12.966   4.202  0.00  0.00          Ve  
-HETATM   17 APOL STP C   3     -14.202  12.998   4.431  0.00  0.00          Ve  
-HETATM   18 APOL STP C   3     -15.071  12.945  11.123  0.00  0.00          Ve  
-HETATM   19 APOL STP C   3     -15.181  12.284   7.101  0.00  0.00          Ve  
-HETATM   20 APOL STP C   3     -14.069  13.525  10.889  0.00  0.00          Ve  
-HETATM   21 APOL STP C   3     -14.486  12.345   9.698  0.00  0.00          Ve  
-HETATM   22 APOL STP C   3     -15.581  11.691   7.702  0.00  0.00          Ve  
-HETATM   23 APOL STP C   3     -13.744  12.589   9.720  0.00  0.00          Ve  
-HETATM   24 APOL STP C   3     -13.903  13.601  10.918  0.00  0.00          Ve  
-HETATM   25 APOL STP C   3     -13.004  13.765  11.916  0.00  0.00          Ve  
-HETATM   26 APOL STP C   3     -12.804  14.399  11.014  0.00  0.00          Ve  
-HETATM   27 APOL STP C   3     -14.691   7.701  13.857  0.00  0.00          Ve  
-HETATM   28 APOL STP C   3     -14.353   7.367  13.918  0.00  0.00          Ve  
-HETATM   29 APOL STP C   3     -14.766   7.663  13.746  0.00  0.00          Ve  
-HETATM   30 APOL STP C   3     -13.822  14.302  10.714  0.00  0.00          Ve  
-HETATM   31 APOL STP C   3     -12.793  14.411  11.014  0.00  0.00          Ve  
-HETATM    1 APOL STP C   4      16.547  23.639  13.890  0.00  0.00          Ve  
-HETATM    2 APOL STP C   4      16.092  23.630  14.033  0.00  0.00          Ve  
-HETATM    3 APOL STP C   4      15.859  23.404  14.170  0.00  0.00          Ve  
-HETATM    4 APOL STP C   4      15.557  23.398  14.576  0.00  0.00          Ve  
-HETATM    5 APOL STP C   4      16.011  22.871  13.482  0.00  0.00          Ve  
-HETATM    6 APOL STP C   4      15.928  23.207  13.765  0.00  0.00          Ve  
-HETATM    7 APOL STP C   4      17.691  22.245  18.072  0.00  0.00          Ve  
-HETATM    8 APOL STP C   4      19.529  21.954  18.755  0.00  0.00          Ve  
-HETATM    9 APOL STP C   4      15.011  22.229  15.825  0.00  0.00          Ve  
-HETATM   10 APOL STP C   4      15.135  20.552  18.741  0.00  0.00          Ve  
-HETATM   11 APOL STP C   4      19.253  21.725  18.788  0.00  0.00          Ve  
-HETATM   12 APOL STP C   4      17.650  21.048  18.652  0.00  0.00          Ve  
-HETATM   13 APOL STP C   4      16.195  21.162  18.168  0.00  0.00          Ve  
-HETATM   14 APOL STP C   4      15.398  20.983  17.666  0.00  0.00          Ve  
-HETATM   15 APOL STP C   4      15.138  20.557  18.735  0.00  0.00          Ve  
-HETATM   16 APOL STP C   4      16.943  21.983  17.981  0.00  0.00          Ve  
-HETATM   17 APOL STP C   4      15.182  22.714  15.737  0.00  0.00          Ve  
-HETATM   18 APOL STP C   4      15.741  24.064  14.855  0.00  0.00          Ve  
-HETATM   19 APOL STP C   4      15.109  20.220  19.179  0.00  0.00          Ve  
-HETATM    1 APOL STP C   5      20.605   6.618  21.102  0.00  0.00          Ve  
-HETATM    2 APOL STP C   5      19.082   9.114  16.906  0.00  0.00          Ve  
-HETATM    3 APOL STP C   5      19.211   8.868  16.477  0.00  0.00          Ve  
-HETATM    4 APOL STP C   5      19.141   9.065  16.855  0.00  0.00          Ve  
-HETATM    5 APOL STP C   5      20.411   8.950  16.497  0.00  0.00          Ve  
-HETATM    6 APOL STP C   5      21.278   7.286  15.271  0.00  0.00          Ve  
-HETATM    7 APOL STP C   5      21.737   8.273  15.966  0.00  0.00          Ve  
-HETATM    8 APOL STP C   5      19.545   9.253  17.348  0.00  0.00          Ve  
-HETATM    9 APOL STP C   5      19.605   9.305  17.253  0.00  0.00          Ve  
-HETATM   10 APOL STP C   5      19.361   9.202  17.087  0.00  0.00          Ve  
-HETATM   11 APOL STP C   5      21.005   6.678  13.902  0.00  0.00          Ve  
-HETATM   12 APOL STP C   5      21.887   7.048  14.721  0.00  0.00          Ve  
-HETATM   13 APOL STP C   5      21.576   8.462  17.094  0.00  0.00          Ve  
-HETATM   14 APOL STP C   5      21.237   8.164  17.688  0.00  0.00          Ve  
-HETATM   15 APOL STP C   5      19.823   9.314  17.205  0.00  0.00          Ve  
-HETATM   16 APOL STP C   5      19.842   9.288  17.195  0.00  0.00          Ve  
-HETATM   17 APOL STP C   5      19.813   9.293  17.207  0.00  0.00          Ve  
-HETATM   18 APOL STP C   5      23.114   7.517  18.754  0.00  0.00          Ve  
-HETATM   19 APOL STP C   5      23.216   7.267  19.612  0.00  0.00          Ve  
-HETATM   20 APOL STP C   5      21.455   7.159  19.578  0.00  0.00          Ve  
-HETATM   21 APOL STP C   5      19.601   8.988  17.728  0.00  0.00          Ve  
-HETATM   22 APOL STP C   5      20.637   6.657  21.076  0.00  0.00          Ve  
-HETATM   23 APOL STP C   5      21.991   6.742  21.095  0.00  0.00          Ve  
-HETATM   24 APOL STP C   5      20.614   6.661  21.080  0.00  0.00          Ve  
-HETATM   25 APOL STP C   5      20.578   6.679  21.067  0.00  0.00          Ve  
-HETATM   26 APOL STP C   5      20.573   6.576  21.121  0.00  0.00          Ve  
-HETATM   27 APOL STP C   5      19.279  10.317  17.326  0.00  0.00          Ve  
-HETATM   28 APOL STP C   5      19.218  10.275  17.340  0.00  0.00          Ve  
-HETATM    1 APOL STP C   6       0.606  30.613  17.291  0.00  0.00          Ve  
-HETATM    2 APOL STP C   6       0.349  29.933  16.102  0.00  0.00          Ve  
-HETATM    3 APOL STP C   6       0.398  29.825  16.006  0.00  0.00          Ve  
-HETATM    4 APOL STP C   6       0.310  30.058  15.886  0.00  0.00          Ve  
-HETATM    5 APOL STP C   6      -2.704  33.369  14.954  0.00  0.00          Ve  
-HETATM    6 APOL STP C   6       0.267  30.094  15.812  0.00  0.00          Ve  
-HETATM    7 APOL STP C   6       0.297  30.167  15.803  0.00  0.00          Ve  
-HETATM    8 APOL STP C   6      -1.603  34.311  14.914  0.00  0.00          Ve  
-HETATM    9 APOL STP C   6      -1.370  34.089  14.976  0.00  0.00          Ve  
-HETATM   10 APOL STP C   6       0.328  30.306  15.653  0.00  0.00          Ve  
-HETATM   11 APOL STP C   6       0.297  30.561  15.738  0.00  0.00          Ve  
-HETATM   12 APOL STP C   6      -0.300  32.461  15.359  0.00  0.00          Ve  
-HETATM   13 APOL STP C   6      -1.581  33.922  14.529  0.00  0.00          Ve  
-HETATM   14 APOL STP C   6      -2.185  34.279  14.137  0.00  0.00          Ve  
-HETATM   15 APOL STP C   6      -3.286  34.022  12.999  0.00  0.00          Ve  
-HETATM   16 APOL STP C   6      -3.344  34.741  12.491  0.00  0.00          Ve  
-HETATM    1 APOL STP C   7      -6.625  24.421  30.057  0.00  0.00          Ve  
-HETATM    2 APOL STP C   7      -5.799  26.309  29.404  0.00  0.00          Ve  
-HETATM    3 APOL STP C   7      -8.308  22.685  29.725  0.00  0.00          Ve  
-HETATM    4 APOL STP C   7      -7.037  21.813  30.245  0.00  0.00          Ve  
-HETATM    5 APOL STP C   7     -10.258  22.548  28.497  0.00  0.00          Ve  
-HETATM    6 APOL STP C   7      -9.562  22.615  29.037  0.00  0.00          Ve  
-HETATM    7 APOL STP C   7      -7.102  21.786  30.244  0.00  0.00          Ve  
-HETATM    8 APOL STP C   7      -8.874  22.184  29.811  0.00  0.00          Ve  
-HETATM    9 APOL STP C   7      -9.225  22.114  29.661  0.00  0.00          Ve  
-HETATM   10 APOL STP C   7      -6.839  21.824  30.201  0.00  0.00          Ve  
-HETATM   11 APOL STP C   7      -6.761  22.668  29.984  0.00  0.00          Ve  
-HETATM   12 APOL STP C   7      -6.848  22.141  30.159  0.00  0.00          Ve  
-HETATM   13 APOL STP C   7      -6.421  23.405  30.062  0.00  0.00          Ve  
-HETATM   14 APOL STP C   7      -5.071  24.416  29.230  0.00  0.00          Ve  
-HETATM   15 APOL STP C   7      -4.870  26.897  28.843  0.00  0.00          Ve  
-HETATM    1 APOL STP C   8      18.480  10.647   8.623  0.00  0.00          Ve  
-HETATM    2 APOL STP C   8      18.473  10.489   8.873  0.00  0.00          Ve  
-HETATM    3 APOL STP C   8      18.698  10.488   9.792  0.00  0.00          Ve  
-HETATM    4 APOL STP C   8      14.943  10.866   4.541  0.00  0.00          Ve  
-HETATM    5 APOL STP C   8      14.875  10.843   4.459  0.00  0.00          Ve  
-HETATM    6 APOL STP C   8      14.864  10.355   4.722  0.00  0.00          Ve  
-HETATM    7 APOL STP C   8      17.917  10.225   9.354  0.00  0.00          Ve  
-HETATM    8 APOL STP C   8      14.939  11.399   5.926  0.00  0.00          Ve  
-HETATM    9 APOL STP C   8      16.088  11.832   6.354  0.00  0.00          Ve  
-HETATM   10 APOL STP C   8      17.345  11.079   8.062  0.00  0.00          Ve  
-HETATM   11 APOL STP C   8      14.302  11.614   6.290  0.00  0.00          Ve  
-HETATM   12 APOL STP C   8      14.169  11.576   6.426  0.00  0.00          Ve  
-HETATM   13 APOL STP C   8      13.282  11.035   4.472  0.00  0.00          Ve  
-HETATM   14 APOL STP C   8      13.297  11.009   4.410  0.00  0.00          Ve  
-HETATM   15 APOL STP C   8      13.187  11.021   4.702  0.00  0.00          Ve  
-HETATM   16 APOL STP C   8      12.553  11.402   3.811  0.00  0.00          Ve  
-HETATM   17 APOL STP C   8      12.615  11.331   3.695  0.00  0.00          Ve  
-HETATM   18 APOL STP C   8      16.085  11.834   6.357  0.00  0.00          Ve  
-HETATM   19 APOL STP C   8      15.342  12.249   7.345  0.00  0.00          Ve  
-HETATM   20 APOL STP C   8      14.506  12.196   7.034  0.00  0.00          Ve  
-HETATM   21 APOL STP C   8      14.353  12.486   7.796  0.00  0.00          Ve  
-HETATM   22 APOL STP C   8      13.277  10.973   4.430  0.00  0.00          Ve  
-HETATM   23 APOL STP C   8      13.182  11.064   3.370  0.00  0.00          Ve  
-HETATM   24 APOL STP C   8      13.287  11.012   4.386  0.00  0.00          Ve  
-HETATM   25 APOL STP C   8      12.716  11.267   3.730  0.00  0.00          Ve  
-HETATM    1 APOL STP C   9      -5.987  21.597  39.224  0.00  0.00          Ve  
-HETATM    2 APOL STP C   9      -6.191  22.298  37.656  0.00  0.00          Ve  
-HETATM    3 APOL STP C   9      -6.290  22.862  37.242  0.00  0.00          Ve  
-HETATM    4 APOL STP C   9      -6.076  21.951  37.687  0.00  0.00          Ve  
-HETATM    5 APOL STP C   9      -4.027  21.397  38.848  0.00  0.00          Ve  
-HETATM    6 APOL STP C   9      -5.569  19.993  39.101  0.00  0.00          Ve  
-HETATM    7 APOL STP C   9      -6.315  20.503  39.256  0.00  0.00          Ve  
-HETATM    8 APOL STP C   9      -6.095  21.897  37.670  0.00  0.00          Ve  
-HETATM    9 APOL STP C   9      -6.531  20.110  38.511  0.00  0.00          Ve  
-HETATM   10 APOL STP C   9      -5.839  22.040  37.133  0.00  0.00          Ve  
-HETATM   11 APOL STP C   9      -6.021  22.227  37.054  0.00  0.00          Ve  
-HETATM   12 APOL STP C   9      -6.062  21.968  37.603  0.00  0.00          Ve  
-HETATM   13 APOL STP C   9      -8.206  18.652  36.918  0.00  0.00          Ve  
-HETATM   14 APOL STP C   9      -8.120  18.521  37.184  0.00  0.00          Ve  
-HETATM   15 APOL STP C   9      -6.229  19.490  37.843  0.00  0.00          Ve  
-HETATM   16 APOL STP C   9      -9.377  17.540  38.316  0.00  0.00          Ve  
-HETATM   17 APOL STP C   9      -9.701  17.858  38.776  0.00  0.00          Ve  
-HETATM    1 APOL STP C  10       7.964  27.871  24.200  0.00  0.00          Ve  
-HETATM    2 APOL STP C  10       9.060  27.846  24.971  0.00  0.00          Ve  
-HETATM    3 APOL STP C  10       8.457  27.440  25.735  0.00  0.00          Ve  
-HETATM    4 APOL STP C  10       8.568  27.505  25.590  0.00  0.00          Ve  
-HETATM    5 APOL STP C  10       8.418  27.411  25.750  0.00  0.00          Ve  
-HETATM    6 APOL STP C  10       9.084  27.764  24.955  0.00  0.00          Ve  
-HETATM    7 APOL STP C  10      10.654  26.047  25.364  0.00  0.00          Ve  
-HETATM    8 APOL STP C  10      10.424  27.853  24.712  0.00  0.00          Ve  
-HETATM    9 APOL STP C  10       9.439  27.576  24.860  0.00  0.00          Ve  
-HETATM   10 APOL STP C  10      10.404  26.714  24.932  0.00  0.00          Ve  
-HETATM   11 APOL STP C  10      10.731  27.817  24.294  0.00  0.00          Ve  
-HETATM   12 APOL STP C  10      10.476  26.400  24.885  0.00  0.00          Ve  
-HETATM   13 APOL STP C  10      11.588  27.014  23.248  0.00  0.00          Ve  
-HETATM   14 APOL STP C  10      11.536  26.189  23.460  0.00  0.00          Ve  
-HETATM   15 APOL STP C  10       8.935  27.351  24.682  0.00  0.00          Ve  
-HETATM   16 APOL STP C  10      10.729  25.699  25.632  0.00  0.00          Ve  
-HETATM   17 APOL STP C  10      10.887  25.711  25.706  0.00  0.00          Ve  
-HETATM   18 APOL STP C  10      10.424  26.232  24.837  0.00  0.00          Ve  
-HETATM   19 APOL STP C  10       8.612  26.736  24.470  0.00  0.00          Ve  
-HETATM    1 APOL STP C  11       3.065   1.680  14.257  0.00  0.00          Ve  
-HETATM    2 APOL STP C  11      -0.262   5.672  13.713  0.00  0.00          Ve  
-HETATM    3 APOL STP C  11       0.191   4.442  13.421  0.00  0.00          Ve  
-HETATM    4 APOL STP C  11       2.560   3.835  10.859  0.00  0.00          Ve  
-HETATM    5 APOL STP C  11      -0.316   5.894  13.740  0.00  0.00          Ve  
-HETATM    6 APOL STP C  11       3.457   4.032   6.967  0.00  0.00          Ve  
-HETATM    7 APOL STP C  11       2.663   3.891  10.841  0.00  0.00          Ve  
-HETATM    8 APOL STP C  11       4.096   4.245  10.995  0.00  0.00          Ve  
-HETATM    9 APOL STP C  11       4.136   4.217  10.924  0.00  0.00          Ve  
-HETATM   10 APOL STP C  11       3.244   4.177  11.181  0.00  0.00          Ve  
-HETATM   11 APOL STP C  11       3.188   4.166  11.182  0.00  0.00          Ve  
-HETATM   12 APOL STP C  11       2.014   3.532  11.198  0.00  0.00          Ve  
-HETATM   13 APOL STP C  11       2.518   3.690  10.662  0.00  0.00          Ve  
-HETATM   14 APOL STP C  11       2.689   3.819  10.691  0.00  0.00          Ve  
-HETATM   15 APOL STP C  11       2.118   3.108   9.175  0.00  0.00          Ve  
-HETATM   16 APOL STP C  11       3.327   3.642   7.482  0.00  0.00          Ve  
-HETATM   17 APOL STP C  11       4.123   4.188  10.873  0.00  0.00          Ve  
-HETATM   18 APOL STP C  11       4.234   4.163  10.882  0.00  0.00          Ve  
-HETATM   19 APOL STP C  11       2.703   1.870  14.067  0.00  0.00          Ve  
-HETATM   20 APOL STP C  11       2.011   3.354  12.335  0.00  0.00          Ve  
-HETATM   21 APOL STP C  11       1.265   3.803  14.371  0.00  0.00          Ve  
-HETATM   22 APOL STP C  11       1.313   3.846  14.395  0.00  0.00          Ve  
-HETATM   23 APOL STP C  11       4.151   4.474  11.146  0.00  0.00          Ve  
-HETATM   24 APOL STP C  11       3.883   4.476  11.221  0.00  0.00          Ve  
-HETATM    1 APOL STP C  12     -12.188  31.839  16.593  0.00  0.00          Ve  
-HETATM    2 APOL STP C  12     -14.197  27.278  17.645  0.00  0.00          Ve  
-HETATM    3 APOL STP C  12     -14.250  26.710  18.687  0.00  0.00          Ve  
-HETATM    4 APOL STP C  12     -14.909  26.223  19.335  0.00  0.00          Ve  
-HETATM    5 APOL STP C  12     -14.382  24.675  18.050  0.00  0.00          Ve  
-HETATM    6 APOL STP C  12     -14.022  26.981  18.887  0.00  0.00          Ve  
-HETATM    7 APOL STP C  12     -13.149  28.055  17.189  0.00  0.00          Ve  
-HETATM    8 APOL STP C  12     -13.848  27.808  17.708  0.00  0.00          Ve  
-HETATM    9 APOL STP C  12     -13.798  28.442  17.460  0.00  0.00          Ve  
-HETATM   10 APOL STP C  12     -13.798  28.303  17.460  0.00  0.00          Ve  
-HETATM   11 APOL STP C  12     -13.804  28.284  17.472  0.00  0.00          Ve  
-HETATM   12 APOL STP C  12     -13.734  30.649  17.420  0.00  0.00          Ve  
-HETATM   13 APOL STP C  12     -13.444  31.621  17.292  0.00  0.00          Ve  
-HETATM   14 APOL STP C  12     -13.757  31.663  17.802  0.00  0.00          Ve  
-HETATM   15 APOL STP C  12     -12.392  31.711  16.849  0.00  0.00          Ve  
-HETATM   16 APOL STP C  12     -14.320  27.344  17.475  0.00  0.00          Ve  
-HETATM   17 APOL STP C  12     -14.498  27.355  17.384  0.00  0.00          Ve  
+HETATM 3557  POL STP C   2      -6.919   6.642  41.684  0.00  0.00          Ve  
+HETATM 3557  POL STP C   2      -6.980   6.668  41.645  0.00  0.00          Ve  
+HETATM 3557  POL STP C   2      -6.526   5.836  41.929  0.00  0.00          Ve  
+HETATM 3557  POL STP C   2      -6.378   5.700  41.831  0.00  0.00          Ve  
+HETATM 3557  POL STP C   2      -7.822   6.625  41.102  0.00  0.00          Ve  
+HETATM 3577  POL STP C   2      -7.825   7.749  41.660  0.00  0.00          Ve  
+HETATM 3578  POL STP C   2      -8.100   8.674  42.098  0.00  0.00          Ve  
+HETATM 3578  POL STP C   2      -8.659   9.530  41.927  0.00  0.00          Ve  
+HETATM 4662  POL STP C   2      -8.737  12.631  40.804  0.00  0.00          Ve  
+HETATM 7611  POL STP C   2     -11.049  12.429  41.049  0.00  0.00          Ve  
+HETATM 7611  POL STP C   2     -11.267  12.028  41.036  0.00  0.00          Ve  
+HETATM 7611  POL STP C   2     -10.890  12.386  41.380  0.00  0.00          Ve  
+HETATM 7612  POL STP C   2      -9.951  10.626  40.848  0.00  0.00          Ve  
+HETATM 7618  POL STP C   2     -10.041   9.901  40.431  0.00  0.00          Ve  
+HETATM 5013  POL STP C   3      21.608   9.684  14.132  0.00  0.00          Ve  
+HETATM    2 APOL STP C   3      19.314  10.586   9.512  0.00  0.00          Ve  
+HETATM    3 APOL STP C   3      19.143  10.766   9.300  0.00  0.00          Ve  
+HETATM 5382  POL STP C   3      22.337  10.819  11.219  0.00  0.00          Ve  
+HETATM 5382  POL STP C   3      21.322  10.417  10.839  0.00  0.00          Ve  
+HETATM 5383  POL STP C   3      22.223   9.452  12.843  0.00  0.00          Ve  
+HETATM    7 APOL STP C   3      20.438   9.717  10.950  0.00  0.00          Ve  
+HETATM    8 APOL STP C   3      19.317  10.526   9.567  0.00  0.00          Ve  
+HETATM    9 APOL STP C   3      20.347   9.733  10.882  0.00  0.00          Ve  
+HETATM 6359  POL STP C   3      20.400   9.647  10.930  0.00  0.00          Ve  
+HETATM   11 APOL STP C   3      18.480  10.647   8.623  0.00  0.00          Ve  
+HETATM   12 APOL STP C   3      18.473  10.489   8.873  0.00  0.00          Ve  
+HETATM   13 APOL STP C   3      19.091  10.740   9.309  0.00  0.00          Ve  
+HETATM   14 APOL STP C   3      19.039  10.663   9.363  0.00  0.00          Ve  
+HETATM   15 APOL STP C   3      18.698  10.488   9.792  0.00  0.00          Ve  
+HETATM   16 APOL STP C   3      20.605   6.618  21.102  0.00  0.00          Ve  
+HETATM   17 APOL STP C   3      14.943  10.866   4.541  0.00  0.00          Ve  
+HETATM 6734  POL STP C   3      14.875  10.843   4.459  0.00  0.00          Ve  
+HETATM 6734  POL STP C   3      14.864  10.355   4.722  0.00  0.00          Ve  
+HETATM   20 APOL STP C   3      18.270  10.051   6.298  0.00  0.00          Ve  
+HETATM   21 APOL STP C   3      17.917  10.225   9.354  0.00  0.00          Ve  
+HETATM   22 APOL STP C   3      14.939  11.399   5.926  0.00  0.00          Ve  
+HETATM   23 APOL STP C   3      16.088  11.832   6.354  0.00  0.00          Ve  
+HETATM   24 APOL STP C   3      17.345  11.079   8.062  0.00  0.00          Ve  
+HETATM   25 APOL STP C   3      14.302  11.614   6.290  0.00  0.00          Ve  
+HETATM   26 APOL STP C   3      14.169  11.576   6.426  0.00  0.00          Ve  
+HETATM   27 APOL STP C   3      21.260   9.781  14.385  0.00  0.00          Ve  
+HETATM 7980  POL STP C   3      19.082   9.114  16.906  0.00  0.00          Ve  
+HETATM   29 APOL STP C   3      23.299   6.241  21.535  0.00  0.00          Ve  
+HETATM   30 APOL STP C   3      19.211   8.868  16.477  0.00  0.00          Ve  
+HETATM 8161  POL STP C   3      19.141   9.065  16.855  0.00  0.00          Ve  
+HETATM   32 APOL STP C   3      20.411   8.950  16.497  0.00  0.00          Ve  
+HETATM   33 APOL STP C   3      21.278   7.286  15.271  0.00  0.00          Ve  
+HETATM   34 APOL STP C   3      21.737   8.273  15.966  0.00  0.00          Ve  
+HETATM   35 APOL STP C   3      19.545   9.253  17.348  0.00  0.00          Ve  
+HETATM   36 APOL STP C   3      19.605   9.305  17.253  0.00  0.00          Ve  
+HETATM   37 APOL STP C   3      19.361   9.202  17.087  0.00  0.00          Ve  
+HETATM 8174  POL STP C   3      21.824   7.092  13.097  0.00  0.00          Ve  
+HETATM 8177  POL STP C   3      21.005   6.678  13.902  0.00  0.00          Ve  
+HETATM   40 APOL STP C   3      21.887   7.048  14.721  0.00  0.00          Ve  
+HETATM 8185  POL STP C   3      21.396   7.252  12.616  0.00  0.00          Ve  
+HETATM   42 APOL STP C   3      13.282  11.035   4.472  0.00  0.00          Ve  
+HETATM 8226  POL STP C   3      13.297  11.009   4.410  0.00  0.00          Ve  
+HETATM   44 APOL STP C   3      13.187  11.021   4.702  0.00  0.00          Ve  
+HETATM   45 APOL STP C   3      12.553  11.402   3.811  0.00  0.00          Ve  
+HETATM   46 APOL STP C   3      12.615  11.331   3.695  0.00  0.00          Ve  
+HETATM   47 APOL STP C   3      16.085  11.834   6.357  0.00  0.00          Ve  
+HETATM   48 APOL STP C   3      15.342  12.249   7.345  0.00  0.00          Ve  
+HETATM   49 APOL STP C   3      14.506  12.196   7.034  0.00  0.00          Ve  
+HETATM   50 APOL STP C   3      14.353  12.486   7.796  0.00  0.00          Ve  
+HETATM   51 APOL STP C   3      21.576   8.462  17.094  0.00  0.00          Ve  
+HETATM   52 APOL STP C   3      21.237   8.164  17.688  0.00  0.00          Ve  
+HETATM   53 APOL STP C   3      19.823   9.314  17.205  0.00  0.00          Ve  
+HETATM   54 APOL STP C   3      19.842   9.288  17.195  0.00  0.00          Ve  
+HETATM   55 APOL STP C   3      19.813   9.293  17.207  0.00  0.00          Ve  
+HETATM   56 APOL STP C   3      23.114   7.517  18.754  0.00  0.00          Ve  
+HETATM   57 APOL STP C   3      23.216   7.267  19.612  0.00  0.00          Ve  
+HETATM   58 APOL STP C   3      21.455   7.159  19.578  0.00  0.00          Ve  
+HETATM   59 APOL STP C   3      19.601   8.988  17.728  0.00  0.00          Ve  
+HETATM   60 APOL STP C   3      20.637   6.657  21.076  0.00  0.00          Ve  
+HETATM   61 APOL STP C   3      21.991   6.742  21.095  0.00  0.00          Ve  
+HETATM   62 APOL STP C   3      20.614   6.661  21.080  0.00  0.00          Ve  
+HETATM 9388  POL STP C   3      13.277  10.973   4.430  0.00  0.00          Ve  
+HETATM   64 APOL STP C   3      13.182  11.064   3.370  0.00  0.00          Ve  
+HETATM 9388  POL STP C   3      13.287  11.012   4.386  0.00  0.00          Ve  
+HETATM   66 APOL STP C   3      12.716  11.267   3.730  0.00  0.00          Ve  
+HETATM   67 APOL STP C   3      20.578   6.679  21.067  0.00  0.00          Ve  
+HETATM   68 APOL STP C   3      20.573   6.576  21.121  0.00  0.00          Ve  
+HETATM 9868  POL STP C   3      19.279  10.317  17.326  0.00  0.00          Ve  
+HETATM   70 APOL STP C   3      19.218  10.275  17.340  0.00  0.00          Ve  
+HETATM 4559  POL STP C   4     -13.394   8.035  11.699  0.00  0.00          Ve  
+HETATM 4559  POL STP C   4     -13.866   8.149  12.756  0.00  0.00          Ve  
+HETATM 4561  POL STP C   4     -13.235   6.985  13.878  0.00  0.00          Ve  
+HETATM    4 APOL STP C   4     -13.396  13.376  12.554  0.00  0.00          Ve  
+HETATM 4639  POL STP C   4     -14.773   7.681  13.727  0.00  0.00          Ve  
+HETATM    6 APOL STP C   4     -14.552   8.323  12.854  0.00  0.00          Ve  
+HETATM    7 APOL STP C   4     -14.690   7.717  13.852  0.00  0.00          Ve  
+HETATM    8 APOL STP C   4     -13.947  10.342   9.126  0.00  0.00          Ve  
+HETATM    9 APOL STP C   4     -12.889   8.488   9.768  0.00  0.00          Ve  
+HETATM 5655  POL STP C   4     -14.059  10.991   9.026  0.00  0.00          Ve  
+HETATM   11 APOL STP C   4     -12.850  13.648  12.578  0.00  0.00          Ve  
+HETATM   12 APOL STP C   4     -12.635  13.830  12.726  0.00  0.00          Ve  
+HETATM   13 APOL STP C   4     -15.321  12.050   6.421  0.00  0.00          Ve  
+HETATM   14 APOL STP C   4     -15.149  12.299   5.990  0.00  0.00          Ve  
+HETATM   15 APOL STP C   4     -14.138  13.128   4.148  0.00  0.00          Ve  
+HETATM 7006  POL STP C   4     -13.842  12.966   4.202  0.00  0.00          Ve  
+HETATM   17 APOL STP C   4     -14.202  12.998   4.431  0.00  0.00          Ve  
+HETATM   18 APOL STP C   4     -15.071  12.945  11.123  0.00  0.00          Ve  
+HETATM   19 APOL STP C   4     -15.181  12.284   7.101  0.00  0.00          Ve  
+HETATM   20 APOL STP C   4     -14.069  13.525  10.889  0.00  0.00          Ve  
+HETATM   21 APOL STP C   4     -14.486  12.345   9.698  0.00  0.00          Ve  
+HETATM   22 APOL STP C   4     -15.581  11.691   7.702  0.00  0.00          Ve  
+HETATM   23 APOL STP C   4     -13.744  12.589   9.720  0.00  0.00          Ve  
+HETATM   24 APOL STP C   4     -13.903  13.601  10.918  0.00  0.00          Ve  
+HETATM   25 APOL STP C   4     -13.004  13.765  11.916  0.00  0.00          Ve  
+HETATM   26 APOL STP C   4     -12.804  14.399  11.014  0.00  0.00          Ve  
+HETATM 8544  POL STP C   4     -14.691   7.701  13.857  0.00  0.00          Ve  
+HETATM 8555  POL STP C   4     -14.353   7.367  13.918  0.00  0.00          Ve  
+HETATM 8555  POL STP C   4     -14.766   7.663  13.746  0.00  0.00          Ve  
+HETATM   30 APOL STP C   4     -13.822  14.302  10.714  0.00  0.00          Ve  
+HETATM   31 APOL STP C   4     -12.793  14.411  11.014  0.00  0.00          Ve  
+HETATM 1872  POL STP C   5      16.547  23.639  13.890  0.00  0.00          Ve  
+HETATM 1873  POL STP C   5      16.092  23.630  14.033  0.00  0.00          Ve  
+HETATM    3 APOL STP C   5      15.859  23.404  14.170  0.00  0.00          Ve  
+HETATM    4 APOL STP C   5      15.557  23.398  14.576  0.00  0.00          Ve  
+HETATM 3663  POL STP C   5      16.011  22.871  13.482  0.00  0.00          Ve  
+HETATM    6 APOL STP C   5      15.928  23.207  13.765  0.00  0.00          Ve  
+HETATM 3702  POL STP C   5      17.691  22.245  18.072  0.00  0.00          Ve  
+HETATM 3702  POL STP C   5      19.529  21.954  18.755  0.00  0.00          Ve  
+HETATM    9 APOL STP C   5      15.011  22.229  15.825  0.00  0.00          Ve  
+HETATM 4994  POL STP C   5      15.135  20.552  18.741  0.00  0.00          Ve  
+HETATM 5018  POL STP C   5      19.253  21.725  18.788  0.00  0.00          Ve  
+HETATM 5018  POL STP C   5      17.650  21.048  18.652  0.00  0.00          Ve  
+HETATM 6334  POL STP C   5      16.195  21.162  18.168  0.00  0.00          Ve  
+HETATM 6334  POL STP C   5      15.398  20.983  17.666  0.00  0.00          Ve  
+HETATM 6334  POL STP C   5      15.138  20.557  18.735  0.00  0.00          Ve  
+HETATM 6334  POL STP C   5      16.943  21.983  17.981  0.00  0.00          Ve  
+HETATM 6334  POL STP C   5      15.182  22.714  15.737  0.00  0.00          Ve  
+HETATM 6335  POL STP C   5      15.741  24.064  14.855  0.00  0.00          Ve  
+HETATM 6367  POL STP C   5      15.109  20.220  19.179  0.00  0.00          Ve  
+HETATM 3339  POL STP C   6     -10.865  18.249   0.469  0.00  0.00          Ve  
+HETATM 4612  POL STP C   6      -9.803  18.840   1.772  0.00  0.00          Ve  
+HETATM 5510  POL STP C   6     -11.664  16.564   0.901  0.00  0.00          Ve  
+HETATM 5510  POL STP C   6     -10.854  18.060   0.590  0.00  0.00          Ve  
+HETATM    5 APOL STP C   6      -9.018  19.707   1.368  0.00  0.00          Ve  
+HETATM 5867  POL STP C   6      -9.656  19.088   1.638  0.00  0.00          Ve  
+HETATM 5868  POL STP C   6     -10.831  18.316   0.411  0.00  0.00          Ve  
+HETATM    8 APOL STP C   6      -8.858  20.212   1.689  0.00  0.00          Ve  
+HETATM    9 APOL STP C   6      -8.626  20.731   1.519  0.00  0.00          Ve  
+HETATM 5869  POL STP C   6      -9.829  18.933   1.649  0.00  0.00          Ve  
+HETATM   11 APOL STP C   6     -12.817  19.837  -0.592  0.00  0.00          Ve  
+HETATM 5876  POL STP C   6     -10.800  18.318   0.530  0.00  0.00          Ve  
+HETATM 5877  POL STP C   6      -9.908  18.876   1.592  0.00  0.00          Ve  
+HETATM 7108  POL STP C   6     -11.221  20.512  -0.292  0.00  0.00          Ve  
+HETATM 7108  POL STP C   6      -8.604  20.710   1.295  0.00  0.00          Ve  
+HETATM 7108  POL STP C   6      -8.165  20.787   0.269  0.00  0.00          Ve  
+HETATM 7109  POL STP C   6      -8.676  20.220   0.368  0.00  0.00          Ve  
+HETATM 2397  POL STP C   7       0.606  30.613  17.291  0.00  0.00          Ve  
+HETATM 2399  POL STP C   7       0.349  29.933  16.102  0.00  0.00          Ve  
+HETATM 2403  POL STP C   7       0.398  29.825  16.006  0.00  0.00          Ve  
+HETATM 2403  POL STP C   7       0.310  30.058  15.886  0.00  0.00          Ve  
+HETATM 2481  POL STP C   7      -2.704  33.369  14.954  0.00  0.00          Ve  
+HETATM 2481  POL STP C   7       0.267  30.094  15.812  0.00  0.00          Ve  
+HETATM 2485  POL STP C   7       0.297  30.167  15.803  0.00  0.00          Ve  
+HETATM 2504  POL STP C   7      -1.603  34.311  14.914  0.00  0.00          Ve  
+HETATM 2504  POL STP C   7      -1.370  34.089  14.976  0.00  0.00          Ve  
+HETATM 3167  POL STP C   7       0.328  30.306  15.653  0.00  0.00          Ve  
+HETATM 3167  POL STP C   7       0.297  30.561  15.738  0.00  0.00          Ve  
+HETATM 3167  POL STP C   7      -0.300  32.461  15.359  0.00  0.00          Ve  
+HETATM 4456  POL STP C   7      -1.581  33.922  14.529  0.00  0.00          Ve  
+HETATM 4459  POL STP C   7      -2.185  34.279  14.137  0.00  0.00          Ve  
+HETATM 4459  POL STP C   7      -3.286  34.022  12.999  0.00  0.00          Ve  
+HETATM 4459  POL STP C   7      -3.344  34.741  12.491  0.00  0.00          Ve  
+HETATM    1 APOL STP C   8     -14.456  28.897   9.357  0.00  0.00          Ve  
+HETATM    2 APOL STP C   8     -13.802  30.114  10.708  0.00  0.00          Ve  
+HETATM    3 APOL STP C   8     -14.824  28.441   8.989  0.00  0.00          Ve  
+HETATM    4 APOL STP C   8     -13.008  26.082  10.497  0.00  0.00          Ve  
+HETATM    5 APOL STP C   8     -14.169  30.414   7.585  0.00  0.00          Ve  
+HETATM 5968  POL STP C   8     -13.292  25.512  10.645  0.00  0.00          Ve  
+HETATM 5971  POL STP C   8     -16.281  25.248   9.782  0.00  0.00          Ve  
+HETATM 5974  POL STP C   8     -13.777  25.706   9.765  0.00  0.00          Ve  
+HETATM 6006  POL STP C   8     -15.422  24.602   9.978  0.00  0.00          Ve  
+HETATM 6011  POL STP C   8     -13.889  25.617   9.542  0.00  0.00          Ve  
+HETATM 6011  POL STP C   8     -13.906  25.623   9.573  0.00  0.00          Ve  
+HETATM 6012  POL STP C   8     -15.206  25.827   9.088  0.00  0.00          Ve  
+HETATM 6013  POL STP C   8     -13.401  24.066  10.900  0.00  0.00          Ve  
+HETATM   14 APOL STP C   8     -13.617  23.729  11.105  0.00  0.00          Ve  
+HETATM   15 APOL STP C   8     -14.727  26.185   8.926  0.00  0.00          Ve  
+HETATM   16 APOL STP C   8     -14.636  26.121   9.005  0.00  0.00          Ve  
+HETATM 6013  POL STP C   8     -14.732  26.170   8.943  0.00  0.00          Ve  
+HETATM   18 APOL STP C   8     -13.644  23.175  11.257  0.00  0.00          Ve  
+HETATM 1757  POL STP C   9      -6.625  24.421  30.057  0.00  0.00          Ve  
+HETATM 1757  POL STP C   9      -5.799  26.309  29.404  0.00  0.00          Ve  
+HETATM 1757  POL STP C   9      -6.778  24.418  30.031  0.00  0.00          Ve  
+HETATM 1757  POL STP C   9      -8.308  22.685  29.725  0.00  0.00          Ve  
+HETATM 1894  POL STP C   9      -7.037  21.813  30.245  0.00  0.00          Ve  
+HETATM    6 APOL STP C   9     -10.258  22.548  28.497  0.00  0.00          Ve  
+HETATM    7 APOL STP C   9      -9.562  22.615  29.037  0.00  0.00          Ve  
+HETATM    8 APOL STP C   9      -7.102  21.786  30.244  0.00  0.00          Ve  
+HETATM    9 APOL STP C   9      -8.874  22.184  29.811  0.00  0.00          Ve  
+HETATM   10 APOL STP C   9      -9.179  22.095  30.112  0.00  0.00          Ve  
+HETATM   11 APOL STP C   9      -9.225  22.114  29.661  0.00  0.00          Ve  
+HETATM   12 APOL STP C   9      -6.839  21.824  30.201  0.00  0.00          Ve  
+HETATM 9192  POL STP C   9      -6.761  22.668  29.984  0.00  0.00          Ve  
+HETATM 9192  POL STP C   9      -6.848  22.141  30.159  0.00  0.00          Ve  
+HETATM 9196  POL STP C   9      -6.421  23.405  30.062  0.00  0.00          Ve  
+HETATM10112  POL STP C   9      -5.071  24.416  29.230  0.00  0.00          Ve  
+HETATM10112  POL STP C   9      -4.870  26.897  28.843  0.00  0.00          Ve  
+HETATM10514  POL STP C  10       7.964  27.871  24.200  0.00  0.00          Ve  
+HETATM10517  POL STP C  10       9.060  27.846  24.971  0.00  0.00          Ve  
+HETATM10948  POL STP C  10       8.457  27.440  25.735  0.00  0.00          Ve  
+HETATM10948  POL STP C  10       8.568  27.505  25.590  0.00  0.00          Ve  
+HETATM10948  POL STP C  10       8.418  27.411  25.750  0.00  0.00          Ve  
+HETATM10949  POL STP C  10       9.084  27.764  24.955  0.00  0.00          Ve  
+HETATM10949  POL STP C  10      10.654  26.047  25.364  0.00  0.00          Ve  
+HETATM11158  POL STP C  10      10.424  27.853  24.712  0.00  0.00          Ve  
+HETATM11158  POL STP C  10       9.439  27.576  24.860  0.00  0.00          Ve  
+HETATM11158  POL STP C  10      10.404  26.714  24.932  0.00  0.00          Ve  
+HETATM11158  POL STP C  10      10.731  27.817  24.294  0.00  0.00          Ve  
+HETATM11159  POL STP C  10      10.476  26.400  24.885  0.00  0.00          Ve  
+HETATM11160  POL STP C  10      11.588  27.014  23.248  0.00  0.00          Ve  
+HETATM11160  POL STP C  10      11.536  26.189  23.460  0.00  0.00          Ve  
+HETATM11160  POL STP C  10       8.935  27.351  24.682  0.00  0.00          Ve  
+HETATM11175  POL STP C  10      10.729  25.699  25.632  0.00  0.00          Ve  
+HETATM11175  POL STP C  10      10.887  25.711  25.706  0.00  0.00          Ve  
+HETATM11262  POL STP C  10      10.424  26.232  24.837  0.00  0.00          Ve  
+HETATM11267  POL STP C  10       8.612  26.736  24.470  0.00  0.00          Ve  
+HETATM 2662  POL STP C  11      -6.365  24.332  39.128  0.00  0.00          Ve  
+HETATM 2662  POL STP C  11      -6.009  21.659  39.280  0.00  0.00          Ve  
+HETATM 2896  POL STP C  11      -5.987  21.597  39.224  0.00  0.00          Ve  
+HETATM    4 APOL STP C  11      -6.191  22.298  37.656  0.00  0.00          Ve  
+HETATM 2896  POL STP C  11      -6.290  22.862  37.242  0.00  0.00          Ve  
+HETATM    6 APOL STP C  11      -6.076  21.951  37.687  0.00  0.00          Ve  
+HETATM 3420  POL STP C  11      -4.027  21.397  38.848  0.00  0.00          Ve  
+HETATM 3422  POL STP C  11      -5.569  19.993  39.101  0.00  0.00          Ve  
+HETATM    9 APOL STP C  11      -6.315  20.503  39.256  0.00  0.00          Ve  
+HETATM   10 APOL STP C  11      -6.095  21.897  37.670  0.00  0.00          Ve  
+HETATM   11 APOL STP C  11      -6.531  20.110  38.511  0.00  0.00          Ve  
+HETATM 3962  POL STP C  11      -5.839  22.040  37.133  0.00  0.00          Ve  
+HETATM 3962  POL STP C  11      -6.021  22.227  37.054  0.00  0.00          Ve  
+HETATM 3962  POL STP C  11      -6.062  21.968  37.603  0.00  0.00          Ve  
+HETATM 3963  POL STP C  11      -8.206  18.652  36.918  0.00  0.00          Ve  
+HETATM 3963  POL STP C  11      -8.120  18.521  37.184  0.00  0.00          Ve  
+HETATM   17 APOL STP C  11      -6.229  19.490  37.843  0.00  0.00          Ve  
+HETATM 4810  POL STP C  11      -9.377  17.540  38.316  0.00  0.00          Ve  
+HETATM   19 APOL STP C  11      -9.701  17.858  38.776  0.00  0.00          Ve  
+HETATM 8383  POL STP C  12       3.065   1.680  14.257  0.00  0.00          Ve  
+HETATM 9036  POL STP C  12      -0.262   5.672  13.713  0.00  0.00          Ve  
+HETATM 9433  POL STP C  12       0.191   4.442  13.421  0.00  0.00          Ve  
+HETATM 9730  POL STP C  12       2.560   3.835  10.859  0.00  0.00          Ve  
+HETATM 9774  POL STP C  12      -0.316   5.894  13.740  0.00  0.00          Ve  
+HETATM10138  POL STP C  12       3.457   4.032   6.967  0.00  0.00          Ve  
+HETATM10140  POL STP C  12       2.663   3.891  10.841  0.00  0.00          Ve  
+HETATM10167  POL STP C  12       4.096   4.245  10.995  0.00  0.00          Ve  
+HETATM10167  POL STP C  12       4.136   4.217  10.924  0.00  0.00          Ve  
+HETATM10168  POL STP C  12       3.244   4.177  11.181  0.00  0.00          Ve  
+HETATM10168  POL STP C  12       3.188   4.166  11.182  0.00  0.00          Ve  
+HETATM10406  POL STP C  12       2.014   3.532  11.198  0.00  0.00          Ve  
+HETATM10420  POL STP C  12       2.518   3.690  10.662  0.00  0.00          Ve  
+HETATM10420  POL STP C  12       2.689   3.819  10.691  0.00  0.00          Ve  
+HETATM10420  POL STP C  12       2.118   3.108   9.175  0.00  0.00          Ve  
+HETATM10422  POL STP C  12       3.327   3.642   7.482  0.00  0.00          Ve  
+HETATM10422  POL STP C  12       4.123   4.188  10.873  0.00  0.00          Ve  
+HETATM10424  POL STP C  12       4.234   4.163  10.882  0.00  0.00          Ve  
+HETATM10834  POL STP C  12       2.703   1.870  14.067  0.00  0.00          Ve  
+HETATM   20 APOL STP C  12       2.011   3.354  12.335  0.00  0.00          Ve  
+HETATM10839  POL STP C  12       1.265   3.803  14.371  0.00  0.00          Ve  
+HETATM10839  POL STP C  12       1.313   3.846  14.395  0.00  0.00          Ve  
+HETATM11109  POL STP C  12       4.151   4.474  11.146  0.00  0.00          Ve  
+HETATM11109  POL STP C  12       3.883   4.476  11.221  0.00  0.00          Ve  
+HETATM 1786  POL STP C  13     -12.188  31.839  16.593  0.00  0.00          Ve  
+HETATM 2012  POL STP C  13     -13.844  30.372  17.279  0.00  0.00          Ve  
+HETATM 2078  POL STP C  13     -14.197  27.278  17.645  0.00  0.00          Ve  
+HETATM 2510  POL STP C  13     -14.250  26.710  18.687  0.00  0.00          Ve  
+HETATM 3269  POL STP C  13     -14.909  26.223  19.335  0.00  0.00          Ve  
+HETATM    6 APOL STP C  13     -14.382  24.675  18.050  0.00  0.00          Ve  
+HETATM 3275  POL STP C  13     -14.022  26.981  18.887  0.00  0.00          Ve  
+HETATM 3278  POL STP C  13     -13.149  28.055  17.189  0.00  0.00          Ve  
+HETATM 3278  POL STP C  13     -13.848  27.808  17.708  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.798  28.442  17.460  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.798  28.303  17.460  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.804  28.284  17.472  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.734  30.649  17.420  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.444  31.621  17.292  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -13.757  31.663  17.802  0.00  0.00          Ve  
+HETATM 3279  POL STP C  13     -12.392  31.711  16.849  0.00  0.00          Ve  
+HETATM   17 APOL STP C  13     -14.327  27.424  17.420  0.00  0.00          Ve  
+HETATM 4553  POL STP C  13     -14.320  27.344  17.475  0.00  0.00          Ve  
+HETATM 4553  POL STP C  13     -14.498  27.355  17.384  0.00  0.00          Ve  

tests/reference_output/1UYD_out/1UYD_pockets.pqr

@@ -168,216 +168,274 @@ ATOM    164    O STP     2     -11.267  12.028  41.036    0.00     4.03
 ATOM    165    O STP     2     -10.890  12.386  41.380    0.00     4.60
 ATOM    166    O STP     2      -9.951  10.626  40.848    0.00     4.18
 ATOM    167    O STP     2     -10.041   9.901  40.431    0.00     3.83
-ATOM    168    O STP     3     -13.394   8.035  11.699    0.00     3.75
-ATOM    169    O STP     3     -13.866   8.149  12.756    0.00     4.22
-ATOM    170    O STP     3     -13.235   6.985  13.878    0.00     3.71
-ATOM    171    C STP     3     -13.396  13.376  12.554    0.00     3.64
-ATOM    172    O STP     3     -14.773   7.681  13.727    0.00     4.61
-ATOM    173    C STP     3     -14.552   8.323  12.854    0.00     4.64
-ATOM    174    C STP     3     -14.690   7.717  13.852    0.00     4.48
-ATOM    175    C STP     3     -13.947  10.342   9.126    0.00     3.72
-ATOM    176    C STP     3     -12.889   8.488   9.768    0.00     3.44
-ATOM    177    O STP     3     -14.059  10.991   9.026    0.00     3.83
-ATOM    178    C STP     3     -12.850  13.648  12.578    0.00     3.53
-ATOM    179    C STP     3     -12.635  13.830  12.726    0.00     3.42
-ATOM    180    C STP     3     -15.321  12.050   6.421    0.00     3.91
-ATOM    181    C STP     3     -15.149  12.299   5.990    0.00     3.77
-ATOM    182    C STP     3     -14.138  13.128   4.148    0.00     3.73
-ATOM    183    O STP     3     -13.842  12.966   4.202    0.00     3.54
-ATOM    184    C STP     3     -14.202  12.998   4.431    0.00     3.63
-ATOM    185    C STP     3     -15.071  12.945  11.123    0.00     4.55
-ATOM    186    C STP     3     -15.181  12.284   7.101    0.00     3.70
-ATOM    187    C STP     3     -14.069  13.525  10.889    0.00     4.05
-ATOM    188    C STP     3     -14.486  12.345   9.698    0.00     4.10
-ATOM    189    C STP     3     -15.581  11.691   7.702    0.00     4.30
-ATOM    190    C STP     3     -13.744  12.589   9.720    0.00     3.59
-ATOM    191    C STP     3     -13.903  13.601  10.918    0.00     3.98
-ATOM    192    C STP     3     -13.004  13.765  11.916    0.00     3.53
-ATOM    193    C STP     3     -12.804  14.399  11.014    0.00     3.51
-ATOM    194    O STP     3     -14.691   7.701  13.857    0.00     4.48
-ATOM    195    O STP     3     -14.353   7.367  13.918    0.00     4.32
-ATOM    196    O STP     3     -14.766   7.663  13.746    0.00     4.60
-ATOM    197    C STP     3     -13.822  14.302  10.714    0.00     3.55
-ATOM    198    C STP     3     -12.793  14.411  11.014    0.00     3.51
-ATOM    199    O STP     4      16.547  23.639  13.890    0.00     4.14
-ATOM    200    O STP     4      16.092  23.630  14.033    0.00     4.24
-ATOM    201    C STP     4      15.859  23.404  14.170    0.00     4.10
-ATOM    202    C STP     4      15.557  23.398  14.576    0.00     4.15
-ATOM    203    O STP     4      16.011  22.871  13.482    0.00     3.59
-ATOM    204    C STP     4      15.928  23.207  13.765    0.00     3.90
-ATOM    205    O STP     4      17.691  22.245  18.072    0.00     3.56
-ATOM    206    O STP     4      19.529  21.954  18.755    0.00     4.34
-ATOM    207    C STP     4      15.011  22.229  15.825    0.00     3.58
-ATOM    208    O STP     4      15.135  20.552  18.741    0.00     3.44
-ATOM    209    O STP     4      19.253  21.725  18.788    0.00     4.16
-ATOM    210    O STP     4      17.650  21.048  18.652    0.00     3.48
-ATOM    211    O STP     4      16.195  21.162  18.168    0.00     3.43
-ATOM    212    O STP     4      15.398  20.983  17.666    0.00     3.45
-ATOM    213    O STP     4      15.138  20.557  18.735    0.00     3.44
-ATOM    214    O STP     4      16.943  21.983  17.981    0.00     3.42
-ATOM    215    O STP     4      15.182  22.714  15.737    0.00     3.78
-ATOM    216    O STP     4      15.741  24.064  14.855    0.00     4.60
-ATOM    217    O STP     4      15.109  20.220  19.179    0.00     3.40
-ATOM    218    C STP     5      20.605   6.618  21.102    0.00     3.76
-ATOM    219    O STP     5      19.082   9.114  16.906    0.00     3.51
-ATOM    220    C STP     5      19.211   8.868  16.477    0.00     3.41
-ATOM    221    O STP     5      19.141   9.065  16.855    0.00     3.52
-ATOM    222    C STP     5      20.411   8.950  16.497    0.00     4.01
-ATOM    223    C STP     5      21.278   7.286  15.271    0.00     3.95
-ATOM    224    C STP     5      21.737   8.273  15.966    0.00     4.55
-ATOM    225    C STP     5      19.545   9.253  17.348    0.00     3.83
-ATOM    226    C STP     5      19.605   9.305  17.253    0.00     3.89
-ATOM    227    C STP     5      19.361   9.202  17.087    0.00     3.71
-ATOM    228    O STP     5      21.005   6.678  13.902    0.00     3.49
-ATOM    229    C STP     5      21.887   7.048  14.721    0.00     4.32
-ATOM    230    C STP     5      21.576   8.462  17.094    0.00     4.39
-ATOM    231    C STP     5      21.237   8.164  17.688    0.00     3.98
-ATOM    232    C STP     5      19.823   9.314  17.205    0.00     3.96
-ATOM    233    C STP     5      19.842   9.288  17.195    0.00     3.97
-ATOM    234    C STP     5      19.813   9.293  17.207    0.00     3.96
-ATOM    235    C STP     5      23.114   7.517  18.754    0.00     4.38
-ATOM    236    C STP     5      23.216   7.267  19.612    0.00     4.27
-ATOM    237    C STP     5      21.455   7.159  19.578    0.00     3.62
-ATOM    238    C STP     5      19.601   8.988  17.728    0.00     3.65
-ATOM    239    C STP     5      20.637   6.657  21.076    0.00     3.77
-ATOM    240    C STP     5      21.991   6.742  21.095    0.00     3.92
-ATOM    241    C STP     5      20.614   6.661  21.080    0.00     3.77
-ATOM    242    C STP     5      20.578   6.679  21.067    0.00     3.75
-ATOM    243    C STP     5      20.573   6.576  21.121    0.00     3.74
-ATOM    244    O STP     5      19.279  10.317  17.326    0.00     3.47
-ATOM    245    C STP     5      19.218  10.275  17.340    0.00     3.46
-ATOM    246    O STP     6       0.606  30.613  17.291    0.00     3.76
-ATOM    247    O STP     6       0.349  29.933  16.102    0.00     3.64
-ATOM    248    O STP     6       0.398  29.825  16.006    0.00     3.59
-ATOM    249    O STP     6       0.310  30.058  15.886    0.00     3.64
-ATOM    250    O STP     6      -2.704  33.369  14.954    0.00     3.46
-ATOM    251    O STP     6       0.267  30.094  15.812    0.00     3.62
-ATOM    252    O STP     6       0.297  30.167  15.803    0.00     3.64
-ATOM    253    O STP     6      -1.603  34.311  14.914    0.00     4.52
-ATOM    254    O STP     6      -1.370  34.089  14.976    0.00     4.40
-ATOM    255    O STP     6       0.328  30.306  15.653    0.00     3.60
-ATOM    256    O STP     6       0.297  30.561  15.738    0.00     3.64
-ATOM    257    O STP     6      -0.300  32.461  15.359    0.00     3.76
-ATOM    258    O STP     6      -1.581  33.922  14.529    0.00     4.09
-ATOM    259    O STP     6      -2.185  34.279  14.137    0.00     4.26
-ATOM    260    O STP     6      -3.286  34.022  12.999    0.00     4.08
-ATOM    261    O STP     6      -3.344  34.741  12.491    0.00     4.54
-ATOM    262    O STP     7      -6.625  24.421  30.057    0.00     3.72
-ATOM    263    O STP     7      -5.799  26.309  29.404    0.00     4.28
-ATOM    264    O STP     7      -8.308  22.685  29.725    0.00     3.61
-ATOM    265    O STP     7      -7.037  21.813  30.245    0.00     3.44
-ATOM    266    C STP     7     -10.258  22.548  28.497    0.00     4.05
-ATOM    267    C STP     7      -9.562  22.615  29.037    0.00     3.80
-ATOM    268    C STP     7      -7.102  21.786  30.244    0.00     3.44
-ATOM    269    C STP     7      -8.874  22.184  29.811    0.00     3.72
-ATOM    270    C STP     7      -9.225  22.114  29.661    0.00     3.78
-ATOM    271    C STP     7      -6.839  21.824  30.201    0.00     3.40
-ATOM    272    O STP     7      -6.761  22.668  29.984    0.00     3.54
-ATOM    273    O STP     7      -6.848  22.141  30.159    0.00     3.46
-ATOM    274    O STP     7      -6.421  23.405  30.062    0.00     3.58
-ATOM    275    O STP     7      -5.071  24.416  29.230    0.00     3.41
-ATOM    276    O STP     7      -4.870  26.897  28.843    0.00     4.69
-ATOM    277    C STP     8      18.480  10.647   8.623    0.00     3.95
-ATOM    278    C STP     8      18.473  10.489   8.873    0.00     3.90
-ATOM    279    C STP     8      18.698  10.488   9.792    0.00     3.67
-ATOM    280    C STP     8      14.943  10.866   4.541    0.00     4.51
-ATOM    281    O STP     8      14.875  10.843   4.459    0.00     4.53
-ATOM    282    O STP     8      14.864  10.355   4.722    0.00     4.07
-ATOM    283    C STP     8      17.917  10.225   9.354    0.00     3.49
-ATOM    284    C STP     8      14.939  11.399   5.926    0.00     4.03
-ATOM    285    C STP     8      16.088  11.832   6.354    0.00     4.19
-ATOM    286    C STP     8      17.345  11.079   8.062    0.00     3.54
-ATOM    287    C STP     8      14.302  11.614   6.290    0.00     3.81
-ATOM    288    C STP     8      14.169  11.576   6.426    0.00     3.68
-ATOM    289    C STP     8      13.282  11.035   4.472    0.00     4.30
-ATOM    290    O STP     8      13.297  11.009   4.410    0.00     4.33
-ATOM    291    C STP     8      13.187  11.021   4.702    0.00     4.11
-ATOM    292    C STP     8      12.553  11.402   3.811    0.00     4.29
-ATOM    293    C STP     8      12.615  11.331   3.695    0.00     4.37
-ATOM    294    C STP     8      16.085  11.834   6.357    0.00     4.19
-ATOM    295    C STP     8      15.342  12.249   7.345    0.00     3.56
-ATOM    296    C STP     8      14.506  12.196   7.034    0.00     3.62
-ATOM    297    C STP     8      14.353  12.486   7.796    0.00     3.41
-ATOM    298    O STP     8      13.277  10.973   4.430    0.00     4.29
-ATOM    299    C STP     8      13.182  11.064   3.370    0.00     4.59
-ATOM    300    O STP     8      13.287  11.012   4.386    0.00     4.34
-ATOM    301    C STP     8      12.716  11.267   3.730    0.00     4.38
-ATOM    302    O STP     9      -5.987  21.597  39.224    0.00     4.67
-ATOM    303    C STP     9      -6.191  22.298  37.656    0.00     3.79
-ATOM    304    O STP     9      -6.290  22.862  37.242    0.00     3.57
-ATOM    305    C STP     9      -6.076  21.951  37.687    0.00     3.87
-ATOM    306    O STP     9      -4.027  21.397  38.848    0.00     3.60
-ATOM    307    O STP     9      -5.569  19.993  39.101    0.00     4.01
-ATOM    308    C STP     9      -6.315  20.503  39.256    0.00     4.60
-ATOM    309    C STP     9      -6.095  21.897  37.670    0.00     3.85
-ATOM    310    C STP     9      -6.531  20.110  38.511    0.00     4.14
-ATOM    311    O STP     9      -5.839  22.040  37.133    0.00     3.50
-ATOM    312    O STP     9      -6.021  22.227  37.054    0.00     3.55
-ATOM    313    O STP     9      -6.062  21.968  37.603    0.00     3.83
-ATOM    314    O STP     9      -8.206  18.652  36.918    0.00     3.45
-ATOM    315    O STP     9      -8.120  18.521  37.184    0.00     3.65
-ATOM    316    C STP     9      -6.229  19.490  37.843    0.00     3.48
-ATOM    317    O STP     9      -9.377  17.540  38.316    0.00     4.06
-ATOM    318    C STP     9      -9.701  17.858  38.776    0.00     4.51
-ATOM    319    O STP    10       7.964  27.871  24.200    0.00     3.67
-ATOM    320    O STP    10       9.060  27.846  24.971    0.00     4.48
-ATOM    321    O STP    10       8.457  27.440  25.735    0.00     3.83
-ATOM    322    O STP    10       8.568  27.505  25.590    0.00     3.93
-ATOM    323    O STP    10       8.418  27.411  25.750    0.00     3.79
-ATOM    324    O STP    10       9.084  27.764  24.955    0.00     4.46
-ATOM    325    O STP    10      10.654  26.047  25.364    0.00     3.76
-ATOM    326    O STP    10      10.424  27.853  24.712    0.00     4.67
-ATOM    327    O STP    10       9.439  27.576  24.860    0.00     4.44
-ATOM    328    O STP    10      10.404  26.714  24.932    0.00     4.18
-ATOM    329    O STP    10      10.731  27.817  24.294    0.00     4.46
-ATOM    330    O STP    10      10.476  26.400  24.885    0.00     4.02
-ATOM    331    O STP    10      11.588  27.014  23.248    0.00     3.77
-ATOM    332    O STP    10      11.536  26.189  23.460    0.00     3.42
-ATOM    333    O STP    10       8.935  27.351  24.682    0.00     4.15
-ATOM    334    O STP    10      10.729  25.699  25.632    0.00     3.55
-ATOM    335    O STP    10      10.887  25.711  25.706    0.00     3.52
-ATOM    336    O STP    10      10.424  26.232  24.837    0.00     3.90
-ATOM    337    O STP    10       8.612  26.736  24.470    0.00     3.66
-ATOM    338    O STP    11       3.065   1.680  14.257    0.00     3.59
-ATOM    339    O STP    11      -0.262   5.672  13.713    0.00     3.61
-ATOM    340    O STP    11       0.191   4.442  13.421    0.00     4.24
-ATOM    341    O STP    11       2.560   3.835  10.859    0.00     4.30
-ATOM    342    O STP    11      -0.316   5.894  13.740    0.00     3.52
-ATOM    343    O STP    11       3.457   4.032   6.967    0.00     3.95
-ATOM    344    O STP    11       2.663   3.891  10.841    0.00     4.26
-ATOM    345    O STP    11       4.096   4.245  10.995    0.00     3.57
-ATOM    346    O STP    11       4.136   4.217  10.924    0.00     3.55
-ATOM    347    O STP    11       3.244   4.177  11.181    0.00     3.96
-ATOM    348    O STP    11       3.188   4.166  11.182    0.00     3.99
-ATOM    349    O STP    11       2.014   3.532  11.198    0.00     4.50
-ATOM    350    O STP    11       2.518   3.690  10.662    0.00     4.31
-ATOM    351    O STP    11       2.689   3.819  10.691    0.00     4.24
-ATOM    352    O STP    11       2.118   3.108   9.175    0.00     4.30
-ATOM    353    O STP    11       3.327   3.642   7.482    0.00     4.08
-ATOM    354    O STP    11       4.123   4.188  10.873    0.00     3.55
-ATOM    355    O STP    11       4.234   4.163  10.882    0.00     3.47
-ATOM    356    O STP    11       2.703   1.870  14.067    0.00     3.79
-ATOM    357    C STP    11       2.011   3.354  12.335    0.00     4.36
-ATOM    358    O STP    11       1.265   3.803  14.371    0.00     4.24
-ATOM    359    O STP    11       1.313   3.846  14.395    0.00     4.19
-ATOM    360    O STP    11       4.151   4.474  11.146    0.00     3.47
-ATOM    361    O STP    11       3.883   4.476  11.221    0.00     3.57
-ATOM    362    O STP    12     -12.188  31.839  16.593    0.00     3.49
-ATOM    363    O STP    12     -14.197  27.278  17.645    0.00     4.05
-ATOM    364    O STP    12     -14.250  26.710  18.687    0.00     4.47
-ATOM    365    O STP    12     -14.909  26.223  19.335    0.00     4.57
-ATOM    366    C STP    12     -14.382  24.675  18.050    0.00     3.53
-ATOM    367    O STP    12     -14.022  26.981  18.887    0.00     4.51
-ATOM    368    O STP    12     -13.149  28.055  17.189    0.00     3.54
-ATOM    369    O STP    12     -13.848  27.808  17.708    0.00     4.07
-ATOM    370    O STP    12     -13.798  28.442  17.460    0.00     3.88
-ATOM    371    O STP    12     -13.798  28.303  17.460    0.00     3.92
-ATOM    372    O STP    12     -13.804  28.284  17.472    0.00     3.93
-ATOM    373    O STP    12     -13.734  30.649  17.420    0.00     3.89
-ATOM    374    O STP    12     -13.444  31.621  17.292    0.00     4.09
-ATOM    375    O STP    12     -13.757  31.663  17.802    0.00     4.23
-ATOM    376    O STP    12     -12.392  31.711  16.849    0.00     3.60
-ATOM    377    O STP    12     -14.320  27.344  17.475    0.00     3.92
-ATOM    378    O STP    12     -14.498  27.355  17.384    0.00     3.78
+ATOM    168    O STP     3      21.608   9.684  14.132    0.00     3.86
+ATOM    169    C STP     3      19.314  10.586   9.512    0.00     3.90
+ATOM    170    C STP     3      19.143  10.766   9.300    0.00     4.01
+ATOM    171    O STP     3      22.337  10.819  11.219    0.00     4.13
+ATOM    172    O STP     3      21.322  10.417  10.839    0.00     3.73
+ATOM    173    O STP     3      22.223   9.452  12.843    0.00     4.32
+ATOM    174    C STP     3      20.438   9.717  10.950    0.00     3.59
+ATOM    175    C STP     3      19.317  10.526   9.567    0.00     3.87
+ATOM    176    C STP     3      20.347   9.733  10.882    0.00     3.58
+ATOM    177    O STP     3      20.400   9.647  10.930    0.00     3.55
+ATOM    178    C STP     3      18.480  10.647   8.623    0.00     3.95
+ATOM    179    C STP     3      18.473  10.489   8.873    0.00     3.90
+ATOM    180    C STP     3      19.091  10.740   9.309    0.00     4.00
+ATOM    181    C STP     3      19.039  10.663   9.363    0.00     3.98
+ATOM    182    C STP     3      18.698  10.488   9.792    0.00     3.67
+ATOM    183    C STP     3      20.605   6.618  21.102    0.00     3.76
+ATOM    184    C STP     3      14.943  10.866   4.541    0.00     4.51
+ATOM    185    O STP     3      14.875  10.843   4.459    0.00     4.53
+ATOM    186    O STP     3      14.864  10.355   4.722    0.00     4.07
+ATOM    187    C STP     3      18.270  10.051   6.298    0.00     3.72
+ATOM    188    C STP     3      17.917  10.225   9.354    0.00     3.49
+ATOM    189    C STP     3      14.939  11.399   5.926    0.00     4.03
+ATOM    190    C STP     3      16.088  11.832   6.354    0.00     4.19
+ATOM    191    C STP     3      17.345  11.079   8.062    0.00     3.54
+ATOM    192    C STP     3      14.302  11.614   6.290    0.00     3.81
+ATOM    193    C STP     3      14.169  11.576   6.426    0.00     3.68
+ATOM    194    C STP     3      21.260   9.781  14.385    0.00     3.65
+ATOM    195    O STP     3      19.082   9.114  16.906    0.00     3.51
+ATOM    196    C STP     3      23.299   6.241  21.535    0.00     4.32
+ATOM    197    C STP     3      19.211   8.868  16.477    0.00     3.41
+ATOM    198    O STP     3      19.141   9.065  16.855    0.00     3.52
+ATOM    199    C STP     3      20.411   8.950  16.497    0.00     4.01
+ATOM    200    C STP     3      21.278   7.286  15.271    0.00     3.95
+ATOM    201    C STP     3      21.737   8.273  15.966    0.00     4.55
+ATOM    202    C STP     3      19.545   9.253  17.348    0.00     3.83
+ATOM    203    C STP     3      19.605   9.305  17.253    0.00     3.89
+ATOM    204    C STP     3      19.361   9.202  17.087    0.00     3.71
+ATOM    205    O STP     3      21.824   7.092  13.097    0.00     4.01
+ATOM    206    O STP     3      21.005   6.678  13.902    0.00     3.49
+ATOM    207    C STP     3      21.887   7.048  14.721    0.00     4.32
+ATOM    208    O STP     3      21.396   7.252  12.616    0.00     3.62
+ATOM    209    C STP     3      13.282  11.035   4.472    0.00     4.30
+ATOM    210    O STP     3      13.297  11.009   4.410    0.00     4.33
+ATOM    211    C STP     3      13.187  11.021   4.702    0.00     4.11
+ATOM    212    C STP     3      12.553  11.402   3.811    0.00     4.29
+ATOM    213    C STP     3      12.615  11.331   3.695    0.00     4.37
+ATOM    214    C STP     3      16.085  11.834   6.357    0.00     4.19
+ATOM    215    C STP     3      15.342  12.249   7.345    0.00     3.56
+ATOM    216    C STP     3      14.506  12.196   7.034    0.00     3.62
+ATOM    217    C STP     3      14.353  12.486   7.796    0.00     3.41
+ATOM    218    C STP     3      21.576   8.462  17.094    0.00     4.39
+ATOM    219    C STP     3      21.237   8.164  17.688    0.00     3.98
+ATOM    220    C STP     3      19.823   9.314  17.205    0.00     3.96
+ATOM    221    C STP     3      19.842   9.288  17.195    0.00     3.97
+ATOM    222    C STP     3      19.813   9.293  17.207    0.00     3.96
+ATOM    223    C STP     3      23.114   7.517  18.754    0.00     4.38
+ATOM    224    C STP     3      23.216   7.267  19.612    0.00     4.27
+ATOM    225    C STP     3      21.455   7.159  19.578    0.00     3.62
+ATOM    226    C STP     3      19.601   8.988  17.728    0.00     3.65
+ATOM    227    C STP     3      20.637   6.657  21.076    0.00     3.77
+ATOM    228    C STP     3      21.991   6.742  21.095    0.00     3.92
+ATOM    229    C STP     3      20.614   6.661  21.080    0.00     3.77
+ATOM    230    O STP     3      13.277  10.973   4.430    0.00     4.29
+ATOM    231    C STP     3      13.182  11.064   3.370    0.00     4.59
+ATOM    232    O STP     3      13.287  11.012   4.386    0.00     4.34
+ATOM    233    C STP     3      12.716  11.267   3.730    0.00     4.38
+ATOM    234    C STP     3      20.578   6.679  21.067    0.00     3.75
+ATOM    235    C STP     3      20.573   6.576  21.121    0.00     3.74
+ATOM    236    O STP     3      19.279  10.317  17.326    0.00     3.47
+ATOM    237    C STP     3      19.218  10.275  17.340    0.00     3.46
+ATOM    238    O STP     4     -13.394   8.035  11.699    0.00     3.75
+ATOM    239    O STP     4     -13.866   8.149  12.756    0.00     4.22
+ATOM    240    O STP     4     -13.235   6.985  13.878    0.00     3.71
+ATOM    241    C STP     4     -13.396  13.376  12.554    0.00     3.64
+ATOM    242    O STP     4     -14.773   7.681  13.727    0.00     4.61
+ATOM    243    C STP     4     -14.552   8.323  12.854    0.00     4.64
+ATOM    244    C STP     4     -14.690   7.717  13.852    0.00     4.48
+ATOM    245    C STP     4     -13.947  10.342   9.126    0.00     3.72
+ATOM    246    C STP     4     -12.889   8.488   9.768    0.00     3.44
+ATOM    247    O STP     4     -14.059  10.991   9.026    0.00     3.83
+ATOM    248    C STP     4     -12.850  13.648  12.578    0.00     3.53
+ATOM    249    C STP     4     -12.635  13.830  12.726    0.00     3.42
+ATOM    250    C STP     4     -15.321  12.050   6.421    0.00     3.91
+ATOM    251    C STP     4     -15.149  12.299   5.990    0.00     3.77
+ATOM    252    C STP     4     -14.138  13.128   4.148    0.00     3.73
+ATOM    253    O STP     4     -13.842  12.966   4.202    0.00     3.54
+ATOM    254    C STP     4     -14.202  12.998   4.431    0.00     3.63
+ATOM    255    C STP     4     -15.071  12.945  11.123    0.00     4.55
+ATOM    256    C STP     4     -15.181  12.284   7.101    0.00     3.70
+ATOM    257    C STP     4     -14.069  13.525  10.889    0.00     4.05
+ATOM    258    C STP     4     -14.486  12.345   9.698    0.00     4.10
+ATOM    259    C STP     4     -15.581  11.691   7.702    0.00     4.30
+ATOM    260    C STP     4     -13.744  12.589   9.720    0.00     3.59
+ATOM    261    C STP     4     -13.903  13.601  10.918    0.00     3.98
+ATOM    262    C STP     4     -13.004  13.765  11.916    0.00     3.53
+ATOM    263    C STP     4     -12.804  14.399  11.014    0.00     3.51
+ATOM    264    O STP     4     -14.691   7.701  13.857    0.00     4.48
+ATOM    265    O STP     4     -14.353   7.367  13.918    0.00     4.32
+ATOM    266    O STP     4     -14.766   7.663  13.746    0.00     4.60
+ATOM    267    C STP     4     -13.822  14.302  10.714    0.00     3.55
+ATOM    268    C STP     4     -12.793  14.411  11.014    0.00     3.51
+ATOM    269    O STP     5      16.547  23.639  13.890    0.00     4.14
+ATOM    270    O STP     5      16.092  23.630  14.033    0.00     4.24
+ATOM    271    C STP     5      15.859  23.404  14.170    0.00     4.10
+ATOM    272    C STP     5      15.557  23.398  14.576    0.00     4.15
+ATOM    273    O STP     5      16.011  22.871  13.482    0.00     3.59
+ATOM    274    C STP     5      15.928  23.207  13.765    0.00     3.90
+ATOM    275    O STP     5      17.691  22.245  18.072    0.00     3.56
+ATOM    276    O STP     5      19.529  21.954  18.755    0.00     4.34
+ATOM    277    C STP     5      15.011  22.229  15.825    0.00     3.58
+ATOM    278    O STP     5      15.135  20.552  18.741    0.00     3.44
+ATOM    279    O STP     5      19.253  21.725  18.788    0.00     4.16
+ATOM    280    O STP     5      17.650  21.048  18.652    0.00     3.48
+ATOM    281    O STP     5      16.195  21.162  18.168    0.00     3.43
+ATOM    282    O STP     5      15.398  20.983  17.666    0.00     3.45
+ATOM    283    O STP     5      15.138  20.557  18.735    0.00     3.44
+ATOM    284    O STP     5      16.943  21.983  17.981    0.00     3.42
+ATOM    285    O STP     5      15.182  22.714  15.737    0.00     3.78
+ATOM    286    O STP     5      15.741  24.064  14.855    0.00     4.60
+ATOM    287    O STP     5      15.109  20.220  19.179    0.00     3.40
+ATOM    288    O STP     6     -10.865  18.249   0.469    0.00     4.11
+ATOM    289    O STP     6      -9.803  18.840   1.772    0.00     3.43
+ATOM    290    O STP     6     -11.664  16.564   0.901    0.00     3.69
+ATOM    291    O STP     6     -10.854  18.060   0.590    0.00     3.96
+ATOM    292    C STP     6      -9.018  19.707   1.368    0.00     3.86
+ATOM    293    O STP     6      -9.656  19.088   1.638    0.00     3.56
+ATOM    294    O STP     6     -10.831  18.316   0.411    0.00     4.14
+ATOM    295    C STP     6      -8.858  20.212   1.689    0.00     3.70
+ATOM    296    C STP     6      -8.626  20.731   1.519    0.00     3.88
+ATOM    297    O STP     6      -9.829  18.933   1.649    0.00     3.53
+ATOM    298    C STP     6     -12.817  19.837  -0.592    0.00     4.00
+ATOM    299    O STP     6     -10.800  18.318   0.530    0.00     4.08
+ATOM    300    O STP     6      -9.908  18.876   1.592    0.00     3.54
+ATOM    301    O STP     6     -11.221  20.512  -0.292    0.00     3.59
+ATOM    302    O STP     6      -8.604  20.710   1.295    0.00     4.00
+ATOM    303    O STP     6      -8.165  20.787   0.269    0.00     4.57
+ATOM    304    O STP     6      -8.676  20.220   0.368    0.00     4.52
+ATOM    305    O STP     7       0.606  30.613  17.291    0.00     3.76
+ATOM    306    O STP     7       0.349  29.933  16.102    0.00     3.64
+ATOM    307    O STP     7       0.398  29.825  16.006    0.00     3.59
+ATOM    308    O STP     7       0.310  30.058  15.886    0.00     3.64
+ATOM    309    O STP     7      -2.704  33.369  14.954    0.00     3.46
+ATOM    310    O STP     7       0.267  30.094  15.812    0.00     3.62
+ATOM    311    O STP     7       0.297  30.167  15.803    0.00     3.64
+ATOM    312    O STP     7      -1.603  34.311  14.914    0.00     4.52
+ATOM    313    O STP     7      -1.370  34.089  14.976    0.00     4.40
+ATOM    314    O STP     7       0.328  30.306  15.653    0.00     3.60
+ATOM    315    O STP     7       0.297  30.561  15.738    0.00     3.64
+ATOM    316    O STP     7      -0.300  32.461  15.359    0.00     3.76
+ATOM    317    O STP     7      -1.581  33.922  14.529    0.00     4.09
+ATOM    318    O STP     7      -2.185  34.279  14.137    0.00     4.26
+ATOM    319    O STP     7      -3.286  34.022  12.999    0.00     4.08
+ATOM    320    O STP     7      -3.344  34.741  12.491    0.00     4.54
+ATOM    321    C STP     8     -14.456  28.897   9.357    0.00     3.95
+ATOM    322    C STP     8     -13.802  30.114  10.708    0.00     3.44
+ATOM    323    C STP     8     -14.824  28.441   8.989    0.00     4.23
+ATOM    324    C STP     8     -13.008  26.082  10.497    0.00     3.45
+ATOM    325    C STP     8     -14.169  30.414   7.585    0.00     4.49
+ATOM    326    O STP     8     -13.292  25.512  10.645    0.00     3.56
+ATOM    327    O STP     8     -16.281  25.248   9.782    0.00     3.64
+ATOM    328    O STP     8     -13.777  25.706   9.765    0.00     4.01
+ATOM    329    O STP     8     -15.422  24.602   9.978    0.00     3.53
+ATOM    330    O STP     8     -13.889  25.617   9.542    0.00     4.12
+ATOM    331    O STP     8     -13.906  25.623   9.573    0.00     4.13
+ATOM    332    O STP     8     -15.206  25.827   9.088    0.00     4.26
+ATOM    333    O STP     8     -13.401  24.066  10.900    0.00     3.67
+ATOM    334    C STP     8     -13.617  23.729  11.105    0.00     3.58
+ATOM    335    C STP     8     -14.727  26.185   8.926    0.00     4.51
+ATOM    336    C STP     8     -14.636  26.121   9.005    0.00     4.46
+ATOM    337    O STP     8     -14.732  26.170   8.943    0.00     4.50
+ATOM    338    C STP     8     -13.644  23.175  11.257    0.00     3.43
+ATOM    339    O STP     9      -6.625  24.421  30.057    0.00     3.72
+ATOM    340    O STP     9      -5.799  26.309  29.404    0.00     4.28
+ATOM    341    O STP     9      -6.778  24.418  30.031    0.00     3.69
+ATOM    342    O STP     9      -8.308  22.685  29.725    0.00     3.61
+ATOM    343    O STP     9      -7.037  21.813  30.245    0.00     3.44
+ATOM    344    C STP     9     -10.258  22.548  28.497    0.00     4.05
+ATOM    345    C STP     9      -9.562  22.615  29.037    0.00     3.80
+ATOM    346    C STP     9      -7.102  21.786  30.244    0.00     3.44
+ATOM    347    C STP     9      -8.874  22.184  29.811    0.00     3.72
+ATOM    348    C STP     9      -9.179  22.095  30.112    0.00     3.56
+ATOM    349    C STP     9      -9.225  22.114  29.661    0.00     3.78
+ATOM    350    C STP     9      -6.839  21.824  30.201    0.00     3.40
+ATOM    351    O STP     9      -6.761  22.668  29.984    0.00     3.54
+ATOM    352    O STP     9      -6.848  22.141  30.159    0.00     3.46
+ATOM    353    O STP     9      -6.421  23.405  30.062    0.00     3.58
+ATOM    354    O STP     9      -5.071  24.416  29.230    0.00     3.41
+ATOM    355    O STP     9      -4.870  26.897  28.843    0.00     4.69
+ATOM    356    O STP    10       7.964  27.871  24.200    0.00     3.67
+ATOM    357    O STP    10       9.060  27.846  24.971    0.00     4.48
+ATOM    358    O STP    10       8.457  27.440  25.735    0.00     3.83
+ATOM    359    O STP    10       8.568  27.505  25.590    0.00     3.93
+ATOM    360    O STP    10       8.418  27.411  25.750    0.00     3.79
+ATOM    361    O STP    10       9.084  27.764  24.955    0.00     4.46
+ATOM    362    O STP    10      10.654  26.047  25.364    0.00     3.76
+ATOM    363    O STP    10      10.424  27.853  24.712    0.00     4.67
+ATOM    364    O STP    10       9.439  27.576  24.860    0.00     4.44
+ATOM    365    O STP    10      10.404  26.714  24.932    0.00     4.18
+ATOM    366    O STP    10      10.731  27.817  24.294    0.00     4.46
+ATOM    367    O STP    10      10.476  26.400  24.885    0.00     4.02
+ATOM    368    O STP    10      11.588  27.014  23.248    0.00     3.77
+ATOM    369    O STP    10      11.536  26.189  23.460    0.00     3.42
+ATOM    370    O STP    10       8.935  27.351  24.682    0.00     4.15
+ATOM    371    O STP    10      10.729  25.699  25.632    0.00     3.55
+ATOM    372    O STP    10      10.887  25.711  25.706    0.00     3.52
+ATOM    373    O STP    10      10.424  26.232  24.837    0.00     3.90
+ATOM    374    O STP    10       8.612  26.736  24.470    0.00     3.66
+ATOM    375    O STP    11      -6.365  24.332  39.128    0.00     4.28
+ATOM    376    O STP    11      -6.009  21.659  39.280    0.00     4.69
+ATOM    377    O STP    11      -5.987  21.597  39.224    0.00     4.67
+ATOM    378    C STP    11      -6.191  22.298  37.656    0.00     3.79
+ATOM    379    O STP    11      -6.290  22.862  37.242    0.00     3.57
+ATOM    380    C STP    11      -6.076  21.951  37.687    0.00     3.87
+ATOM    381    O STP    11      -4.027  21.397  38.848    0.00     3.60
+ATOM    382    O STP    11      -5.569  19.993  39.101    0.00     4.01
+ATOM    383    C STP    11      -6.315  20.503  39.256    0.00     4.60
+ATOM    384    C STP    11      -6.095  21.897  37.670    0.00     3.85
+ATOM    385    C STP    11      -6.531  20.110  38.511    0.00     4.14
+ATOM    386    O STP    11      -5.839  22.040  37.133    0.00     3.50
+ATOM    387    O STP    11      -6.021  22.227  37.054    0.00     3.55
+ATOM    388    O STP    11      -6.062  21.968  37.603    0.00     3.83
+ATOM    389    O STP    11      -8.206  18.652  36.918    0.00     3.45
+ATOM    390    O STP    11      -8.120  18.521  37.184    0.00     3.65
+ATOM    391    C STP    11      -6.229  19.490  37.843    0.00     3.48
+ATOM    392    O STP    11      -9.377  17.540  38.316    0.00     4.06
+ATOM    393    C STP    11      -9.701  17.858  38.776    0.00     4.51
+ATOM    394    O STP    12       3.065   1.680  14.257    0.00     3.59
+ATOM    395    O STP    12      -0.262   5.672  13.713    0.00     3.61
+ATOM    396    O STP    12       0.191   4.442  13.421    0.00     4.24
+ATOM    397    O STP    12       2.560   3.835  10.859    0.00     4.30
+ATOM    398    O STP    12      -0.316   5.894  13.740    0.00     3.52
+ATOM    399    O STP    12       3.457   4.032   6.967    0.00     3.95
+ATOM    400    O STP    12       2.663   3.891  10.841    0.00     4.26
+ATOM    401    O STP    12       4.096   4.245  10.995    0.00     3.57
+ATOM    402    O STP    12       4.136   4.217  10.924    0.00     3.55
+ATOM    403    O STP    12       3.244   4.177  11.181    0.00     3.96
+ATOM    404    O STP    12       3.188   4.166  11.182    0.00     3.99
+ATOM    405    O STP    12       2.014   3.532  11.198    0.00     4.50
+ATOM    406    O STP    12       2.518   3.690  10.662    0.00     4.31
+ATOM    407    O STP    12       2.689   3.819  10.691    0.00     4.24
+ATOM    408    O STP    12       2.118   3.108   9.175    0.00     4.30
+ATOM    409    O STP    12       3.327   3.642   7.482    0.00     4.08
+ATOM    410    O STP    12       4.123   4.188  10.873    0.00     3.55
+ATOM    411    O STP    12       4.234   4.163  10.882    0.00     3.47
+ATOM    412    O STP    12       2.703   1.870  14.067    0.00     3.79
+ATOM    413    C STP    12       2.011   3.354  12.335    0.00     4.36
+ATOM    414    O STP    12       1.265   3.803  14.371    0.00     4.24
+ATOM    415    O STP    12       1.313   3.846  14.395    0.00     4.19
+ATOM    416    O STP    12       4.151   4.474  11.146    0.00     3.47
+ATOM    417    O STP    12       3.883   4.476  11.221    0.00     3.57
+ATOM    418    O STP    13     -12.188  31.839  16.593    0.00     3.49
+ATOM    419    O STP    13     -13.844  30.372  17.279    0.00     3.73
+ATOM    420    O STP    13     -14.197  27.278  17.645    0.00     4.05
+ATOM    421    O STP    13     -14.250  26.710  18.687    0.00     4.47
+ATOM    422    O STP    13     -14.909  26.223  19.335    0.00     4.57
+ATOM    423    C STP    13     -14.382  24.675  18.050    0.00     3.53
+ATOM    424    O STP    13     -14.022  26.981  18.887    0.00     4.51
+ATOM    425    O STP    13     -13.149  28.055  17.189    0.00     3.54
+ATOM    426    O STP    13     -13.848  27.808  17.708    0.00     4.07
+ATOM    427    O STP    13     -13.798  28.442  17.460    0.00     3.88
+ATOM    428    O STP    13     -13.798  28.303  17.460    0.00     3.92
+ATOM    429    O STP    13     -13.804  28.284  17.472    0.00     3.93
+ATOM    430    O STP    13     -13.734  30.649  17.420    0.00     3.89
+ATOM    431    O STP    13     -13.444  31.621  17.292    0.00     4.09
+ATOM    432    O STP    13     -13.757  31.663  17.802    0.00     4.23
+ATOM    433    O STP    13     -12.392  31.711  16.849    0.00     3.60
+ATOM    434    C STP    13     -14.327  27.424  17.420    0.00     3.87
+ATOM    435    O STP    13     -14.320  27.344  17.475    0.00     3.92
+ATOM    436    O STP    13     -14.498  27.355  17.384    0.00     3.78
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket10_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of alpha spheres           :    19
 HEADER 3  - Mean alpha-sphere radius          : 3.9820
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5960
-HEADER 5  - Mean B-factor of pocket residues  : 0.1384
+HEADER 5  - Mean B-factor of pocket residues  : 0.0832
 HEADER 6  - Hydrophobicity Score              : 10.6250
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Amino Acid based volume Score     : 3.3750
-HEADER 9  - Pocket volume (Monte Carlo)       : 188.7581
-HEADER 10  -Pocket volume (convex hull)       : 5.5840
+HEADER 9  - Pocket volume (Monte Carlo)       : 190.2617
+HEADER 10 - Pocket volume (convex hull)       : 5.5840
 HEADER 11 - Charge Score                      :     0
 HEADER 12 - Local hydrophobic density Score   : 0.0000
 HEADER 13 - Number of apolar alpha sphere     :     0

tests/reference_output/1UYD_out/pockets/pocket10_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of V. Vertices             :    19
 HEADER 3  - Mean alpha-sphere radius          : 3.9820
 HEADER 4  - Mean alpha-sphere SA              : 0.5960
-HEADER 5  - Mean B-factor                     : 0.1384
+HEADER 5  - Mean B-factor                     : 0.0832
 HEADER 6  - Hydrophobicity Score              : 10.6250
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 3.3750
-HEADER 9  - Real volume (approximation)       : 188.7581
+HEADER 9  - Real volume (approximation)       : 190.2617
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 0.0000
 HEADER 12 - Number of apolar alpha sphere     :     0

tests/reference_output/1UYD_out/pockets/pocket11_atm.pdb

@@ -3,43 +3,37 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    11:
-HEADER 0  - Pocket Score                      : -0.0850
-HEADER 1  - Drug Score                        : 0.0001
-HEADER 2  - Number of alpha spheres           :    24
-HEADER 3  - Mean alpha-sphere radius          : 3.9413
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6305
-HEADER 5  - Mean B-factor of pocket residues  : 0.4193
-HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 0  - Pocket Score                      : -0.0709
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9530
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5838
+HEADER 5  - Mean B-factor of pocket residues  : 0.4039
+HEADER 6  - Hydrophobicity Score              : -8.6667
 HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Amino Acid based volume Score     : 3.5714
-HEADER 9  - Pocket volume (Monte Carlo)       : 314.7152
-HEADER 10  -Pocket volume (convex hull)       : 23.7268
-HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 0.0000
-HEADER 13 - Number of apolar alpha sphere     :     1
-HEADER 14 - Proportion of apolar alpha sphere : 0.0417
-ATOM    905   CG GLN A 133       5.839   1.301  12.015  0.00  0.00           C 0
-ATOM    900    N GLN A 133       6.065   3.614  13.906  0.65  2.19           N 0
-ATOM    899    O GLY A 132       5.184   4.004  15.981  0.41  9.64           O 0
-ATOM    901   CA GLN A 133       6.602   2.274  14.225  0.00  0.00           C 0
-ATOM    288   CB SER A  50      -2.318   6.388  16.587  0.00  0.00           C 0
-ATOM    266  OE1 GLU A  47       2.544   7.847  14.341  0.46  3.21           O 0
-ATOM    289   OG SER A  50      -1.198   5.792  17.193  0.42  8.57           O 0
-ATOM    254   CD ARG A  46      -1.055   7.401  10.651  0.00  0.00           C 0
-ATOM    267  OE2 GLU A  47       2.264   7.922  12.168  0.62  2.14           O 0
-ATOM    256   CZ ARG A  46       0.655   7.138   8.868  0.00  0.00           C 0
-ATOM    258  NH2 ARG A  46       1.902   7.340   8.454  0.00  0.00           N 0
-ATOM    251    O ARG A  46      -2.341   8.640  14.586  0.42  1.07           O 0
-ATOM    877    O SER A 129       4.713   7.157   9.023  0.00  0.00           O 0
-ATOM    885   CG MET A 130       7.387   4.013   7.315  0.00  0.00           C 0
-ATOM    879   OG SER A 129       5.275   7.233   5.546  0.00  0.00           O 0
-ATOM    883    O MET A 130       7.577   4.779  11.583  0.00  0.00           O 0
-ATOM    881   CA MET A 130       7.027   5.523   9.334  0.00  0.00           C 0
-ATOM    897   CA GLY A 132       5.029   5.773  14.338  0.00  0.00           C 0
-ATOM    255   NE ARG A  46       0.290   7.541  10.087  0.49  1.09           N 0
-ATOM    908  NE2 GLN A 133       6.088   1.519   9.608  0.00  0.00           N 0
-ATOM    257  NH1 ARG A  46      -0.217   6.541   8.063  0.00  0.00           N 0
-ATOM    898    C GLY A 132       5.444   4.381  14.811  0.00  0.00           C 0
-ATOM    896    N GLY A 132       5.940   6.411  13.397  0.00  0.00           N 0
+HEADER 8  - Amino Acid based volume Score     : 3.3333
+HEADER 9  - Pocket volume (Monte Carlo)       : 327.2880
+HEADER 10 - Pocket volume (convex hull)       : 18.5031
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 6.0000
+HEADER 13 - Number of apolar alpha sphere     :     7
+HEADER 14 - Proportion of apolar alpha sphere : 0.3684
+ATOM   1248    O GLY A 177      -7.087  25.609  35.109  0.58  3.21           O 0
+ATOM   1263   CG PRO A 179      -9.842  23.072  36.977  0.00  0.00           C 0
+ATOM   1233    O ASP A 175      -2.967  23.964  36.554  0.52  6.43           O 0
+ATOM   1241    O THR A 176      -5.738  27.556  36.386  0.54  9.64           O 0
+ATOM   1262   CB PRO A 179      -9.732  21.711  36.429  0.00  0.00           C 0
+ATOM   1106  OE2 GLU A 158      -2.440  19.673  41.584  0.00  0.00           O 0
+ATOM   1111   CB GLN A 159      -3.563  19.835  35.636  0.00  0.00           C 0
+ATOM   1259   CA PRO A 179      -8.962  21.849  35.105  0.00  0.00           C 0
+ATOM   1107    N GLN A 159      -2.228  18.673  37.326  0.63  2.19           N 0
+ATOM   1062   CE LYS A 153      -5.591  16.089  38.200  0.00  0.00           C 0
+ATOM   1114  OE1 GLN A 159      -6.210  19.893  34.388  0.76  2.14           O 0
+ATOM   1113   CD GLN A 159      -5.304  20.600  33.983  0.00  0.00           C 0
+ATOM   1273    N GLY A 181      -9.984  17.239  34.316  0.59  3.28           N 0
+ATOM   1265    N MET A 180      -8.985  19.796  33.754  0.61  1.09           N 0
+ATOM   1061   CD LYS A 153      -4.956  16.412  36.840  0.00  0.00           C 0
+ATOM   1274   CA GLY A 181     -10.573  15.994  34.761  0.00  0.00           C 0
+ATOM   1276    O GLY A 181      -9.088  14.413  35.748  0.70  5.36           O 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket11_vert.pqr

@@ -4,43 +4,38 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    11:
-HEADER 0  - Pocket Score                      : -0.0850
-HEADER 1  - Drug Score                        : 0.0001
-HEADER 2  - Number of V. Vertices             :    24
-HEADER 3  - Mean alpha-sphere radius          : 3.9413
-HEADER 4  - Mean alpha-sphere SA              : 0.6305
-HEADER 5  - Mean B-factor                     : 0.4193
-HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 0  - Pocket Score                      : -0.0709
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9530
+HEADER 4  - Mean alpha-sphere SA              : 0.5838
+HEADER 5  - Mean B-factor                     : 0.4039
+HEADER 6  - Hydrophobicity Score              : -8.6667
 HEADER 7  - Polarity Score                    :     5
-HEADER 8  - Volume Score                      : 3.5714
-HEADER 9  - Real volume (approximation)       : 314.7152
-HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 0.0000
-HEADER 12 - Number of apolar alpha sphere     :     1
-HEADER 13 - Proportion of apolar alpha sphere : 0.0417
-ATOM      1    O STP    11       3.065   1.680  14.257    0.00     3.59
-ATOM      2    O STP    11      -0.262   5.672  13.713    0.00     3.61
-ATOM      3    O STP    11       0.191   4.442  13.421    0.00     4.24
-ATOM      4    O STP    11       2.560   3.835  10.859    0.00     4.30
-ATOM      5    O STP    11      -0.316   5.894  13.740    0.00     3.52
-ATOM      6    O STP    11       3.457   4.032   6.967    0.00     3.95
-ATOM      7    O STP    11       2.663   3.891  10.841    0.00     4.26
-ATOM      8    O STP    11       4.096   4.245  10.995    0.00     3.57
-ATOM      9    O STP    11       4.136   4.217  10.924    0.00     3.55
-ATOM     10    O STP    11       3.244   4.177  11.181    0.00     3.96
-ATOM     11    O STP    11       3.188   4.166  11.182    0.00     3.99
-ATOM     12    O STP    11       2.014   3.532  11.198    0.00     4.50
-ATOM     13    O STP    11       2.518   3.690  10.662    0.00     4.31
-ATOM     14    O STP    11       2.689   3.819  10.691    0.00     4.24
-ATOM     15    O STP    11       2.118   3.108   9.175    0.00     4.30
-ATOM     16    O STP    11       3.327   3.642   7.482    0.00     4.08
-ATOM     17    O STP    11       4.123   4.188  10.873    0.00     3.55
-ATOM     18    O STP    11       4.234   4.163  10.882    0.00     3.47
-ATOM     19    O STP    11       2.703   1.870  14.067    0.00     3.79
-ATOM     20    C STP    11       2.011   3.354  12.335    0.00     4.36
-ATOM     21    O STP    11       1.265   3.803  14.371    0.00     4.24
-ATOM     22    O STP    11       1.313   3.846  14.395    0.00     4.19
-ATOM     23    O STP    11       4.151   4.474  11.146    0.00     3.47
-ATOM     24    O STP    11       3.883   4.476  11.221    0.00     3.57
+HEADER 8  - Volume Score                      : 3.3333
+HEADER 9  - Real volume (approximation)       : 327.2880
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 6.0000
+HEADER 12 - Number of apolar alpha sphere     :     7
+HEADER 13 - Proportion of apolar alpha sphere : 0.3684
+ATOM      1    O STP    11      -6.365  24.332  39.128    0.00     4.28
+ATOM      2    O STP    11      -6.009  21.659  39.280    0.00     4.69
+ATOM      3    O STP    11      -5.987  21.597  39.224    0.00     4.67
+ATOM      4    C STP    11      -6.191  22.298  37.656    0.00     3.79
+ATOM      5    O STP    11      -6.290  22.862  37.242    0.00     3.57
+ATOM      6    C STP    11      -6.076  21.951  37.687    0.00     3.87
+ATOM      7    O STP    11      -4.027  21.397  38.848    0.00     3.60
+ATOM      8    O STP    11      -5.569  19.993  39.101    0.00     4.01
+ATOM      9    C STP    11      -6.315  20.503  39.256    0.00     4.60
+ATOM     10    C STP    11      -6.095  21.897  37.670    0.00     3.85
+ATOM     11    C STP    11      -6.531  20.110  38.511    0.00     4.14
+ATOM     12    O STP    11      -5.839  22.040  37.133    0.00     3.50
+ATOM     13    O STP    11      -6.021  22.227  37.054    0.00     3.55
+ATOM     14    O STP    11      -6.062  21.968  37.603    0.00     3.83
+ATOM     15    O STP    11      -8.206  18.652  36.918    0.00     3.45
+ATOM     16    O STP    11      -8.120  18.521  37.184    0.00     3.65
+ATOM     17    C STP    11      -6.229  19.490  37.843    0.00     3.48
+ATOM     18    O STP    11      -9.377  17.540  38.316    0.00     4.06
+ATOM     19    C STP    11      -9.701  17.858  38.776    0.00     4.51
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket12_atm.pdb

@@ -3,35 +3,43 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket    12:
-HEADER 0  - Pocket Score                      : -0.0943
+HEADER 0  - Pocket Score                      : -0.0850
 HEADER 1  - Drug Score                        : 0.0001
-HEADER 2  - Number of alpha spheres           :    17
-HEADER 3  - Mean alpha-sphere radius          : 3.9685
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4690
-HEADER 5  - Mean B-factor of pocket residues  : 0.6813
-HEADER 6  - Hydrophobicity Score              : 17.1250
-HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Amino Acid based volume Score     : 4.3750
-HEADER 9  - Pocket volume (Monte Carlo)       : 258.9960
-HEADER 10  -Pocket volume (convex hull)       : 6.1907
+HEADER 2  - Number of alpha spheres           :    24
+HEADER 3  - Mean alpha-sphere radius          : 3.9413
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6305
+HEADER 5  - Mean B-factor of pocket residues  : 0.2519
+HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.5714
+HEADER 9  - Pocket volume (Monte Carlo)       : 318.5220
+HEADER 10 - Pocket volume (convex hull)       : 23.7268
 HEADER 11 - Charge Score                      :     0
 HEADER 12 - Local hydrophobic density Score   : 0.0000
 HEADER 13 - Number of apolar alpha sphere     :     1
-HEADER 14 - Proportion of apolar alpha sphere : 0.0588
-ATOM    546  OD1 ASN A  83      -9.060  30.353  17.010  0.00  0.00           O 0
-ATOM    564  OE1 GLN A  85     -11.154  34.993  17.665  0.00  0.00           O 0
-ATOM    561   CB GLN A  85      -9.191  33.552  16.094  0.00  0.00           C 0
-ATOM   1635  OE1 GLU A 223     -12.191  29.432  14.068  0.69  6.43           O 0
-ATOM   1624    O VAL A 222     -16.483  24.967  15.232  0.41  9.64           O 0
-ATOM    536    O PRO A  82     -10.987  25.587  15.850  0.58  5.36           O 0
-ATOM   1633   CG GLU A 223     -13.156  27.273  13.733  0.00  0.00           C 0
-ATOM   1640    O LYS A 224     -17.476  29.652  17.739  0.00  0.00           O 0
-ATOM    531  CG2 ILE A  81     -11.338  23.371  19.262  0.00  0.00           C 0
-ATOM   1617  CD2 PHE A 221     -15.287  21.681  19.679  0.00  0.00           C 0
-ATOM   1614   CB PHE A 221     -14.726  21.255  17.261  0.00  0.00           C 0
-ATOM    547  ND2 ASN A  83     -10.255  29.459  18.675  0.00  0.00           N 0
-ATOM   1638   CA LYS A 224     -16.885  29.440  15.328  0.00  0.00           C 0
-ATOM   1641   CB LYS A 224     -16.523  30.812  14.719  0.00  0.00           C 0
-ATOM   1629   CA GLU A 223     -15.616  27.088  13.785  0.00  0.00           C 0
+HEADER 14 - Proportion of apolar alpha sphere : 0.0417
+ATOM    905   CG GLN A 133       5.839   1.301  12.015  0.00  0.00           C 0
+ATOM    900    N GLN A 133       6.065   3.614  13.906  0.65  2.19           N 0
+ATOM    899    O GLY A 132       5.184   4.004  15.981  0.41  9.64           O 0
+ATOM    901   CA GLN A 133       6.602   2.274  14.225  0.00  0.00           C 0
+ATOM    288   CB SER A  50      -2.318   6.388  16.587  0.00  0.00           C 0
+ATOM    266  OE1 GLU A  47       2.544   7.847  14.341  0.46  3.21           O 0
+ATOM    289   OG SER A  50      -1.198   5.792  17.193  0.42  8.57           O 0
+ATOM    254   CD ARG A  46      -1.055   7.401  10.651  0.00  0.00           C 0
+ATOM    267  OE2 GLU A  47       2.264   7.922  12.168  0.62  2.14           O 0
+ATOM    256   CZ ARG A  46       0.655   7.138   8.868  0.00  0.00           C 0
+ATOM    258  NH2 ARG A  46       1.902   7.340   8.454  0.00  0.00           N 0
+ATOM    251    O ARG A  46      -2.341   8.640  14.586  0.42  1.07           O 0
+ATOM    877    O SER A 129       4.713   7.157   9.023  0.00  0.00           O 0
+ATOM    885   CG MET A 130       7.387   4.013   7.315  0.00  0.00           C 0
+ATOM    879   OG SER A 129       5.275   7.233   5.546  0.00  0.00           O 0
+ATOM    883    O MET A 130       7.577   4.779  11.583  0.00  0.00           O 0
+ATOM    881   CA MET A 130       7.027   5.523   9.334  0.00  0.00           C 0
+ATOM    897   CA GLY A 132       5.029   5.773  14.338  0.00  0.00           C 0
+ATOM    255   NE ARG A  46       0.290   7.541  10.087  0.49  1.09           N 0
+ATOM    908  NE2 GLN A 133       6.088   1.519   9.608  0.00  0.00           N 0
+ATOM    257  NH1 ARG A  46      -0.217   6.541   8.063  0.00  0.00           N 0
+ATOM    898    C GLY A 132       5.444   4.381  14.811  0.00  0.00           C 0
+ATOM    896    N GLY A 132       5.940   6.411  13.397  0.00  0.00           N 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket12_vert.pqr

@@ -4,36 +4,43 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket    12:
-HEADER 0  - Pocket Score                      : -0.0943
+HEADER 0  - Pocket Score                      : -0.0850
 HEADER 1  - Drug Score                        : 0.0001
-HEADER 2  - Number of V. Vertices             :    17
-HEADER 3  - Mean alpha-sphere radius          : 3.9685
-HEADER 4  - Mean alpha-sphere SA              : 0.4690
-HEADER 5  - Mean B-factor                     : 0.6813
-HEADER 6  - Hydrophobicity Score              : 17.1250
-HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Volume Score                      : 4.3750
-HEADER 9  - Real volume (approximation)       : 258.9960
+HEADER 2  - Number of V. Vertices             :    24
+HEADER 3  - Mean alpha-sphere radius          : 3.9413
+HEADER 4  - Mean alpha-sphere SA              : 0.6305
+HEADER 5  - Mean B-factor                     : 0.2519
+HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.5714
+HEADER 9  - Real volume (approximation)       : 318.5220
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 0.0000
 HEADER 12 - Number of apolar alpha sphere     :     1
-HEADER 13 - Proportion of apolar alpha sphere : 0.0588
-ATOM      1    O STP    12     -12.188  31.839  16.593    0.00     3.49
-ATOM      2    O STP    12     -14.197  27.278  17.645    0.00     4.05
-ATOM      3    O STP    12     -14.250  26.710  18.687    0.00     4.47
-ATOM      4    O STP    12     -14.909  26.223  19.335    0.00     4.57
-ATOM      5    C STP    12     -14.382  24.675  18.050    0.00     3.53
-ATOM      6    O STP    12     -14.022  26.981  18.887    0.00     4.51
-ATOM      7    O STP    12     -13.149  28.055  17.189    0.00     3.54
-ATOM      8    O STP    12     -13.848  27.808  17.708    0.00     4.07
-ATOM      9    O STP    12     -13.798  28.442  17.460    0.00     3.88
-ATOM     10    O STP    12     -13.798  28.303  17.460    0.00     3.92
-ATOM     11    O STP    12     -13.804  28.284  17.472    0.00     3.93
-ATOM     12    O STP    12     -13.734  30.649  17.420    0.00     3.89
-ATOM     13    O STP    12     -13.444  31.621  17.292    0.00     4.09
-ATOM     14    O STP    12     -13.757  31.663  17.802    0.00     4.23
-ATOM     15    O STP    12     -12.392  31.711  16.849    0.00     3.60
-ATOM     16    O STP    12     -14.320  27.344  17.475    0.00     3.92
-ATOM     17    O STP    12     -14.498  27.355  17.384    0.00     3.78
+HEADER 13 - Proportion of apolar alpha sphere : 0.0417
+ATOM      1    O STP    12       3.065   1.680  14.257    0.00     3.59
+ATOM      2    O STP    12      -0.262   5.672  13.713    0.00     3.61
+ATOM      3    O STP    12       0.191   4.442  13.421    0.00     4.24
+ATOM      4    O STP    12       2.560   3.835  10.859    0.00     4.30
+ATOM      5    O STP    12      -0.316   5.894  13.740    0.00     3.52
+ATOM      6    O STP    12       3.457   4.032   6.967    0.00     3.95
+ATOM      7    O STP    12       2.663   3.891  10.841    0.00     4.26
+ATOM      8    O STP    12       4.096   4.245  10.995    0.00     3.57
+ATOM      9    O STP    12       4.136   4.217  10.924    0.00     3.55
+ATOM     10    O STP    12       3.244   4.177  11.181    0.00     3.96
+ATOM     11    O STP    12       3.188   4.166  11.182    0.00     3.99
+ATOM     12    O STP    12       2.014   3.532  11.198    0.00     4.50
+ATOM     13    O STP    12       2.518   3.690  10.662    0.00     4.31
+ATOM     14    O STP    12       2.689   3.819  10.691    0.00     4.24
+ATOM     15    O STP    12       2.118   3.108   9.175    0.00     4.30
+ATOM     16    O STP    12       3.327   3.642   7.482    0.00     4.08
+ATOM     17    O STP    12       4.123   4.188  10.873    0.00     3.55
+ATOM     18    O STP    12       4.234   4.163  10.882    0.00     3.47
+ATOM     19    O STP    12       2.703   1.870  14.067    0.00     3.79
+ATOM     20    C STP    12       2.011   3.354  12.335    0.00     4.36
+ATOM     21    O STP    12       1.265   3.803  14.371    0.00     4.24
+ATOM     22    O STP    12       1.313   3.846  14.395    0.00     4.19
+ATOM     23    O STP    12       4.151   4.474  11.146    0.00     3.47
+ATOM     24    O STP    12       3.883   4.476  11.221    0.00     3.57
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket13_atm.pdb

@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    13:
+HEADER 0  - Pocket Score                      : -0.0959
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9509
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4966
+HEADER 5  - Mean B-factor of pocket residues  : 0.4094
+HEADER 6  - Hydrophobicity Score              : 17.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 4.3750
+HEADER 9  - Pocket volume (Monte Carlo)       : 255.7915
+HEADER 10 - Pocket volume (convex hull)       : 6.3124
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.1053
+ATOM    546  OD1 ASN A  83      -9.060  30.353  17.010  0.00  0.00           O 0
+ATOM    564  OE1 GLN A  85     -11.154  34.993  17.665  0.00  0.00           O 0
+ATOM    561   CB GLN A  85      -9.191  33.552  16.094  0.00  0.00           C 0
+ATOM   1635  OE1 GLU A 223     -12.191  29.432  14.068  0.68  7.50           O 0
+ATOM   1638   CA LYS A 224     -16.885  29.440  15.328  0.00  0.00           C 0
+ATOM   1641   CB LYS A 224     -16.523  30.812  14.719  0.00  0.00           C 0
+ATOM   1640    O LYS A 224     -17.476  29.652  17.739  0.00  0.00           O 0
+ATOM   1624    O VAL A 222     -16.483  24.967  15.232  0.41  9.64           O 0
+ATOM    536    O PRO A  82     -10.987  25.587  15.850  0.58  5.36           O 0
+ATOM   1633   CG GLU A 223     -13.156  27.273  13.733  0.00  0.00           C 0
+ATOM    531  CG2 ILE A  81     -11.338  23.371  19.262  0.00  0.00           C 0
+ATOM   1617  CD2 PHE A 221     -15.287  21.681  19.679  0.00  0.00           C 0
+ATOM   1614   CB PHE A 221     -14.726  21.255  17.261  0.00  0.00           C 0
+ATOM    547  ND2 ASN A  83     -10.255  29.459  18.675  0.00  0.00           N 0
+ATOM   1629   CA GLU A 223     -15.616  27.088  13.785  0.00  0.00           C 0
+TER
+END

tests/reference_output/1UYD_out/pockets/pocket13_vert.pqr

@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    13:
+HEADER 0  - Pocket Score                      : -0.0959
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9509
+HEADER 4  - Mean alpha-sphere SA              : 0.4966
+HEADER 5  - Mean B-factor                     : 0.4094
+HEADER 6  - Hydrophobicity Score              : 17.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 4.3750
+HEADER 9  - Real volume (approximation)       : 255.7915
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.1053
+ATOM      1    O STP    13     -12.188  31.839  16.593    0.00     3.49
+ATOM      2    O STP    13     -13.844  30.372  17.279    0.00     3.73
+ATOM      3    O STP    13     -14.197  27.278  17.645    0.00     4.05
+ATOM      4    O STP    13     -14.250  26.710  18.687    0.00     4.47
+ATOM      5    O STP    13     -14.909  26.223  19.335    0.00     4.57
+ATOM      6    C STP    13     -14.382  24.675  18.050    0.00     3.53
+ATOM      7    O STP    13     -14.022  26.981  18.887    0.00     4.51
+ATOM      8    O STP    13     -13.149  28.055  17.189    0.00     3.54
+ATOM      9    O STP    13     -13.848  27.808  17.708    0.00     4.07
+ATOM     10    O STP    13     -13.798  28.442  17.460    0.00     3.88
+ATOM     11    O STP    13     -13.798  28.303  17.460    0.00     3.92
+ATOM     12    O STP    13     -13.804  28.284  17.472    0.00     3.93
+ATOM     13    O STP    13     -13.734  30.649  17.420    0.00     3.89
+ATOM     14    O STP    13     -13.444  31.621  17.292    0.00     4.09
+ATOM     15    O STP    13     -13.757  31.663  17.802    0.00     4.23
+ATOM     16    O STP    13     -12.392  31.711  16.849    0.00     3.60
+ATOM     17    C STP    13     -14.327  27.424  17.420    0.00     3.87
+ATOM     18    O STP    13     -14.320  27.344  17.475    0.00     3.92
+ATOM     19    O STP    13     -14.498  27.355  17.384    0.00     3.78
+TER
+END

tests/reference_output/1UYD_out/pockets/pocket1_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.8551
 HEADER 2  - Number of alpha spheres           :   143
 HEADER 3  - Mean alpha-sphere radius          : 3.9767
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4511
-HEADER 5  - Mean B-factor of pocket residues  : 0.2270
+HEADER 5  - Mean B-factor of pocket residues  : 0.1364
 HEADER 6  - Hydrophobicity Score              : 39.7273
 HEADER 7  - Polarity Score                    :    13
 HEADER 8  - Amino Acid based volume Score     : 3.9394
-HEADER 9  - Pocket volume (Monte Carlo)       : 1437.6858
-HEADER 10  -Pocket volume (convex hull)       : 806.5479
+HEADER 9  - Pocket volume (Monte Carlo)       : 1455.5071
+HEADER 10 - Pocket volume (convex hull)       : 806.5479
 HEADER 11 - Charge Score                      :    -2
 HEADER 12 - Local hydrophobic density Score   : 53.0833
 HEADER 13 - Number of apolar alpha sphere     :    72

tests/reference_output/1UYD_out/pockets/pocket1_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.8551
 HEADER 2  - Number of V. Vertices             :   143
 HEADER 3  - Mean alpha-sphere radius          : 3.9767
 HEADER 4  - Mean alpha-sphere SA              : 0.4511
-HEADER 5  - Mean B-factor                     : 0.2270
+HEADER 5  - Mean B-factor                     : 0.1364
 HEADER 6  - Hydrophobicity Score              : 39.7273
 HEADER 7  - Polarity Score                    :    13
 HEADER 8  - Volume Score                      : 3.9394
-HEADER 9  - Real volume (approximation)       : 1437.6858
+HEADER 9  - Real volume (approximation)       : 1455.5071
 HEADER 10 - Charge Score                      :    -2
 HEADER 11 - Local hydrophobic density Score   : 53.0833
 HEADER 12 - Number of apolar alpha sphere     :    72

tests/reference_output/1UYD_out/pockets/pocket2_atm.pdb

@@ -8,12 +8,12 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of alpha spheres           :    24
 HEADER 3  - Mean alpha-sphere radius          : 4.0106
 HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5440
-HEADER 5  - Mean B-factor of pocket residues  : 0.6012
+HEADER 5  - Mean B-factor of pocket residues  : 0.3613
 HEADER 6  - Hydrophobicity Score              : -15.7273
 HEADER 7  - Polarity Score                    :    10
 HEADER 8  - Amino Acid based volume Score     : 3.7273
-HEADER 9  - Pocket volume (Monte Carlo)       : 425.4238
-HEADER 10  -Pocket volume (convex hull)       : 41.3760
+HEADER 9  - Pocket volume (Monte Carlo)       : 419.0484
+HEADER 10 - Pocket volume (convex hull)       : 41.3760
 HEADER 11 - Charge Score                      :    -1
 HEADER 12 - Local hydrophobic density Score   : 2.0000
 HEADER 13 - Number of apolar alpha sphere     :     3

tests/reference_output/1UYD_out/pockets/pocket2_vert.pqr

@@ -9,11 +9,11 @@ HEADER 1  - Drug Score                        : 0.0001
 HEADER 2  - Number of V. Vertices             :    24
 HEADER 3  - Mean alpha-sphere radius          : 4.0106
 HEADER 4  - Mean alpha-sphere SA              : 0.5440
-HEADER 5  - Mean B-factor                     : 0.6012
+HEADER 5  - Mean B-factor                     : 0.3613
 HEADER 6  - Hydrophobicity Score              : -15.7273
 HEADER 7  - Polarity Score                    :    10
 HEADER 8  - Volume Score                      : 3.7273
-HEADER 9  - Real volume (approximation)       : 425.4238
+HEADER 9  - Real volume (approximation)       : 419.0484
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 2.0000
 HEADER 12 - Number of apolar alpha sphere     :     3

tests/reference_output/1UYD_out/pockets/pocket3_atm.pdb

@@ -3,49 +3,67 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     3:
-HEADER 0  - Pocket Score                      : 0.0502
-HEADER 1  - Drug Score                        : 0.0138
-HEADER 2  - Number of alpha spheres           :    31
-HEADER 3  - Mean alpha-sphere radius          : 3.9139
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6054
-HEADER 5  - Mean B-factor of pocket residues  : 0.2848
-HEADER 6  - Hydrophobicity Score              : 39.9091
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.8182
-HEADER 9  - Pocket volume (Monte Carlo)       : 438.3710
-HEADER 10  -Pocket volume (convex hull)       : 60.7327
-HEADER 11 - Charge Score                      :     1
-HEADER 12 - Local hydrophobic density Score   : 19.4545
-HEADER 13 - Number of apolar alpha sphere     :    22
-HEADER 14 - Proportion of apolar alpha sphere : 0.7097
-ATOM   1500  CG1 VAL A 207     -11.010  10.906  11.334  0.00  0.00           C 0
-ATOM   1533    O SER A 211      -9.891   6.827  12.276  0.55  1.07           O 0
-ATOM   1539    O GLN A 212     -12.672   4.377  11.298  0.00  0.00           O 0
-ATOM   1537   CA GLN A 212     -11.070   5.585  10.068  0.00  0.00           C 0
-ATOM   1594  CD1 ILE A 218     -10.824   9.348  15.419  0.00  0.00           C 0
-ATOM   1559    O ILE A 214     -12.563   4.175  16.207  0.48  6.43           O 0
-ATOM   1606   CB LEU A 220     -14.074  16.914  13.109  0.00  0.00           C 0
-ATOM   1593  CG2 ILE A 218     -11.852  12.231  15.651  0.00  0.00           C 0
-ATOM   1590    O ILE A 218     -15.064  12.371  15.635  0.00  0.00           O 0
-ATOM   1587    N ILE A 218     -14.467  10.181  17.586  0.59  5.47           N 0
-ATOM   1591   CB ILE A 218     -12.641  10.969  16.152  0.00  0.00           C 0
-ATOM   1592  CG1 ILE A 218     -11.762   9.770  16.549  0.00  0.00           C 0
-ATOM   1503   CA LYS A 208     -11.107   9.334   6.950  0.00  0.00           C 0
-ATOM   1502    N LYS A 208     -10.517  10.430   7.696  0.00  0.00           N 0
-ATOM   1506   CB LYS A 208     -12.107   9.883   5.929  0.00  0.00           C 0
-ATOM   1498    O VAL A 207      -9.553   9.082   9.177  0.00  0.00           O 0
-ATOM   1472    O LYS A 204     -11.546  12.938   6.899  0.55  4.29           O 0
-ATOM   1501  CG2 VAL A 207      -9.586  13.044  11.381  0.00  0.00           C 0
-ATOM    523  CD1 LEU A  80      -9.898  15.086  14.356  0.00  0.00           C 0
-ATOM   1508   CD LYS A 208     -13.692   9.431   4.022  0.00  0.00           C 0
-ATOM   1475   CD LYS A 204     -16.021  15.874   6.811  0.00  0.00           C 0
-ATOM   1473   CB LYS A 204     -13.540  15.591   6.878  0.00  0.00           C 0
-ATOM   1478    N GLU A 205     -11.077  14.716   5.558  0.00  0.00           N 0
-ATOM   1471    C LYS A 204     -11.587  14.151   6.663  0.00  0.00           C 0
-ATOM   1474   CG LYS A 204     -14.759  15.911   7.688  0.00  0.00           C 0
-ATOM   1470   CA LYS A 204     -12.281  15.108   7.616  0.00  0.00           C 0
-ATOM   1499   CB VAL A 207     -10.284  12.010  10.498  0.00  0.00           C 0
-ATOM   1571    O TYR A 216     -13.684   6.959  18.163  0.00  0.00           O 0
-ATOM   1609  CD2 LEU A 220     -13.507  17.839  10.826  0.00  0.00           C 0
+HEADER 0  - Pocket Score                      : 0.0868
+HEADER 1  - Drug Score                        : 0.1155
+HEADER 2  - Number of alpha spheres           :    70
+HEADER 3  - Mean alpha-sphere radius          : 3.9288
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5299
+HEADER 5  - Mean B-factor of pocket residues  : 0.4841
+HEADER 6  - Hydrophobicity Score              : 20.9333
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Amino Acid based volume Score     : 4.4000
+HEADER 9  - Pocket volume (Monte Carlo)       : 748.9551
+HEADER 10 - Pocket volume (convex hull)       : 184.9001
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 27.4815
+HEADER 13 - Number of apolar alpha sphere     :    54
+HEADER 14 - Proportion of apolar alpha sphere : 0.7714
+ATOM    809   CB MET A 119      18.047   8.438  13.304  0.00  0.00           C 0
+ATOM    812   CE MET A 119      18.896  12.204  13.031  0.00  0.00           C 0
+ATOM    103  OE1 GLN A  28      21.519  12.799  16.414  0.00  0.00           O 0
+ATOM    104  NE2 GLN A  28      22.157  13.501  14.352  0.00  0.00           N 0
+ATOM    840   CG GLN A 123      20.411   7.331   7.673  0.00  0.00           C 0
+ATOM    841   CD GLN A 123      21.740   7.846   8.175  0.00  0.00           C 0
+ATOM    843  NE2 GLN A 123      22.244   8.929   7.550  0.00  0.00           N 0
+ATOM    133  CD1 LEU A  32      17.260  14.294   9.535  0.00  0.00           C 0
+ATOM    842  OE1 GLN A 123      22.317   7.267   9.116  0.48  8.57           O 0
+ATOM    808    O MET A 119      18.239   6.888  10.339  0.60  1.07           O 0
+ATOM    134  CD2 LEU A  32      15.972  12.683  10.900  0.00  0.00           C 0
+ATOM    831   CB LEU A 122      15.645   7.979   7.938  0.00  0.00           C 0
+ATOM    810   CG MET A 119      17.406   9.804  13.159  0.00  0.00           C 0
+ATOM    784   CB LYS A 116      19.005   4.904  18.162  0.00  0.00           C 0
+ATOM    761   CE LYS A 112      20.763   7.806  24.667  0.00  0.00           C 0
+ATOM    759   CG LYS A 112      18.345   7.905  23.819  0.00  0.00           C 0
+ATOM    786   CD LYS A 116      21.107   3.626  18.880  0.00  0.00           C 0
+ATOM    830    O LEU A 122      16.827   6.812   5.159  0.00  0.00           O 0
+ATOM    834  CD2 LEU A 122      13.141   8.318   7.801  0.00  0.00           C 0
+ATOM    165  CG2 THR A  36      13.954  15.228   5.144  0.00  0.00           C 0
+ATOM    856    O ALA A 126      13.064   6.701   4.796  0.00  0.00           O 0
+ATOM    829    C LEU A 122      16.982   6.557   6.366  0.00  0.00           C 0
+ATOM    833  CD1 LEU A 122      14.496   9.519   9.463  0.00  0.00           C 0
+ATOM    873  CD1 ILE A 128      11.138  13.485   7.280  0.00  0.00           C 0
+ATOM    871  CG1 ILE A 128      10.835  12.117   7.893  0.00  0.00           C 0
+ATOM    811   SD MET A 119      17.851  11.068  14.259  0.00  0.00           S 0
+ATOM    779  CG2 THR A 115      15.826   9.929  17.943  0.00  0.00           C 0
+ATOM    780    N LYS A 116      17.048   6.386  17.780  0.61  1.09           N 0
+ATOM    776    O THR A 115      16.217   7.347  15.900  0.00  0.00           O 0
+ATOM     81  OE1 GLU A  25      22.506  10.395  22.432  0.00  0.00           O 0
+ATOM    787   CE LYS A 116      22.558   3.176  18.577  0.00  0.00           C 0
+ATOM    781   CA LYS A 116      18.173   5.688  17.126  0.00  0.00           C 0
+ATOM    783    O LYS A 116      18.078   5.007  14.822  0.00  0.00           O 0
+ATOM    785   CG LYS A 116      20.367   4.281  17.674  0.00  0.00           C 0
+ATOM     78   CB GLU A  25      19.262  11.053  20.713  0.00  0.00           C 0
+ATOM    813    N GLU A 120      18.338   5.404  12.039  0.00  0.00           N 0
+ATOM    818   CG GLU A 120      20.403   3.337  13.075  0.00  0.00           C 0
+ATOM    807    C MET A 119      18.017   6.580  11.507  0.00  0.00           C 0
+ATOM    866    N ILE A 128       9.827   9.471   6.497  0.00  0.00           N 0
+ATOM    183  CD1 TYR A  38       8.575  12.993   3.679  0.00  0.00           C 0
+ATOM    862   CB ASP A 127       9.804   7.990   3.839  0.00  0.00           C 0
+ATOM    164  OG1 THR A  36      14.951  15.781   7.174  0.77  3.21           O 0
+ATOM    132   CG LEU A  32      15.981  14.083  10.326  0.00  0.00           C 0
+ATOM     79   CG GLU A  25      20.650  10.425  20.910  0.00  0.00           C 0
+ATOM    859   CA ASP A 127      10.629   7.660   5.095  0.00  0.00           C 0
+ATOM    757    O LYS A 112      16.831   6.525  21.054  0.75  2.14           O 0
+ATOM     77    O GLU A  25      17.500  12.958  18.695  0.00  0.00           O 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket3_vert.pqr

@@ -4,50 +4,89 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     3:
-HEADER 0  - Pocket Score                      : 0.0502
-HEADER 1  - Drug Score                        : 0.0138
-HEADER 2  - Number of V. Vertices             :    31
-HEADER 3  - Mean alpha-sphere radius          : 3.9139
-HEADER 4  - Mean alpha-sphere SA              : 0.6054
-HEADER 5  - Mean B-factor                     : 0.2848
-HEADER 6  - Hydrophobicity Score              : 39.9091
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.8182
-HEADER 9  - Real volume (approximation)       : 438.3710
-HEADER 10 - Charge Score                      :     1
-HEADER 11 - Local hydrophobic density Score   : 19.4545
-HEADER 12 - Number of apolar alpha sphere     :    22
-HEADER 13 - Proportion of apolar alpha sphere : 0.7097
-ATOM      1    O STP     3     -13.394   8.035  11.699    0.00     3.75
-ATOM      2    O STP     3     -13.866   8.149  12.756    0.00     4.22
-ATOM      3    O STP     3     -13.235   6.985  13.878    0.00     3.71
-ATOM      4    C STP     3     -13.396  13.376  12.554    0.00     3.64
-ATOM      5    O STP     3     -14.773   7.681  13.727    0.00     4.61
-ATOM      6    C STP     3     -14.552   8.323  12.854    0.00     4.64
-ATOM      7    C STP     3     -14.690   7.717  13.852    0.00     4.48
-ATOM      8    C STP     3     -13.947  10.342   9.126    0.00     3.72
-ATOM      9    C STP     3     -12.889   8.488   9.768    0.00     3.44
-ATOM     10    O STP     3     -14.059  10.991   9.026    0.00     3.83
-ATOM     11    C STP     3     -12.850  13.648  12.578    0.00     3.53
-ATOM     12    C STP     3     -12.635  13.830  12.726    0.00     3.42
-ATOM     13    C STP     3     -15.321  12.050   6.421    0.00     3.91
-ATOM     14    C STP     3     -15.149  12.299   5.990    0.00     3.77
-ATOM     15    C STP     3     -14.138  13.128   4.148    0.00     3.73
-ATOM     16    O STP     3     -13.842  12.966   4.202    0.00     3.54
-ATOM     17    C STP     3     -14.202  12.998   4.431    0.00     3.63
-ATOM     18    C STP     3     -15.071  12.945  11.123    0.00     4.55
-ATOM     19    C STP     3     -15.181  12.284   7.101    0.00     3.70
-ATOM     20    C STP     3     -14.069  13.525  10.889    0.00     4.05
-ATOM     21    C STP     3     -14.486  12.345   9.698    0.00     4.10
-ATOM     22    C STP     3     -15.581  11.691   7.702    0.00     4.30
-ATOM     23    C STP     3     -13.744  12.589   9.720    0.00     3.59
-ATOM     24    C STP     3     -13.903  13.601  10.918    0.00     3.98
-ATOM     25    C STP     3     -13.004  13.765  11.916    0.00     3.53
-ATOM     26    C STP     3     -12.804  14.399  11.014    0.00     3.51
-ATOM     27    O STP     3     -14.691   7.701  13.857    0.00     4.48
-ATOM     28    O STP     3     -14.353   7.367  13.918    0.00     4.32
-ATOM     29    O STP     3     -14.766   7.663  13.746    0.00     4.60
-ATOM     30    C STP     3     -13.822  14.302  10.714    0.00     3.55
-ATOM     31    C STP     3     -12.793  14.411  11.014    0.00     3.51
+HEADER 0  - Pocket Score                      : 0.0868
+HEADER 1  - Drug Score                        : 0.1155
+HEADER 2  - Number of V. Vertices             :    70
+HEADER 3  - Mean alpha-sphere radius          : 3.9288
+HEADER 4  - Mean alpha-sphere SA              : 0.5299
+HEADER 5  - Mean B-factor                     : 0.4841
+HEADER 6  - Hydrophobicity Score              : 20.9333
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Volume Score                      : 4.4000
+HEADER 9  - Real volume (approximation)       : 748.9551
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 27.4815
+HEADER 12 - Number of apolar alpha sphere     :    54
+HEADER 13 - Proportion of apolar alpha sphere : 0.7714
+ATOM      1    O STP     3      21.608   9.684  14.132    0.00     3.86
+ATOM      2    C STP     3      19.314  10.586   9.512    0.00     3.90
+ATOM      3    C STP     3      19.143  10.766   9.300    0.00     4.01
+ATOM      4    O STP     3      22.337  10.819  11.219    0.00     4.13
+ATOM      5    O STP     3      21.322  10.417  10.839    0.00     3.73
+ATOM      6    O STP     3      22.223   9.452  12.843    0.00     4.32
+ATOM      7    C STP     3      20.438   9.717  10.950    0.00     3.59
+ATOM      8    C STP     3      19.317  10.526   9.567    0.00     3.87
+ATOM      9    C STP     3      20.347   9.733  10.882    0.00     3.58
+ATOM     10    O STP     3      20.400   9.647  10.930    0.00     3.55
+ATOM     11    C STP     3      18.480  10.647   8.623    0.00     3.95
+ATOM     12    C STP     3      18.473  10.489   8.873    0.00     3.90
+ATOM     13    C STP     3      19.091  10.740   9.309    0.00     4.00
+ATOM     14    C STP     3      19.039  10.663   9.363    0.00     3.98
+ATOM     15    C STP     3      18.698  10.488   9.792    0.00     3.67
+ATOM     16    C STP     3      20.605   6.618  21.102    0.00     3.76
+ATOM     17    C STP     3      14.943  10.866   4.541    0.00     4.51
+ATOM     18    O STP     3      14.875  10.843   4.459    0.00     4.53
+ATOM     19    O STP     3      14.864  10.355   4.722    0.00     4.07
+ATOM     20    C STP     3      18.270  10.051   6.298    0.00     3.72
+ATOM     21    C STP     3      17.917  10.225   9.354    0.00     3.49
+ATOM     22    C STP     3      14.939  11.399   5.926    0.00     4.03
+ATOM     23    C STP     3      16.088  11.832   6.354    0.00     4.19
+ATOM     24    C STP     3      17.345  11.079   8.062    0.00     3.54
+ATOM     25    C STP     3      14.302  11.614   6.290    0.00     3.81
+ATOM     26    C STP     3      14.169  11.576   6.426    0.00     3.68
+ATOM     27    C STP     3      21.260   9.781  14.385    0.00     3.65
+ATOM     28    O STP     3      19.082   9.114  16.906    0.00     3.51
+ATOM     29    C STP     3      23.299   6.241  21.535    0.00     4.32
+ATOM     30    C STP     3      19.211   8.868  16.477    0.00     3.41
+ATOM     31    O STP     3      19.141   9.065  16.855    0.00     3.52
+ATOM     32    C STP     3      20.411   8.950  16.497    0.00     4.01
+ATOM     33    C STP     3      21.278   7.286  15.271    0.00     3.95
+ATOM     34    C STP     3      21.737   8.273  15.966    0.00     4.55
+ATOM     35    C STP     3      19.545   9.253  17.348    0.00     3.83
+ATOM     36    C STP     3      19.605   9.305  17.253    0.00     3.89
+ATOM     37    C STP     3      19.361   9.202  17.087    0.00     3.71
+ATOM     38    O STP     3      21.824   7.092  13.097    0.00     4.01
+ATOM     39    O STP     3      21.005   6.678  13.902    0.00     3.49
+ATOM     40    C STP     3      21.887   7.048  14.721    0.00     4.32
+ATOM     41    O STP     3      21.396   7.252  12.616    0.00     3.62
+ATOM     42    C STP     3      13.282  11.035   4.472    0.00     4.30
+ATOM     43    O STP     3      13.297  11.009   4.410    0.00     4.33
+ATOM     44    C STP     3      13.187  11.021   4.702    0.00     4.11
+ATOM     45    C STP     3      12.553  11.402   3.811    0.00     4.29
+ATOM     46    C STP     3      12.615  11.331   3.695    0.00     4.37
+ATOM     47    C STP     3      16.085  11.834   6.357    0.00     4.19
+ATOM     48    C STP     3      15.342  12.249   7.345    0.00     3.56
+ATOM     49    C STP     3      14.506  12.196   7.034    0.00     3.62
+ATOM     50    C STP     3      14.353  12.486   7.796    0.00     3.41
+ATOM     51    C STP     3      21.576   8.462  17.094    0.00     4.39
+ATOM     52    C STP     3      21.237   8.164  17.688    0.00     3.98
+ATOM     53    C STP     3      19.823   9.314  17.205    0.00     3.96
+ATOM     54    C STP     3      19.842   9.288  17.195    0.00     3.97
+ATOM     55    C STP     3      19.813   9.293  17.207    0.00     3.96
+ATOM     56    C STP     3      23.114   7.517  18.754    0.00     4.38
+ATOM     57    C STP     3      23.216   7.267  19.612    0.00     4.27
+ATOM     58    C STP     3      21.455   7.159  19.578    0.00     3.62
+ATOM     59    C STP     3      19.601   8.988  17.728    0.00     3.65
+ATOM     60    C STP     3      20.637   6.657  21.076    0.00     3.77
+ATOM     61    C STP     3      21.991   6.742  21.095    0.00     3.92
+ATOM     62    C STP     3      20.614   6.661  21.080    0.00     3.77
+ATOM     63    O STP     3      13.277  10.973   4.430    0.00     4.29
+ATOM     64    C STP     3      13.182  11.064   3.370    0.00     4.59
+ATOM     65    O STP     3      13.287  11.012   4.386    0.00     4.34
+ATOM     66    C STP     3      12.716  11.267   3.730    0.00     4.38
+ATOM     67    C STP     3      20.578   6.679  21.067    0.00     3.75
+ATOM     68    C STP     3      20.573   6.576  21.121    0.00     3.74
+ATOM     69    O STP     3      19.279  10.317  17.326    0.00     3.47
+ATOM     70    C STP     3      19.218  10.275  17.340    0.00     3.46
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket4_atm.pdb

@@ -3,37 +3,49 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     4:
-HEADER 0  - Pocket Score                      : 0.0422
-HEADER 1  - Drug Score                        : 0.0003
-HEADER 2  - Number of alpha spheres           :    19
-HEADER 3  - Mean alpha-sphere radius          : 3.8010
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4900
-HEADER 5  - Mean B-factor of pocket residues  : 0.2299
-HEADER 6  - Hydrophobicity Score              : 27.7500
-HEADER 7  - Polarity Score                    :     2
-HEADER 8  - Amino Acid based volume Score     : 2.6250
-HEADER 9  - Pocket volume (Monte Carlo)       : 275.1293
-HEADER 10  -Pocket volume (convex hull)       : 12.3309
-HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 3.0000
-HEADER 13 - Number of apolar alpha sphere     :     4
-HEADER 14 - Proportion of apolar alpha sphere : 0.2105
-ATOM    125   CB SER A  31      17.326  19.576  14.038  0.00  0.00           C 0
-ATOM    126   OG SER A  31      17.732  19.950  15.347  0.00  0.00           O 0
-ATOM    158  ND2 ASN A  35      17.494  21.267  10.632  0.00  0.00           N 0
-ATOM    157  OD1 ASN A  35      15.956  22.734   9.894  0.00  0.00           O 0
-ATOM    149  CG2 ILE A  34      12.680  22.906  11.627  0.00  0.00           C 0
-ATOM    122   CA SER A  31      15.810  19.311  13.908  0.00  0.00           C 0
-ATOM    150  CD1 ILE A  34      11.667  21.954  14.572  0.00  0.00           C 0
-ATOM   1177    N GLY A 168      16.023  22.831  21.164  0.73  2.19           N 0
-ATOM   1175    C GLY A 167      16.348  24.073  20.818  0.00  0.00           C 0
-ATOM   1174   CA GLY A 167      15.573  24.649  19.628  0.00  0.00           C 0
-ATOM   1178   CA GLY A 168      16.782  22.051  22.118  0.00  0.00           C 0
-ATOM   1172   CB ALA A 166      12.281  22.382  18.138  0.00  0.00           C 0
-ATOM     94    O ALA A  27      16.870  17.872  17.453  0.55  1.07           O 0
-ATOM    117   CB MET A  30      13.128  18.094  17.405  0.00  0.00           C 0
-ATOM     95   CB ALA A  27      18.043  18.164  20.565  0.00  0.00           C 0
-ATOM   1173    N GLY A 167      14.393  23.879  19.246  0.38  2.19           N 0
-ATOM     92   CA ALA A  27      16.913  17.410  19.844  0.00  0.00           C 0
+HEADER 0  - Pocket Score                      : 0.0502
+HEADER 1  - Drug Score                        : 0.0138
+HEADER 2  - Number of alpha spheres           :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.9139
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6054
+HEADER 5  - Mean B-factor of pocket residues  : 0.1711
+HEADER 6  - Hydrophobicity Score              : 39.9091
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.8182
+HEADER 9  - Pocket volume (Monte Carlo)       : 434.5795
+HEADER 10 - Pocket volume (convex hull)       : 60.7327
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 19.4545
+HEADER 13 - Number of apolar alpha sphere     :    22
+HEADER 14 - Proportion of apolar alpha sphere : 0.7097
+ATOM   1500  CG1 VAL A 207     -11.010  10.906  11.334  0.00  0.00           C 0
+ATOM   1533    O SER A 211      -9.891   6.827  12.276  0.55  1.07           O 0
+ATOM   1539    O GLN A 212     -12.672   4.377  11.298  0.00  0.00           O 0
+ATOM   1537   CA GLN A 212     -11.070   5.585  10.068  0.00  0.00           C 0
+ATOM   1594  CD1 ILE A 218     -10.824   9.348  15.419  0.00  0.00           C 0
+ATOM   1559    O ILE A 214     -12.563   4.175  16.207  0.48  6.43           O 0
+ATOM   1606   CB LEU A 220     -14.074  16.914  13.109  0.00  0.00           C 0
+ATOM   1593  CG2 ILE A 218     -11.852  12.231  15.651  0.00  0.00           C 0
+ATOM   1590    O ILE A 218     -15.064  12.371  15.635  0.00  0.00           O 0
+ATOM   1587    N ILE A 218     -14.467  10.181  17.586  0.59  5.47           N 0
+ATOM   1591   CB ILE A 218     -12.641  10.969  16.152  0.00  0.00           C 0
+ATOM   1592  CG1 ILE A 218     -11.762   9.770  16.549  0.00  0.00           C 0
+ATOM   1503   CA LYS A 208     -11.107   9.334   6.950  0.00  0.00           C 0
+ATOM   1502    N LYS A 208     -10.517  10.430   7.696  0.00  0.00           N 0
+ATOM   1506   CB LYS A 208     -12.107   9.883   5.929  0.00  0.00           C 0
+ATOM   1498    O VAL A 207      -9.553   9.082   9.177  0.00  0.00           O 0
+ATOM   1472    O LYS A 204     -11.546  12.938   6.899  0.55  4.29           O 0
+ATOM   1501  CG2 VAL A 207      -9.586  13.044  11.381  0.00  0.00           C 0
+ATOM    523  CD1 LEU A  80      -9.898  15.086  14.356  0.00  0.00           C 0
+ATOM   1508   CD LYS A 208     -13.692   9.431   4.022  0.00  0.00           C 0
+ATOM   1475   CD LYS A 204     -16.021  15.874   6.811  0.00  0.00           C 0
+ATOM   1473   CB LYS A 204     -13.540  15.591   6.878  0.00  0.00           C 0
+ATOM   1478    N GLU A 205     -11.077  14.716   5.558  0.00  0.00           N 0
+ATOM   1471    C LYS A 204     -11.587  14.151   6.663  0.00  0.00           C 0
+ATOM   1474   CG LYS A 204     -14.759  15.911   7.688  0.00  0.00           C 0
+ATOM   1470   CA LYS A 204     -12.281  15.108   7.616  0.00  0.00           C 0
+ATOM   1499   CB VAL A 207     -10.284  12.010  10.498  0.00  0.00           C 0
+ATOM   1571    O TYR A 216     -13.684   6.959  18.163  0.00  0.00           O 0
+ATOM   1609  CD2 LEU A 220     -13.507  17.839  10.826  0.00  0.00           C 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket4_vert.pqr

@@ -4,38 +4,50 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     4:
-HEADER 0  - Pocket Score                      : 0.0422
-HEADER 1  - Drug Score                        : 0.0003
-HEADER 2  - Number of V. Vertices             :    19
-HEADER 3  - Mean alpha-sphere radius          : 3.8010
-HEADER 4  - Mean alpha-sphere SA              : 0.4900
-HEADER 5  - Mean B-factor                     : 0.2299
-HEADER 6  - Hydrophobicity Score              : 27.7500
-HEADER 7  - Polarity Score                    :     2
-HEADER 8  - Volume Score                      : 2.6250
-HEADER 9  - Real volume (approximation)       : 275.1293
-HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 3.0000
-HEADER 12 - Number of apolar alpha sphere     :     4
-HEADER 13 - Proportion of apolar alpha sphere : 0.2105
-ATOM      1    O STP     4      16.547  23.639  13.890    0.00     4.14
-ATOM      2    O STP     4      16.092  23.630  14.033    0.00     4.24
-ATOM      3    C STP     4      15.859  23.404  14.170    0.00     4.10
-ATOM      4    C STP     4      15.557  23.398  14.576    0.00     4.15
-ATOM      5    O STP     4      16.011  22.871  13.482    0.00     3.59
-ATOM      6    C STP     4      15.928  23.207  13.765    0.00     3.90
-ATOM      7    O STP     4      17.691  22.245  18.072    0.00     3.56
-ATOM      8    O STP     4      19.529  21.954  18.755    0.00     4.34
-ATOM      9    C STP     4      15.011  22.229  15.825    0.00     3.58
-ATOM     10    O STP     4      15.135  20.552  18.741    0.00     3.44
-ATOM     11    O STP     4      19.253  21.725  18.788    0.00     4.16
-ATOM     12    O STP     4      17.650  21.048  18.652    0.00     3.48
-ATOM     13    O STP     4      16.195  21.162  18.168    0.00     3.43
-ATOM     14    O STP     4      15.398  20.983  17.666    0.00     3.45
-ATOM     15    O STP     4      15.138  20.557  18.735    0.00     3.44
-ATOM     16    O STP     4      16.943  21.983  17.981    0.00     3.42
-ATOM     17    O STP     4      15.182  22.714  15.737    0.00     3.78
-ATOM     18    O STP     4      15.741  24.064  14.855    0.00     4.60
-ATOM     19    O STP     4      15.109  20.220  19.179    0.00     3.40
+HEADER 0  - Pocket Score                      : 0.0502
+HEADER 1  - Drug Score                        : 0.0138
+HEADER 2  - Number of V. Vertices             :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.9139
+HEADER 4  - Mean alpha-sphere SA              : 0.6054
+HEADER 5  - Mean B-factor                     : 0.1711
+HEADER 6  - Hydrophobicity Score              : 39.9091
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.8182
+HEADER 9  - Real volume (approximation)       : 434.5795
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 19.4545
+HEADER 12 - Number of apolar alpha sphere     :    22
+HEADER 13 - Proportion of apolar alpha sphere : 0.7097
+ATOM      1    O STP     4     -13.394   8.035  11.699    0.00     3.75
+ATOM      2    O STP     4     -13.866   8.149  12.756    0.00     4.22
+ATOM      3    O STP     4     -13.235   6.985  13.878    0.00     3.71
+ATOM      4    C STP     4     -13.396  13.376  12.554    0.00     3.64
+ATOM      5    O STP     4     -14.773   7.681  13.727    0.00     4.61
+ATOM      6    C STP     4     -14.552   8.323  12.854    0.00     4.64
+ATOM      7    C STP     4     -14.690   7.717  13.852    0.00     4.48
+ATOM      8    C STP     4     -13.947  10.342   9.126    0.00     3.72
+ATOM      9    C STP     4     -12.889   8.488   9.768    0.00     3.44
+ATOM     10    O STP     4     -14.059  10.991   9.026    0.00     3.83
+ATOM     11    C STP     4     -12.850  13.648  12.578    0.00     3.53
+ATOM     12    C STP     4     -12.635  13.830  12.726    0.00     3.42
+ATOM     13    C STP     4     -15.321  12.050   6.421    0.00     3.91
+ATOM     14    C STP     4     -15.149  12.299   5.990    0.00     3.77
+ATOM     15    C STP     4     -14.138  13.128   4.148    0.00     3.73
+ATOM     16    O STP     4     -13.842  12.966   4.202    0.00     3.54
+ATOM     17    C STP     4     -14.202  12.998   4.431    0.00     3.63
+ATOM     18    C STP     4     -15.071  12.945  11.123    0.00     4.55
+ATOM     19    C STP     4     -15.181  12.284   7.101    0.00     3.70
+ATOM     20    C STP     4     -14.069  13.525  10.889    0.00     4.05
+ATOM     21    C STP     4     -14.486  12.345   9.698    0.00     4.10
+ATOM     22    C STP     4     -15.581  11.691   7.702    0.00     4.30
+ATOM     23    C STP     4     -13.744  12.589   9.720    0.00     3.59
+ATOM     24    C STP     4     -13.903  13.601  10.918    0.00     3.98
+ATOM     25    C STP     4     -13.004  13.765  11.916    0.00     3.53
+ATOM     26    C STP     4     -12.804  14.399  11.014    0.00     3.51
+ATOM     27    O STP     4     -14.691   7.701  13.857    0.00     4.48
+ATOM     28    O STP     4     -14.353   7.367  13.918    0.00     4.32
+ATOM     29    O STP     4     -14.766   7.663  13.746    0.00     4.60
+ATOM     30    C STP     4     -13.822  14.302  10.714    0.00     3.55
+ATOM     31    C STP     4     -12.793  14.411  11.014    0.00     3.51
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket5_atm.pdb

@@ -3,41 +3,37 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     5:
-HEADER 0  - Pocket Score                      : -0.0120
-HEADER 1  - Drug Score                        : 0.0106
-HEADER 2  - Number of alpha spheres           :    28
-HEADER 3  - Mean alpha-sphere radius          : 3.8577
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5218
-HEADER 5  - Mean B-factor of pocket residues  : 0.7484
-HEADER 6  - Hydrophobicity Score              : -4.4286
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.5714
-HEADER 9  - Pocket volume (Monte Carlo)       : 314.3672
-HEADER 10  -Pocket volume (convex hull)       : 22.9942
+HEADER 0  - Pocket Score                      : 0.0422
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.8010
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4900
+HEADER 5  - Mean B-factor of pocket residues  : 0.1381
+HEADER 6  - Hydrophobicity Score              : 27.7500
+HEADER 7  - Polarity Score                    :     2
+HEADER 8  - Amino Acid based volume Score     : 2.6250
+HEADER 9  - Pocket volume (Monte Carlo)       : 275.3307
+HEADER 10 - Pocket volume (convex hull)       : 12.3309
 HEADER 11 - Charge Score                      :     0
-HEADER 12 - Local hydrophobic density Score   : 23.0000
-HEADER 13 - Number of apolar alpha sphere     :    24
-HEADER 14 - Proportion of apolar alpha sphere : 0.8571
-ATOM    784   CB LYS A 116      19.005   4.904  18.162  0.00  0.00           C 0
-ATOM    761   CE LYS A 112      20.763   7.806  24.667  0.00  0.00           C 0
-ATOM    759   CG LYS A 112      18.345   7.905  23.819  0.00  0.00           C 0
-ATOM    786   CD LYS A 116      21.107   3.626  18.880  0.00  0.00           C 0
-ATOM    779  CG2 THR A 115      15.826   9.929  17.943  0.00  0.00           C 0
-ATOM    811   SD MET A 119      17.851  11.068  14.259  0.00  0.00           S 0
-ATOM    780    N LYS A 116      17.048   6.386  17.780  0.61  1.09           N 0
-ATOM    776    O THR A 115      16.217   7.347  15.900  0.00  0.00           O 0
-ATOM    781   CA LYS A 116      18.173   5.688  17.126  0.00  0.00           C 0
-ATOM    809   CB MET A 119      18.047   8.438  13.304  0.00  0.00           C 0
-ATOM    103  OE1 GLN A  28      21.519  12.799  16.414  0.00  0.00           O 0
-ATOM    783    O LYS A 116      18.078   5.007  14.822  0.00  0.00           O 0
-ATOM    785   CG LYS A 116      20.367   4.281  17.674  0.00  0.00           C 0
-ATOM     78   CB GLU A  25      19.262  11.053  20.713  0.00  0.00           C 0
-ATOM    818   CG GLU A 120      20.403   3.337  13.075  0.00  0.00           C 0
-ATOM    813    N GLU A 120      18.338   5.404  12.039  0.00  0.00           N 0
-ATOM     79   CG GLU A  25      20.650  10.425  20.910  0.00  0.00           C 0
-ATOM    787   CE LYS A 116      22.558   3.176  18.577  0.00  0.00           C 0
-ATOM     81  OE1 GLU A  25      22.506  10.395  22.432  0.00  0.00           O 0
-ATOM    757    O LYS A 112      16.831   6.525  21.054  0.75  2.14           O 0
-ATOM     77    O GLU A  25      17.500  12.958  18.695  0.00  0.00           O 0
+HEADER 12 - Local hydrophobic density Score   : 3.0000
+HEADER 13 - Number of apolar alpha sphere     :     4
+HEADER 14 - Proportion of apolar alpha sphere : 0.2105
+ATOM    125   CB SER A  31      17.326  19.576  14.038  0.00  0.00           C 0
+ATOM    126   OG SER A  31      17.732  19.950  15.347  0.00  0.00           O 0
+ATOM    158  ND2 ASN A  35      17.494  21.267  10.632  0.00  0.00           N 0
+ATOM    157  OD1 ASN A  35      15.956  22.734   9.894  0.00  0.00           O 0
+ATOM    149  CG2 ILE A  34      12.680  22.906  11.627  0.00  0.00           C 0
+ATOM    122   CA SER A  31      15.810  19.311  13.908  0.00  0.00           C 0
+ATOM    150  CD1 ILE A  34      11.667  21.954  14.572  0.00  0.00           C 0
+ATOM   1177    N GLY A 168      16.023  22.831  21.164  0.73  2.19           N 0
+ATOM   1175    C GLY A 167      16.348  24.073  20.818  0.00  0.00           C 0
+ATOM   1174   CA GLY A 167      15.573  24.649  19.628  0.00  0.00           C 0
+ATOM   1178   CA GLY A 168      16.782  22.051  22.118  0.00  0.00           C 0
+ATOM   1172   CB ALA A 166      12.281  22.382  18.138  0.00  0.00           C 0
+ATOM     94    O ALA A  27      16.870  17.872  17.453  0.55  1.07           O 0
+ATOM    117   CB MET A  30      13.128  18.094  17.405  0.00  0.00           C 0
+ATOM     95   CB ALA A  27      18.043  18.164  20.565  0.00  0.00           C 0
+ATOM   1173    N GLY A 167      14.393  23.879  19.246  0.38  2.19           N 0
+ATOM     92   CA ALA A  27      16.913  17.410  19.844  0.00  0.00           C 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket5_vert.pqr

@@ -4,47 +4,38 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     5:
-HEADER 0  - Pocket Score                      : -0.0120
-HEADER 1  - Drug Score                        : 0.0106
-HEADER 2  - Number of V. Vertices             :    28
-HEADER 3  - Mean alpha-sphere radius          : 3.8577
-HEADER 4  - Mean alpha-sphere SA              : 0.5218
-HEADER 5  - Mean B-factor                     : 0.7484
-HEADER 6  - Hydrophobicity Score              : -4.4286
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.5714
-HEADER 9  - Real volume (approximation)       : 314.3672
+HEADER 0  - Pocket Score                      : 0.0422
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.8010
+HEADER 4  - Mean alpha-sphere SA              : 0.4900
+HEADER 5  - Mean B-factor                     : 0.1381
+HEADER 6  - Hydrophobicity Score              : 27.7500
+HEADER 7  - Polarity Score                    :     2
+HEADER 8  - Volume Score                      : 2.6250
+HEADER 9  - Real volume (approximation)       : 275.3307
 HEADER 10 - Charge Score                      :     0
-HEADER 11 - Local hydrophobic density Score   : 23.0000
-HEADER 12 - Number of apolar alpha sphere     :    24
-HEADER 13 - Proportion of apolar alpha sphere : 0.8571
-ATOM      1    C STP     5      20.605   6.618  21.102    0.00     3.76
-ATOM      2    O STP     5      19.082   9.114  16.906    0.00     3.51
-ATOM      3    C STP     5      19.211   8.868  16.477    0.00     3.41
-ATOM      4    O STP     5      19.141   9.065  16.855    0.00     3.52
-ATOM      5    C STP     5      20.411   8.950  16.497    0.00     4.01
-ATOM      6    C STP     5      21.278   7.286  15.271    0.00     3.95
-ATOM      7    C STP     5      21.737   8.273  15.966    0.00     4.55
-ATOM      8    C STP     5      19.545   9.253  17.348    0.00     3.83
-ATOM      9    C STP     5      19.605   9.305  17.253    0.00     3.89
-ATOM     10    C STP     5      19.361   9.202  17.087    0.00     3.71
-ATOM     11    O STP     5      21.005   6.678  13.902    0.00     3.49
-ATOM     12    C STP     5      21.887   7.048  14.721    0.00     4.32
-ATOM     13    C STP     5      21.576   8.462  17.094    0.00     4.39
-ATOM     14    C STP     5      21.237   8.164  17.688    0.00     3.98
-ATOM     15    C STP     5      19.823   9.314  17.205    0.00     3.96
-ATOM     16    C STP     5      19.842   9.288  17.195    0.00     3.97
-ATOM     17    C STP     5      19.813   9.293  17.207    0.00     3.96
-ATOM     18    C STP     5      23.114   7.517  18.754    0.00     4.38
-ATOM     19    C STP     5      23.216   7.267  19.612    0.00     4.27
-ATOM     20    C STP     5      21.455   7.159  19.578    0.00     3.62
-ATOM     21    C STP     5      19.601   8.988  17.728    0.00     3.65
-ATOM     22    C STP     5      20.637   6.657  21.076    0.00     3.77
-ATOM     23    C STP     5      21.991   6.742  21.095    0.00     3.92
-ATOM     24    C STP     5      20.614   6.661  21.080    0.00     3.77
-ATOM     25    C STP     5      20.578   6.679  21.067    0.00     3.75
-ATOM     26    C STP     5      20.573   6.576  21.121    0.00     3.74
-ATOM     27    O STP     5      19.279  10.317  17.326    0.00     3.47
-ATOM     28    C STP     5      19.218  10.275  17.340    0.00     3.46
+HEADER 11 - Local hydrophobic density Score   : 3.0000
+HEADER 12 - Number of apolar alpha sphere     :     4
+HEADER 13 - Proportion of apolar alpha sphere : 0.2105
+ATOM      1    O STP     5      16.547  23.639  13.890    0.00     4.14
+ATOM      2    O STP     5      16.092  23.630  14.033    0.00     4.24
+ATOM      3    C STP     5      15.859  23.404  14.170    0.00     4.10
+ATOM      4    C STP     5      15.557  23.398  14.576    0.00     4.15
+ATOM      5    O STP     5      16.011  22.871  13.482    0.00     3.59
+ATOM      6    C STP     5      15.928  23.207  13.765    0.00     3.90
+ATOM      7    O STP     5      17.691  22.245  18.072    0.00     3.56
+ATOM      8    O STP     5      19.529  21.954  18.755    0.00     4.34
+ATOM      9    C STP     5      15.011  22.229  15.825    0.00     3.58
+ATOM     10    O STP     5      15.135  20.552  18.741    0.00     3.44
+ATOM     11    O STP     5      19.253  21.725  18.788    0.00     4.16
+ATOM     12    O STP     5      17.650  21.048  18.652    0.00     3.48
+ATOM     13    O STP     5      16.195  21.162  18.168    0.00     3.43
+ATOM     14    O STP     5      15.398  20.983  17.666    0.00     3.45
+ATOM     15    O STP     5      15.138  20.557  18.735    0.00     3.44
+ATOM     16    O STP     5      16.943  21.983  17.981    0.00     3.42
+ATOM     17    O STP     5      15.182  22.714  15.737    0.00     3.78
+ATOM     18    O STP     5      15.741  24.064  14.855    0.00     4.60
+ATOM     19    O STP     5      15.109  20.220  19.179    0.00     3.40
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket6_atm.pdb

@@ -3,34 +3,38 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     6:
-HEADER 0  - Pocket Score                      : -0.0207
-HEADER 1  - Drug Score                        : 0.0000
-HEADER 2  - Number of alpha spheres           :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.8891
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5474
-HEADER 5  - Mean B-factor of pocket residues  : 0.6196
-HEADER 6  - Hydrophobicity Score              : -4.0000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Amino Acid based volume Score     : 4.7143
-HEADER 9  - Pocket volume (Monte Carlo)       : 256.7571
-HEADER 10  -Pocket volume (convex hull)       : 6.4999
-HEADER 11 - Charge Score                      :     1
-HEADER 12 - Local hydrophobic density Score   : 0.0000
-HEADER 13 - Number of apolar alpha sphere     :     0
-HEADER 14 - Proportion of apolar alpha sphere : 0.0000
-ATOM   1335   CB HIS A 189       1.397  27.011  18.007  0.00  0.00           C 0
-ATOM   1009  OE2 GLU A 146       3.925  30.351  15.551  0.00  0.00           O 0
-ATOM    569    O ASP A  86      -3.134  30.577  16.949  0.33  9.64           O 0
-ATOM   1337  ND1 HIS A 189       0.040  27.983  19.913  0.77  5.47           N 0
-ATOM    577    O ARG A  87      -2.431  27.764  15.190  0.00  0.00           O 0
-ATOM   1344    O LEU A 190       1.574  28.168  13.041  0.74  1.07           O 0
-ATOM    578   CB ARG A  87      -2.813  30.073  13.913  0.00  0.00           C 0
-ATOM    560    O GLN A  85      -5.938  33.818  16.095  0.00  0.00           O 0
-ATOM    568    C ASP A  86      -4.287  30.742  16.552  0.00  0.00           C 0
-ATOM    584  NH2 ARG A  87       0.614  32.921  11.229  0.09  5.47           N 0
-ATOM    582   CZ ARG A  87       0.454  31.713  11.756  0.00  0.00           C 0
-ATOM    583  NH1 ARG A  87       1.503  31.117  12.350  0.41  2.19           N 0
-ATOM    581   NE ARG A  87      -0.749  31.111  11.680  0.24  2.19           N 0
-ATOM    551    O LYS A  84      -6.645  31.712  13.194  0.00  0.00           O 0
+HEADER 0  - Pocket Score                      : -0.0143
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8923
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6748
+HEADER 5  - Mean B-factor of pocket residues  : 0.3830
+HEADER 6  - Hydrophobicity Score              : -22.5000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 5.5000
+HEADER 9  - Pocket volume (Monte Carlo)       : 243.4480
+HEADER 10 - Pocket volume (convex hull)       : 5.7693
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 3.0000
+HEADER 13 - Number of apolar alpha sphere     :     4
+HEADER 14 - Proportion of apolar alpha sphere : 0.2353
+ATOM   1485  OE1 GLU A 205      -7.708  16.135   2.041  0.00  0.00           O 0
+ATOM   1441    O ARG A 201     -11.435  17.477   4.467  0.00  0.00           O 0
+ATOM   1442   CB ARG A 201     -13.137  20.046   3.387  0.00  0.00           C 0
+ATOM   1486  OE2 GLU A 205      -8.401  14.963   0.277  0.48  9.64           O 0
+ATOM   1440    C ARG A 201     -11.508  18.675   4.747  0.00  0.00           C 0
+ATOM   1449    N ARG A 202     -10.457  19.424   5.091  0.00  0.00           N 0
+ATOM   1484   CD GLU A 205      -8.306  15.169   1.516  0.00  0.00           C 0
+ATOM   1482   CB GLU A 205      -9.706  14.909   3.552  0.00  0.00           C 0
+ATOM   1443   CG ARG A 201     -12.137  21.172   3.114  0.00  0.00           C 0
+ATOM   1450   CA ARG A 202      -9.085  18.912   5.148  0.00  0.00           C 0
+ATOM   1455   CD ARG A 202      -6.251  18.804   3.909  0.00  0.00           C 0
+ATOM   1453   CB ARG A 202      -8.058  20.067   5.301  0.00  0.00           C 0
+ATOM   1427  OE1 GLU A 199      -9.058  24.242   3.117  0.00  0.00           O 0
+ATOM   1444   CD ARG A 201     -12.683  22.428   2.449  0.00  0.00           C 0
+ATOM   1447  NH1 ARG A 201     -12.652  23.792  -0.034  0.00  0.00           N 0
+ATOM   1445   NE ARG A 201     -11.596  23.281   1.959  0.00  0.00           N 0
+ATOM   1446   CZ ARG A 201     -11.611  23.912   0.786  0.00  0.00           C 0
+ATOM   1448  NH2 ARG A 201     -10.576  24.661   0.428  0.00  0.00           N 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket6_vert.pqr

@@ -4,35 +4,36 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     6:
-HEADER 0  - Pocket Score                      : -0.0207
-HEADER 1  - Drug Score                        : 0.0000
-HEADER 2  - Number of V. Vertices             :    16
-HEADER 3  - Mean alpha-sphere radius          : 3.8891
-HEADER 4  - Mean alpha-sphere SA              : 0.5474
-HEADER 5  - Mean B-factor                     : 0.6196
-HEADER 6  - Hydrophobicity Score              : -4.0000
-HEADER 7  - Polarity Score                    :     6
-HEADER 8  - Volume Score                      : 4.7143
-HEADER 9  - Real volume (approximation)       : 256.7571
-HEADER 10 - Charge Score                      :     1
-HEADER 11 - Local hydrophobic density Score   : 0.0000
-HEADER 12 - Number of apolar alpha sphere     :     0
-HEADER 13 - Proportion of apolar alpha sphere : 0.0000
-ATOM      1    O STP     6       0.606  30.613  17.291    0.00     3.76
-ATOM      2    O STP     6       0.349  29.933  16.102    0.00     3.64
-ATOM      3    O STP     6       0.398  29.825  16.006    0.00     3.59
-ATOM      4    O STP     6       0.310  30.058  15.886    0.00     3.64
-ATOM      5    O STP     6      -2.704  33.369  14.954    0.00     3.46
-ATOM      6    O STP     6       0.267  30.094  15.812    0.00     3.62
-ATOM      7    O STP     6       0.297  30.167  15.803    0.00     3.64
-ATOM      8    O STP     6      -1.603  34.311  14.914    0.00     4.52
-ATOM      9    O STP     6      -1.370  34.089  14.976    0.00     4.40
-ATOM     10    O STP     6       0.328  30.306  15.653    0.00     3.60
-ATOM     11    O STP     6       0.297  30.561  15.738    0.00     3.64
-ATOM     12    O STP     6      -0.300  32.461  15.359    0.00     3.76
-ATOM     13    O STP     6      -1.581  33.922  14.529    0.00     4.09
-ATOM     14    O STP     6      -2.185  34.279  14.137    0.00     4.26
-ATOM     15    O STP     6      -3.286  34.022  12.999    0.00     4.08
-ATOM     16    O STP     6      -3.344  34.741  12.491    0.00     4.54
+HEADER 0  - Pocket Score                      : -0.0143
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8923
+HEADER 4  - Mean alpha-sphere SA              : 0.6748
+HEADER 5  - Mean B-factor                     : 0.3830
+HEADER 6  - Hydrophobicity Score              : -22.5000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 5.5000
+HEADER 9  - Real volume (approximation)       : 243.4480
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 3.0000
+HEADER 12 - Number of apolar alpha sphere     :     4
+HEADER 13 - Proportion of apolar alpha sphere : 0.2353
+ATOM      1    O STP     6     -10.865  18.249   0.469    0.00     4.11
+ATOM      2    O STP     6      -9.803  18.840   1.772    0.00     3.43
+ATOM      3    O STP     6     -11.664  16.564   0.901    0.00     3.69
+ATOM      4    O STP     6     -10.854  18.060   0.590    0.00     3.96
+ATOM      5    C STP     6      -9.018  19.707   1.368    0.00     3.86
+ATOM      6    O STP     6      -9.656  19.088   1.638    0.00     3.56
+ATOM      7    O STP     6     -10.831  18.316   0.411    0.00     4.14
+ATOM      8    C STP     6      -8.858  20.212   1.689    0.00     3.70
+ATOM      9    C STP     6      -8.626  20.731   1.519    0.00     3.88
+ATOM     10    O STP     6      -9.829  18.933   1.649    0.00     3.53
+ATOM     11    C STP     6     -12.817  19.837  -0.592    0.00     4.00
+ATOM     12    O STP     6     -10.800  18.318   0.530    0.00     4.08
+ATOM     13    O STP     6      -9.908  18.876   1.592    0.00     3.54
+ATOM     14    O STP     6     -11.221  20.512  -0.292    0.00     3.59
+ATOM     15    O STP     6      -8.604  20.710   1.295    0.00     4.00
+ATOM     16    O STP     6      -8.165  20.787   0.269    0.00     4.57
+ATOM     17    O STP     6      -8.676  20.220   0.368    0.00     4.52
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket7_atm.pdb

@@ -3,36 +3,34 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     7:
-HEADER 0  - Pocket Score                      : -0.0338
-HEADER 1  - Drug Score                        : 0.0006
-HEADER 2  - Number of alpha spheres           :    15
-HEADER 3  - Mean alpha-sphere radius          : 3.7280
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4019
-HEADER 5  - Mean B-factor of pocket residues  : 0.7160
-HEADER 6  - Hydrophobicity Score              : 7.7143
-HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Amino Acid based volume Score     : 4.0000
-HEADER 9  - Pocket volume (Monte Carlo)       : 262.3640
-HEADER 10  -Pocket volume (convex hull)       : 6.7930
-HEADER 11 - Charge Score                      :    -1
-HEADER 12 - Local hydrophobic density Score   : 5.0000
-HEADER 13 - Number of apolar alpha sphere     :     6
-HEADER 14 - Proportion of apolar alpha sphere : 0.4000
-ATOM   1307   NZ LYS A 185      -6.814  23.332  26.506  0.00  0.00           N 0
-ATOM   1237  OD2 ASP A 175      -3.713  23.987  32.328  0.00  0.00           O 0
-ATOM   1249    N GLU A 178      -7.967  26.111  33.085  0.00  0.00           N 0
-ATOM   1252    O GLU A 178      -7.954  23.140  33.285  0.64  2.14           O 0
-ATOM   1246   CA GLY A 177      -5.755  26.984  33.627  0.00  0.00           C 0
-ATOM   1253   CB GLU A 178      -9.877  25.079  31.919  0.00  0.00           C 0
-ATOM   1305   CD LYS A 185      -6.913  20.867  26.939  0.00  0.00           C 0
-ATOM   1271   SD MET A 180      -5.989  18.540  30.424  0.00  0.00           S 0
-ATOM   1115  NE2 GLN A 159      -5.515  21.745  33.331  0.00  0.00           N 0
-ATOM   1254   CG GLU A 178     -11.190  24.323  32.022  0.00  0.00           C 0
-ATOM   1306   CE LYS A 185      -7.179  21.983  25.920  0.00  0.00           C 0
-ATOM   1269   CB MET A 180      -8.472  18.896  31.501  0.00  0.00           C 0
-ATOM   1046  CG2 ILE A 151      -3.467  21.394  30.249  0.00  0.00           C 0
-ATOM   1047  CD1 ILE A 151      -1.923  23.263  28.606  0.00  0.00           C 0
-ATOM   1045  CG1 ILE A 151      -2.748  22.280  27.937  0.00  0.00           C 0
-ATOM   1236  OD1 ASP A 175      -2.222  25.511  32.451  0.50  2.14           O 0
+HEADER 0  - Pocket Score                      : -0.0207
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8891
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5474
+HEADER 5  - Mean B-factor of pocket residues  : 0.3723
+HEADER 6  - Hydrophobicity Score              : -4.0000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.7143
+HEADER 9  - Pocket volume (Monte Carlo)       : 252.0875
+HEADER 10 - Pocket volume (convex hull)       : 6.4999
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     0
+HEADER 14 - Proportion of apolar alpha sphere : 0.0000
+ATOM   1335   CB HIS A 189       1.397  27.011  18.007  0.00  0.00           C 0
+ATOM   1009  OE2 GLU A 146       3.925  30.351  15.551  0.00  0.00           O 0
+ATOM    569    O ASP A  86      -3.134  30.577  16.949  0.33  9.64           O 0
+ATOM   1337  ND1 HIS A 189       0.040  27.983  19.913  0.77  5.47           N 0
+ATOM    577    O ARG A  87      -2.431  27.764  15.190  0.00  0.00           O 0
+ATOM   1344    O LEU A 190       1.574  28.168  13.041  0.74  1.07           O 0
+ATOM    578   CB ARG A  87      -2.813  30.073  13.913  0.00  0.00           C 0
+ATOM    560    O GLN A  85      -5.938  33.818  16.095  0.00  0.00           O 0
+ATOM    568    C ASP A  86      -4.287  30.742  16.552  0.00  0.00           C 0
+ATOM    584  NH2 ARG A  87       0.614  32.921  11.229  0.09  7.66           N 0
+ATOM    582   CZ ARG A  87       0.454  31.713  11.756  0.00  0.00           C 0
+ATOM    583  NH1 ARG A  87       1.503  31.117  12.350  0.00  0.00           N 0
+ATOM    581   NE ARG A  87      -0.749  31.111  11.680  0.24  2.19           N 0
+ATOM    551    O LYS A  84      -6.645  31.712  13.194  0.00  0.00           O 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket7_vert.pqr

@@ -4,34 +4,35 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     7:
-HEADER 0  - Pocket Score                      : -0.0338
-HEADER 1  - Drug Score                        : 0.0006
-HEADER 2  - Number of V. Vertices             :    15
-HEADER 3  - Mean alpha-sphere radius          : 3.7280
-HEADER 4  - Mean alpha-sphere SA              : 0.4019
-HEADER 5  - Mean B-factor                     : 0.7160
-HEADER 6  - Hydrophobicity Score              : 7.7143
-HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 262.3640
-HEADER 10 - Charge Score                      :    -1
-HEADER 11 - Local hydrophobic density Score   : 5.0000
-HEADER 12 - Number of apolar alpha sphere     :     6
-HEADER 13 - Proportion of apolar alpha sphere : 0.4000
-ATOM      1    O STP     7      -6.625  24.421  30.057    0.00     3.72
-ATOM      2    O STP     7      -5.799  26.309  29.404    0.00     4.28
-ATOM      3    O STP     7      -8.308  22.685  29.725    0.00     3.61
-ATOM      4    O STP     7      -7.037  21.813  30.245    0.00     3.44
-ATOM      5    C STP     7     -10.258  22.548  28.497    0.00     4.05
-ATOM      6    C STP     7      -9.562  22.615  29.037    0.00     3.80
-ATOM      7    C STP     7      -7.102  21.786  30.244    0.00     3.44
-ATOM      8    C STP     7      -8.874  22.184  29.811    0.00     3.72
-ATOM      9    C STP     7      -9.225  22.114  29.661    0.00     3.78
-ATOM     10    C STP     7      -6.839  21.824  30.201    0.00     3.40
-ATOM     11    O STP     7      -6.761  22.668  29.984    0.00     3.54
-ATOM     12    O STP     7      -6.848  22.141  30.159    0.00     3.46
-ATOM     13    O STP     7      -6.421  23.405  30.062    0.00     3.58
-ATOM     14    O STP     7      -5.071  24.416  29.230    0.00     3.41
-ATOM     15    O STP     7      -4.870  26.897  28.843    0.00     4.69
+HEADER 0  - Pocket Score                      : -0.0207
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8891
+HEADER 4  - Mean alpha-sphere SA              : 0.5474
+HEADER 5  - Mean B-factor                     : 0.3723
+HEADER 6  - Hydrophobicity Score              : -4.0000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.7143
+HEADER 9  - Real volume (approximation)       : 252.0875
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     0
+HEADER 13 - Proportion of apolar alpha sphere : 0.0000
+ATOM      1    O STP     7       0.606  30.613  17.291    0.00     3.76
+ATOM      2    O STP     7       0.349  29.933  16.102    0.00     3.64
+ATOM      3    O STP     7       0.398  29.825  16.006    0.00     3.59
+ATOM      4    O STP     7       0.310  30.058  15.886    0.00     3.64
+ATOM      5    O STP     7      -2.704  33.369  14.954    0.00     3.46
+ATOM      6    O STP     7       0.267  30.094  15.812    0.00     3.62
+ATOM      7    O STP     7       0.297  30.167  15.803    0.00     3.64
+ATOM      8    O STP     7      -1.603  34.311  14.914    0.00     4.52
+ATOM      9    O STP     7      -1.370  34.089  14.976    0.00     4.40
+ATOM     10    O STP     7       0.328  30.306  15.653    0.00     3.60
+ATOM     11    O STP     7       0.297  30.561  15.738    0.00     3.64
+ATOM     12    O STP     7      -0.300  32.461  15.359    0.00     3.76
+ATOM     13    O STP     7      -1.581  33.922  14.529    0.00     4.09
+ATOM     14    O STP     7      -2.185  34.279  14.137    0.00     4.26
+ATOM     15    O STP     7      -3.286  34.022  12.999    0.00     4.08
+ATOM     16    O STP     7      -3.344  34.741  12.491    0.00     4.54
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket8_atm.pdb

@@ -3,40 +3,37 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     8:
-HEADER 0  - Pocket Score                      : -0.0391
-HEADER 1  - Drug Score                        : 0.0087
-HEADER 2  - Number of alpha spheres           :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0460
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5630
-HEADER 5  - Mean B-factor of pocket residues  : 0.6875
-HEADER 6  - Hydrophobicity Score              : 46.5556
+HEADER 0  - Pocket Score                      : -0.0379
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.9420
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4848
+HEADER 5  - Mean B-factor of pocket residues  : 0.5112
+HEADER 6  - Hydrophobicity Score              : 14.8750
 HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Amino Acid based volume Score     : 4.3333
-HEADER 9  - Pocket volume (Monte Carlo)       : 292.0643
-HEADER 10  -Pocket volume (convex hull)       : 11.0907
-HEADER 11 - Charge Score                      :    -1
-HEADER 12 - Local hydrophobic density Score   : 18.5000
-HEADER 13 - Number of apolar alpha sphere     :    20
-HEADER 14 - Proportion of apolar alpha sphere : 0.8000
-ATOM    134  CD2 LEU A  32      15.972  12.683  10.900  0.00  0.00           C 0
-ATOM    831   CB LEU A 122      15.645   7.979   7.938  0.00  0.00           C 0
-ATOM    133  CD1 LEU A  32      17.260  14.294   9.535  0.00  0.00           C 0
-ATOM    840   CG GLN A 123      20.411   7.331   7.673  0.00  0.00           C 0
-ATOM    808    O MET A 119      18.239   6.888  10.339  0.59  1.07           O 0
-ATOM    810   CG MET A 119      17.406   9.804  13.159  0.00  0.00           C 0
-ATOM    812   CE MET A 119      18.896  12.204  13.031  0.00  0.00           C 0
-ATOM    830    O LEU A 122      16.827   6.812   5.159  0.00  0.00           O 0
-ATOM    834  CD2 LEU A 122      13.141   8.318   7.801  0.00  0.00           C 0
-ATOM    165  CG2 THR A  36      13.954  15.228   5.144  0.00  0.00           C 0
-ATOM    856    O ALA A 126      13.064   6.701   4.796  0.00  0.00           O 0
-ATOM    833  CD1 LEU A 122      14.496   9.519   9.463  0.00  0.00           C 0
-ATOM    873  CD1 ILE A 128      11.138  13.485   7.280  0.00  0.00           C 0
-ATOM    871  CG1 ILE A 128      10.835  12.117   7.893  0.00  0.00           C 0
-ATOM    866    N ILE A 128       9.827   9.471   6.497  0.00  0.00           N 0
-ATOM    183  CD1 TYR A  38       8.575  12.993   3.679  0.00  0.00           C 0
-ATOM    862   CB ASP A 127       9.804   7.990   3.839  0.00  0.00           C 0
-ATOM    164  OG1 THR A  36      14.951  15.781   7.174  0.77  3.21           O 0
-ATOM    132   CG LEU A  32      15.981  14.083  10.326  0.00  0.00           C 0
-ATOM    859   CA ASP A 127      10.629   7.660   5.095  0.00  0.00           C 0
+HEADER 8  - Amino Acid based volume Score     : 4.7500
+HEADER 9  - Pocket volume (Monte Carlo)       : 284.5030
+HEADER 10 - Pocket volume (convex hull)       : 14.8121
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 7.5556
+HEADER 13 - Number of apolar alpha sphere     :     9
+HEADER 14 - Proportion of apolar alpha sphere : 0.5000
+ATOM    554   CD LYS A  84     -10.564  29.203   9.966  0.00  0.00           C 0
+ATOM    555   CE LYS A  84     -10.617  28.047   8.968  0.00  0.00           C 0
+ATOM   1632   CB GLU A 223     -14.450  27.765  13.143  0.00  0.00           C 0
+ATOM   1644   CE LYS A 224     -16.928  31.544  10.938  0.00  0.00           C 0
+ATOM   1643   CD LYS A 224     -16.362  31.743  12.340  0.00  0.00           C 0
+ATOM   1631    O GLU A 223     -17.365  27.664  12.274  0.00  0.00           O 0
+ATOM   1415    O LEU A 198      -9.906  24.668   9.956  0.69  1.07           O 0
+ATOM   1633   CG GLU A 223     -13.156  27.273  13.733  0.00  0.00           C 0
+ATOM    556   NZ LYS A  84     -10.127  28.466   7.603  0.00  5.47           N 0
+ATOM   1628    N GLU A 223     -15.619  25.690  13.330  0.55  2.19           N 0
+ATOM   1436  OE1 GLU A 200     -17.093  22.138   8.081  0.00  0.00           O 0
+ATOM   1625   CB VAL A 222     -17.369  23.118  12.521  0.00  0.00           C 0
+ATOM   1433   CB GLU A 200     -14.329  21.747   8.212  0.00  0.00           C 0
+ATOM   1429    N GLU A 200     -12.069  22.448   7.649  0.00  0.00           N 0
+ATOM    538   CG PRO A  82     -11.246  23.110  13.712  0.00  0.00           C 0
+ATOM   1622   CA VAL A 222     -16.212  23.301  13.531  0.00  0.00           C 0
+ATOM   1613    O PHE A 221     -14.238  21.495  14.191  0.74  3.21           O 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket8_vert.pqr

@@ -4,44 +4,37 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     8:
-HEADER 0  - Pocket Score                      : -0.0391
-HEADER 1  - Drug Score                        : 0.0087
-HEADER 2  - Number of V. Vertices             :    25
-HEADER 3  - Mean alpha-sphere radius          : 4.0460
-HEADER 4  - Mean alpha-sphere SA              : 0.5630
-HEADER 5  - Mean B-factor                     : 0.6875
-HEADER 6  - Hydrophobicity Score              : 46.5556
+HEADER 0  - Pocket Score                      : -0.0379
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.9420
+HEADER 4  - Mean alpha-sphere SA              : 0.4848
+HEADER 5  - Mean B-factor                     : 0.5112
+HEADER 6  - Hydrophobicity Score              : 14.8750
 HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Volume Score                      : 4.3333
-HEADER 9  - Real volume (approximation)       : 292.0643
-HEADER 10 - Charge Score                      :    -1
-HEADER 11 - Local hydrophobic density Score   : 18.5000
-HEADER 12 - Number of apolar alpha sphere     :    20
-HEADER 13 - Proportion of apolar alpha sphere : 0.8000
-ATOM      1    C STP     8      18.480  10.647   8.623    0.00     3.95
-ATOM      2    C STP     8      18.473  10.489   8.873    0.00     3.90
-ATOM      3    C STP     8      18.698  10.488   9.792    0.00     3.67
-ATOM      4    C STP     8      14.943  10.866   4.541    0.00     4.51
-ATOM      5    O STP     8      14.875  10.843   4.459    0.00     4.53
-ATOM      6    O STP     8      14.864  10.355   4.722    0.00     4.07
-ATOM      7    C STP     8      17.917  10.225   9.354    0.00     3.49
-ATOM      8    C STP     8      14.939  11.399   5.926    0.00     4.03
-ATOM      9    C STP     8      16.088  11.832   6.354    0.00     4.19
-ATOM     10    C STP     8      17.345  11.079   8.062    0.00     3.54
-ATOM     11    C STP     8      14.302  11.614   6.290    0.00     3.81
-ATOM     12    C STP     8      14.169  11.576   6.426    0.00     3.68
-ATOM     13    C STP     8      13.282  11.035   4.472    0.00     4.30
-ATOM     14    O STP     8      13.297  11.009   4.410    0.00     4.33
-ATOM     15    C STP     8      13.187  11.021   4.702    0.00     4.11
-ATOM     16    C STP     8      12.553  11.402   3.811    0.00     4.29
-ATOM     17    C STP     8      12.615  11.331   3.695    0.00     4.37
-ATOM     18    C STP     8      16.085  11.834   6.357    0.00     4.19
-ATOM     19    C STP     8      15.342  12.249   7.345    0.00     3.56
-ATOM     20    C STP     8      14.506  12.196   7.034    0.00     3.62
-ATOM     21    C STP     8      14.353  12.486   7.796    0.00     3.41
-ATOM     22    O STP     8      13.277  10.973   4.430    0.00     4.29
-ATOM     23    C STP     8      13.182  11.064   3.370    0.00     4.59
-ATOM     24    O STP     8      13.287  11.012   4.386    0.00     4.34
-ATOM     25    C STP     8      12.716  11.267   3.730    0.00     4.38
+HEADER 8  - Volume Score                      : 4.7500
+HEADER 9  - Real volume (approximation)       : 284.5030
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 7.5556
+HEADER 12 - Number of apolar alpha sphere     :     9
+HEADER 13 - Proportion of apolar alpha sphere : 0.5000
+ATOM      1    C STP     8     -14.456  28.897   9.357    0.00     3.95
+ATOM      2    C STP     8     -13.802  30.114  10.708    0.00     3.44
+ATOM      3    C STP     8     -14.824  28.441   8.989    0.00     4.23
+ATOM      4    C STP     8     -13.008  26.082  10.497    0.00     3.45
+ATOM      5    C STP     8     -14.169  30.414   7.585    0.00     4.49
+ATOM      6    O STP     8     -13.292  25.512  10.645    0.00     3.56
+ATOM      7    O STP     8     -16.281  25.248   9.782    0.00     3.64
+ATOM      8    O STP     8     -13.777  25.706   9.765    0.00     4.01
+ATOM      9    O STP     8     -15.422  24.602   9.978    0.00     3.53
+ATOM     10    O STP     8     -13.889  25.617   9.542    0.00     4.12
+ATOM     11    O STP     8     -13.906  25.623   9.573    0.00     4.13
+ATOM     12    O STP     8     -15.206  25.827   9.088    0.00     4.26
+ATOM     13    O STP     8     -13.401  24.066  10.900    0.00     3.67
+ATOM     14    C STP     8     -13.617  23.729  11.105    0.00     3.58
+ATOM     15    C STP     8     -14.727  26.185   8.926    0.00     4.51
+ATOM     16    C STP     8     -14.636  26.121   9.005    0.00     4.46
+ATOM     17    O STP     8     -14.732  26.170   8.943    0.00     4.50
+ATOM     18    C STP     8     -13.644  23.175  11.257    0.00     3.43
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket9_atm.pdb

@@ -3,36 +3,36 @@ HEADER This is a pdb format file writen by the programm fpocket.
 HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
 HEADER                                                                           
 HEADER Information about the pocket     9:
-HEADER 0  - Pocket Score                      : -0.0597
-HEADER 1  - Drug Score                        : 0.0005
+HEADER 0  - Pocket Score                      : -0.0423
+HEADER 1  - Drug Score                        : 0.0007
 HEADER 2  - Number of alpha spheres           :    17
-HEADER 3  - Mean alpha-sphere radius          : 3.8905
-HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5932
-HEADER 5  - Mean B-factor of pocket residues  : 0.6375
-HEADER 6  - Hydrophobicity Score              : -11.3750
+HEADER 3  - Mean alpha-sphere radius          : 3.7157
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4200
+HEADER 5  - Mean B-factor of pocket residues  : 0.4302
+HEADER 6  - Hydrophobicity Score              : 7.7143
 HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Amino Acid based volume Score     : 3.3750
-HEADER 9  - Pocket volume (Monte Carlo)       : 280.7654
-HEADER 10  -Pocket volume (convex hull)       : 12.8403
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 259.3035
+HEADER 10 - Pocket volume (convex hull)       : 7.7394
 HEADER 11 - Charge Score                      :    -1
 HEADER 12 - Local hydrophobic density Score   : 6.0000
 HEADER 13 - Number of apolar alpha sphere     :     7
 HEADER 14 - Proportion of apolar alpha sphere : 0.4118
-ATOM   1262   CB PRO A 179      -9.732  21.711  36.429  0.00  0.00           C 0
-ATOM   1111   CB GLN A 159      -3.563  19.835  35.636  0.00  0.00           C 0
-ATOM   1233    O ASP A 175      -2.967  23.964  36.554  0.34  7.50           O 0
-ATOM   1106  OE2 GLU A 158      -2.440  19.673  41.584  0.00  0.00           O 0
-ATOM   1259   CA PRO A 179      -8.962  21.849  35.105  0.00  0.00           C 0
-ATOM   1263   CG PRO A 179      -9.842  23.072  36.977  0.00  0.00           C 0
-ATOM   1248    O GLY A 177      -7.087  25.609  35.109  0.40  4.29           O 0
-ATOM   1107    N GLN A 159      -2.228  18.673  37.326  0.63  2.19           N 0
-ATOM   1062   CE LYS A 153      -5.591  16.089  38.200  0.00  0.00           C 0
-ATOM   1114  OE1 GLN A 159      -6.210  19.893  34.388  0.76  2.14           O 0
-ATOM   1113   CD GLN A 159      -5.304  20.600  33.983  0.00  0.00           C 0
-ATOM   1273    N GLY A 181      -9.984  17.239  34.316  0.59  3.28           N 0
-ATOM   1265    N MET A 180      -8.985  19.796  33.754  0.61  1.09           N 0
-ATOM   1061   CD LYS A 153      -4.956  16.412  36.840  0.00  0.00           C 0
-ATOM   1274   CA GLY A 181     -10.573  15.994  34.761  0.00  0.00           C 0
-ATOM   1276    O GLY A 181      -9.088  14.413  35.748  0.70  5.36           O 0
+ATOM   1307   NZ LYS A 185      -6.814  23.332  26.506  0.00  0.00           N 0
+ATOM   1237  OD2 ASP A 175      -3.713  23.987  32.328  0.00  0.00           O 0
+ATOM   1249    N GLU A 178      -7.967  26.111  33.085  0.00  0.00           N 0
+ATOM   1252    O GLU A 178      -7.954  23.140  33.285  0.66  2.14           O 0
+ATOM   1246   CA GLY A 177      -5.755  26.984  33.627  0.00  0.00           C 0
+ATOM   1253   CB GLU A 178      -9.877  25.079  31.919  0.00  0.00           C 0
+ATOM   1305   CD LYS A 185      -6.913  20.867  26.939  0.00  0.00           C 0
+ATOM   1271   SD MET A 180      -5.989  18.540  30.424  0.00  0.00           S 0
+ATOM   1115  NE2 GLN A 159      -5.515  21.745  33.331  0.00  0.00           N 0
+ATOM   1254   CG GLU A 178     -11.190  24.323  32.022  0.00  0.00           C 0
+ATOM   1306   CE LYS A 185      -7.179  21.983  25.920  0.00  0.00           C 0
+ATOM   1269   CB MET A 180      -8.472  18.896  31.501  0.00  0.00           C 0
+ATOM   1046  CG2 ILE A 151      -3.467  21.394  30.249  0.00  0.00           C 0
+ATOM   1047  CD1 ILE A 151      -1.923  23.263  28.606  0.00  0.00           C 0
+ATOM   1045  CG1 ILE A 151      -2.748  22.280  27.937  0.00  0.00           C 0
+ATOM   1236  OD1 ASP A 175      -2.222  25.511  32.451  0.50  2.14           O 0
 TER
 END

tests/reference_output/1UYD_out/pockets/pocket9_vert.pqr

@@ -4,36 +4,36 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     9:
-HEADER 0  - Pocket Score                      : -0.0597
-HEADER 1  - Drug Score                        : 0.0005
+HEADER 0  - Pocket Score                      : -0.0423
+HEADER 1  - Drug Score                        : 0.0007
 HEADER 2  - Number of V. Vertices             :    17
-HEADER 3  - Mean alpha-sphere radius          : 3.8905
-HEADER 4  - Mean alpha-sphere SA              : 0.5932
-HEADER 5  - Mean B-factor                     : 0.6375
-HEADER 6  - Hydrophobicity Score              : -11.3750
+HEADER 3  - Mean alpha-sphere radius          : 3.7157
+HEADER 4  - Mean alpha-sphere SA              : 0.4200
+HEADER 5  - Mean B-factor                     : 0.4302
+HEADER 6  - Hydrophobicity Score              : 7.7143
 HEADER 7  - Polarity Score                    :     4
-HEADER 8  - Volume Score                      : 3.3750
-HEADER 9  - Real volume (approximation)       : 280.7654
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 259.3035
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7
 HEADER 13 - Proportion of apolar alpha sphere : 0.4118
-ATOM      1    O STP     9      -5.987  21.597  39.224    0.00     4.67
-ATOM      2    C STP     9      -6.191  22.298  37.656    0.00     3.79
-ATOM      3    O STP     9      -6.290  22.862  37.242    0.00     3.57
-ATOM      4    C STP     9      -6.076  21.951  37.687    0.00     3.87
-ATOM      5    O STP     9      -4.027  21.397  38.848    0.00     3.60
-ATOM      6    O STP     9      -5.569  19.993  39.101    0.00     4.01
-ATOM      7    C STP     9      -6.315  20.503  39.256    0.00     4.60
-ATOM      8    C STP     9      -6.095  21.897  37.670    0.00     3.85
-ATOM      9    C STP     9      -6.531  20.110  38.511    0.00     4.14
-ATOM     10    O STP     9      -5.839  22.040  37.133    0.00     3.50
-ATOM     11    O STP     9      -6.021  22.227  37.054    0.00     3.55
-ATOM     12    O STP     9      -6.062  21.968  37.603    0.00     3.83
-ATOM     13    O STP     9      -8.206  18.652  36.918    0.00     3.45
-ATOM     14    O STP     9      -8.120  18.521  37.184    0.00     3.65
-ATOM     15    C STP     9      -6.229  19.490  37.843    0.00     3.48
-ATOM     16    O STP     9      -9.377  17.540  38.316    0.00     4.06
-ATOM     17    C STP     9      -9.701  17.858  38.776    0.00     4.51
+ATOM      1    O STP     9      -6.625  24.421  30.057    0.00     3.72
+ATOM      2    O STP     9      -5.799  26.309  29.404    0.00     4.28
+ATOM      3    O STP     9      -6.778  24.418  30.031    0.00     3.69
+ATOM      4    O STP     9      -8.308  22.685  29.725    0.00     3.61
+ATOM      5    O STP     9      -7.037  21.813  30.245    0.00     3.44
+ATOM      6    C STP     9     -10.258  22.548  28.497    0.00     4.05
+ATOM      7    C STP     9      -9.562  22.615  29.037    0.00     3.80
+ATOM      8    C STP     9      -7.102  21.786  30.244    0.00     3.44
+ATOM      9    C STP     9      -8.874  22.184  29.811    0.00     3.72
+ATOM     10    C STP     9      -9.179  22.095  30.112    0.00     3.56
+ATOM     11    C STP     9      -9.225  22.114  29.661    0.00     3.78
+ATOM     12    C STP     9      -6.839  21.824  30.201    0.00     3.40
+ATOM     13    O STP     9      -6.761  22.668  29.984    0.00     3.54
+ATOM     14    O STP     9      -6.848  22.141  30.159    0.00     3.46
+ATOM     15    O STP     9      -6.421  23.405  30.062    0.00     3.58
+ATOM     16    O STP     9      -5.071  24.416  29.230    0.00     3.41
+ATOM     17    O STP     9      -4.870  26.897  28.843    0.00     4.69
 TER
 END

tests/reference_output/2P0R_mod_out/2P0R_mod_info.txt

@@ -5,7 +5,7 @@ Pocket 1 :
 	Total SASA : 	195.984
 	Polar SASA : 	87.297
 	Apolar SASA : 	108.687
-	Volume : 	1933.883
+	Volume : 	1910.432
 	Mean local hydrophobic density : 	19.643
 	Mean alpha sphere radius :	4.224
 	Mean alp. sph. solvent access : 	0.508

tests/reference_output/2P0R_mod_out/2P0R_mod_out.pdb

@@ -5119,103 +5119,103 @@ ATOM   5151   CB LEU E 357      -0.639  18.231  62.969  0.00  0.00           C 0
 ATOM   5152   CG LEU E 357      -1.271  18.582  64.323  0.00  0.00           C 0
 ATOM   5153  CD1 LEU E 357      -0.477  17.951  65.443  0.00  0.00           C 0
 ATOM   5154  CD2 LEU E 357      -1.370  20.078  64.523  0.00  0.00           C 0
-HETATM    1 APOL STP C   1      -7.927  25.710  29.491  0.00  0.00          Ve  
-HETATM    2 APOL STP C   1      -0.944  21.557  24.346  0.00  0.00          Ve  
+HETATM 6185  POL STP C   1      -7.927  25.710  29.491  0.00  0.00          Ve  
+HETATM 6714  POL STP C   1      -0.944  21.557  24.346  0.00  0.00          Ve  
 HETATM    3 APOL STP C   1      -0.390  21.119  25.163  0.00  0.00          Ve  
 HETATM    4 APOL STP C   1      -0.497  19.750  26.137  0.00  0.00          Ve  
-HETATM    5 APOL STP C   1      -1.505  21.560  24.468  0.00  0.00          Ve  
-HETATM    6 APOL STP C   1      -7.006  23.099  31.939  0.00  0.00          Ve  
+HETATM 8321  POL STP C   1      -1.505  21.560  24.468  0.00  0.00          Ve  
+HETATM10203  POL STP C   1      -7.006  23.099  31.939  0.00  0.00          Ve  
 HETATM    7 APOL STP C   1      -2.421  19.598  26.681  0.00  0.00          Ve  
-HETATM    8 APOL STP C   1      -1.904  20.950  25.868  0.00  0.00          Ve  
-HETATM    9 APOL STP C   1      -1.138  19.994  26.698  0.00  0.00          Ve  
-HETATM   10 APOL STP C   1      -0.610  21.340  26.848  0.00  0.00          Ve  
-HETATM   11 APOL STP C   1      -1.105  20.703  26.217  0.00  0.00          Ve  
+HETATM10206  POL STP C   1      -1.904  20.950  25.868  0.00  0.00          Ve  
+HETATM10206  POL STP C   1      -1.138  19.994  26.698  0.00  0.00          Ve  
+HETATM10206  POL STP C   1      -0.610  21.340  26.848  0.00  0.00          Ve  
+HETATM10206  POL STP C   1      -1.105  20.703  26.217  0.00  0.00          Ve  
 HETATM   12 APOL STP C   1      -2.450  19.593  26.684  0.00  0.00          Ve  
 HETATM   13 APOL STP C   1      -0.703  20.660  31.637  0.00  0.00          Ve  
-HETATM   14 APOL STP C   1      -0.812  20.704  31.050  0.00  0.00          Ve  
+HETATM12214  POL STP C   1      -0.812  20.704  31.050  0.00  0.00          Ve  
 HETATM   15 APOL STP C   1      -0.219  20.522  28.381  0.00  0.00          Ve  
-HETATM   16 APOL STP C   1      -0.246  20.464  28.365  0.00  0.00          Ve  
-HETATM   17 APOL STP C   1       2.253  18.734  33.805  0.00  0.00          Ve  
-HETATM   18 APOL STP C   1       2.716  18.560  34.058  0.00  0.00          Ve  
-HETATM   19 APOL STP C   1      -2.017  21.009  25.831  0.00  0.00          Ve  
+HETATM12216  POL STP C   1      -0.246  20.464  28.365  0.00  0.00          Ve  
+HETATM12223  POL STP C   1       2.253  18.734  33.805  0.00  0.00          Ve  
+HETATM12272  POL STP C   1       2.716  18.560  34.058  0.00  0.00          Ve  
+HETATM13862  POL STP C   1      -2.017  21.009  25.831  0.00  0.00          Ve  
 HETATM   20 APOL STP C   1      -7.684  25.074  29.391  0.00  0.00          Ve  
 HETATM   21 APOL STP C   1      -5.738  21.726  22.846  0.00  0.00          Ve  
-HETATM   22 APOL STP C   1      -4.802  20.822  26.086  0.00  0.00          Ve  
-HETATM   23 APOL STP C   1      -3.784  20.874  25.890  0.00  0.00          Ve  
-HETATM   24 APOL STP C   1      -2.002  21.755  24.422  0.00  0.00          Ve  
-HETATM   25 APOL STP C   1      -3.770  21.486  26.150  0.00  0.00          Ve  
-HETATM   26 APOL STP C   1      -3.053  21.034  25.802  0.00  0.00          Ve  
-HETATM   27 APOL STP C   1      -2.286  21.303  25.452  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -4.802  20.822  26.086  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -3.784  20.874  25.890  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -2.002  21.755  24.422  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -3.770  21.486  26.150  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -3.053  21.034  25.802  0.00  0.00          Ve  
+HETATM15419  POL STP C   1      -2.286  21.303  25.452  0.00  0.00          Ve  
 HETATM   28 APOL STP C   1      -2.467  19.582  26.696  0.00  0.00          Ve  
 HETATM   29 APOL STP C   1      -3.065  18.013  27.593  0.00  0.00          Ve  
-HETATM   30 APOL STP C   1      -4.069  15.575  26.940  0.00  0.00          Ve  
-HETATM   31 APOL STP C   1      -3.587  13.987  38.073  0.00  0.00          Ve  
-HETATM   32 APOL STP C   1      -3.704  14.174  38.166  0.00  0.00          Ve  
-HETATM   33 APOL STP C   1      -5.656  15.984  36.278  0.00  0.00          Ve  
-HETATM   34 APOL STP C   1      -5.504  16.518  38.204  0.00  0.00          Ve  
+HETATM15453  POL STP C   1      -4.069  15.575  26.940  0.00  0.00          Ve  
+HETATM16574  POL STP C   1      -3.587  13.987  38.073  0.00  0.00          Ve  
+HETATM16574  POL STP C   1      -3.704  14.174  38.166  0.00  0.00          Ve  
+HETATM16574  POL STP C   1      -5.656  15.984  36.278  0.00  0.00          Ve  
+HETATM16574  POL STP C   1      -5.504  16.518  38.204  0.00  0.00          Ve  
 HETATM   35 APOL STP C   1      -6.227  18.398  36.193  0.00  0.00          Ve  
-HETATM   36 APOL STP C   1      -3.847  18.514  36.288  0.00  0.00          Ve  
-HETATM   37 APOL STP C   1      -5.712  16.109  39.065  0.00  0.00          Ve  
-HETATM   38 APOL STP C   1      -3.819  14.133  38.275  0.00  0.00          Ve  
-HETATM   39 APOL STP C   1      -4.642  15.555  38.606  0.00  0.00          Ve  
-HETATM   40 APOL STP C   1      -4.979  16.043  38.743  0.00  0.00          Ve  
-HETATM   41 APOL STP C   1      -4.914  16.042  38.749  0.00  0.00          Ve  
-HETATM   42 APOL STP C   1      -4.641  18.226  28.432  0.00  0.00          Ve  
+HETATM16574  POL STP C   1      -3.847  18.514  36.288  0.00  0.00          Ve  
+HETATM16576  POL STP C   1      -5.712  16.109  39.065  0.00  0.00          Ve  
+HETATM16576  POL STP C   1      -3.819  14.133  38.275  0.00  0.00          Ve  
+HETATM16576  POL STP C   1      -4.642  15.555  38.606  0.00  0.00          Ve  
+HETATM16576  POL STP C   1      -4.979  16.043  38.743  0.00  0.00          Ve  
+HETATM16576  POL STP C   1      -4.914  16.042  38.749  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -4.641  18.226  28.432  0.00  0.00          Ve  
 HETATM   43 APOL STP C   1      -3.129  18.059  27.644  0.00  0.00          Ve  
-HETATM   44 APOL STP C   1      -2.825  18.832  27.555  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -2.825  18.832  27.555  0.00  0.00          Ve  
 HETATM   45 APOL STP C   1      -3.030  18.141  27.600  0.00  0.00          Ve  
-HETATM   46 APOL STP C   1      -1.764  19.741  31.334  0.00  0.00          Ve  
-HETATM   47 APOL STP C   1      -1.278  19.903  31.356  0.00  0.00          Ve  
-HETATM   48 APOL STP C   1      -1.286  19.922  31.268  0.00  0.00          Ve  
-HETATM   49 APOL STP C   1      -0.653  19.833  28.635  0.00  0.00          Ve  
-HETATM   50 APOL STP C   1      -1.291  18.558  33.444  0.00  0.00          Ve  
-HETATM   51 APOL STP C   1       0.141  18.540  33.212  0.00  0.00          Ve  
-HETATM   52 APOL STP C   1      -0.337  17.740  33.506  0.00  0.00          Ve  
-HETATM   53 APOL STP C   1      -0.856  18.760  27.475  0.00  0.00          Ve  
-HETATM   54 APOL STP C   1      -2.728  14.181  37.978  0.00  0.00          Ve  
-HETATM   55 APOL STP C   1      -0.221  17.529  33.664  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -1.764  19.741  31.334  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -1.278  19.903  31.356  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -1.286  19.922  31.268  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -0.653  19.833  28.635  0.00  0.00          Ve  
+HETATM16589  POL STP C   1      -1.291  18.558  33.444  0.00  0.00          Ve  
+HETATM16590  POL STP C   1       0.141  18.540  33.212  0.00  0.00          Ve  
+HETATM16590  POL STP C   1      -0.337  17.740  33.506  0.00  0.00          Ve  
+HETATM16592  POL STP C   1      -0.856  18.760  27.475  0.00  0.00          Ve  
+HETATM16620  POL STP C   1      -2.728  14.181  37.978  0.00  0.00          Ve  
+HETATM16621  POL STP C   1      -0.221  17.529  33.664  0.00  0.00          Ve  
 HETATM   56 APOL STP C   1      -3.437  18.918  36.407  0.00  0.00          Ve  
-HETATM   57 APOL STP C   1      -2.278  19.673  36.184  0.00  0.00          Ve  
+HETATM18803  POL STP C   1      -2.278  19.673  36.184  0.00  0.00          Ve  
 HETATM   58 APOL STP C   1      -4.398  20.219  36.733  0.00  0.00          Ve  
-HETATM   59 APOL STP C   1      -1.215  19.866  26.768  0.00  0.00          Ve  
+HETATM19660  POL STP C   1      -1.215  19.866  26.768  0.00  0.00          Ve  
 HETATM   60 APOL STP C   1      -2.296  19.575  26.726  0.00  0.00          Ve  
 HETATM   61 APOL STP C   1      -0.463  19.697  26.108  0.00  0.00          Ve  
-HETATM   62 APOL STP C   1      -0.646  18.417  26.693  0.00  0.00          Ve  
-HETATM   63 APOL STP C   1      -1.504  19.313  27.220  0.00  0.00          Ve  
-HETATM   64 APOL STP C   1      -1.799  19.199  27.242  0.00  0.00          Ve  
-HETATM   65 APOL STP C   1      -1.195  18.862  27.071  0.00  0.00          Ve  
+HETATM19662  POL STP C   1      -0.646  18.417  26.693  0.00  0.00          Ve  
+HETATM19663  POL STP C   1      -1.504  19.313  27.220  0.00  0.00          Ve  
+HETATM19663  POL STP C   1      -1.799  19.199  27.242  0.00  0.00          Ve  
+HETATM19663  POL STP C   1      -1.195  18.862  27.071  0.00  0.00          Ve  
 HETATM   66 APOL STP C   1      -1.255  18.277  26.909  0.00  0.00          Ve  
-HETATM   67 APOL STP C   1      -1.374  19.085  27.170  0.00  0.00          Ve  
+HETATM19663  POL STP C   1      -1.374  19.085  27.170  0.00  0.00          Ve  
 HETATM   68 APOL STP C   1      -1.665  18.991  27.195  0.00  0.00          Ve  
 HETATM   69 APOL STP C   1       0.538  20.926  24.251  0.00  0.00          Ve  
-HETATM   70 APOL STP C   1      -4.253  16.196  38.650  0.00  0.00          Ve  
+HETATM21839  POL STP C   1      -4.253  16.196  38.650  0.00  0.00          Ve  
 HETATM   71 APOL STP C   1      -0.660  17.674  41.151  0.00  0.00          Ve  
-HETATM   72 APOL STP C   1      -0.665  17.381  41.718  0.00  0.00          Ve  
-HETATM   73 APOL STP C   1      -2.320  14.385  37.937  0.00  0.00          Ve  
-HETATM   74 APOL STP C   1      -3.527  17.299  37.574  0.00  0.00          Ve  
-HETATM   75 APOL STP C   1       1.896  18.908  33.762  0.00  0.00          Ve  
+HETATM21839  POL STP C   1      -0.665  17.381  41.718  0.00  0.00          Ve  
+HETATM21839  POL STP C   1      -2.320  14.385  37.937  0.00  0.00          Ve  
+HETATM21840  POL STP C   1      -3.527  17.299  37.574  0.00  0.00          Ve  
+HETATM24188  POL STP C   1       1.896  18.908  33.762  0.00  0.00          Ve  
 HETATM   76 APOL STP C   1      -0.502  20.722  31.885  0.00  0.00          Ve  
-HETATM   77 APOL STP C   1      -0.828  18.820  33.297  0.00  0.00          Ve  
-HETATM   78 APOL STP C   1      -0.715  19.279  32.645  0.00  0.00          Ve  
-HETATM   79 APOL STP C   1      -0.068  18.700  33.204  0.00  0.00          Ve  
-HETATM   80 APOL STP C   1       2.761  18.546  34.093  0.00  0.00          Ve  
-HETATM   81 APOL STP C   1       2.783  18.567  34.049  0.00  0.00          Ve  
+HETATM24191  POL STP C   1      -0.828  18.820  33.297  0.00  0.00          Ve  
+HETATM24191  POL STP C   1      -0.715  19.279  32.645  0.00  0.00          Ve  
+HETATM24191  POL STP C   1      -0.068  18.700  33.204  0.00  0.00          Ve  
+HETATM27229  POL STP C   1       2.761  18.546  34.093  0.00  0.00          Ve  
+HETATM27230  POL STP C   1       2.783  18.567  34.049  0.00  0.00          Ve  
 HETATM   82 APOL STP C   1      -4.983  18.148  28.557  0.00  0.00          Ve  
 HETATM   83 APOL STP C   1      -6.697  18.281  32.723  0.00  0.00          Ve  
-HETATM   84 APOL STP C   1      -6.877  15.226  26.592  0.00  0.00          Ve  
-HETATM   85 APOL STP C   1      -5.571  16.002  26.870  0.00  0.00          Ve  
-HETATM   86 APOL STP C   1      -4.952  18.143  28.746  0.00  0.00          Ve  
+HETATM27380  POL STP C   1      -6.877  15.226  26.592  0.00  0.00          Ve  
+HETATM27383  POL STP C   1      -5.571  16.002  26.870  0.00  0.00          Ve  
+HETATM27383  POL STP C   1      -4.952  18.143  28.746  0.00  0.00          Ve  
 HETATM   87 APOL STP C   1      -4.516  15.952  27.324  0.00  0.00          Ve  
 HETATM   88 APOL STP C   1      -6.455  17.186  32.808  0.00  0.00          Ve  
 HETATM   89 APOL STP C   1      -6.466  17.333  32.806  0.00  0.00          Ve  
-HETATM   90 APOL STP C   1      -5.335  18.346  31.496  0.00  0.00          Ve  
-HETATM   91 APOL STP C   1      -5.324  18.315  31.552  0.00  0.00          Ve  
-HETATM   92 APOL STP C   1      -3.887  15.796  31.076  0.00  0.00          Ve  
+HETATM27384  POL STP C   1      -5.335  18.346  31.496  0.00  0.00          Ve  
+HETATM27384  POL STP C   1      -5.324  18.315  31.552  0.00  0.00          Ve  
+HETATM27384  POL STP C   1      -3.887  15.796  31.076  0.00  0.00          Ve  
 HETATM   93 APOL STP C   1      -3.831  15.614  31.082  0.00  0.00          Ve  
-HETATM   94 APOL STP C   1      -5.263  16.341  42.194  0.00  0.00          Ve  
-HETATM   95 APOL STP C   1      -4.438  16.373  40.937  0.00  0.00          Ve  
-HETATM   96 APOL STP C   1      -4.111  16.415  42.058  0.00  0.00          Ve  
-HETATM   97 APOL STP C   1      -6.809  16.200  40.052  0.00  0.00          Ve  
-HETATM   98 APOL STP C   1      -6.390  16.221  39.684  0.00  0.00          Ve  
-HETATM   99 APOL STP C   1       2.836  18.727  33.815  0.00  0.00          Ve  
-HETATM  100 APOL STP C   1       2.888  18.613  33.980  0.00  0.00          Ve  
+HETATM28623  POL STP C   1      -5.263  16.341  42.194  0.00  0.00          Ve  
+HETATM28626  POL STP C   1      -4.438  16.373  40.937  0.00  0.00          Ve  
+HETATM28626  POL STP C   1      -4.111  16.415  42.058  0.00  0.00          Ve  
+HETATM28630  POL STP C   1      -6.809  16.200  40.052  0.00  0.00          Ve  
+HETATM28630  POL STP C   1      -6.390  16.221  39.684  0.00  0.00          Ve  
+HETATM35227  POL STP C   1       2.836  18.727  33.815  0.00  0.00          Ve  
+HETATM35227  POL STP C   1       2.888  18.613  33.980  0.00  0.00          Ve  

tests/reference_output/2P0R_mod_out/pockets/pocket1_atm.pdb

@@ -12,8 +12,8 @@ HEADER 5  - Mean B-factor of pocket residues  : 0.0000
 HEADER 6  - Hydrophobicity Score              : 12.9615
 HEADER 7  - Polarity Score                    :    15
 HEADER 8  - Amino Acid based volume Score     : 3.4615
-HEADER 9  - Pocket volume (Monte Carlo)       : 1933.8832
-HEADER 10  -Pocket volume (convex hull)       : 700.1219
+HEADER 9  - Pocket volume (Monte Carlo)       : 1910.4324
+HEADER 10 - Pocket volume (convex hull)       : 700.1219
 HEADER 11 - Charge Score                      :    -2
 HEADER 12 - Local hydrophobic density Score   : 19.6429
 HEADER 13 - Number of apolar alpha sphere     :    28

tests/reference_output/2P0R_mod_out/pockets/pocket1_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0000
 HEADER 6  - Hydrophobicity Score              : 12.9615
 HEADER 7  - Polarity Score                    :    15
 HEADER 8  - Volume Score                      : 3.4615
-HEADER 9  - Real volume (approximation)       : 1933.8832
+HEADER 9  - Real volume (approximation)       : 1910.4324
 HEADER 10 - Charge Score                      :    -2
 HEADER 11 - Local hydrophobic density Score   : 19.6429
 HEADER 12 - Number of apolar alpha sphere     :    28

tests/reference_output/2P0R_out/2P0R_info.txt

@@ -5,7 +5,7 @@ Pocket 1 :
 	Total SASA : 	56.959
 	Polar SASA : 	36.430
 	Apolar SASA : 	20.530
-	Volume : 	386.650
+	Volume : 	403.684
 	Mean local hydrophobic density : 	14.625
 	Mean alpha sphere radius :	3.873
 	Mean alp. sph. solvent access : 	0.467
@@ -17,7 +17,7 @@ Pocket 1 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	3.695
 	Cent. of mass - Alpha Sphere max dist: 	8.946
-	Flexibility : 	0.704
+	Flexibility : 	0.535
 
 Pocket 2 :
 	Score : 	0.322
@@ -26,7 +26,7 @@ Pocket 2 :
 	Total SASA : 	228.206
 	Polar SASA : 	123.142
 	Apolar SASA : 	105.064
-	Volume : 	933.613
+	Volume : 	949.979
 	Mean local hydrophobic density : 	9.059
 	Mean alpha sphere radius :	4.049
 	Mean alp. sph. solvent access : 	0.543
@@ -38,7 +38,7 @@ Pocket 2 :
 	Proportion of polar atoms: 	49.020
 	Alpha sphere density : 	7.507
 	Cent. of mass - Alpha Sphere max dist: 	20.590
-	Flexibility : 	0.533
+	Flexibility : 	0.405
 
 Pocket 3 :
 	Score : 	0.308
@@ -47,7 +47,7 @@ Pocket 3 :
 	Total SASA : 	175.232
 	Polar SASA : 	94.974
 	Apolar SASA : 	80.258
-	Volume : 	801.518
+	Volume : 	784.998
 	Mean local hydrophobic density : 	14.000
 	Mean alpha sphere radius :	3.962
 	Mean alp. sph. solvent access : 	0.466
@@ -59,7 +59,7 @@ Pocket 3 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	6.192
 	Cent. of mass - Alpha Sphere max dist: 	15.864
-	Flexibility : 	0.538
+	Flexibility : 	0.409
 
 Pocket 4 :
 	Score : 	0.236
@@ -68,7 +68,7 @@ Pocket 4 :
 	Total SASA : 	59.367
 	Polar SASA : 	27.969
 	Apolar SASA : 	31.398
-	Volume : 	273.478
+	Volume : 	268.599
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	4.070
 	Mean alp. sph. solvent access : 	0.587
@@ -80,16 +80,58 @@ Pocket 4 :
 	Proportion of polar atoms: 	46.667
 	Alpha sphere density : 	2.572
 	Cent. of mass - Alpha Sphere max dist: 	6.347
-	Flexibility : 	0.466
+	Flexibility : 	0.354
 
 Pocket 5 :
+	Score : 	0.232
+	Druggability Score : 	0.171
+	Number of Alpha Spheres : 	56
+	Total SASA : 	147.910
+	Polar SASA : 	69.414
+	Apolar SASA : 	78.496
+	Volume : 	551.668
+	Mean local hydrophobic density : 	20.200
+	Mean alpha sphere radius :	3.851
+	Mean alp. sph. solvent access : 	0.514
+	Apolar alpha sphere proportion : 	0.536
+	Hydrophobicity score:	43.000
+	Volume score: 	 4.250
+	Polarity score:	 6
+	Charge score :	 1
+	Proportion of polar atoms: 	34.211
+	Alpha sphere density : 	5.248
+	Cent. of mass - Alpha Sphere max dist: 	11.947
+	Flexibility : 	0.585
+
+Pocket 6 :
+	Score : 	0.210
+	Druggability Score : 	0.088
+	Number of Alpha Spheres : 	44
+	Total SASA : 	124.563
+	Polar SASA : 	59.351
+	Apolar SASA : 	65.212
+	Volume : 	511.022
+	Mean local hydrophobic density : 	18.917
+	Mean alpha sphere radius :	3.912
+	Mean alp. sph. solvent access : 	0.568
+	Apolar alpha sphere proportion : 	0.545
+	Hydrophobicity score:	27.214
+	Volume score: 	 4.714
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	33.333
+	Alpha sphere density : 	5.014
+	Cent. of mass - Alpha Sphere max dist: 	10.663
+	Flexibility : 	0.592
+
+Pocket 7 :
 	Score : 	0.181
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	18
 	Total SASA : 	86.033
 	Polar SASA : 	58.257
 	Apolar SASA : 	27.775
-	Volume : 	419.163
+	Volume : 	423.183
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.979
 	Mean alp. sph. solvent access : 	0.692
@@ -101,37 +143,16 @@ Pocket 5 :
 	Proportion of polar atoms: 	65.000
 	Alpha sphere density : 	4.911
 	Cent. of mass - Alpha Sphere max dist: 	10.576
-	Flexibility : 	0.580
+	Flexibility : 	0.440
 
-Pocket 6 :
-	Score : 	0.152
-	Druggability Score : 	0.006
-	Number of Alpha Spheres : 	27
-	Total SASA : 	70.207
-	Polar SASA : 	30.355
-	Apolar SASA : 	39.852
-	Volume : 	252.148
-	Mean local hydrophobic density : 	6.667
-	Mean alpha sphere radius :	3.668
-	Mean alp. sph. solvent access : 	0.402
-	Apolar alpha sphere proportion : 	0.333
-	Hydrophobicity score:	49.333
-	Volume score: 	 4.778
-	Polarity score:	 5
-	Charge score :	 1
-	Proportion of polar atoms: 	40.000
-	Alpha sphere density : 	3.400
-	Cent. of mass - Alpha Sphere max dist: 	8.144
-	Flexibility : 	0.719
-
-Pocket 7 :
+Pocket 8 :
 	Score : 	0.151
 	Druggability Score : 	0.348
 	Number of Alpha Spheres : 	59
 	Total SASA : 	179.558
 	Polar SASA : 	88.590
 	Apolar SASA : 	90.968
-	Volume : 	645.087
+	Volume : 	666.014
 	Mean local hydrophobic density : 	25.000
 	Mean alpha sphere radius :	3.965
 	Mean alp. sph. solvent access : 	0.500
@@ -143,16 +164,16 @@ Pocket 7 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	5.590
 	Cent. of mass - Alpha Sphere max dist: 	14.341
-	Flexibility : 	0.408
+	Flexibility : 	0.310
 
-Pocket 8 :
+Pocket 9 :
 	Score : 	0.138
 	Druggability Score : 	0.001
 	Number of Alpha Spheres : 	42
 	Total SASA : 	132.756
 	Polar SASA : 	90.489
 	Apolar SASA : 	42.267
-	Volume : 	477.150
+	Volume : 	484.920
 	Mean local hydrophobic density : 	2.800
 	Mean alpha sphere radius :	3.936
 	Mean alp. sph. solvent access : 	0.547
@@ -164,28 +185,7 @@ Pocket 8 :
 	Proportion of polar atoms: 	55.172
 	Alpha sphere density : 	4.899
 	Cent. of mass - Alpha Sphere max dist: 	14.694
-	Flexibility : 	0.915
-
-Pocket 9 :
-	Score : 	0.129
-	Druggability Score : 	0.006
-	Number of Alpha Spheres : 	18
-	Total SASA : 	51.800
-	Polar SASA : 	20.402
-	Apolar SASA : 	31.398
-	Volume : 	216.365
-	Mean local hydrophobic density : 	10.000
-	Mean alpha sphere radius :	3.909
-	Mean alp. sph. solvent access : 	0.554
-	Apolar alpha sphere proportion : 	0.611
-	Hydrophobicity score:	48.500
-	Volume score: 	 4.750
-	Polarity score:	 2
-	Charge score :	 -1
-	Proportion of polar atoms: 	29.412
-	Alpha sphere density : 	2.994
-	Cent. of mass - Alpha Sphere max dist: 	6.481
-	Flexibility : 	0.699
+	Flexibility : 	0.695
 
 Pocket 10 :
 	Score : 	0.097
@@ -194,7 +194,7 @@ Pocket 10 :
 	Total SASA : 	70.487
 	Polar SASA : 	36.673
 	Apolar SASA : 	33.814
-	Volume : 	241.612
+	Volume : 	239.490
 	Mean local hydrophobic density : 	17.000
 	Mean alpha sphere radius :	4.036
 	Mean alp. sph. solvent access : 	0.559
@@ -206,7 +206,7 @@ Pocket 10 :
 	Proportion of polar atoms: 	30.435
 	Alpha sphere density : 	2.440
 	Cent. of mass - Alpha Sphere max dist: 	5.602
-	Flexibility : 	0.482
+	Flexibility : 	0.366
 
 Pocket 11 :
 	Score : 	0.093
@@ -215,7 +215,7 @@ Pocket 11 :
 	Total SASA : 	233.274
 	Polar SASA : 	106.473
 	Apolar SASA : 	126.801
-	Volume : 	832.296
+	Volume : 	840.390
 	Mean local hydrophobic density : 	3.556
 	Mean alpha sphere radius :	4.073
 	Mean alp. sph. solvent access : 	0.681
@@ -227,7 +227,7 @@ Pocket 11 :
 	Proportion of polar atoms: 	47.059
 	Alpha sphere density : 	6.966
 	Cent. of mass - Alpha Sphere max dist: 	19.633
-	Flexibility : 	0.409
+	Flexibility : 	0.310
 
 Pocket 12 :
 	Score : 	0.087
@@ -236,7 +236,7 @@ Pocket 12 :
 	Total SASA : 	52.033
 	Polar SASA : 	38.750
 	Apolar SASA : 	13.284
-	Volume : 	130.401
+	Volume : 	130.600
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.639
 	Mean alp. sph. solvent access : 	0.469
@@ -248,7 +248,7 @@ Pocket 12 :
 	Proportion of polar atoms: 	52.632
 	Alpha sphere density : 	2.073
 	Cent. of mass - Alpha Sphere max dist: 	4.278
-	Flexibility : 	0.509
+	Flexibility : 	0.387
 
 Pocket 13 :
 	Score : 	0.082
@@ -257,7 +257,7 @@ Pocket 13 :
 	Total SASA : 	38.749
 	Polar SASA : 	27.880
 	Apolar SASA : 	10.869
-	Volume : 	119.578
+	Volume : 	121.121
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.723
 	Mean alp. sph. solvent access : 	0.436
@@ -269,7 +269,7 @@ Pocket 13 :
 	Proportion of polar atoms: 	56.250
 	Alpha sphere density : 	1.703
 	Cent. of mass - Alpha Sphere max dist: 	3.731
-	Flexibility : 	0.378
+	Flexibility : 	0.287
 
 Pocket 14 :
 	Score : 	0.080
@@ -278,7 +278,7 @@ Pocket 14 :
 	Total SASA : 	42.368
 	Polar SASA : 	29.084
 	Apolar SASA : 	13.284
-	Volume : 	118.943
+	Volume : 	118.067
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.698
 	Mean alp. sph. solvent access : 	0.488
@@ -290,7 +290,7 @@ Pocket 14 :
 	Proportion of polar atoms: 	68.750
 	Alpha sphere density : 	1.567
 	Cent. of mass - Alpha Sphere max dist: 	3.471
-	Flexibility : 	0.729
+	Flexibility : 	0.554
 
 Pocket 15 :
 	Score : 	0.077
@@ -299,7 +299,7 @@ Pocket 15 :
 	Total SASA : 	135.418
 	Polar SASA : 	78.659
 	Apolar SASA : 	56.759
-	Volume : 	508.468
+	Volume : 	496.615
 	Mean local hydrophobic density : 	8.000
 	Mean alpha sphere radius :	3.823
 	Mean alp. sph. solvent access : 	0.435
@@ -311,7 +311,7 @@ Pocket 15 :
 	Proportion of polar atoms: 	48.387
 	Alpha sphere density : 	3.920
 	Cent. of mass - Alpha Sphere max dist: 	10.386
-	Flexibility : 	0.795
+	Flexibility : 	0.604
 
 Pocket 16 :
 	Score : 	0.074
@@ -320,7 +320,7 @@ Pocket 16 :
 	Total SASA : 	63.026
 	Polar SASA : 	40.892
 	Apolar SASA : 	22.133
-	Volume : 	166.282
+	Volume : 	170.154
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.696
 	Mean alp. sph. solvent access : 	0.392
@@ -332,7 +332,7 @@ Pocket 16 :
 	Proportion of polar atoms: 	60.000
 	Alpha sphere density : 	2.748
 	Cent. of mass - Alpha Sphere max dist: 	5.469
-	Flexibility : 	0.476
+	Flexibility : 	0.362
 
 Pocket 17 :
 	Score : 	0.073
@@ -341,7 +341,7 @@ Pocket 17 :
 	Total SASA : 	98.912
 	Polar SASA : 	71.137
 	Apolar SASA : 	27.775
-	Volume : 	320.310
+	Volume : 	308.789
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.874
 	Mean alp. sph. solvent access : 	0.623
@@ -353,7 +353,7 @@ Pocket 17 :
 	Proportion of polar atoms: 	52.941
 	Alpha sphere density : 	4.470
 	Cent. of mass - Alpha Sphere max dist: 	10.659
-	Flexibility : 	0.614
+	Flexibility : 	0.466
 
 Pocket 18 :
 	Score : 	0.070
@@ -362,7 +362,7 @@ Pocket 18 :
 	Total SASA : 	78.181
 	Polar SASA : 	26.986
 	Apolar SASA : 	51.195
-	Volume : 	284.181
+	Volume : 	285.409
 	Mean local hydrophobic density : 	16.000
 	Mean alpha sphere radius :	3.875
 	Mean alp. sph. solvent access : 	0.568
@@ -374,7 +374,7 @@ Pocket 18 :
 	Proportion of polar atoms: 	28.571
 	Alpha sphere density : 	3.012
 	Cent. of mass - Alpha Sphere max dist: 	7.183
-	Flexibility : 	0.775
+	Flexibility : 	0.589
 
 Pocket 19 :
 	Score : 	0.054
@@ -383,7 +383,7 @@ Pocket 19 :
 	Total SASA : 	104.741
 	Polar SASA : 	74.550
 	Apolar SASA : 	30.191
-	Volume : 	370.999
+	Volume : 	368.619
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	4.001
 	Mean alp. sph. solvent access : 	0.533
@@ -395,7 +395,7 @@ Pocket 19 :
 	Proportion of polar atoms: 	56.000
 	Alpha sphere density : 	3.323
 	Cent. of mass - Alpha Sphere max dist: 	7.437
-	Flexibility : 	0.801
+	Flexibility : 	0.608
 
 Pocket 20 :
 	Score : 	0.048
@@ -404,7 +404,7 @@ Pocket 20 :
 	Total SASA : 	82.549
 	Polar SASA : 	55.981
 	Apolar SASA : 	26.568
-	Volume : 	279.142
+	Volume : 	285.215
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	4.020
 	Mean alp. sph. solvent access : 	0.698
@@ -416,7 +416,7 @@ Pocket 20 :
 	Proportion of polar atoms: 	57.895
 	Alpha sphere density : 	3.081
 	Cent. of mass - Alpha Sphere max dist: 	6.744
-	Flexibility : 	0.509
+	Flexibility : 	0.387
 
 Pocket 21 :
 	Score : 	0.047
@@ -425,7 +425,7 @@ Pocket 21 :
 	Total SASA : 	113.874
 	Polar SASA : 	47.454
 	Apolar SASA : 	66.420
-	Volume : 	359.691
+	Volume : 	362.104
 	Mean local hydrophobic density : 	12.000
 	Mean alpha sphere radius :	3.928
 	Mean alp. sph. solvent access : 	0.660
@@ -437,7 +437,7 @@ Pocket 21 :
 	Proportion of polar atoms: 	47.826
 	Alpha sphere density : 	4.119
 	Cent. of mass - Alpha Sphere max dist: 	11.144
-	Flexibility : 	0.448
+	Flexibility : 	0.340
 
 Pocket 22 :
 	Score : 	0.044
@@ -446,7 +446,7 @@ Pocket 22 :
 	Total SASA : 	55.714
 	Polar SASA : 	19.485
 	Apolar SASA : 	36.229
-	Volume : 	231.692
+	Volume : 	228.186
 	Mean local hydrophobic density : 	12.000
 	Mean alpha sphere radius :	4.067
 	Mean alp. sph. solvent access : 	0.673
@@ -458,7 +458,7 @@ Pocket 22 :
 	Proportion of polar atoms: 	41.176
 	Alpha sphere density : 	2.248
 	Cent. of mass - Alpha Sphere max dist: 	5.161
-	Flexibility : 	0.522
+	Flexibility : 	0.396
 
 Pocket 23 :
 	Score : 	0.043
@@ -467,7 +467,7 @@ Pocket 23 :
 	Total SASA : 	110.639
 	Polar SASA : 	65.956
 	Apolar SASA : 	44.682
-	Volume : 	373.423
+	Volume : 	387.846
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	4.152
 	Mean alp. sph. solvent access : 	0.666
@@ -479,7 +479,7 @@ Pocket 23 :
 	Proportion of polar atoms: 	42.857
 	Alpha sphere density : 	4.071
 	Cent. of mass - Alpha Sphere max dist: 	10.454
-	Flexibility : 	0.621
+	Flexibility : 	0.472
 
 Pocket 24 :
 	Score : 	0.040
@@ -488,7 +488,7 @@ Pocket 24 :
 	Total SASA : 	52.460
 	Polar SASA : 	25.892
 	Apolar SASA : 	26.568
-	Volume : 	201.565
+	Volume : 	193.355
 	Mean local hydrophobic density : 	6.000
 	Mean alpha sphere radius :	3.959
 	Mean alp. sph. solvent access : 	0.551
@@ -500,7 +500,7 @@ Pocket 24 :
 	Proportion of polar atoms: 	53.333
 	Alpha sphere density : 	1.785
 	Cent. of mass - Alpha Sphere max dist: 	3.872
-	Flexibility : 	0.657
+	Flexibility : 	0.499
 
 Pocket 25 :
 	Score : 	0.039
@@ -509,7 +509,7 @@ Pocket 25 :
 	Total SASA : 	52.442
 	Polar SASA : 	35.535
 	Apolar SASA : 	16.907
-	Volume : 	238.630
+	Volume : 	233.317
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.883
 	Mean alp. sph. solvent access : 	0.594
@@ -521,7 +521,7 @@ Pocket 25 :
 	Proportion of polar atoms: 	57.143
 	Alpha sphere density : 	2.162
 	Cent. of mass - Alpha Sphere max dist: 	4.767
-	Flexibility : 	0.324
+	Flexibility : 	0.246
 
 Pocket 26 :
 	Score : 	0.035
@@ -530,7 +530,7 @@ Pocket 26 :
 	Total SASA : 	91.621
 	Polar SASA : 	60.223
 	Apolar SASA : 	31.398
-	Volume : 	357.614
+	Volume : 	354.787
 	Mean local hydrophobic density : 	1.000
 	Mean alpha sphere radius :	3.998
 	Mean alp. sph. solvent access : 	0.463
@@ -542,7 +542,7 @@ Pocket 26 :
 	Proportion of polar atoms: 	60.000
 	Alpha sphere density : 	3.042
 	Cent. of mass - Alpha Sphere max dist: 	6.995
-	Flexibility : 	0.440
+	Flexibility : 	0.334
 
 Pocket 27 :
 	Score : 	0.030
@@ -551,7 +551,7 @@ Pocket 27 :
 	Total SASA : 	49.108
 	Polar SASA : 	12.880
 	Apolar SASA : 	36.229
-	Volume : 	197.723
+	Volume : 	202.557
 	Mean local hydrophobic density : 	4.000
 	Mean alpha sphere radius :	3.928
 	Mean alp. sph. solvent access : 	0.629
@@ -563,7 +563,7 @@ Pocket 27 :
 	Proportion of polar atoms: 	42.857
 	Alpha sphere density : 	2.002
 	Cent. of mass - Alpha Sphere max dist: 	4.999
-	Flexibility : 	0.702
+	Flexibility : 	0.533
 
 Pocket 28 :
 	Score : 	0.028
@@ -572,7 +572,7 @@ Pocket 28 :
 	Total SASA : 	95.771
 	Polar SASA : 	37.567
 	Apolar SASA : 	58.204
-	Volume : 	272.798
+	Volume : 	272.290
 	Mean local hydrophobic density : 	13.000
 	Mean alpha sphere radius :	3.876
 	Mean alp. sph. solvent access : 	0.490
@@ -584,7 +584,7 @@ Pocket 28 :
 	Proportion of polar atoms: 	33.333
 	Alpha sphere density : 	2.525
 	Cent. of mass - Alpha Sphere max dist: 	5.760
-	Flexibility : 	0.428
+	Flexibility : 	0.325
 
 Pocket 29 :
 	Score : 	0.024
@@ -593,7 +593,7 @@ Pocket 29 :
 	Total SASA : 	113.046
 	Polar SASA : 	71.987
 	Apolar SASA : 	41.059
-	Volume : 	382.428
+	Volume : 	380.582
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	4.070
 	Mean alp. sph. solvent access : 	0.694
@@ -605,7 +605,7 @@ Pocket 29 :
 	Proportion of polar atoms: 	57.143
 	Alpha sphere density : 	3.541
 	Cent. of mass - Alpha Sphere max dist: 	7.664
-	Flexibility : 	0.809
+	Flexibility : 	0.614
 
 Pocket 30 :
 	Score : 	0.022
@@ -614,7 +614,7 @@ Pocket 30 :
 	Total SASA : 	126.450
 	Polar SASA : 	43.124
 	Apolar SASA : 	83.326
-	Volume : 	415.124
+	Volume : 	411.148
 	Mean local hydrophobic density : 	7.000
 	Mean alpha sphere radius :	4.025
 	Mean alp. sph. solvent access : 	0.620
@@ -626,7 +626,7 @@ Pocket 30 :
 	Proportion of polar atoms: 	47.826
 	Alpha sphere density : 	4.752
 	Cent. of mass - Alpha Sphere max dist: 	12.329
-	Flexibility : 	0.419
+	Flexibility : 	0.319
 
 Pocket 31 :
 	Score : 	0.013
@@ -635,7 +635,7 @@ Pocket 31 :
 	Total SASA : 	105.586
 	Polar SASA : 	54.866
 	Apolar SASA : 	50.720
-	Volume : 	376.423
+	Volume : 	384.491
 	Mean local hydrophobic density : 	3.000
 	Mean alpha sphere radius :	3.971
 	Mean alp. sph. solvent access : 	0.594
@@ -647,7 +647,7 @@ Pocket 31 :
 	Proportion of polar atoms: 	42.857
 	Alpha sphere density : 	3.649
 	Cent. of mass - Alpha Sphere max dist: 	9.255
-	Flexibility : 	0.610
+	Flexibility : 	0.464
 
 Pocket 32 :
 	Score : 	0.011
@@ -656,7 +656,7 @@ Pocket 32 :
 	Total SASA : 	84.302
 	Polar SASA : 	51.696
 	Apolar SASA : 	32.606
-	Volume : 	243.039
+	Volume : 	242.765
 	Mean local hydrophobic density : 	4.000
 	Mean alpha sphere radius :	3.851
 	Mean alp. sph. solvent access : 	0.583
@@ -668,7 +668,7 @@ Pocket 32 :
 	Proportion of polar atoms: 	44.444
 	Alpha sphere density : 	3.116
 	Cent. of mass - Alpha Sphere max dist: 	6.911
-	Flexibility : 	0.754
+	Flexibility : 	0.573
 
 Pocket 33 :
 	Score : 	0.006
@@ -677,7 +677,7 @@ Pocket 33 :
 	Total SASA : 	78.442
 	Polar SASA : 	28.929
 	Apolar SASA : 	49.513
-	Volume : 	227.359
+	Volume : 	218.631
 	Mean local hydrophobic density : 	11.000
 	Mean alpha sphere radius :	3.905
 	Mean alp. sph. solvent access : 	0.622
@@ -689,37 +689,58 @@ Pocket 33 :
 	Proportion of polar atoms: 	33.333
 	Alpha sphere density : 	2.894
 	Cent. of mass - Alpha Sphere max dist: 	6.487
-	Flexibility : 	0.378
+	Flexibility : 	0.287
 
 Pocket 34 :
-	Score : 	-0.002
-	Druggability Score : 	0.034
-	Number of Alpha Spheres : 	27
-	Total SASA : 	81.212
-	Polar SASA : 	40.153
-	Apolar SASA : 	41.059
-	Volume : 	281.548
-	Mean local hydrophobic density : 	20.000
-	Mean alpha sphere radius :	4.025
-	Mean alp. sph. solvent access : 	0.619
-	Apolar alpha sphere proportion : 	0.778
-	Hydrophobicity score:	31.000
-	Volume score: 	 4.600
-	Polarity score:	 3
-	Charge score :	 1
-	Proportion of polar atoms: 	27.778
-	Alpha sphere density : 	2.216
-	Cent. of mass - Alpha Sphere max dist: 	6.237
-	Flexibility : 	0.813
+	Score : 	-0.004
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	21
+	Total SASA : 	67.132
+	Polar SASA : 	24.865
+	Apolar SASA : 	42.267
+	Volume : 	246.548
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	3.929
+	Mean alp. sph. solvent access : 	0.500
+	Apolar alpha sphere proportion : 	0.286
+	Hydrophobicity score:	14.167
+	Volume score: 	 4.833
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	46.154
+	Alpha sphere density : 	2.031
+	Cent. of mass - Alpha Sphere max dist: 	4.691
+	Flexibility : 	0.776
 
 Pocket 35 :
+	Score : 	-0.020
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	18
+	Total SASA : 	60.438
+	Polar SASA : 	29.040
+	Apolar SASA : 	31.398
+	Volume : 	208.154
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	4.142
+	Mean alp. sph. solvent access : 	0.600
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	-32.833
+	Volume score: 	 4.333
+	Polarity score:	 6
+	Charge score :	 -1
+	Proportion of polar atoms: 	56.250
+	Alpha sphere density : 	1.755
+	Cent. of mass - Alpha Sphere max dist: 	3.686
+	Flexibility : 	0.691
+
+Pocket 36 :
 	Score : 	-0.020
 	Druggability Score : 	0.001
 	Number of Alpha Spheres : 	16
 	Total SASA : 	55.577
 	Polar SASA : 	11.786
 	Apolar SASA : 	43.791
-	Volume : 	155.436
+	Volume : 	155.244
 	Mean local hydrophobic density : 	5.000
 	Mean alpha sphere radius :	3.819
 	Mean alp. sph. solvent access : 	0.487
@@ -731,16 +752,16 @@ Pocket 35 :
 	Proportion of polar atoms: 	41.667
 	Alpha sphere density : 	1.680
 	Cent. of mass - Alpha Sphere max dist: 	4.107
-	Flexibility : 	0.271
+	Flexibility : 	0.206
 
-Pocket 36 :
+Pocket 37 :
 	Score : 	-0.021
 	Druggability Score : 	0.194
 	Number of Alpha Spheres : 	26
 	Total SASA : 	93.206
 	Polar SASA : 	26.786
 	Apolar SASA : 	66.420
-	Volume : 	302.742
+	Volume : 	290.469
 	Mean local hydrophobic density : 	21.000
 	Mean alpha sphere radius :	4.066
 	Mean alp. sph. solvent access : 	0.589
@@ -752,28 +773,7 @@ Pocket 36 :
 	Proportion of polar atoms: 	40.000
 	Alpha sphere density : 	2.663
 	Cent. of mass - Alpha Sphere max dist: 	7.896
-	Flexibility : 	0.760
-
-Pocket 37 :
-	Score : 	-0.026
-	Druggability Score : 	0.000
-	Number of Alpha Spheres : 	16
-	Total SASA : 	53.873
-	Polar SASA : 	23.683
-	Apolar SASA : 	30.191
-	Volume : 	165.159
-	Mean local hydrophobic density : 	5.000
-	Mean alpha sphere radius :	4.147
-	Mean alp. sph. solvent access : 	0.584
-	Apolar alpha sphere proportion : 	0.375
-	Hydrophobicity score:	-32.833
-	Volume score: 	 4.333
-	Polarity score:	 6
-	Charge score :	 -1
-	Proportion of polar atoms: 	53.333
-	Alpha sphere density : 	1.534
-	Cent. of mass - Alpha Sphere max dist: 	3.589
-	Flexibility : 	0.901
+	Flexibility : 	0.577
 
 Pocket 38 :
 	Score : 	-0.028
@@ -782,7 +782,7 @@ Pocket 38 :
 	Total SASA : 	118.852
 	Polar SASA : 	64.509
 	Apolar SASA : 	54.343
-	Volume : 	373.641
+	Volume : 	381.890
 	Mean local hydrophobic density : 	6.000
 	Mean alpha sphere radius :	3.944
 	Mean alp. sph. solvent access : 	0.571
@@ -794,7 +794,7 @@ Pocket 38 :
 	Proportion of polar atoms: 	42.857
 	Alpha sphere density : 	3.875
 	Cent. of mass - Alpha Sphere max dist: 	9.016
-	Flexibility : 	0.547
+	Flexibility : 	0.415
 
 Pocket 39 :
 	Score : 	-0.029
@@ -803,7 +803,7 @@ Pocket 39 :
 	Total SASA : 	108.466
 	Polar SASA : 	42.858
 	Apolar SASA : 	65.608
-	Volume : 	289.661
+	Volume : 	292.747
 	Mean local hydrophobic density : 	2.000
 	Mean alpha sphere radius :	3.867
 	Mean alp. sph. solvent access : 	0.434
@@ -815,37 +815,16 @@ Pocket 39 :
 	Proportion of polar atoms: 	42.105
 	Alpha sphere density : 	3.379
 	Cent. of mass - Alpha Sphere max dist: 	6.950
-	Flexibility : 	0.612
+	Flexibility : 	0.465
 
 Pocket 40 :
-	Score : 	-0.030
-	Druggability Score : 	0.000
-	Number of Alpha Spheres : 	17
-	Total SASA : 	80.399
-	Polar SASA : 	45.377
-	Apolar SASA : 	35.021
-	Volume : 	265.301
-	Mean local hydrophobic density : 	5.000
-	Mean alpha sphere radius :	4.033
-	Mean alp. sph. solvent access : 	0.543
-	Apolar alpha sphere proportion : 	0.353
-	Hydrophobicity score:	13.857
-	Volume score: 	 4.429
-	Polarity score:	 5
-	Charge score :	 -1
-	Proportion of polar atoms: 	40.000
-	Alpha sphere density : 	2.550
-	Cent. of mass - Alpha Sphere max dist: 	4.655
-	Flexibility : 	0.731
-
-Pocket 41 :
 	Score : 	-0.030
 	Druggability Score : 	0.014
 	Number of Alpha Spheres : 	20
 	Total SASA : 	63.323
 	Polar SASA : 	5.357
 	Apolar SASA : 	57.966
-	Volume : 	196.956
+	Volume : 	191.823
 	Mean local hydrophobic density : 	14.000
 	Mean alpha sphere radius :	3.894
 	Mean alp. sph. solvent access : 	0.592
@@ -857,16 +836,16 @@ Pocket 41 :
 	Proportion of polar atoms: 	26.667
 	Alpha sphere density : 	1.653
 	Cent. of mass - Alpha Sphere max dist: 	4.670
-	Flexibility : 	0.499
+	Flexibility : 	0.379
 
-Pocket 42 :
+Pocket 41 :
 	Score : 	-0.033
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	23
 	Total SASA : 	104.224
 	Polar SASA : 	51.089
 	Apolar SASA : 	53.136
-	Volume : 	285.535
+	Volume : 	277.900
 	Mean local hydrophobic density : 	6.000
 	Mean alpha sphere radius :	3.937
 	Mean alp. sph. solvent access : 	0.636
@@ -878,16 +857,16 @@ Pocket 42 :
 	Proportion of polar atoms: 	50.000
 	Alpha sphere density : 	3.185
 	Cent. of mass - Alpha Sphere max dist: 	8.525
-	Flexibility : 	0.631
+	Flexibility : 	0.479
 
-Pocket 43 :
+Pocket 42 :
 	Score : 	-0.034
 	Druggability Score : 	0.000
 	Number of Alpha Spheres : 	17
 	Total SASA : 	105.087
 	Polar SASA : 	70.065
 	Apolar SASA : 	35.021
-	Volume : 	265.080
+	Volume : 	271.683
 	Mean local hydrophobic density : 	0.000
 	Mean alpha sphere radius :	3.836
 	Mean alp. sph. solvent access : 	0.381
@@ -899,16 +878,16 @@ Pocket 43 :
 	Proportion of polar atoms: 	58.824
 	Alpha sphere density : 	3.579
 	Cent. of mass - Alpha Sphere max dist: 	8.402
-	Flexibility : 	0.506
+	Flexibility : 	0.385
 
-Pocket 44 :
+Pocket 43 :
 	Score : 	-0.068
 	Druggability Score : 	0.007
 	Number of Alpha Spheres : 	24
 	Total SASA : 	99.271
 	Polar SASA : 	36.474
 	Apolar SASA : 	62.797
-	Volume : 	258.754
+	Volume : 	260.496
 	Mean local hydrophobic density : 	12.000
 	Mean alpha sphere radius :	3.905
 	Mean alp. sph. solvent access : 	0.573
@@ -920,5 +899,5 @@ Pocket 44 :
 	Proportion of polar atoms: 	38.095
 	Alpha sphere density : 	2.492
 	Cent. of mass - Alpha Sphere max dist: 	5.483
-	Flexibility : 	0.656
+	Flexibility : 	0.499