fixing reference test

Issue observed while running fpocket on the PDB 7uit

.github/workflows/c-cpp.yml

@@ -15,10 +15,10 @@ jobs:
       run: sudo apt-get install libnetcdf-dev
     - name: make
       run: make fpocket
-    - name: Set up Python 3.7
+    - name: Set up Python 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.12
     - name: create conda environment
       run: conda env update -f ./tests/environment.yml   
     - name : activate

Dockerfile-debian-slim

@@ -1,4 +1,4 @@
-FROM debian:bullseye-slim
+FROM debian:bookworm-slim
 RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
 RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
 

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/atom.h

@@ -37,12 +37,14 @@ typedef struct s_atm
     char name[5],		/**< Atom name */
          type[7],		/**< Atom type */
          chain[16],		/**< Chain name */
+         label_asym_id[16],
          symbol[3],		/**< Chemical symbol of the atom */
          res_name[8];		/**< Atom residue name */
 
     int id,			/**< Atom id */
         seen,                   /**< Say if we have seen this atom during a neighbor search */
         res_id,			/**< Atom residue ID */
+        label_seq_id,   /**<MMCIF label seq ID*/
         atype,
         charge,                 /**< Atom charge */
         abpa;                   /**< 1 if atom is an abpa, 0 otherwise*/	

headers/fparams.h

@@ -30,84 +30,90 @@ 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_MAX_CHAIN_NAME_LENGTH 20
+#define M_MAX_LIG_RESNAME_LENGTH 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"
 
@@ -117,11 +123,11 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
 #define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
 
-#define M_PAR_WRITE_MODE 'w' /**flag, to define which chains are defined as a ligand*/
+#define M_PAR_WRITE_MODE 'w' /**flag, to define write mode for pocket output: d->same as input, b or both -> both (pdb & cif), p or pdb ->pdb, m or cif -> mmcif*/
 #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 +170,85 @@ 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;
+	char *xlig_resname;
+	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 */
+	unsigned short
+		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 */
-	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*/
+		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*/
+	unsigned short n_chains_to_delete;
+	unsigned short n_chains_as_ligand;
+	char *chain_as_ligand[M_MAX_CHAINS_DELETE];
+	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/refine.h

@@ -31,7 +31,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* --------------------------PROTOTYPES---------------------------------------*/
 
 void refinePockets(c_lst_pockets *pockets, s_fparams *params);
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params);
+void apply_clustering(c_lst_pockets *pockets);
 void reIndexPockets(c_lst_pockets *pockets);
 void dropSmallNpolarPockets(c_lst_pockets *pockets, s_fparams *params);
 void drop_tiny(c_lst_pockets *pockets, s_fparams *params) ;

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*/
 
@@ -140,10 +142,10 @@ s_min_max_coords *float_get_min_max_from_pdb(s_pdb *pdb);
 void init_coord_grid(s_pdb *pdb);
 void create_coord_grid(s_pdb *pdb);
 void fill_coord_grid(s_pdb *pdb);
-s_atom_ptr_list *init_atom_ptr_list(void);
+// s_atom_ptr_list *init_atom_ptr_list(void);
 
 
 short get_mm_type_from_element(char *symbol);
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept);
-int is_ligand(char *chains_selected, char current_line_chain);
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete);
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand);
 #endif

headers/utils.h

@@ -33,8 +33,8 @@ 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_PDB_NAME_LEN 2000  /**< 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);

headers/writepdb.h

@@ -28,6 +28,6 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
 
 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[], 
 						 char alt_loc, const char res_name[], const char chain[], 
-						 int res_id, const char insert, float x, float y, float z, float occ, 
+						 int res_id,  const char label_asym_id[],int label_seq_id, const char insert, float x, float y, float z, float occ, 
 						 float bfactor, int abpa, const char *symbol, int charge,float abpa_prob) ;
 #endif

headers/writepocket.h

@@ -40,6 +40,7 @@ void write_pdb_atoms(FILE *f, s_atm *atoms, int natoms) ;
 void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets,s_pdb *pdb);
 void write_pocket_pqr_DB(const char out[], s_pocket *pocket);
 void write_pocket_pdb_DB(const char out[], s_pocket *pocket,s_pdb *pdb);
+void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb);
 
 void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms);
 void write_pockets_single_mmcif(const char out[], s_pdb *pdb, c_lst_pockets *pockets);

makefile

@@ -47,7 +47,7 @@ COS         = -DM_OS_LINUX
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -W -Wextra -Wwrite-strings -Wstrict-prototypes
 
-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=gnu99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
 QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 

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)
@@ -87,36 +87,44 @@ 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;
+    par->n_chains_to_delete=0;
+    par->n_chains_as_ligand=0;
     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;
-
+    const char *separators = ",:";
     static struct option fplong_options[] = {/*long options args located in fparams.h*/
                                              {"file", required_argument, 0, M_PAR_PDB_FILE},
                                              {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
@@ -133,6 +141,8 @@ 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 +155,7 @@ 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 +164,6 @@ 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"))
@@ -166,108 +175,149 @@ 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*/
-            pt = strtok(par->chain_as_ligand, separatorss);
+            pt = strtok(optarg, separators);
             int nn = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_as_ligand[nn]), pt, 1);
+                par->chain_as_ligand[nn] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_as_ligand[nn], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_as_ligand[nn][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nn++;
-                pt = strtok(NULL, separatorss);
+                pt = strtok(NULL, separators);
             }
+            par->n_chains_as_ligand=nn;
             par->xlig_resnumber = 0;
-            //printf("lig %s\n",par->chain_as_ligand);
-      break;
-           
-
-
-           
+            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);
-            const char *separators = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separators);
+            pt = strtok(optarg, separators);
             int n = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[n]), pt,1);
-                
+                par->chain_delete[n] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[n], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[n][M_MAX_CHAIN_NAME_LENGTH]='\0';
+
                 n++;
                 pt = strtok(NULL, separators);
             }
             par->chain_is_kept = 0;
-            
-            //printf("%s\n",par->chain_delete);
+            par->n_chains_to_delete=n;
             status++;
             break;
 
         case M_PAR_KEEP_CHAINS: /*option with -k "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);
-            const char *separator = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separator);
+            pt = strtok(optarg, separators);
             int nk = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[nk]), pt, 1);
+                
+                par->chain_delete[nk] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[nk], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[nk][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nk++;
-                pt = strtok(NULL, separator);
+                pt = strtok(NULL, separators);
             }
-            //printf("%s\n",par->chain_delete);
+            par->n_chains_to_delete=nk;
+            // 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);
-            pt = strtok(par->custom_ligand, ":");
+            // strcpy(par->custom_ligand, optarg);
+            // printf("%s and %s",par->custom_ligand,optarg);
+            pt = strtok(optarg, ":");
 
             while (pt != NULL)
             {
                 custom_ligand_i++;
                 if (custom_ligand_i == 1)
                     par->xlig_resnumber = atoi(pt);
-                else if (custom_ligand_i == 2)
-                    strncpy(&(par->xlig_resname), pt, 3);
-                else if (custom_ligand_i == 3)
-                    strncpy(&(par->xlig_chain_code), pt, 1);
-                /*int a = atoi(pt);
-                    printf("%d\n", a);*/
+                else if (custom_ligand_i == 2){
+                    par->xlig_resname= (char *)malloc((M_MAX_LIG_RESNAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_resname, pt, M_MAX_LIG_RESNAME_LENGTH);
+                    par->xlig_resname[M_MAX_LIG_RESNAME_LENGTH]='\0';
+                }
+                else if (custom_ligand_i == 3){
+                    par->xlig_chain_code= (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_chain_code, pt, M_MAX_CHAIN_NAME_LENGTH);
+                    par->xlig_chain_code[M_MAX_CHAIN_NAME_LENGTH]='\0';
+                }
                 pt = strtok(NULL, ":");
             }
 
             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 +351,7 @@ 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 +385,7 @@ 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 +398,45 @@ 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 +447,7 @@ 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 +576,19 @@ 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 +606,19 @@ 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 +651,20 @@ 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 +686,19 @@ 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 +716,19 @@ 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 +746,20 @@ 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 +777,19 @@ 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 +807,19 @@ 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 +837,19 @@ 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 +869,17 @@ 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 +902,18 @@ 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 +934,18 @@ 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 +972,21 @@ 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 +1016,7 @@ 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 +1025,18 @@ 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);
@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
                 }
                 else
                 {
-                        if (params->pdb_path == NULL || strlen(params->pdb_path) <= 0)
+                        if (!params->pdb_path[0] || strlen(params->pdb_path) <= 0)
                         {
                                 fprintf(stdout, "! Invalid pdb name given.\n");
                                 print_pocket_usage(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);
@@ -223,30 +222,30 @@ void process_pdb(char *pdbname, s_fparams *params)
                         print_number_of_objects_in_memory();
                 }
         }
-        else
-                fprintf(stderr, "! PDB reading failed!\n");
+        else {
+                fprintf(stderr, "! Structure reading failed!\n");
+                exit( EXIT_FAILURE );
+        }
 }
 
 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) {
+
+    apply_clustering(pockets);
+    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[0])
+            calculate_pocket_energy_grids(pockets, params, pdb);
+        // params->fpocket_running &&
     }
 
     return pockets;
 }
-

src/fpout.c

@@ -58,6 +58,7 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
    char pdb_code[350] = "";
    char pdb_path[350] = "";
    char out_path[350] = "";
+   char out_path_tmp[350] = "";
    char pdb_out_path[350] = "";
    char info_out_path[350] = "";
    char mmcif_out_path[350] = "";
@@ -85,34 +86,34 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
          return;
       }
 
-      sprintf(out_path, "%s/%s", out_path, pdb_code);
-      sprintf(pdb_out_path, "%s_out.pdb", out_path);
+      sprintf(out_path_tmp, "%s/%s", out_path, pdb_code);
+      sprintf(pdb_out_path, "%s_out.pdb", out_path_tmp);
 
-      sprintf(mmcif_out_path, "%s_out.cif", out_path);
+      sprintf(mmcif_out_path, "%s_out.cif", out_path_tmp);
       
       /* Write vmd and pymol scripts */
       sprintf(fout, "%s_out.pdb", pdb_code);
-      write_visualization(out_path, fout);
+      write_visualization(out_path_tmp, fout);
       
       /* Writing full pdb */
       //printf("%s\n",write_mode);
       if(write_mode[0] == 'p' || write_mode[0] == 'b'){
-      sprintf(pdb_out_path, "%s_out.pdb", out_path);
+      sprintf(pdb_out_path, "%s_out.pdb", out_path_tmp);
 
       write_pockets_single_pdb(pdb_out_path, pdb, pockets);
       }
 
       /*Writing full mmcif*/
       if(write_mode[0] == 'm' || write_mode[0] == 'b'){
-      sprintf(mmcif_out_path, "%s_out.cif", out_path);
+      sprintf(mmcif_out_path, "%s_out.cif", out_path_tmp);
       write_pockets_single_mmcif(mmcif_out_path, pdb, pockets);
       }
 
-      sprintf(info_out_path, "%s_info.txt", out_path);
+      sprintf(info_out_path, "%s_info.txt", out_path_tmp);
       write_out_fpocket_info_file(pockets, info_out_path);
 
       /* Writing pockets as a single pqr */
-      sprintf(fout, "%s_pockets.pqr", out_path);
+      sprintf(fout, "%s_pockets.pqr", out_path_tmp);
       write_pockets_single_pqr(fout, pockets);
 
       /* Writing individual pockets pqr */
@@ -121,14 +122,14 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
       else
          sprintf(out_path, "%s_out", pdb_code);
 
-      sprintf(out_path, "%s/pockets", out_path);
-      sprintf(command, "mkdir %s", out_path);
+      sprintf(out_path_tmp, "%s/pockets", out_path);
+      sprintf(command, "mkdir %s", out_path_tmp);
       status = system(command);
       /*if(status != 0) {
 			return ;
 		}*/
 
-      write_each_pocket(out_path, pockets);
+      write_each_pocket(out_path_tmp, pockets);
    }
 }
 /**

src/mdparams.c

@@ -256,7 +256,7 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
                 par = NULL;
                 print_mdpocket_usage(stdout);
             }
-        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path)) {
+        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path[0])) {
             fprintf(stdout, "! No input file given... Try again :).%d %d %s\n",traj_file_defined,traj_format_defined,par->fpar->pdb_path);
             free_mdparams(par);
             par = NULL;

src/pertable.c

@@ -265,10 +265,13 @@ char *pte_get_element_from_number(int atomicnumber)
 	
 		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
 		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
-		tmp[2] = '\0';
 		return tmp;
-	} 
-	return -1 ;
+	} else {
+		tmp[0]='-';
+		tmp[1]='1';
+	}
+	tmp[2]='\0';
+	return tmp;
 }
 
 /**

src/qhull/src/qconvex/qconvex.c

@@ -42,7 +42,7 @@ int run_qconvex(FILE *fin,FILE *fout) {
   boolT ismalloc;
 
   int argc=2;
-  char *argv[2];
+  const char *argv[2];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qconvex\0";
   argv[1]=malloc(sizeof(char)*2);

src/qhull/src/qvoronoi/qvoronoi.c

@@ -239,7 +239,7 @@ int run_qvoronoi(FILE *fin,FILE *fout) {
   coordT *points;
   boolT ismalloc;
   int argc=6;
-  char *argv[6];
+  const char *argv[6];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qvoronoi\0";
   argv[1]=malloc(sizeof(char)*2);

src/read_mmcif.c

@@ -56,38 +56,39 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
 
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
     // printf("%s | %s |%d", fpath, filetype, inatoms);
     // printf("\n");
     void *h_in;
     molfile_timestep_t ts_in;
     molfile_atom_t *at_in;
-    int optflags = 0x0040;
+    int optflags[] = {0x0001,0x0040};
     int rc;
     int rc2;
     int j;
     int k;
-
     h_in = api->open_file_read(fpath, filetype, &inatoms);
+    if(inatoms==0){
+        fprintf(stderr, "! Structure reading failed or file is empty!\n");
+        exit( EXIT_FAILURE );
+    }
     at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
-    rc2 = api->read_structure(h_in, &optflags, at_in);
+    rc2 = api->read_structure(h_in, optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
     if (!model_number)
         model_number = 1;
     model_flag = 1;
     for (i = 0; i < inatoms; i++) /*loop to go through all atoms*/
     {
-
         if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
-        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
         {
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
-
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '?')
             {
-                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Atom entry: check if there is a ligand in there (just in case)... */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -99,7 +100,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                         }
                         /*check this function*/
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -114,13 +115,7 @@ 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]))
+                    if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
                     }
@@ -129,26 +124,25 @@ 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]))
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && 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]) || (par->xlig_chain_code!=NULL && 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])))
+        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_auth,par->n_chains_as_ligand)))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == '?' || at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
             {
-
-                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
                     {
                         natm_lig++;
                         natoms++;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
                         if (keep_lig)
                             natm_lig++;
@@ -157,13 +151,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     else
                     {
                         /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)))
                         {
 
                             natoms++;
                             nhetatm++;
                         }
-                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                         {
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
                             {
@@ -178,14 +172,14 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     }
                 }
 
-                if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                 {
                     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]))
+            {   
+                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (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])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && 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++;
                 }
@@ -260,7 +254,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     /*******************************************************************************/
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
 
     void *h_in;
@@ -277,6 +271,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
     rc2 = api->read_structure(h_in, &optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
+
     // printf("READ : %s | %s |%d\n", pdb->fname, filetype, inatoms);
     /* Loop over the pdb file */
     model_flag = 1;
@@ -285,25 +280,26 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ; /*here we indicate that a particular model should be read only*/
     for (i = 0; i < inatoms; i++)
     {
+
         if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
 
-        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] == '?')
             { /*if within first occurence*/
                 /* Enter this if when arg in command line is -r */
 
                 /* Enter this if when arg in command line is -a */
-                if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(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 (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in such an entry */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -317,8 +313,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -342,7 +340,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ligfound = 1;
                         }
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -354,8 +352,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -398,13 +398,13 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
-                        // fflush(stdout);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
-                        atom->res_id = at_in[i].resid;
+
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
-                        // printf("ins:%s",at_in[i].insertion);
 
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
@@ -434,9 +434,10 @@ 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])
-                {
+                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
 
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && 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]))
+                {
                     *(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];
@@ -444,23 +445,22 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                 }
             }
         }
-        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])))
+        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_auth,params->n_chains_as_ligand)))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] =='?')
             { /*first occurence*/
 
-                if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(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];
 
-                    // printf("%d\n", i_explicit_ligand_atom);
                     i_explicit_ligand_atom++;
                 }
                 // fflush(stdout);
-                if (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in HETATM entry */
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -472,9 +472,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
+
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
                         atom->z = ts_in.coords[(3 * i) + 2];
@@ -496,7 +499,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         iatoms++;
                         ligfound = 1;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
 
                         if (keep_lig)
@@ -509,8 +512,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -538,7 +543,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     {
 
                         /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand)))
                         {
 
                             atom = atoms + iatoms;
@@ -547,9 +552,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
+
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
                             atom->z = ts_in.coords[(3 * i) + 2];
@@ -569,7 +577,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ihetatm++;
                             iatoms++;
                         }
-                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                         {
 
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
@@ -585,8 +593,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                     strcpy(atom->name, at_in[i].type);
                                     atom->pdb_aloc = at_in[i].altloc[0];
                                     strcpy(atom->res_name, at_in[i].resname);
-                                    strncpy(atom->chain, at_in[i].chain, 2);
-                                    atom->res_id = at_in[i].resid;
+                                    strcpy(atom->chain, at_in[i].chain_auth);
+                                    strcpy(atom->label_asym_id, at_in[i].chain);
+                                    atom->res_id = at_in[i].resid_auth;
+                                    atom->label_seq_id=at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
                                     atom->y = ts_in.coords[(3 * i) + 1];
@@ -614,16 +624,18 @@ 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]) {
 
+                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
+
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && 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]) || (params->xlig_chain_code!=NULL && 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]))
+                {
+                                        
                     *(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++;
                 }
             }
@@ -638,6 +650,9 @@ 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;
@@ -651,6 +666,12 @@ 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/refine.c

@@ -55,7 +55,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 	void
 
 */
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params)
+void apply_clustering(c_lst_pockets *pockets)
 {
 	node_pocket *nextPocket;
 	node_pocket *curMobilePocket;

src/rpdb.c

@@ -186,13 +186,6 @@ s_min_max_coords *float_get_min_max_from_pdb(s_pdb *pdb)
     return (NULL);
 }
 
-s_atom_ptr_list *init_atom_ptr_list()
-{
-    s_atom_ptr_list *ret = my_malloc(sizeof(s_atom_ptr_list));
-    ret->natoms = 0;
-    ret->latoms = (s_atm **)my_malloc(sizeof(s_atm *));
-    return (ret);
-}
 
 void create_coord_grid(s_pdb *pdb)
 {
@@ -284,7 +277,8 @@ void init_coord_grid(s_pdb *pdb)
             g->atom_ptr[cx][cy] = (s_atom_ptr_list *)my_malloc(sizeof(s_atom_ptr_list) * g->nz);
             for (cz = 0; cz < g->nz; cz++)
             {
-                g->atom_ptr[cx][cy][cz] = *init_atom_ptr_list();
+                g->atom_ptr[cx][cy][cz].natoms = 0;
+                g->atom_ptr[cx][cy][cz].latoms = (s_atm **)my_malloc(sizeof(s_atm *));
             }
         }
     }
@@ -809,6 +803,8 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
     int i;
     float x, y, z;
     int resnbuf = 0;
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
@@ -854,12 +850,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         }
         if (pdb->model_flag == 0 || model_read == 1)
         {
-
-            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, buf[21]))
+            chainbuf[0]=buf[21];
+            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
             {
 
                 // printf("%s",par->chain_delete ); // deleting the chains we want to delete from pdb file
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Check if this is the first occurence of this atom*/
                     rpdb_extract_atm_resname(buf, resb);
@@ -868,7 +864,7 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         /* Atom entry: check if there is a ligand in there (just in case)... */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -897,20 +893,9 @@ 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 (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 (is_ligand(par->chain_as_ligand, buf[21]))
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                         {
                             pdb->n_xlig_atoms++;
-                            // fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
                         }
                     }
                 }
@@ -918,7 +903,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 {
                     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])
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
+                        {
+                            pdb->n_xlig_atoms++;
+                        }
+                        else if (par->xlig_chain_code!=NULL && 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++;
                         }
@@ -926,11 +915,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
             }
 
-            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, buf[21])))
+            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
             {
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
-                {
 
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
+                {
                     /*Check again for the first occurence*/
                     rpdb_extract_atom_coordinates(buf, &x, &y, &z); /*extract and double check coordinates to avoid issues with wrong coordinates*/
                     resnbuf = rpdb_extract_atm_resumber(buf);
@@ -938,11 +927,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
                     /* Hetatom entry: check if there is a ligand in there too... */
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         rpdb_extract_atm_resname(buf, resb);
 
-                        // printf("%s ",ligan);
+                        
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
                             natm_lig++;
@@ -957,13 +947,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         else
                         {
                             /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, buf[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
                             {
-                                // printf("%s|%c ",resb,buf[21]);
                                 natoms++;
                                 nhetatm++;
                             }
-                            else if (!is_ligand(par->chain_as_ligand, buf[21]))
+                            else if (!is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                             {
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
                                 {
@@ -978,19 +967,9 @@ 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 (is_ligand(par->chain_as_ligand, buf[21]))
+                    if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
-                        // fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
                     }
                 }
                 if (x < 9990 && y < 9990 && z < 9990)
@@ -1000,9 +979,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
 
                     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])
+                        unsigned short is_chain_ligand=(is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+                        if (is_chain_ligand || (par->xlig_chain_code!=NULL && 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++;
                         }
                     }
@@ -1105,6 +1084,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     s_atm *atom = NULL;
     s_atm *atoms = pdb->latoms;
     s_atm **atoms_p = pdb->latoms_p;
@@ -1131,10 +1112,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         if (pdb->model_flag == 0 || model_read == 1)
         {
 
-            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, pdb_line[21]))
+            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
             {
-
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     // printf("%s\n",params->chain_delete);
 
@@ -1145,30 +1126,20 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*if within first occurence*/
                     /* Store ATOM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
 
                         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])
-                    //     {
-
-                    //         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]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
                         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++;
                     }
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in such an entry */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1190,6 +1161,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+
 
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
@@ -1218,7 +1192,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
 
@@ -1244,6 +1220,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             // printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain  : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
                             // atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
                             // printf("electroneg : %s\n",atom->symbol);
@@ -1258,8 +1237,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
+                        
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
 
-                        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 (is_chain_ligand || (params->xlig_chain_code!=NULL && (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));
@@ -1268,33 +1249,25 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
-            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, pdb_line[21])))
+
+            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
             {
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     rpdb_extract_atom_coordinates(pdb_line, &tmpx, &tmpy, &tmpz); /*extract and double check coordinates to avoid issues with wrong coordinates*/
+                    resnbuf = rpdb_extract_atm_resumber(pdb_line);
                 }
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*first occurence*/
                     /* Check HETATM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
-                        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]) {
-
-                    //         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++;
-                    //     }
-                    // }
-                    if (is_ligand(params->chain_as_ligand, pdb_line[21]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
 
                         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));
@@ -1302,7 +1275,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         i_explicit_ligand_atom++;
                     }
                     // fflush(stdout);
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in HETATM entry */
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1319,7 +1292,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
-
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             atoms_p[iatoms] = atom;
                             atm_lig[iatm_lig] = atom;
 
@@ -1345,7 +1320,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 atm_lig[iatm_lig] = atom;
 
@@ -1356,9 +1333,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                         else if (pdb->lhetatm)
                         {
-
                             /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, pdb_line[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
                             {
 
                                 atom = atoms + iatoms;
@@ -1374,13 +1350,15 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 pdb->lhetatm[ihetatm] = atom;
                                 ihetatm++;
                                 iatoms++;
                             }
-                            else if (!is_ligand(params->chain_as_ligand, pdb_line[21]))
+                            else if (!is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                             {
 
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
@@ -1402,7 +1380,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                         atom->radius = pte_get_vdw_ray(atom->symbol);
                                         atom->electroneg = pte_get_enegativity(atom->symbol);
                                         atom->sort_x = -1;
-
+                                        atom->label_seq_id=atom->res_id;
+                                        strcpy(atom->label_asym_id, atom->chain);
+                                
                                         atoms_p[iatoms] = atom;
                                         pdb->lhetatm[ihetatm] = atom;
                                         ihetatm++;
@@ -1422,7 +1402,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         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])
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+
+                        if (is_chain_ligand || (params->xlig_chain_code!=NULL && (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));
@@ -1432,6 +1414,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
+            
             else if (strncmp(pdb_line, "CRYST1", 6) == 0)
             {
                 rpdb_extract_cryst1(pdb_line, &(pdb->alpha), &(pdb->beta), &(pdb->gamma),
@@ -1444,6 +1427,8 @@ 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;
@@ -1457,15 +1442,16 @@ 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;
     pdb->avg_bfactor /= (iatoms - num_h_atoms);
-    //        pdb->avg_bfactor=0.0;
-
-    /*if(guess_flag>0) {
-        fprintf(stderr, ">! Warning: You did not provide a standard PDB file.\nElements were guessed by fpocket, because not provided in the PDB file. \nThere is no guarantee on the results!\n");
-    }*/
 
     if (ligan && keep_lig && (ligfound == 0 || pdb->natm_lig <= 0))
     {
@@ -1572,50 +1558,49 @@ void free_pdb_atoms(s_pdb *pdb)
         int
 
  */
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept)
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete)
 { /*deletes the chains selected by command -c, returns true if the chain correspond false if not*/
 
     if (is_chain_kept == 0)
     {
         int is_deleted = 1;
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
                 is_deleted = 0;
             }
         }
-        // printf("\n");
         return is_deleted;
     }
     else
     {
-        int is_deleted = 0;
+        int is_kept = 0;
+
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
-                is_deleted = 1;
+                is_kept = 1;
             }
         }
-        // printf("\n");
-        return is_deleted;
+        return is_kept;
     }
 }
 
-int is_ligand(char *chains_selected, char current_line_chain)
+
+
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand)
 {
+    
     int is_a_ligand = 0;
     int i;
-    for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+    for (i = 0; i < n_chains_as_ligand; i++)
     {
-        if (chains_selected[i] == current_line_chain)
+        if (!strcmp(chains_selected[i],current_line_chain))
         {
-            // printf("%c_%c ", chains_selected[i],current_line_chain);
             is_a_ligand = 1;
         }
     }

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)
@@ -1523,23 +1488,23 @@ void write_mmcif_vert(FILE *f, s_vvertice *v, int i)
     if (v->electrostatic_energy <= -0.05)
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, " POL",
-                              ' ', "ACC", "O", v->resid, ' ',
+        write_mmcif_atom_line(f, "HETATM", i, "POL",
+                              '.', "ACC", "O", v->resid, "O",v->resid,'.',
                               v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
     else if (v->electrostatic_energy >= 0.05)
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "POL", '.', "DON", "N",
+                              v->resid, "N",v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
     else
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "APOL", '.', "STP", "C",
+                              v->resid, "C", v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
 }

src/write_visu.c

@@ -61,7 +61,7 @@ void write_visualization(char *pdb_name, char *pdb_out_name)
 	}
 
 	if(write_mode[0] == 'm' || write_mode[0] == 'b'){
-	char *ext_cif = ".cif";
+	const char *ext_cif = ".cif";
 	remove_ext(pdb_out_name); 
 	strcat(pdb_out_name,ext_cif); /*put the .cif file extension*/
 	

src/writepdb.c

@@ -206,7 +206,7 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
 
 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
 						   char alt_loc, const char res_name[], const char chain[],
-						   int res_id, const char insert, float x, float y, float z, float occ,
+						   int res_id, const char label_asym_id[],int label_seq_id, char insert, float x, float y, float z, float occ,
 						   float bfactor, int abpa, const char *symbol, int charge, float abpa_prob)
 {
 	int status = 0;
@@ -226,7 +226,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 	else
 		sprintf(res_id_buf, "****");
 
-	alt_loc = (alt_loc == '\0') ? ' ' : alt_loc;
+	alt_loc = (alt_loc == '\0' || (alt_loc == ' '))  ? '?' : alt_loc;
+	insert = (insert == '\0' || insert==' ') ? '?' : insert;
 
 	if (charge == -1)
 		sprintf(charge_buf, " 0");
@@ -237,14 +238,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 	if (abpa)
 		finalabpa = abpa_prob;
 
-	//status = fprintf(f, "%-7s %6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %4s %4s %2s %4s\n",
-	//				 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, res_id_buf, res_name, chain, atom_name);
+	status = fprintf(f, "%-7s %-6s %3s %4s %c %4s %6s %d %c %8.3f %8.3f %8.3f %6.2f %2s %d %s\n",
+					 rec_name, id_buf, symbol, atom_name,alt_loc, res_name, label_asym_id, label_seq_id,insert, x, y, z, occ, charge_buf, res_id,chain);
 
-	status = fprintf(f, "%-7s %-6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s  %2s\n",
-					 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, chain);
+}
 
-	/*"ATOM %d %s %s . %s %s . %d ? %f %f %f %f %f %s\n",
-            i + 1, atoms[i].name, atoms[i].type, atoms[i].resname, atoms[i].chain,
-            atoms[i].resid, *x, *y, *z, atoms[i].occupancy,
-            atoms[i].charge, atoms[i].chain);*/
-}

src/writepocket.c

@@ -44,7 +44,6 @@ static const char atomSiteHeader[] =
     "_atom_site.label_alt_id\n"
     "_atom_site.label_comp_id\n"
     "_atom_site.label_asym_id\n"
-    "_atom_site.label_entity_id\n"
     "_atom_site.label_seq_id\n"
     "_atom_site.pdbx_PDB_ins_code\n"
     "_atom_site.Cartn_x\n"
@@ -52,6 +51,7 @@ static const char atomSiteHeader[] =
     "_atom_site.Cartn_z\n"
     "_atom_site.occupancy\n"
     "_atom_site.pdbx_formal_charge\n"
+    "_atom_site.auth_seq_id\n"
     "_atom_site.auth_asym_id\n";
 
     /*static const char atomSiteHeader[] =
@@ -83,7 +83,6 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
     out[0] = '\0';
 
     node_pocket *pcur;
-
     int i = 0;
     if (pockets) {
         pcur = pockets->first;
@@ -92,13 +91,26 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i + 1);
             write_pocket_pqr_DB(out, pcur->pocket);
 
-            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
-            write_pocket_pdb_DB(out, pcur->pocket, pdb);
-
-            
+            if(write_mode[0] == 'p' || write_mode[0] == 'b'){
+        
             sprintf(out, "%s/pocket%d_atm.pdb", out_path, i + 1);
             write_pocket_pdb(out, pcur->pocket);
 
+            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
+            write_pocket_pdb_DB(out, pcur->pocket, pdb);
+            // sprintf(out, "%s/pocket%d_atm.pdb", out_path, i+1);
+            // write_pocket_pdb_DB(out, pcur->pocket);
+            }
+
+            if(write_mode[0] == 'm' || write_mode[0] == 'b'){
+            sprintf(out, "%s/pocket%d_atm.cif", out_path, i + 1);
+            write_pocket_mmcif(out, pcur->pocket);
+
+            sprintf(out, "%s/pocket%d_env_atm.cif", out_path, i+1);
+            write_pocket_mmcif_DB(out, pcur->pocket,pdb);
+            }
+
+
             pcur = pcur->next;
             i++;
         }
@@ -144,14 +156,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
 
         node_vertice *nvcur = pocket->v_lst->first;
 
-       /* 
-                                fprintf(stdout, "A Pocket:\n") ;
-        */
         while (nvcur) {
-            /*
-                                            fprintf(stdout, "Vertice %d: %p %d %f\n", i, nvcur->vertice, nvcur->vertice->id, nvcur->vertice->ray) ;
-                                            fprintf(stdout, "Atom %s\n", nvcur->vertice->neigh[0]->name) ;
-             */
 
             tab_vert[nvert] = nvcur->vertice;
             nvcur = nvcur->next;
@@ -159,7 +164,6 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
         }
         sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
         for (i = 0; i < n_sa; i++) {
-            //atom = pocket->sou_atoms[i] ;
             atom = pdb->latoms_p[sa[i]];
             write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
                     atom->res_name, atom->chain, atom->res_id,
@@ -167,36 +171,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);
         }
-        /*
-                    vcur = pocket->v_lst->first ;
-
-                        while(vcur){
-                                for(i = 0 ; i < 4 ; i++) {
-                                        if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
-                                                if(cur_size >= cur_allocated-1) {
-                                                        cur_allocated *= 2 ;
-                                                        atms = (s_atm**) my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
-                                                }
-                                                atms[cur_size] = vcur->vertice->neigh[i] ;
-                                                cur_size ++ ;
-                                        }
-
-                                }
-                                vcur = vcur->next ;
-                        }
-         */
-        // Then write atoms...
-        /*
-                        for(i = 0 ; i < cur_size ; i++) {
-                                atom = atms[i] ;
-
-                                write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                                                                                atom->res_name, atom->chain, atom->res_id,
-                                                                                atom->pdb_insert, atom->x, atom->y, atom->z,
-                                                                                atom->occupancy, atom->bfactor, atom->symbol,
-                                                                                atom->charge);
-                        }
-         */
+        
         fprintf(f, "TER\nEND\n");
         fclose(f);
     } else {
@@ -207,6 +182,56 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
     my_free(atms);
 }
 
+
+
+void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
+    int i = 0, nvert = 0;
+    s_atm **atms = (s_atm **) my_malloc(sizeof (s_atm*)*10);
+    s_atm *atom = NULL;
+    int n_sa = 0;
+    int *sa = NULL; /*surrounding atoms container*/
+    s_vvertice **tab_vert = NULL;
+    char tmp[250];
+    strcpy(tmp,out);
+    remove_ext(tmp);
+    remove_path(tmp);
+    FILE *f = fopen(out, "w");
+    fprintf(f,"data_%s\n# \n",tmp);
+    fprintf(f,"%s",atomSiteHeader);/*print the header*/
+    if (f && pocket) {
+        // First get the list of atoms
+        tab_vert = (s_vvertice **) my_malloc(pocket->v_lst->n_vertices * sizeof (s_vvertice*));
+
+        node_vertice *nvcur = pocket->v_lst->first;
+
+        while (nvcur) {
+
+            tab_vert[nvert] = nvcur->vertice;
+            nvcur = nvcur->next;
+            nvert++;
+        }
+        sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
+        for (i = 0; i < n_sa; i++) {
+            atom = pdb->latoms_p[sa[i]];
+            write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
+                    atom->pdb_insert, atom->x, atom->y, atom->z,
+                    atom->dA, atom->a0, atom->abpa, atom->symbol,
+                    atom->charge, atom->abpa_sourrounding_prob);
+        }
+        
+        fprintf(f, "#\n");
+        fclose(f);
+    } else {
+        if (!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
+        else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
+    }
+
+    my_free(atms);
+}
+
+
+
 /**
    ## FUNCTION: 
         write_single_pdb
@@ -350,9 +375,9 @@ void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms) {
     for (i = 0; i < natoms; i++) {
         atom = atoms + i;
         //atom->chain[1]='\0';
-        //printf("%d:%s|symb:%s\t",i,atom->chain,atom->symbol);
+        // printf("%d:%s vs %s\n",i,atom->chain,atom->label_asym_id);
         write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                atom->res_name, atom->chain, atom->res_id,
+                atom->res_name, atom->chain,atom->res_id,atom->label_asym_id,atom->label_seq_id,
                 atom->pdb_insert, atom->x, atom->y, atom->z,
                 atom->dA, atom->a0, atom->abpa, atom->symbol,
                 atom->charge, atom->abpa_sourrounding_prob);
@@ -483,7 +508,7 @@ void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
     int i = 1;
     if (pockets) {
         pcur = pockets->first;
-        
+
         while (pcur) {
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i);
 
@@ -524,6 +549,7 @@ 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 +633,7 @@ 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);
@@ -716,7 +742,7 @@ void write_pocket_mmcif(const char out[], s_pocket *pocket) {
             atom = atms[i];
 
             write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                    atom->res_name, atom->chain, atom->res_id,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
                     atom->pdb_insert, atom->x, atom->y, atom->z,
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);

tests/environment.yml

@@ -2,5 +2,5 @@ name: fpocket_test
 channels:
   - defaults
 dependencies:
-  - python=3.7
+  - python=3.12
   - pytest

tests/reference_output/123abc_out/pocket10_atm.cif

@@ -0,0 +1,76 @@
+data_pocket10_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    10:
+0  - Pocket Score                      : 0.0405
+1  - Drug Score                        : 0.0230
+2  - Number of alpha spheres           :    57
+3  - Mean alpha-sphere radius          : 3.8604
+4  - Mean alpha-sphere Solvent Acc.    : 0.4592
+5  - Mean B-factor of pocket residues  : 0.2769
+6  - Hydrophobicity Score              : 40.0769
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 427.0346
+10  -Pocket volume (convex hull)       : 76.0139
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 32.4571
+13 - Number of apolar alpha sphere     :    35
+14 - Proportion of apolar alpha sphere : 0.6140
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3335    C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM     3339    O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM     1238    O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM     3399    C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM     3397    C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM     3345    C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM     3378    C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM     3332    O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM     3735    C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM     3729    O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM     1239    C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM     3454    O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM     3488    O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM     3380    C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM     3460    O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM     3458    C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM     3348    C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM     1241    C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM     3760    C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM     3756    N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM     3398    C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM     3463    C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM     3737    O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM     3728    C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM     3730    C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM     3738    C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM     3346    C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM     3464    C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM     3734    N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM     1247    C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM     3461    C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM     1250    N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM     1255    N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM     1237    C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+# 

tests/reference_output/123abc_out/pocket10_env_atm.cif

@@ -0,0 +1,91 @@
+data_pocket10_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1236    C   CA ?  ALA    Axp 168 ?   21.345   31.742   30.855   0.00  0 395 A
+ATOM     1237    C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+ATOM     1238    O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM     1239    C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM     1240    N    N ?  HIS    Axp 169 ?   19.130   32.633   31.043   0.00  0 396 A
+ATOM     1241    C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM     1242    C    C ?  HIS    Axp 169 ?   17.124   32.937   32.241   0.00  0 396 A
+ATOM     1244    C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM     1245    C   CG ?  HIS    Axp 169 ?   16.104   34.797   30.229   0.00  0 396 A
+ATOM     1247    C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM     1249    N  NE2 ?  HIS    Axp 169 ?   14.590   36.367   30.529   0.00  0 396 A
+ATOM     1250    N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM     1251    C   CA ?  ALA    Axp 170 ?   16.342   32.830   34.571   0.00  0 397 A
+ATOM     1252    C    C ?  ALA    Axp 170 ?   16.105   31.311   34.539   0.00  0 397 A
+ATOM     1254    C   CB ?  ALA    Axp 170 ?   15.038   33.564   34.528   0.00  0 397 A
+ATOM     1255    N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM     3331    C    C ?  THR    Bxp 167 ?   22.771   43.904   32.327   0.00  0 394 B
+ATOM     3332    O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM     3333    C   CB ?  THR    Bxp 167 ?   23.958   42.338   33.911   0.00  0 394 B
+ATOM     3335    C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM     3338    C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM     3339    O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM     3341    N    N ?  HIS    Bxp 169 ?   19.743   43.280   29.949   0.00  0 396 B
+ATOM     3342    C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM     3345    C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM     3346    C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM     3347    N  ND1 ?  HIS    Bxp 169 ?   15.399   41.864   29.978  -2.19  0 396 B
+ATOM     3348    C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM     3349    C  CE1 ?  HIS    Bxp 169 ?   14.459   40.980   29.690   0.00  0 396 B
+ATOM     3350    N  NE2 ?  HIS    Bxp 169 ?   14.959   39.769   29.859   0.00  0 396 B
+ATOM     3374    N    N ?  PHE    Bxp 174 ?   19.806   45.500   34.237   0.00  0 401 B
+ATOM     3375    C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM     3377    O    O ?  PHE    Bxp 174 ?   21.500   44.304   36.088   0.00  0 401 B
+ATOM     3378    C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM     3379    C   CG ?  PHE    Bxp 174 ?   17.076   44.325   34.855   0.00  0 401 B
+ATOM     3380    C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM     3382    C  CE1 ?  PHE    Bxp 174 ?   15.273   43.909   33.319   0.00  0 401 B
+ATOM     3396    C   CB ?  ILE    Bxp 176 ?   21.966   39.989   38.044   0.00  0 403 B
+ATOM     3397    C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM     3398    C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM     3399    C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM     3453    C    C ?  SER    Bxp 183 ?   12.616   39.571   36.930   0.00  0 410 B
+ATOM     3454    O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM     3457    N    N ?  LEU    Bxp 184 ?   13.478   38.624   37.304   0.00  0 411 B
+ATOM     3458    C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM     3459    C    C ?  LEU    Bxp 184 ?   13.764   37.165   35.433   0.00  0 411 B
+ATOM     3460    O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM     3461    C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM     3462    C   CG ?  LEU    Bxp 184 ?   16.587   38.098   37.951   0.00  0 411 B
+ATOM     3463    C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM     3464    C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM     3488    O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM     3727    C   CA ?  LEU    Bxp 218 ?   25.851   36.423   37.264   0.00  0 445 B
+ATOM     3728    C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM     3729    O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM     3730    C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM     3734    N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM     3735    C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM     3736    C    C ?  SER    Bxp 219 ?   24.150   32.474   35.811   0.00  0 446 B
+ATOM     3737    O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM     3738    C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM     3751    C    C ?  VAL    Bxp 221 ?   21.031   32.982   40.538   0.00  0 448 B
+ATOM     3753    C   CB ?  VAL    Bxp 221 ?   22.559   35.077   40.397   0.00  0 448 B
+ATOM     3756    N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM     3757    C   CA ?  TYR    Bxp 222 ?   18.886   32.708   39.432   0.00  0 449 B
+ATOM     3760    C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM     3761    C   CG ?  TYR    Bxp 222 ?   16.811   32.522   38.032   0.00  0 449 B
+ATOM     3762    C  CD1 ?  TYR    Bxp 222 ?   15.795   33.459   38.329   0.00  0 449 B
+ATOM     3768    N    N ?  GLU    Bxp 223 ?   19.652   30.471   39.123   0.00  0 450 B
+ATOM     3773    C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM     3776    O  OE2 ?  GLU    Bxp 223 ?   21.549   28.266   34.820   0.00  0 450 B
+#

tests/reference_output/123abc_out/pocket10_vert.pqr

@@ -0,0 +1,59 @@
+ATOM      1    O STP    10      21.702  37.817  31.893    0.00     4.09
+ATOM      2    C STP    10      19.673  40.504  33.491    0.00     3.60
+ATOM      3    C STP    10      19.762  41.204  33.656    0.00     3.56
+ATOM      4    O STP    10      19.774  41.436  33.555    0.00     3.45
+ATOM      5    O STP    10      19.888  41.310  33.676    0.00     3.53
+ATOM      6    O STP    10      20.810  34.601  34.374    0.00     3.89
+ATOM      7    O STP    10      22.171  36.269  33.386    0.00     3.87
+ATOM      8    O STP    10      15.383  40.306  33.837    0.00     3.41
+ATOM      9    O STP    10      15.487  40.276  33.991    0.00     3.41
+ATOM     10    O STP    10      15.519  40.241  33.611    0.00     3.44
+ATOM     11    C STP    10      19.399  38.571  32.764    0.00     4.21
+ATOM     12    O STP    10      19.631  37.930  32.444    0.00     4.45
+ATOM     13    C STP    10      19.282  37.676  32.828    0.00     4.53
+ATOM     14    O STP    10      20.160  35.844  37.073    0.00     3.59
+ATOM     15    C STP    10      20.138  35.856  37.103    0.00     3.58
+ATOM     16    C STP    10      20.119  35.880  36.964    0.00     3.63
+ATOM     17    O STP    10      20.785  34.426  34.531    0.00     3.86
+ATOM     18    C STP    10      24.048  36.964  33.366    0.00     3.71
+ATOM     19    C STP    10      23.766  36.842  33.568    0.00     3.56
+ATOM     20    C STP    10      23.470  37.040  32.145    0.00     4.32
+ATOM     21    C STP    10      22.938  36.606  32.779    0.00     4.02
+ATOM     22    C STP    10      24.363  37.273  32.697    0.00     4.10
+ATOM     23    C STP    10      24.101  36.997  33.214    0.00     3.80
+ATOM     24    C STP    10      17.002  40.176  33.584    0.00     3.41
+ATOM     25    C STP    10      17.136  40.046  33.708    0.00     3.55
+ATOM     26    C STP    10      16.167  40.018  33.979    0.00     3.53
+ATOM     27    C STP    10      16.305  39.958  33.848    0.00     3.58
+ATOM     28    C STP    10      19.086  39.525  33.553    0.00     3.89
+ATOM     29    C STP    10      19.053  38.731  33.178    0.00     4.19
+ATOM     30    C STP    10      18.646  40.617  34.047    0.00     3.63
+ATOM     31    C STP    10      18.847  40.579  34.038    0.00     3.69
+ATOM     32    C STP    10      20.140  36.950  36.141    0.00     3.43
+ATOM     33    C STP    10      20.148  36.427  35.991    0.00     3.81
+ATOM     34    C STP    10      19.995  36.133  36.373    0.00     3.82
+ATOM     35    C STP    10      19.906  35.986  36.229    0.00     3.90
+ATOM     36    C STP    10      24.433  36.790  33.463    0.00     3.48
+ATOM     37    C STP    10      24.463  36.791  33.428    0.00     3.49
+ATOM     38    C STP    10      17.930  37.771  33.253    0.00     4.01
+ATOM     39    C STP    10      19.259  37.654  32.729    0.00     4.47
+ATOM     40    C STP    10      19.138  37.660  32.994    0.00     4.54
+ATOM     41    C STP    10      19.116  37.654  33.024    0.00     4.54
+ATOM     42    C STP    10      19.115  37.662  33.021    0.00     4.54
+ATOM     43    C STP    10      18.498  35.757  35.907    0.00     3.54
+ATOM     44    O STP    10      18.041  37.280  33.428    0.00     4.04
+ATOM     45    C STP    10      18.664  37.361  33.249    0.00     4.29
+ATOM     46    O STP    10      17.586  36.737  34.326    0.00     3.53
+ATOM     47    C STP    10      18.506  35.744  35.825    0.00     3.58
+ATOM     48    C STP    10      19.301  37.188  33.471    0.00     4.39
+ATOM     49    O STP    10      19.927  36.095  35.154    0.00     4.20
+ATOM     50    O STP    10      19.807  35.859  35.537    0.00     4.14
+ATOM     51    O STP    10      19.624  36.886  33.557    0.00     4.29
+ATOM     52    O STP    10      20.418  35.977  34.266    0.00     4.22
+ATOM     53    O STP    10      20.780  34.426  34.534    0.00     3.86
+ATOM     54    O STP    10      20.507  34.155  35.241    0.00     3.80
+ATOM     55    O STP    10      20.041  32.362  35.203    0.00     3.42
+ATOM     56    O STP    10      20.690  34.424  34.197    0.00     3.70
+ATOM     57    O STP    10      20.804  34.600  34.377    0.00     3.90
+TER
+END

tests/reference_output/123abc_out/pocket11_atm.cif

@@ -0,0 +1,63 @@
+data_pocket11_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    11:
+0  - Pocket Score                      : 0.0388
+1  - Drug Score                        : 0.0007
+2  - Number of alpha spheres           :    30
+3  - Mean alpha-sphere radius          : 3.6177
+4  - Mean alpha-sphere Solvent Acc.    : 0.4151
+5  - Mean B-factor of pocket residues  : 0.1046
+6  - Hydrophobicity Score              : 17.4167
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.8333
+9  - Pocket volume (Monte Carlo)       : 160.2332
+10  -Pocket volume (convex hull)       : 11.3291
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.2000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1405    C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM     1435    O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM     1407    C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM      996    O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM     1436    C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM     1329    N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM     1327    O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM     1290    C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM     1323    C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM     1437    O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM     1289    C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM     1312    C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM     1005    C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM     1311    O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM     1471    C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+ATOM     1355    O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM     1012    N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM     1444    O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM      995    C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM      994    C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM     1328    C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+# 

tests/reference_output/123abc_out/pocket11_env_atm.cif

@@ -0,0 +1,64 @@
+data_pocket11_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM      993    N    N ?  ARG    Axp 135 ?   10.598   26.723   18.417   0.00  0 362 A
+ATOM      994    C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM      995    C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM      996    O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM      997    C   CB ?  ARG    Axp 135 ?   10.850   26.919   20.881   0.00  0 362 A
+ATOM     1004    N    N ?  ASP    Axp 136 ?   13.515   26.641   18.666   0.00  0 363 A
+ATOM     1005    C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM     1006    C    C ?  ASP    Axp 136 ?   15.413   26.185   17.291   0.00  0 363 A
+ATOM     1008    C   CB ?  ASP    Axp 136 ?   15.490   25.673   19.755   0.00  0 363 A
+ATOM     1009    C   CG ?  ASP    Axp 136 ?   16.996   25.759   19.996   0.00  0 363 A
+ATOM     1010    O  OD1 ?  ASP    Axp 136 ?   17.712   26.739   19.639   0.00  0 363 A
+ATOM     1012    N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM     1014    C    C ?  LEU    Axp 137 ?   16.652   27.030   14.689   0.00  0 364 A
+ATOM     1015    O    O ?  LEU    Axp 137 ?   16.968   28.209   14.932   0.00  0 364 A
+ATOM     1280    C  CD2 ?  PHE    Axp 174 ?   15.409   30.643   25.623   0.00  0 401 A
+ATOM     1287    O    O ?  PRO    Axp 175 ?   19.472   32.424   20.666   0.00  0 402 A
+ATOM     1289    C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM     1290    C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM     1309    C   CA ?  TRP    Axp 178 ?   18.854   33.025   17.137   0.00  0 405 A
+ATOM     1310    C    C ?  TRP    Axp 178 ?   17.481   33.558   17.564   0.00  0 405 A
+ATOM     1311    O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM     1312    C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM     1322    N    N ?  THR    Axp 179 ?   17.421   34.347   18.657   0.00  0 406 A
+ATOM     1323    C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM     1324    C    C ?  THR    Axp 179 ?   15.545   35.958   19.044   0.00  0 406 A
+ATOM     1326    C   CB ?  THR    Axp 179 ?   16.508   34.581   20.893   0.00  0 406 A
+ATOM     1327    O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM     1328    C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+ATOM     1329    N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM     1333    C   CB ?  ALA    Axp 180 ?   12.155   36.812   17.751   0.00  0 407 A
+ATOM     1354    C   CB ?  SER    Axp 183 ?   11.829   35.508   22.060   0.00  0 410 A
+ATOM     1355    O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM     1405    C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM     1407    C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM     1408    C   CZ ?  PHE    Axp 189 ?   12.053   32.229   24.016   0.00  0 416 A
+ATOM     1433    C   CA ?  SER    Axp 193 ?    9.893   34.090   16.472   0.00  0 420 A
+ATOM     1434    C    C ?  SER    Axp 193 ?   10.658   32.899   15.802   0.00  0 420 A
+ATOM     1435    O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM     1436    C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM     1437    O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM     1438    N    N ?  ASP    Axp 194 ?    9.907   31.853   15.450   0.00  0 421 A
+ATOM     1439    C   CA ?  ASP    Axp 194 ?   10.435   30.800   14.622   0.00  0 421 A
+ATOM     1444    O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM     1471    C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+#

tests/reference_output/123abc_out/pocket11_vert.pqr

@@ -0,0 +1,32 @@
+ATOM      1    O STP    11      12.898  31.662  19.017    0.00     3.84
+ATOM      2    O STP    11      13.150  32.247  19.120    0.00     3.85
+ATOM      3    O STP    11      15.088  30.679  21.810    0.00     3.40
+ATOM      4    O STP    11      14.161  31.633  19.836    0.00     3.64
+ATOM      5    O STP    11      13.387  31.848  19.044    0.00     3.96
+ATOM      6    O STP    11      13.175  32.231  19.116    0.00     3.86
+ATOM      7    O STP    11      12.808  31.604  18.987    0.00     3.81
+ATOM      8    O STP    11      12.873  31.765  19.036    0.00     3.81
+ATOM      9    C STP    11      12.557  32.462  19.477    0.00     3.41
+ATOM     10    O STP    11      12.931  31.991  19.076    0.00     3.80
+ATOM     11    C STP    11      16.028  30.026  18.804    0.00     3.56
+ATOM     12    O STP    11      13.473  31.801  18.968    0.00     3.94
+ATOM     13    O STP    11      13.537  32.512  18.591    0.00     3.49
+ATOM     14    O STP    11      15.773  30.122  18.478    0.00     3.59
+ATOM     15    O STP    11      14.671  31.353  19.355    0.00     3.61
+ATOM     16    O STP    11      15.838  30.562  19.199    0.00     3.61
+ATOM     17    O STP    11      15.915  30.373  18.983    0.00     3.61
+ATOM     18    O STP    11      16.143  30.691  19.153    0.00     3.44
+ATOM     19    O STP    11      13.668  31.316  18.409    0.00     3.75
+ATOM     20    O STP    11      15.536  30.118  18.260    0.00     3.56
+ATOM     21    C STP    11      15.745  30.047  18.174    0.00     3.54
+ATOM     22    O STP    11      12.904  32.687  19.451    0.00     3.57
+ATOM     23    C STP    11      15.940  29.800  17.882    0.00     3.41
+ATOM     24    O STP    11      12.225  30.961  18.523    0.00     3.60
+ATOM     25    O STP    11      12.987  30.452  17.753    0.00     3.52
+ATOM     26    O STP    11      12.997  30.420  17.738    0.00     3.50
+ATOM     27    O STP    11      11.766  30.743  19.000    0.00     3.41
+ATOM     28    O STP    11      11.834  30.739  18.825    0.00     3.44
+ATOM     29    C STP    11      13.290  32.673  19.656    0.00     3.51
+ATOM     30    C STP    11      14.144  31.854  20.011    0.00     3.50
+TER
+END

tests/reference_output/123abc_out/pocket12_atm.cif

@@ -0,0 +1,61 @@
+data_pocket12_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    12:
+0  - Pocket Score                      : 0.0380
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    22
+3  - Mean alpha-sphere radius          : 4.0091
+4  - Mean alpha-sphere Solvent Acc.    : 0.5656
+5  - Mean B-factor of pocket residues  : 0.1891
+6  - Hydrophobicity Score              : 14.1667
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.4167
+9  - Pocket volume (Monte Carlo)       : 293.7227
+10  -Pocket volume (convex hull)       : 19.5893
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.0909
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3242    O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM     3271    O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM     3255    C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM     3241    O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM     3383    C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM     3094    O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM     3097    C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM     3504    C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM     3368    O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM     3109    O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM     3258    N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM     3095    C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM     3084    O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM     3381    C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM     3270    C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM     3326    C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM     3391    C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM     3106    C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM     3107    C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+# 

tests/reference_output/123abc_out/pocket12_env_atm.cif

@@ -0,0 +1,58 @@
+data_pocket12_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3084    O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM     3092    C   CA ?  ARG    Bxp 135 ?   12.705   49.230   41.141   0.00  0 362 B
+ATOM     3093    C    C ?  ARG    Bxp 135 ?   14.235   49.115   41.170   0.00  0 362 B
+ATOM     3094    O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM     3095    C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM     3096    C   CG ?  ARG    Bxp 135 ?   10.987   49.132   39.313   0.00  0 362 B
+ATOM     3097    C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM     3098    N   NE ?  ARG    Bxp 135 ?    9.837   48.697   37.316  -3.28  0 362 B
+ATOM     3099    C   CZ ?  ARG    Bxp 135 ?    9.680   48.564   36.008   0.00  0 362 B
+ATOM     3100    N  NH1 ?  ARG    Bxp 135 ?   10.479   49.242   35.166   0.00  0 362 B
+ATOM     3102    N    N ?  ASP    Bxp 136 ?   14.929   49.943   41.933   0.00  0 363 B
+ATOM     3103    C   CA ?  ASP    Bxp 136 ?   16.383   49.878   41.974   0.00  0 363 B
+ATOM     3106    C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM     3107    C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+ATOM     3108    O  OD1 ?  ASP    Bxp 136 ?   19.011   49.469   41.230  -2.14  0 363 B
+ATOM     3109    O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM     3240    C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM     3241    O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM     3242    O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM     3254    N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM     3255    C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM     3256    C    C ?  GLY    Bxp 156 ?   20.360   55.778   36.866   0.00  0 383 B
+ATOM     3258    N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM     3266    N    N ?  SER    Bxp 158 ?   21.413   52.688   36.129   0.00  0 385 B
+ATOM     3267    C   CA ?  SER    Bxp 158 ?   21.516   51.514   35.236   0.00  0 385 B
+ATOM     3270    C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM     3271    O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM     3324    C  CD2 ?  TYR    Bxp 166 ?   21.644   48.614   37.025   0.00  0 393 B
+ATOM     3326    C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM     3368    O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM     3375    C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM     3381    C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM     3383    C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM     3390    C   CG ?  PRO    Bxp 175 ?   19.698   46.334   39.774   0.00  0 402 B
+ATOM     3391    C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM     3502    C  CD2 ?  PHE    Bxp 189 ?   11.410   45.318   38.790   0.00  0 416 B
+ATOM     3504    C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM     3505    C   CZ ?  PHE    Bxp 189 ?   12.791   44.477   36.970   0.00  0 416 B
+#

tests/reference_output/123abc_out/pocket12_vert.pqr

@@ -0,0 +1,24 @@
+ATOM      1    O STP    12      15.798  53.375  36.448    0.00     4.45
+ATOM      2    C STP    12      13.890  48.091  37.059    0.00     3.51
+ATOM      3    O STP    12      15.723  50.129  36.349    0.00     4.58
+ATOM      4    O STP    12      16.096  50.102  36.606    0.00     4.44
+ATOM      5    O STP    12      15.901  52.536  36.959    0.00     4.46
+ATOM      6    O STP    12      16.813  53.016  37.079    0.00     3.99
+ATOM      7    O STP    12      18.001  53.059  37.147    0.00     3.44
+ATOM      8    C STP    12      14.176  48.608  36.866    0.00     3.64
+ATOM      9    O STP    12      12.896  52.943  37.474    0.00     3.99
+ATOM     10    O STP    12      16.135  49.273  36.737    0.00     4.06
+ATOM     11    O STP    12      17.906  49.419  37.009    0.00     3.41
+ATOM     12    O STP    12      16.145  50.097  36.607    0.00     4.40
+ATOM     13    O STP    12      17.037  48.850  37.404    0.00     3.82
+ATOM     14    O STP    12      16.872  48.623  37.320    0.00     3.77
+ATOM     15    O STP    12      17.737  48.872  37.372    0.00     3.51
+ATOM     16    O STP    12      15.994  50.263  36.624    0.00     4.46
+ATOM     17    O STP    12      15.478  50.742  36.523    0.00     4.67
+ATOM     18    O STP    12      15.879  52.513  36.955    0.00     4.47
+ATOM     19    O STP    12      14.645  52.046  38.693    0.00     3.48
+ATOM     20    O STP    12      15.903  52.532  37.000    0.00     4.43
+ATOM     21    O STP    12      16.777  49.342  37.774    0.00     3.49
+ATOM     22    O STP    12      17.097  48.804  37.592    0.00     3.71
+TER
+END

tests/reference_output/123abc_out/pocket13_atm.cif

@@ -0,0 +1,74 @@
+data_pocket13_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    13:
+0  - Pocket Score                      : 0.0342
+1  - Drug Score                        : 0.3180
+2  - Number of alpha spheres           :    51
+3  - Mean alpha-sphere radius          : 3.7908
+4  - Mean alpha-sphere Solvent Acc.    : 0.4415
+5  - Mean B-factor of pocket residues  : 0.1092
+6  - Hydrophobicity Score              : 59.0769
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 406.5184
+10  -Pocket volume (convex hull)       : 39.2787
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 37.1163
+13 - Number of apolar alpha sphere     :    43
+14 - Proportion of apolar alpha sphere : 0.8431
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7064    N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM     7069    C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM     7068    C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM     7063    C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM     8096    C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM     7780    O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM     7784    C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM     7814    C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM     7081    O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM     7086    N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM     7087    C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM     7080    C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM     7062    O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM     7093    C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM     8079    C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM     7061    C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM     8080    C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM     8067    O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM     7060    C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM     7084    C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM     7817    C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM     7819    O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM     8069    C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM     7118    C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM     7820    C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM     8073    S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM     7816    N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM     7065    C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM     7082    C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM     8097    C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM     7092    C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM     8308    C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+# 

tests/reference_output/123abc_out/pocket13_env_atm.cif

@@ -0,0 +1,70 @@
+data_pocket13_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7059    N    N ?  ALA    Dxp 110 ?   48.007   27.461   23.893  -1.09  0 337 D
+ATOM     7060    C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM     7061    C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM     7062    O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM     7063    C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM     7064    N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM     7065    C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM     7068    C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM     7069    C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM     7079    C   CA ?  LEU    Dxp 113 ?   48.430   23.739   28.221   0.00  0 340 D
+ATOM     7080    C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM     7081    O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM     7082    C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM     7083    C   CG ?  LEU    Dxp 113 ?   47.664   26.335   28.429   0.00  0 340 D
+ATOM     7084    C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM     7086    N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM     7087    C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM     7090    C   CB ?  LEU    Dxp 114 ?   46.375   20.660   25.286   0.00  0 341 D
+ATOM     7091    C   CG ?  LEU    Dxp 114 ?   45.386   19.662   24.699   0.00  0 341 D
+ATOM     7092    C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM     7093    C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM     7118    C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM     7778    C   CA ?  LEU    Dxp 202 ?   42.652   21.867   34.762   0.00  0 429 D
+ATOM     7779    C    C ?  LEU    Dxp 202 ?   42.175   23.314   34.680   0.00  0 429 D
+ATOM     7780    O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM     7781    C   CB ?  LEU    Dxp 202 ?   41.521   21.052   34.137   0.00  0 429 D
+ATOM     7784    C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM     7810    C    C ?  ILE    Dxp 205 ?   45.268   26.571   32.956   0.00  0 432 D
+ATOM     7812    C   CB ?  ILE    Dxp 205 ?   46.098   24.078   33.335   0.00  0 432 D
+ATOM     7814    C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM     7816    N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM     7817    C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM     7818    C    C ?  ALA    Dxp 206 ?   43.351   28.736   31.982   0.00  0 433 D
+ATOM     7819    O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM     7820    C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM     8066    C    C ?  GLY    Dxp 236 ?   39.903   29.189   26.105   0.00  0 463 D
+ATOM     8067    O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM     8068    N    N ?  CYS    Dxp 237 ?   39.113   28.714   27.084   0.00  0 464 D
+ATOM     8069    C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM     8072    C   CB ?  CYS    Dxp 237 ?   38.727   27.002   28.857   0.00  0 464 D
+ATOM     8073    S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM     8074    N    N ?  PRO    Dxp 238 ?   38.989   25.529   25.691   0.00  0 465 D
+ATOM     8079    C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM     8080    C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM     8095    C   CB ?  VAL    Dxp 241 ?   39.605   21.580   27.947   0.00  0 468 D
+ATOM     8096    C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM     8097    C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM     8306    C  CD1 ?  PHE    Dxp 266 ?   43.156   16.946   28.042   0.00  0 493 D
+ATOM     8308    C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+ATOM     8310    C   CZ ?  PHE    Dxp 266 ?   42.081   17.395   30.126   0.00  0 493 D
+#

tests/reference_output/123abc_out/pocket13_vert.pqr

@@ -0,0 +1,53 @@
+ATOM      1    C STP    13      46.059  24.382  19.261    0.00     4.26
+ATOM      2    C STP    13      43.573  22.870  30.504    0.00     3.60
+ATOM      3    C STP    13      43.984  22.433  29.906    0.00     3.75
+ATOM      4    O STP    13      43.952  22.288  28.531    0.00     3.75
+ATOM      5    O STP    13      43.955  22.851  28.597    0.00     3.86
+ATOM      6    C STP    13      43.827  23.601  22.719    0.00     3.82
+ATOM      7    C STP    13      45.118  23.290  19.762    0.00     4.69
+ATOM      8    C STP    13      45.149  23.388  21.337    0.00     3.78
+ATOM      9    C STP    13      44.874  23.447  21.846    0.00     3.63
+ATOM     10    C STP    13      43.793  26.502  25.724    0.00     3.65
+ATOM     11    C STP    13      43.786  25.191  24.960    0.00     3.45
+ATOM     12    C STP    13      43.895  25.524  25.355    0.00     3.52
+ATOM     13    O STP    13      42.903  27.502  28.148    0.00     3.58
+ATOM     14    C STP    13      43.879  26.514  26.051    0.00     3.75
+ATOM     15    C STP    13      44.061  25.792  26.172    0.00     3.74
+ATOM     16    C STP    13      42.795  26.738  28.029    0.00     3.72
+ATOM     17    C STP    13      43.975  21.875  29.579    0.00     3.64
+ATOM     18    C STP    13      43.957  21.481  28.872    0.00     3.66
+ATOM     19    C STP    13      42.130  24.737  28.746    0.00     3.54
+ATOM     20    C STP    13      43.487  23.966  29.665    0.00     3.86
+ATOM     21    C STP    13      43.458  23.963  30.068    0.00     3.66
+ATOM     22    C STP    13      43.369  23.803  30.112    0.00     3.73
+ATOM     23    O STP    13      43.391  23.850  30.163    0.00     3.68
+ATOM     24    O STP    13      42.594  27.525  28.277    0.00     3.50
+ATOM     25    O STP    13      42.505  27.578  28.306    0.00     3.46
+ATOM     26    C STP    13      42.795  26.735  28.032    0.00     3.72
+ATOM     27    C STP    13      42.802  26.839  28.057    0.00     3.69
+ATOM     28    C STP    13      42.795  26.746  28.033    0.00     3.71
+ATOM     29    C STP    13      45.471  23.095  20.260    0.00     4.20
+ATOM     30    O STP    13      43.876  23.748  26.816    0.00     3.91
+ATOM     31    C STP    13      44.046  25.266  26.548    0.00     3.74
+ATOM     32    C STP    13      43.944  22.937  28.572    0.00     3.88
+ATOM     33    C STP    13      43.723  23.220  27.954    0.00     3.96
+ATOM     34    C STP    13      43.497  23.681  27.807    0.00     4.03
+ATOM     35    C STP    13      43.694  23.535  27.272    0.00     3.99
+ATOM     36    C STP    13      43.249  24.512  28.561    0.00     4.10
+ATOM     37    C STP    13      43.261  24.584  28.537    0.00     4.08
+ATOM     38    C STP    13      43.457  24.225  29.088    0.00     3.99
+ATOM     39    C STP    13      43.380  24.593  28.735    0.00     3.98
+ATOM     40    C STP    13      43.972  23.122  29.275    0.00     3.89
+ATOM     41    C STP    13      43.957  22.936  28.651    0.00     3.88
+ATOM     42    C STP    13      43.579  24.045  29.361    0.00     3.97
+ATOM     43    C STP    13      43.373  23.252  26.343    0.00     3.58
+ATOM     44    C STP    13      43.788  23.106  24.178    0.00     3.50
+ATOM     45    C STP    13      43.744  23.515  26.179    0.00     3.74
+ATOM     46    C STP    13      43.710  23.456  26.998    0.00     3.93
+ATOM     47    O STP    13      43.820  23.548  26.634    0.00     3.88
+ATOM     48    C STP    13      43.834  22.399  28.195    0.00     3.75
+ATOM     49    C STP    13      43.828  22.419  28.181    0.00     3.75
+ATOM     50    C STP    13      43.887  21.298  28.775    0.00     3.63
+ATOM     51    C STP    13      43.778  21.088  28.773    0.00     3.55
+TER
+END

tests/reference_output/123abc_out/pocket14_atm.cif

@@ -0,0 +1,55 @@
+data_pocket14_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    14:
+0  - Pocket Score                      : 0.0287
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    20
+3  - Mean alpha-sphere radius          : 3.7199
+4  - Mean alpha-sphere Solvent Acc.    : 0.5390
+5  - Mean B-factor of pocket residues  : 0.2120
+6  - Hydrophobicity Score              : -27.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.5000
+9  - Pocket volume (Monte Carlo)       : 157.1661
+10  -Pocket volume (convex hull)       : 1.4197
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     0
+14 - Proportion of apolar alpha sphere : 0.0000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3238    O    O ?  ASP    Bxp 154 ?   17.212   58.730   41.018  -2.14  0 381 B
+ATOM     3240    C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM     3255    C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM     3241    O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM     2491    O  OE1 ?  GLU    Bxp 59 ?   14.831   61.607   36.581   0.00  0 286 B
+ATOM     3242    O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM     2492    O  OE2 ?  GLU    Bxp 59 ?   15.137   61.777   38.754  -1.07  0 286 B
+ATOM     2389    N   NZ ?  LYS    Bxp 44 ?   17.801   61.554   36.438  -1.51  0 271 B
+ATOM     3254    N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM     2489    C   CG ?  GLU    Bxp 59 ?   12.912   61.584   38.000   0.00  0 286 B
+ATOM     2490    C   CD ?  GLU    Bxp 59 ?   14.404   61.663   37.759   0.00  0 286 B
+ATOM     3239    C   CB ?  ASP    Bxp 154 ?   15.520   56.620   41.941   0.00  0 381 B
+ATOM     2488    C   CB ?  GLU    Bxp 59 ?   12.087   61.638   36.697   0.00  0 286 B
+# 

tests/reference_output/123abc_out/pocket14_env_atm.cif

@@ -0,0 +1,38 @@
+data_pocket14_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     2389    N   NZ ?  LYS    Bxp 44 ?   17.801   61.554   36.438  -1.51  0 271 B
+ATOM     2454    O    O ?  GLU    Bxp 55 ?   11.608   61.345   33.284  -1.88  0 282 B
+ATOM     2485    C   CA ?  GLU    Bxp 59 ?   10.598   61.833   36.936   0.00  0 286 B
+ATOM     2488    C   CB ?  GLU    Bxp 59 ?   12.087   61.638   36.697   0.00  0 286 B
+ATOM     2489    C   CG ?  GLU    Bxp 59 ?   12.912   61.584   38.000   0.00  0 286 B
+ATOM     2490    C   CD ?  GLU    Bxp 59 ?   14.404   61.663   37.759   0.00  0 286 B
+ATOM     2491    O  OE1 ?  GLU    Bxp 59 ?   14.831   61.607   36.581   0.00  0 286 B
+ATOM     2492    O  OE2 ?  GLU    Bxp 59 ?   15.137   61.777   38.754  -1.07  0 286 B
+ATOM     3237    C    C ?  ASP    Bxp 154 ?   17.708   57.721   41.604   0.00  0 381 B
+ATOM     3238    O    O ?  ASP    Bxp 154 ?   17.212   58.730   41.018  -2.14  0 381 B
+ATOM     3239    C   CB ?  ASP    Bxp 154 ?   15.520   56.620   41.941   0.00  0 381 B
+ATOM     3240    C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM     3241    O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM     3242    O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM     3245    C    C ?  PHE    Bxp 155 ?   19.859   57.712   39.087   0.00  0 382 B
+ATOM     3246    O    O ?  PHE    Bxp 155 ?   20.558   58.316   38.318  -3.21  0 382 B
+ATOM     3254    N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM     3255    C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+#

tests/reference_output/123abc_out/pocket14_vert.pqr

@@ -0,0 +1,22 @@
+ATOM      1    O STP    14      15.638  57.796  37.788    0.00     3.71
+ATOM      2    O STP    14      15.454  57.900  37.633    0.00     3.90
+ATOM      3    O STP    14      15.381  57.358  37.454    0.00     3.78
+ATOM      4    O STP    14      15.235  57.694  37.383    0.00     4.01
+ATOM      5    O STP    14      16.323  58.738  37.710    0.00     3.43
+ATOM      6    O STP    14      15.737  57.770  37.853    0.00     3.62
+ATOM      7    O STP    14      16.292  58.564  37.614    0.00     3.53
+ATOM      8    O STP    14      16.315  58.581  37.608    0.00     3.52
+ATOM      9    O STP    14      16.316  58.585  37.615    0.00     3.52
+ATOM     10    O STP    14      13.739  57.551  37.046    0.00     4.23
+ATOM     11    O STP    14      14.038  58.408  39.176    0.00     3.57
+ATOM     12    O STP    14      15.123  57.787  37.536    0.00     3.95
+ATOM     13    O STP    14      14.177  58.373  39.077    0.00     3.55
+ATOM     14    O STP    14      15.440  57.907  37.645    0.00     3.90
+ATOM     15    O STP    14      15.908  58.512  37.786    0.00     3.49
+ATOM     16    O STP    14      14.441  58.331  38.888    0.00     3.52
+ATOM     17    O STP    14      14.088  58.418  39.234    0.00     3.55
+ATOM     18    O STP    14      14.004  58.433  39.269    0.00     3.57
+ATOM     19    O STP    14      14.203  58.428  39.237    0.00     3.51
+ATOM     20    O STP    14      13.408  57.299  36.594    0.00     4.54
+TER
+END

tests/reference_output/123abc_out/pocket15_atm.cif

@@ -0,0 +1,67 @@
+data_pocket15_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    15:
+0  - Pocket Score                      : 0.0219
+1  - Drug Score                        : 0.0431
+2  - Number of alpha spheres           :    39
+3  - Mean alpha-sphere radius          : 3.7453
+4  - Mean alpha-sphere Solvent Acc.    : 0.4087
+5  - Mean B-factor of pocket residues  : 0.1166
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 223.1380
+10  -Pocket volume (convex hull)       : 14.5929
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 33.0000
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8718
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3639    C   CA ?  ALA    Bxp 206 ?   25.485   44.511   57.685   0.00  0 433 B
+ATOM     2914    C  CD1 ?  LEU    Bxp 113 ?   26.128   47.415   60.882   0.00  0 340 B
+ATOM     3642    C   CB ?  ALA    Bxp 206 ?   24.633   43.235   57.872   0.00  0 433 B
+ATOM     3641    O    O ?  ALA    Bxp 206 ?   27.664   43.745   58.449  -4.29  0 433 B
+ATOM     2922    C  CD1 ?  LEU    Bxp 114 ?   18.369   46.670   63.743   0.00  0 341 B
+ATOM     3902    C   CD ?  PRO    Bxp 238 ?   22.462   42.067   63.671   0.00  0 465 B
+ATOM     2892    O    O ?  ALA    Bxp 110 ?   23.079   48.277   64.744  -3.21  0 337 B
+ATOM     3901    C   CG ?  PRO    Bxp 238 ?   21.818   42.336   65.023   0.00  0 465 B
+ATOM     3919    C  CG2 ?  VAL    Bxp 241 ?   18.754   43.171   62.407   0.00  0 468 B
+ATOM     2890    C   CA ?  ALA    Bxp 110 ?   25.351   47.954   65.540   0.00  0 337 B
+ATOM     3918    C  CG1 ?  VAL    Bxp 241 ?   19.352   42.826   59.944   0.00  0 468 B
+ATOM     3895    S   SG ?  CYS    Bxp 237 ?   22.468   40.332   60.148   0.00  0 464 B
+ATOM     2893    C   CB ?  ALA    Bxp 110 ?   25.301   47.008   66.740   0.00  0 337 B
+ATOM     2916    N    N ?  LEU    Bxp 114 ?   21.229   49.545   62.399  -2.19  0 341 B
+ATOM     3889    O    O ?  GLY    Bxp 236 ?   25.751   41.531   64.057   0.00  0 463 B
+ATOM     2912    C   CB ?  LEU    Bxp 113 ?   24.074   48.764   61.348   0.00  0 340 B
+ATOM     2917    C   CA ?  LEU    Bxp 114 ?   19.825   49.298   62.629   0.00  0 341 B
+ATOM     4130    C  CE1 ?  PHE    Bxp 266 ?   16.326   46.124   60.459   0.00  0 493 B
+ATOM     2948    C   CB ?  ALA    Bxp 117 ?   17.953   48.663   58.385   0.00  0 344 B
+ATOM     2910    C    C ?  LEU    Bxp 113 ?   21.785   49.807   61.241   0.00  0 340 B
+ATOM     3891    C   CA ?  CYS    Bxp 237 ?   24.487   40.444   62.093   0.00  0 464 B
+ATOM     2911    O    O ?  LEU    Bxp 113 ?   21.152   49.905   60.239   0.00  0 340 B
+ATOM     3636    C  CG2 ?  ILE    Bxp 205 ?   23.388   48.453   57.534   0.00  0 432 B
+ATOM     3602    O    O ?  LEU    Bxp 202 ?   22.353   44.476   55.620  -1.07  0 429 B
+ATOM     3606    C  CD2 ?  LEU    Bxp 202 ?   18.004   45.680   56.609   0.00  0 429 B
+# 

tests/reference_output/123abc_out/pocket15_env_atm.cif

@@ -0,0 +1,67 @@
+data_pocket15_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     2889    N    N ?  ALA    Bxp 110 ?   26.627   48.705   65.568  -4.79  0 337 B
+ATOM     2890    C   CA ?  ALA    Bxp 110 ?   25.351   47.954   65.540   0.00  0 337 B
+ATOM     2891    C    C ?  ALA    Bxp 110 ?   24.009   48.706   65.482   0.00  0 337 B
+ATOM     2892    O    O ?  ALA    Bxp 110 ?   23.079   48.277   64.744  -3.21  0 337 B
+ATOM     2893    C   CB ?  ALA    Bxp 110 ?   25.301   47.008   66.740   0.00  0 337 B
+ATOM     2909    C   CA ?  LEU    Bxp 113 ?   23.279   50.062   61.281   0.00  0 340 B
+ATOM     2910    C    C ?  LEU    Bxp 113 ?   21.785   49.807   61.241   0.00  0 340 B
+ATOM     2911    O    O ?  LEU    Bxp 113 ?   21.152   49.905   60.239   0.00  0 340 B
+ATOM     2912    C   CB ?  LEU    Bxp 113 ?   24.074   48.764   61.348   0.00  0 340 B
+ATOM     2913    C   CG ?  LEU    Bxp 113 ?   25.603   48.823   61.065   0.00  0 340 B
+ATOM     2914    C  CD1 ?  LEU    Bxp 113 ?   26.128   47.415   60.882   0.00  0 340 B
+ATOM     2916    N    N ?  LEU    Bxp 114 ?   21.229   49.545   62.399  -2.19  0 341 B
+ATOM     2917    C   CA ?  LEU    Bxp 114 ?   19.825   49.298   62.629   0.00  0 341 B
+ATOM     2920    C   CB ?  LEU    Bxp 114 ?   19.727   48.806   64.061   0.00  0 341 B
+ATOM     2921    C   CG ?  LEU    Bxp 114 ?   18.632   47.903   64.623   0.00  0 341 B
+ATOM     2922    C  CD1 ?  LEU    Bxp 114 ?   18.369   46.670   63.743   0.00  0 341 B
+ATOM     2923    C  CD2 ?  LEU    Bxp 114 ?   19.208   47.511   65.968   0.00  0 341 B
+ATOM     2948    C   CB ?  ALA    Bxp 117 ?   17.953   48.663   58.385   0.00  0 344 B
+ATOM     3600    C   CA ?  LEU    Bxp 202 ?   20.271   44.948   54.579   0.00  0 429 B
+ATOM     3601    C    C ?  LEU    Bxp 202 ?   21.600   44.222   54.708   0.00  0 429 B
+ATOM     3602    O    O ?  LEU    Bxp 202 ?   22.353   44.476   55.620  -1.07  0 429 B
+ATOM     3603    C   CB ?  LEU    Bxp 202 ?   19.212   44.020   55.190   0.00  0 429 B
+ATOM     3604    C   CG ?  LEU    Bxp 202 ?   17.876   44.597   55.580   0.00  0 429 B
+ATOM     3606    C  CD2 ?  LEU    Bxp 202 ?   18.004   45.680   56.609   0.00  0 429 B
+ATOM     3632    C    C ?  ILE    Bxp 205 ?   25.327   46.616   56.447   0.00  0 432 B
+ATOM     3634    C   CB ?  ILE    Bxp 205 ?   23.228   47.890   56.077   0.00  0 432 B
+ATOM     3636    C  CG2 ?  ILE    Bxp 205 ?   23.388   48.453   57.534   0.00  0 432 B
+ATOM     3638    N    N ?  ALA    Bxp 206 ?   24.907   45.366   56.637   0.00  0 433 B
+ATOM     3639    C   CA ?  ALA    Bxp 206 ?   25.485   44.511   57.685   0.00  0 433 B
+ATOM     3640    C    C ?  ALA    Bxp 206 ?   26.979   44.157   57.488   0.00  0 433 B
+ATOM     3641    O    O ?  ALA    Bxp 206 ?   27.664   43.745   58.449  -4.29  0 433 B
+ATOM     3642    C   CB ?  ALA    Bxp 206 ?   24.633   43.235   57.872   0.00  0 433 B
+ATOM     3888    C    C ?  GLY    Bxp 236 ?   26.369   40.695   63.407   0.00  0 463 B
+ATOM     3889    O    O ?  GLY    Bxp 236 ?   25.751   41.531   64.057   0.00  0 463 B
+ATOM     3890    N    N ?  CYS    Bxp 237 ?   25.765   39.993   62.462   0.00  0 464 B
+ATOM     3891    C   CA ?  CYS    Bxp 237 ?   24.487   40.444   62.093   0.00  0 464 B
+ATOM     3894    C   CB ?  CYS    Bxp 237 ?   24.207   40.164   60.619   0.00  0 464 B
+ATOM     3895    S   SG ?  CYS    Bxp 237 ?   22.468   40.332   60.148   0.00  0 464 B
+ATOM     3896    N    N ?  PRO    Bxp 238 ?   22.623   40.597   63.684   0.00  0 465 B
+ATOM     3901    C   CG ?  PRO    Bxp 238 ?   21.818   42.336   65.023   0.00  0 465 B
+ATOM     3902    C   CD ?  PRO    Bxp 238 ?   22.462   42.067   63.671   0.00  0 465 B
+ATOM     3917    C   CB ?  VAL    Bxp 241 ?   19.067   42.132   61.337   0.00  0 468 B
+ATOM     3918    C  CG1 ?  VAL    Bxp 241 ?   19.352   42.826   59.944   0.00  0 468 B
+ATOM     3919    C  CG2 ?  VAL    Bxp 241 ?   18.754   43.171   62.407   0.00  0 468 B
+ATOM     4128    C  CD1 ?  PHE    Bxp 266 ?   15.519   46.953   61.239   0.00  0 493 B
+ATOM     4130    C  CE1 ?  PHE    Bxp 266 ?   16.326   46.124   60.459   0.00  0 493 B
+ATOM     4132    C   CZ ?  PHE    Bxp 266 ?   15.850   45.610   59.310   0.00  0 493 B
+#

tests/reference_output/123abc_out/pocket15_vert.pqr

@@ -0,0 +1,41 @@
+ATOM      1    C STP    15      25.498  44.063  61.072    0.00     3.42
+ATOM      2    C STP    15      21.594  45.420  63.446    0.00     3.47
+ATOM      3    C STP    15      21.796  45.620  62.175    0.00     3.91
+ATOM      4    C STP    15      24.445  45.165  63.287    0.00     3.70
+ATOM      5    C STP    15      22.618  43.763  60.648    0.00     3.47
+ATOM      6    C STP    15      24.119  45.045  64.169    0.00     3.44
+ATOM      7    C STP    15      21.189  45.892  61.289    0.00     3.82
+ATOM      8    O STP    15      25.479  43.886  61.327    0.00     3.62
+ATOM      9    C STP    15      24.693  45.025  63.344    0.00     3.72
+ATOM     10    C STP    15      24.584  44.857  64.041    0.00     3.53
+ATOM     11    C STP    15      23.191  45.482  60.247    0.00     3.57
+ATOM     12    C STP    15      23.648  45.360  62.614    0.00     3.66
+ATOM     13    C STP    15      22.621  45.013  60.900    0.00     4.05
+ATOM     14    C STP    15      23.032  44.964  61.045    0.00     3.95
+ATOM     15    C STP    15      21.946  45.398  61.542    0.00     3.99
+ATOM     16    C STP    15      21.541  45.755  61.393    0.00     3.93
+ATOM     17    C STP    15      21.818  45.628  62.116    0.00     3.94
+ATOM     18    C STP    15      21.801  45.644  62.113    0.00     3.94
+ATOM     19    C STP    15      21.750  45.675  62.018    0.00     3.92
+ATOM     20    O STP    15      21.788  45.682  62.115    0.00     3.91
+ATOM     21    C STP    15      20.869  46.082  61.014    0.00     3.75
+ATOM     22    C STP    15      19.950  46.367  60.487    0.00     3.63
+ATOM     23    C STP    15      19.968  46.395  60.418    0.00     3.65
+ATOM     24    C STP    15      21.427  45.953  60.939    0.00     3.88
+ATOM     25    O STP    15      25.507  43.765  61.288    0.00     3.57
+ATOM     26    C STP    15      24.640  44.083  61.469    0.00     3.70
+ATOM     27    C STP    15      25.193  43.940  61.393    0.00     3.63
+ATOM     28    C STP    15      24.744  44.082  61.604    0.00     3.68
+ATOM     29    C STP    15      21.494  46.039  60.350    0.00     3.88
+ATOM     30    C STP    15      20.052  46.404  60.380    0.00     3.67
+ATOM     31    O STP    15      20.804  46.198  60.745    0.00     3.76
+ATOM     32    O STP    15      20.903  46.173  60.737    0.00     3.77
+ATOM     33    C STP    15      22.790  45.692  59.848    0.00     3.65
+ATOM     34    C STP    15      21.608  46.023  60.034    0.00     3.91
+ATOM     35    C STP    15      21.924  45.444  59.210    0.00     3.74
+ATOM     36    C STP    15      22.210  45.561  59.963    0.00     3.96
+ATOM     37    C STP    15      21.006  45.904  58.749    0.00     3.69
+ATOM     38    C STP    15      20.765  46.243  59.136    0.00     3.79
+ATOM     39    C STP    15      20.779  46.268  59.216    0.00     3.80
+TER
+END

tests/reference_output/123abc_out/pocket16_atm.cif

@@ -0,0 +1,63 @@
+data_pocket16_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    16:
+0  - Pocket Score                      : 0.0116
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    28
+3  - Mean alpha-sphere radius          : 3.7712
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.1225
+6  - Hydrophobicity Score              : 11.6923
+7  - Polarity Score                    :     9
+8  - Amino Acid based volume Score     : 4.5385
+9  - Pocket volume (Monte Carlo)       : 373.4439
+10  -Pocket volume (convex hull)       : 34.1542
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 6.5000
+13 - Number of apolar alpha sphere     :     8
+14 - Proportion of apolar alpha sphere : 0.2857
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7853    C   CA ?  SER    Dxp 211 ?   42.974   31.063   42.423   0.00  0 438 D
+ATOM     7600    C  CH2 ?  TRP    Dxp 178 ?   43.960   26.363   45.206   0.00  0 405 D
+ATOM     7847    O    O ?  MET    Dxp 210 ?   44.036   29.741   40.141  -1.07  0 437 D
+ATOM     7857    O   OG ?  SER    Dxp 211 ?   44.316   32.109   43.942   0.00  0 438 D
+ATOM     7598    C  CZ2 ?  TRP    Dxp 178 ?   44.202   25.607   44.069   0.00  0 405 D
+ATOM     7864    C   CD ?  PRO    Dxp 212 ?   41.974   28.366   43.102   0.00  0 439 D
+ATOM     7302    C   CB ?  ARG    Dxp 140 ?   50.864   24.591   44.728   0.00  0 367 D
+ATOM     6415    N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM     6936    N  ND2 ?  ASN    Dxp 95 ?   54.321   26.577   41.672   0.00  0 322 D
+ATOM     6952    C  CD2 ?  LEU    Dxp 97 ?   49.815   28.277   43.031   0.00  0 324 D
+ATOM     7493    O  OG1 ?  THR    Dxp 165 ?   46.860   28.337   49.111  -0.95  0 392 D
+ATOM     7307    N  NH1 ?  ARG    Dxp 140 ?   46.275   24.168   46.062   0.00  0 367 D
+ATOM     7304    C   CD ?  ARG    Dxp 140 ?   49.165   24.333   46.741   0.00  0 367 D
+ATOM     7468    C   CE ?  MET    Dxp 161 ?   51.743   26.507   49.224   0.00  0 388 D
+ATOM     6959    O  OD1 ?  ASP    Dxp 98 ?   54.141   30.867   42.252  -4.02  0 325 D
+ATOM     7806    O  OE1 ?  GLU    Dxp 204 ?   46.278   25.826   41.102  -2.14  0 431 D
+ATOM     6960    O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM     6991    N  NH2 ?  ARG    Dxp 101 ?   47.806   31.880   42.344  -2.61  0 328 D
+ATOM     6951    C  CD1 ?  LEU    Dxp 97 ?   48.963   28.362   40.622   0.00  0 324 D
+ATOM     6990    N  NH1 ?  ARG    Dxp 101 ?   49.983   32.573   42.931  -3.70  0 328 D
+ATOM     7467    S   SD ?  MET    Dxp 161 ?   50.163   27.152   49.858   0.00  0 388 D
+# 

tests/reference_output/123abc_out/pocket16_env_atm.cif

@@ -0,0 +1,65 @@
+data_pocket16_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     6412    C   CG ?  GLN    Dxp 25 ?   57.187   27.871   48.035   0.00  0 252 D
+ATOM     6413    C   CD ?  GLN    Dxp 25 ?   57.407   27.989   46.515   0.00  0 252 D
+ATOM     6415    N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM     6934    C   CG ?  ASN    Dxp 95 ?   55.423   26.157   42.216   0.00  0 322 D
+ATOM     6935    O  OD1 ?  ASN    Dxp 95 ?   56.159   26.889   42.866  -2.14  0 322 D
+ATOM     6936    N  ND2 ?  ASN    Dxp 95 ?   54.321   26.577   41.672   0.00  0 322 D
+ATOM     6949    C   CB ?  LEU    Dxp 97 ?   51.235   27.362   41.089   0.00  0 324 D
+ATOM     6950    C   CG ?  LEU    Dxp 97 ?   50.200   28.423   41.537   0.00  0 324 D
+ATOM     6951    C  CD1 ?  LEU    Dxp 97 ?   48.963   28.362   40.622   0.00  0 324 D
+ATOM     6952    C  CD2 ?  LEU    Dxp 97 ?   49.815   28.277   43.031   0.00  0 324 D
+ATOM     6958    C   CG ?  ASP    Dxp 98 ?   55.143   30.209   41.861   0.00  0 325 D
+ATOM     6959    O  OD1 ?  ASP    Dxp 98 ?   54.141   30.867   42.252  -4.02  0 325 D
+ATOM     6960    O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM     6989    C   CZ ?  ARG    Dxp 101 ?   49.039   32.250   41.984   0.00  0 328 D
+ATOM     6990    N  NH1 ?  ARG    Dxp 101 ?   49.983   32.573   42.931  -3.70  0 328 D
+ATOM     6991    N  NH2 ?  ARG    Dxp 101 ?   47.806   31.880   42.344  -2.61  0 328 D
+ATOM     7299    C   CA ?  ARG    Dxp 140 ?   51.455   23.903   43.460   0.00  0 367 D
+ATOM     7302    C   CB ?  ARG    Dxp 140 ?   50.864   24.591   44.728   0.00  0 367 D
+ATOM     7303    C   CG ?  ARG    Dxp 140 ?   49.872   23.765   45.486   0.00  0 367 D
+ATOM     7304    C   CD ?  ARG    Dxp 140 ?   49.165   24.333   46.741   0.00  0 367 D
+ATOM     7305    N   NE ?  ARG    Dxp 140 ?   48.155   23.363   47.248   0.00  0 367 D
+ATOM     7306    C   CZ ?  ARG    Dxp 140 ?   46.851   23.301   46.920   0.00  0 367 D
+ATOM     7307    N  NH1 ?  ARG    Dxp 140 ?   46.275   24.168   46.062   0.00  0 367 D
+ATOM     7466    C   CG ?  MET    Dxp 161 ?   50.568   27.737   51.524   0.00  0 388 D
+ATOM     7467    S   SD ?  MET    Dxp 161 ?   50.163   27.152   49.858   0.00  0 388 D
+ATOM     7468    C   CE ?  MET    Dxp 161 ?   51.743   26.507   49.224   0.00  0 388 D
+ATOM     7486    O  OD1 ?  ASP    Dxp 164 ?   44.010   31.506   50.068   0.00  0 391 D
+ATOM     7492    C   CB ?  THR    Dxp 165 ?   46.378   27.253   49.907   0.00  0 392 D
+ATOM     7493    O  OG1 ?  THR    Dxp 165 ?   46.860   28.337   49.111  -0.95  0 392 D
+ATOM     7494    C  CG2 ?  THR    Dxp 165 ?   46.295   26.043   49.013   0.00  0 392 D
+ATOM     7598    C  CZ2 ?  TRP    Dxp 178 ?   44.202   25.607   44.069   0.00  0 405 D
+ATOM     7599    C  CZ3 ?  TRP    Dxp 178 ?   43.261   25.813   46.311   0.00  0 405 D
+ATOM     7600    C  CH2 ?  TRP    Dxp 178 ?   43.960   26.363   45.206   0.00  0 405 D
+ATOM     7805    C   CD ?  GLU    Dxp 204 ?   45.509   25.019   40.553   0.00  0 431 D
+ATOM     7806    O  OE1 ?  GLU    Dxp 204 ?   46.278   25.826   41.102  -2.14  0 431 D
+ATOM     7843    O    O ?  GLY    Dxp 209 ?   46.861   31.370   39.639  -1.07  0 436 D
+ATOM     7846    C    C ?  MET    Dxp 210 ?   43.952   30.964   40.187   0.00  0 437 D
+ATOM     7847    O    O ?  MET    Dxp 210 ?   44.036   29.741   40.141  -1.07  0 437 D
+ATOM     7852    N    N ?  SER    Dxp 211 ?   43.574   31.652   41.258  -1.51  0 438 D
+ATOM     7853    C   CA ?  SER    Dxp 211 ?   42.974   31.063   42.423   0.00  0 438 D
+ATOM     7854    C    C ?  SER    Dxp 211 ?   41.591   30.664   42.075   0.00  0 438 D
+ATOM     7856    C   CB ?  SER    Dxp 211 ?   42.985   32.055   43.579   0.00  0 438 D
+ATOM     7857    O   OG ?  SER    Dxp 211 ?   44.316   32.109   43.942   0.00  0 438 D
+ATOM     7858    N    N ?  PRO    Dxp 212 ?   41.244   29.428   42.388   0.00  0 439 D
+ATOM     7864    C   CD ?  PRO    Dxp 212 ?   41.974   28.366   43.102   0.00  0 439 D
+#

tests/reference_output/123abc_out/pocket16_vert.pqr

@@ -0,0 +1,30 @@
+ATOM      1    O STP    16      45.737  28.840  43.225    0.00     3.64
+ATOM      2    C STP    16      45.399  28.690  43.120    0.00     3.44
+ATOM      3    C STP    16      45.409  28.722  43.141    0.00     3.45
+ATOM      4    O STP    16      52.890  27.607  44.851    0.00     3.64
+ATOM      5    O STP    16      46.687  29.229  45.260    0.00     3.96
+ATOM      6    O STP    16      47.688  27.428  45.764    0.00     3.57
+ATOM      7    O STP    16      47.345  27.600  45.596    0.00     3.62
+ATOM      8    O STP    16      52.565  29.668  46.222    0.00     4.44
+ATOM      9    C STP    16      52.572  27.916  45.719    0.00     3.87
+ATOM     10    C STP    16      50.256  27.540  46.333    0.00     3.41
+ATOM     11    C STP    16      46.342  28.344  43.550    0.00     3.51
+ATOM     12    O STP    16      45.740  28.740  43.159    0.00     3.61
+ATOM     13    O STP    16      45.872  28.831  43.221    0.00     3.70
+ATOM     14    O STP    16      53.073  28.298  44.594    0.00     3.61
+ATOM     15    O STP    16      53.061  28.327  44.518    0.00     3.57
+ATOM     16    O STP    16      53.063  28.360  44.636    0.00     3.62
+ATOM     17    O STP    16      45.887  28.838  43.215    0.00     3.70
+ATOM     18    O STP    16      46.398  28.774  42.900    0.00     3.46
+ATOM     19    O STP    16      46.389  29.033  44.284    0.00     3.73
+ATOM     20    O STP    16      46.157  28.734  43.395    0.00     3.70
+ATOM     21    O STP    16      45.895  28.832  43.234    0.00     3.71
+ATOM     22    O STP    16      46.919  29.535  45.370    0.00     3.93
+ATOM     23    O STP    16      48.488  30.553  46.122    0.00     4.06
+ATOM     24    O STP    16      47.776  32.161  46.864    0.00     4.53
+ATOM     25    O STP    16      50.088  30.509  46.900    0.00     4.47
+ATOM     26    C STP    16      51.345  30.458  46.827    0.00     4.64
+ATOM     27    C STP    16      49.231  27.875  46.510    0.00     3.55
+ATOM     28    C STP    16      50.049  27.669  46.434    0.00     3.46
+TER
+END

tests/reference_output/123abc_out/pocket17_atm.cif

@@ -0,0 +1,57 @@
+data_pocket17_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    17:
+0  - Pocket Score                      : 0.0075
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    19
+3  - Mean alpha-sphere radius          : 3.5999
+4  - Mean alpha-sphere Solvent Acc.    : 0.4164
+5  - Mean B-factor of pocket residues  : 0.1872
+6  - Hydrophobicity Score              : 12.0000
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 154.3036
+10  -Pocket volume (convex hull)       : 5.2942
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     1
+14 - Proportion of apolar alpha sphere : 0.0526
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3171    O    O ?  GLY    Bxp 145 ?   24.279   62.076   57.870   0.00  0 372 B
+ATOM     2751    C  CE1 ?  TYR    Bxp 93 ?   27.916   64.065   57.675   0.00  0 320 B
+ATOM     3181    N    N ?  ASN    Bxp 147 ?   24.353   63.017   61.460  -3.03  0 374 B
+ATOM     3189    N    N ?  HIS    Bxp 148 ?   23.808   60.293   60.791   0.00  0 375 B
+ATOM     2872    O  OE1 ?  GLU    Bxp 107 ?   31.484   58.761   62.681  -0.95  0 334 B
+ATOM     2752    C  CE2 ?  TYR    Bxp 93 ?   30.166   63.254   57.309   0.00  0 320 B
+ATOM     2873    O  OE2 ?  GLU    Bxp 107 ?   29.348   59.201   62.656  -7.90  0 334 B
+ATOM     2754    O   OH ?  TYR    Bxp 93 ?   29.703   64.823   59.044   0.00  0 320 B
+ATOM     2753    C   CZ ?  TYR    Bxp 93 ?   29.259   64.044   58.017   0.00  0 320 B
+ATOM     2837    N    N ?  ASN    Bxp 104 ?   33.994   55.404   60.098  -1.09  0 331 B
+ATOM     2835    C   CB ?  CYS    Bxp 103 ?   31.652   54.686   58.227   0.00  0 330 B
+ATOM     2832    C   CA ?  CYS    Bxp 103 ?   33.088   55.081   57.860   0.00  0 330 B
+ATOM     3198    N  NE2 ?  HIS    Bxp 148 ?   27.061   57.958   62.310   0.00  0 375 B
+ATOM     2802    O   OH ?  TYR    Bxp 99 ?   28.273   57.952   59.075  -7.50  0 326 B
+ATOM     2799    C  CE1 ?  TYR    Bxp 99 ?   29.022   58.408   56.848   0.00  0 326 B
+# 

tests/reference_output/123abc_out/pocket17_env_atm.cif

@@ -0,0 +1,54 @@
+data_pocket17_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     2748    C   CG ?  TYR    Bxp 93 ?   28.347   62.433   55.906   0.00  0 320 B
+ATOM     2749    C  CD1 ?  TYR    Bxp 93 ?   27.464   63.247   56.634   0.00  0 320 B
+ATOM     2750    C  CD2 ?  TYR    Bxp 93 ?   29.699   62.458   56.235   0.00  0 320 B
+ATOM     2751    C  CE1 ?  TYR    Bxp 93 ?   27.916   64.065   57.675   0.00  0 320 B
+ATOM     2752    C  CE2 ?  TYR    Bxp 93 ?   30.166   63.254   57.309   0.00  0 320 B
+ATOM     2753    C   CZ ?  TYR    Bxp 93 ?   29.259   64.044   58.017   0.00  0 320 B
+ATOM     2754    O   OH ?  TYR    Bxp 93 ?   29.703   64.823   59.044   0.00  0 320 B
+ATOM     2797    C  CD1 ?  TYR    Bxp 99 ?   29.075   58.066   55.512   0.00  0 326 B
+ATOM     2799    C  CE1 ?  TYR    Bxp 99 ?   29.022   58.408   56.848   0.00  0 326 B
+ATOM     2801    C   CZ ?  TYR    Bxp 99 ?   28.332   57.583   57.750   0.00  0 326 B
+ATOM     2802    O   OH ?  TYR    Bxp 99 ?   28.273   57.952   59.075  -7.50  0 326 B
+ATOM     2832    C   CA ?  CYS    Bxp 103 ?   33.088   55.081   57.860   0.00  0 330 B
+ATOM     2833    C    C ?  CYS    Bxp 103 ?   34.047   54.644   59.003   0.00  0 330 B
+ATOM     2835    C   CB ?  CYS    Bxp 103 ?   31.652   54.686   58.227   0.00  0 330 B
+ATOM     2837    N    N ?  ASN    Bxp 104 ?   33.994   55.404   60.098  -1.09  0 331 B
+ATOM     2841    C   CB ?  ASN    Bxp 104 ?   34.555   56.312   62.312   0.00  0 331 B
+ATOM     2871    C   CD ?  GLU    Bxp 107 ?   30.339   58.618   63.162   0.00  0 334 B
+ATOM     2872    O  OE1 ?  GLU    Bxp 107 ?   31.484   58.761   62.681  -0.95  0 334 B
+ATOM     2873    O  OE2 ?  GLU    Bxp 107 ?   29.348   59.201   62.656  -7.90  0 334 B
+ATOM     2880    C  CG2 ?  VAL    Bxp 108 ?   29.169   55.016   60.859   0.00  0 335 B
+ATOM     3170    C    C ?  GLY    Bxp 145 ?   23.940   63.150   57.410   0.00  0 372 B
+ATOM     3171    O    O ?  GLY    Bxp 145 ?   24.279   62.076   57.870   0.00  0 372 B
+ATOM     3173    C   CA ?  GLU    Bxp 146 ?   24.527   64.377   59.465   0.00  0 373 B
+ATOM     3174    C    C ?  GLU    Bxp 146 ?   23.693   63.539   60.431   0.00  0 373 B
+ATOM     3181    N    N ?  ASN    Bxp 147 ?   24.353   63.017   61.460  -3.03  0 374 B
+ATOM     3182    C   CA ?  ASN    Bxp 147 ?   23.727   62.121   62.392   0.00  0 374 B
+ATOM     3183    C    C ?  ASN    Bxp 147 ?   23.179   60.827   61.846   0.00  0 374 B
+ATOM     3189    N    N ?  HIS    Bxp 148 ?   23.808   60.293   60.791   0.00  0 375 B
+ATOM     3190    C   CA ?  HIS    Bxp 148 ?   23.386   59.007   60.237   0.00  0 375 B
+ATOM     3194    C   CG ?  HIS    Bxp 148 ?   24.910   57.903   61.905   0.00  0 375 B
+ATOM     3195    N  ND1 ?  HIS    Bxp 148 ?   25.150   58.412   63.173   0.00  0 375 B
+ATOM     3196    C  CD2 ?  HIS    Bxp 148 ?   26.118   57.632   61.362   0.00  0 375 B
+ATOM     3197    C  CE1 ?  HIS    Bxp 148 ?   26.449   58.390   63.404   0.00  0 375 B
+ATOM     3198    N  NE2 ?  HIS    Bxp 148 ?   27.061   57.958   62.310   0.00  0 375 B
+#

tests/reference_output/123abc_out/pocket17_vert.pqr

@@ -0,0 +1,21 @@
+ATOM      1    O STP    17      27.163  61.333  59.924    0.00     3.62
+ATOM      2    O STP    17      31.006  61.727  60.553    0.00     3.68
+ATOM      3    O STP    17      27.926  62.162  60.926    0.00     3.71
+ATOM      4    O STP    17      27.805  62.375  60.817    0.00     3.57
+ATOM      5    O STP    17      27.823  61.963  60.720    0.00     3.70
+ATOM      6    O STP    17      30.094  61.665  60.366    0.00     3.45
+ATOM      7    O STP    17      31.821  58.024  59.274    0.00     3.50
+ATOM      8    O STP    17      27.219  60.940  60.519    0.00     3.48
+ATOM      9    O STP    17      27.963  61.404  60.134    0.00     3.62
+ATOM     10    O STP    17      30.769  60.519  59.600    0.00     3.62
+ATOM     11    O STP    17      27.177  61.306  59.910    0.00     3.63
+ATOM     12    O STP    17      27.305  61.186  60.407    0.00     3.63
+ATOM     13    O STP    17      27.507  61.408  60.269    0.00     3.74
+ATOM     14    O STP    17      27.200  61.318  59.955    0.00     3.64
+ATOM     15    O STP    17      29.234  61.147  59.842    0.00     3.42
+ATOM     16    O STP    17      31.798  58.067  59.233    0.00     3.53
+ATOM     17    C STP    17      31.733  58.066  58.976    0.00     3.46
+ATOM     18    O STP    17      31.231  60.238  59.252    0.00     3.74
+ATOM     19    O STP    17      31.905  58.310  59.084    0.00     3.65
+TER
+END

tests/reference_output/123abc_out/pocket18_atm.cif

@@ -0,0 +1,65 @@
+data_pocket18_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    18:
+0  - Pocket Score                      : 0.0041
+1  - Drug Score                        : 0.0027
+2  - Number of alpha spheres           :    33
+3  - Mean alpha-sphere radius          : 3.9082
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.2780
+6  - Hydrophobicity Score              : 53.6000
+7  - Polarity Score                    :     4
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 282.9662
+10  -Pocket volume (convex hull)       : 22.1820
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 17.8947
+13 - Number of apolar alpha sphere     :    19
+14 - Proportion of apolar alpha sphere : 0.5758
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1359    O    O ?  LEU    Axp 184 ?   14.349   39.319   26.613  -1.07  0 411 A
+ATOM     3348    C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM     1363    C  CD2 ?  LEU    Axp 184 ?   17.375   37.076   23.709   0.00  0 411 A
+ATOM     3351    N    N ?  ALA    Bxp 170 ?   17.691   42.856   27.354  -6.98  0 397 B
+ATOM     3340    C   CB ?  ALA    Bxp 168 ?   22.786   43.694   28.595   0.00  0 395 B
+ATOM     1640    O    O ?  SER    Axp 219 ?   23.891   43.579   25.385  -1.07  0 446 A
+ATOM     1638    C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM     1632    O    O ?  LEU    Axp 218 ?   23.990   39.840   23.886   0.00  0 445 A
+ATOM     3339    O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM     3338    C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM     1298    C  CD1 ?  ILE    Axp 176 ?   20.379   35.378   24.896   0.00  0 403 A
+ATOM     1238    O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM     1279    C  CD1 ?  PHE    Axp 174 ?   15.732   32.610   26.953   0.00  0 401 A
+ATOM     1244    C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM     3342    C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM     1297    C  CG2 ?  ILE    Axp 176 ?   21.592   37.080   22.335   0.00  0 403 A
+ATOM     1663    C   CB ?  TYR    Axp 222 ?   18.792   43.075   23.036   0.00  0 449 A
+ATOM     1659    N    N ?  TYR    Axp 222 ?   20.759   42.581   21.578  -1.09  0 449 A
+ATOM     1362    C  CD1 ?  LEU    Axp 184 ?   17.407   38.949   21.882   0.00  0 411 A
+ATOM     1247    C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM     1357    C   CA ?  LEU    Axp 184 ?   14.567   38.323   24.463   0.00  0 411 A
+ATOM     1353    O    O ?  SER    Axp 183 ?   12.402   36.556   25.117   0.00  0 410 A
+ATOM     1360    C   CB ?  LEU    Axp 184 ?   15.704   39.018   23.710   0.00  0 411 A
+# 

tests/reference_output/123abc_out/pocket18_env_atm.cif

@@ -0,0 +1,75 @@
+data_pocket18_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1237    C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+ATOM     1238    O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM     1241    C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM     1244    C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM     1245    C   CG ?  HIS    Axp 169 ?   16.104   34.797   30.229   0.00  0 396 A
+ATOM     1246    N  ND1 ?  HIS    Axp 169 ?   14.891   34.244   30.609   0.00  0 396 A
+ATOM     1247    C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM     1248    C  CE1 ?  HIS    Axp 169 ?   14.000   35.208   30.775   0.00  0 396 A
+ATOM     1249    N  NE2 ?  HIS    Axp 169 ?   14.590   36.367   30.529   0.00  0 396 A
+ATOM     1277    C   CB ?  PHE    Axp 174 ?   17.509   31.996   25.288   0.00  0 401 A
+ATOM     1278    C   CG ?  PHE    Axp 174 ?   16.182   31.763   25.962   0.00  0 401 A
+ATOM     1279    C  CD1 ?  PHE    Axp 174 ?   15.732   32.610   26.953   0.00  0 401 A
+ATOM     1281    C  CE1 ?  PHE    Axp 174 ?   14.531   32.366   27.594   0.00  0 401 A
+ATOM     1295    C   CB ?  ILE    Axp 176 ?   21.717   35.588   22.696   0.00  0 403 A
+ATOM     1296    C  CG1 ?  ILE    Axp 176 ?   21.726   35.377   24.235   0.00  0 403 A
+ATOM     1297    C  CG2 ?  ILE    Axp 176 ?   21.592   37.080   22.335   0.00  0 403 A
+ATOM     1298    C  CD1 ?  ILE    Axp 176 ?   20.379   35.378   24.896   0.00  0 403 A
+ATOM     1352    C    C ?  SER    Axp 183 ?   12.496   37.011   23.965   0.00  0 410 A
+ATOM     1353    O    O ?  SER    Axp 183 ?   12.402   36.556   25.117   0.00  0 410 A
+ATOM     1356    N    N ?  LEU    Axp 184 ?   13.536   37.768   23.548   0.00  0 411 A
+ATOM     1357    C   CA ?  LEU    Axp 184 ?   14.567   38.323   24.463   0.00  0 411 A
+ATOM     1358    C    C ?  LEU    Axp 184 ?   13.995   39.330   25.444   0.00  0 411 A
+ATOM     1359    O    O ?  LEU    Axp 184 ?   14.349   39.319   26.613  -1.07  0 411 A
+ATOM     1360    C   CB ?  LEU    Axp 184 ?   15.704   39.018   23.710   0.00  0 411 A
+ATOM     1361    C   CG ?  LEU    Axp 184 ?   16.583   38.094   22.866   0.00  0 411 A
+ATOM     1362    C  CD1 ?  LEU    Axp 184 ?   17.407   38.949   21.882   0.00  0 411 A
+ATOM     1363    C  CD2 ?  LEU    Axp 184 ?   17.375   37.076   23.709   0.00  0 411 A
+ATOM     1387    O  OD1 ?  ASN    Axp 187 ?   11.727   35.895   28.835  -1.07  0 414 A
+ATOM     1631    C    C ?  LEU    Axp 218 ?   25.155   39.717   24.180   0.00  0 445 A
+ATOM     1632    O    O ?  LEU    Axp 218 ?   23.990   39.840   23.886   0.00  0 445 A
+ATOM     1637    N    N ?  SER    Axp 219 ?   25.769   40.519   25.023   0.00  0 446 A
+ATOM     1638    C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM     1639    C    C ?  SER    Axp 219 ?   24.704   42.744   24.987   0.00  0 446 A
+ATOM     1640    O    O ?  SER    Axp 219 ?   23.891   43.579   25.385  -1.07  0 446 A
+ATOM     1641    C   CB ?  SER    Axp 219 ?   25.796   41.724   27.105   0.00  0 446 A
+ATOM     1656    C   CB ?  VAL    Axp 221 ?   22.834   40.427   20.388   0.00  0 448 A
+ATOM     1659    N    N ?  TYR    Axp 222 ?   20.759   42.581   21.578  -1.09  0 449 A
+ATOM     1660    C   CA ?  TYR    Axp 222 ?   19.471   43.262   21.673   0.00  0 449 A
+ATOM     1663    C   CB ?  TYR    Axp 222 ?   18.792   43.075   23.036   0.00  0 449 A
+ATOM     1664    C   CG ?  TYR    Axp 222 ?   17.328   43.572   23.026   0.00  0 449 A
+ATOM     1665    C  CD1 ?  TYR    Axp 222 ?   16.254   42.671   22.864   0.00  0 449 A
+ATOM     3337    C   CA ?  ALA    Bxp 168 ?   22.105   43.779   29.982   0.00  0 395 B
+ATOM     3338    C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM     3339    O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM     3340    C   CB ?  ALA    Bxp 168 ?   22.786   43.694   28.595   0.00  0 395 B
+ATOM     3341    N    N ?  HIS    Bxp 169 ?   19.743   43.280   29.949   0.00  0 396 B
+ATOM     3342    C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM     3343    C    C ?  HIS    Bxp 169 ?   17.666   43.282   28.628   0.00  0 396 B
+ATOM     3345    C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM     3346    C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM     3348    C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM     3350    N  NE2 ?  HIS    Bxp 169 ?   14.959   39.769   29.859   0.00  0 396 B
+ATOM     3351    N    N ?  ALA    Bxp 170 ?   17.691   42.856   27.354  -6.98  0 397 B
+ATOM     3352    C   CA ?  ALA    Bxp 170 ?   16.780   43.344   26.347   0.00  0 397 B
+ATOM     3355    C   CB ?  ALA    Bxp 170 ?   15.447   42.648   26.503   0.00  0 397 B
+#

tests/reference_output/123abc_out/pocket18_vert.pqr

@@ -0,0 +1,35 @@
+ATOM      1    O STP    18      18.224  39.001  27.002    0.00     3.91
+ATOM      2    O STP    18      21.233  40.946  26.362    0.00     3.87
+ATOM      3    O STP    18      21.243  40.700  26.566    0.00     3.93
+ATOM      4    O STP    18      20.826  41.301  26.894    0.00     3.53
+ATOM      5    O STP    18      21.028  40.969  26.290    0.00     3.98
+ATOM      6    O STP    18      21.022  40.772  26.450    0.00     4.03
+ATOM      7    O STP    18      19.759  37.862  28.486    0.00     4.41
+ATOM      8    C STP    18      17.513  35.624  26.891    0.00     3.50
+ATOM      9    C STP    18      19.490  38.703  27.575    0.00     4.36
+ATOM     10    C STP    18      20.247  39.399  25.373    0.00     4.05
+ATOM     11    O STP    18      20.152  39.594  25.894    0.00     4.34
+ATOM     12    O STP    18      20.463  39.491  26.549    0.00     4.43
+ATOM     13    O STP    18      19.717  39.010  27.197    0.00     4.35
+ATOM     14    C STP    18      19.294  38.813  27.333    0.00     4.35
+ATOM     15    C STP    18      19.164  38.794  27.249    0.00     4.32
+ATOM     16    O STP    18      20.838  41.174  25.766    0.00     3.91
+ATOM     17    O STP    18      20.056  39.848  25.500    0.00     4.25
+ATOM     18    O STP    18      20.384  40.004  24.085    0.00     3.62
+ATOM     19    C STP    18      20.172  39.935  23.822    0.00     3.52
+ATOM     20    C STP    18      20.103  39.773  24.930    0.00     4.03
+ATOM     21    C STP    18      20.007  39.763  24.636    0.00     3.87
+ATOM     22    C STP    18      16.143  36.437  26.813    0.00     3.40
+ATOM     23    C STP    18      15.955  36.071  26.718    0.00     3.48
+ATOM     24    C STP    18      15.288  35.989  26.843    0.00     3.41
+ATOM     25    C STP    18      17.790  37.902  27.398    0.00     3.80
+ATOM     26    C STP    18      17.239  35.779  26.967    0.00     3.51
+ATOM     27    C STP    18      18.501  37.831  27.548    0.00     4.07
+ATOM     28    C STP    18      17.669  36.047  27.103    0.00     3.56
+ATOM     29    C STP    18      19.261  36.968  28.314    0.00     3.93
+ATOM     30    C STP    18      19.565  37.710  28.464    0.00     4.34
+ATOM     31    O STP    18      18.004  39.306  26.537    0.00     3.66
+ATOM     32    C STP    18      18.911  40.087  25.220    0.00     3.70
+ATOM     33    C STP    18      18.881  40.061  24.922    0.00     3.56
+TER
+END

tests/reference_output/123abc_out/pocket19_atm.cif

@@ -0,0 +1,74 @@
+data_pocket19_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    19:
+0  - Pocket Score                      : 0.0000
+1  - Drug Score                        : 0.0491
+2  - Number of alpha spheres           :    40
+3  - Mean alpha-sphere radius          : 3.9057
+4  - Mean alpha-sphere Solvent Acc.    : 0.5724
+5  - Mean B-factor of pocket residues  : 0.2564
+6  - Hydrophobicity Score              : 62.1111
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 4.3333
+9  - Pocket volume (Monte Carlo)       : 420.3820
+10  -Pocket volume (convex hull)       : 67.6357
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 28.1176
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8500
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7944    C   CZ ?  TYR    Dxp 222 ?   28.663   18.750   51.374   0.00  0 449 D
+ATOM     7943    C  CE2 ?  TYR    Dxp 222 ?   27.884   19.861   51.731   0.00  0 449 D
+ATOM     7945    O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM     7647    C   CB ?  ALA    Dxp 185 ?   30.355   15.757   53.617   0.00  0 412 D
+ATOM     7644    C   CA ?  ALA    Dxp 185 ?   31.641   16.003   54.405   0.00  0 412 D
+ATOM     7942    C  CE1 ?  TYR    Dxp 222 ?   29.998   18.906   51.064   0.00  0 449 D
+ATOM     7940    C  CD1 ?  TYR    Dxp 222 ?   30.563   20.141   51.099   0.00  0 449 D
+ATOM     7941    C  CD2 ?  TYR    Dxp 222 ?   28.465   21.119   51.770   0.00  0 449 D
+ATOM     7577    C  CD1 ?  ILE    Dxp 176 ?   37.672   25.382   53.690   0.00  0 403 D
+ATOM     7576    C  CG2 ?  ILE    Dxp 176 ?   36.592   24.562   50.949   0.00  0 403 D
+ATOM     7575    C  CG1 ?  ILE    Dxp 176 ?   38.212   24.231   52.898   0.00  0 403 D
+ATOM     7642    C  CD2 ?  LEU    Dxp 184 ?   36.369   20.233   52.078   0.00  0 411 D
+ATOM     7641    C  CD1 ?  LEU    Dxp 184 ?   34.448   20.808   50.650   0.00  0 411 D
+ATOM     7938    C   CB ?  TYR    Dxp 222 ?   30.486   22.638   51.402   0.00  0 449 D
+ATOM     7934    N    N ?  TYR    Dxp 222 ?   31.202   24.455   49.938  -1.09  0 449 D
+ATOM     7907    O    O ?  LEU    Dxp 218 ?   34.008   27.525   52.271  -0.40  0 445 D
+ATOM     7639    C   CB ?  LEU    Dxp 184 ?   34.244   18.838   52.215   0.00  0 411 D
+ATOM     7939    C   CG ?  TYR    Dxp 222 ?   29.832   21.273   51.448   0.00  0 449 D
+ATOM     7560    C  CE1 ?  PHE    Dxp 174 ?   39.595   17.433   56.140   0.00  0 401 D
+ATOM     7638    O    O ?  LEU    Dxp 184 ?   33.870   17.251   55.188   0.00  0 411 D
+ATOM     7525    N  ND1 ?  HIS    Dxp 169 ?   36.365   20.155   60.429  -1.93  0 396 D
+ATOM     7558    C  CD1 ?  PHE    Dxp 174 ?   39.696   18.611   55.390   0.00  0 401 D
+ATOM     7524    C   CG ?  HIS    Dxp 169 ?   36.743   21.442   60.097   0.00  0 396 D
+ATOM     7527    C  CE1 ?  HIS    Dxp 169 ?   35.170   20.180   60.996   0.00  0 396 D
+ATOM     7528    N  NE2 ?  HIS    Dxp 169 ?   34.778   21.438   61.089   0.00  0 396 D
+ATOM     7526    C  CD2 ?  HIS    Dxp 169 ?   35.750   22.249   60.547   0.00  0 396 D
+ATOM     7637    C    C ?  LEU    Dxp 184 ?   33.727   17.072   53.991   0.00  0 411 D
+ATOM     7523    C   CB ?  HIS    Dxp 169 ?   38.074   21.770   59.468   0.00  0 396 D
+ATOM     7556    C   CB ?  PHE    Dxp 174 ?   40.965   20.182   53.857   0.00  0 401 D
+ATOM     7513    C  CG2 ?  THR    Dxp 167 ?   39.795   26.405   56.782   0.00  0 394 D
+ATOM     7510    O    O ?  THR    Dxp 167 ?   41.927   23.289   56.784   0.00  0 394 D
+ATOM     7517    O    O ?  ALA    Dxp 168 ?   40.187   24.764   60.121  -3.35  0 395 D
+# 

tests/reference_output/123abc_out/pocket19_env_atm.cif

@@ -0,0 +1,69 @@
+data_pocket19_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7508    C   CA ?  THR    Dxp 167 ?   42.083   25.551   56.067   0.00  0 394 D
+ATOM     7509    C    C ?  THR    Dxp 167 ?   42.091   24.462   57.107   0.00  0 394 D
+ATOM     7510    O    O ?  THR    Dxp 167 ?   41.927   23.289   56.784   0.00  0 394 D
+ATOM     7511    C   CB ?  THR    Dxp 167 ?   40.671   25.960   55.612   0.00  0 394 D
+ATOM     7513    C  CG2 ?  THR    Dxp 167 ?   39.795   26.405   56.782   0.00  0 394 D
+ATOM     7516    C    C ?  ALA    Dxp 168 ?   40.899   23.759   59.909   0.00  0 395 D
+ATOM     7517    O    O ?  ALA    Dxp 168 ?   40.187   24.764   60.121  -3.35  0 395 D
+ATOM     7519    N    N ?  HIS    Dxp 169 ?   40.449   22.501   59.939   0.00  0 396 D
+ATOM     7520    C   CA ?  HIS    Dxp 169 ?   39.141   22.139   60.511   0.00  0 396 D
+ATOM     7523    C   CB ?  HIS    Dxp 169 ?   38.074   21.770   59.468   0.00  0 396 D
+ATOM     7524    C   CG ?  HIS    Dxp 169 ?   36.743   21.442   60.097   0.00  0 396 D
+ATOM     7525    N  ND1 ?  HIS    Dxp 169 ?   36.365   20.155   60.429  -1.93  0 396 D
+ATOM     7526    C  CD2 ?  HIS    Dxp 169 ?   35.750   22.249   60.547   0.00  0 396 D
+ATOM     7527    C  CE1 ?  HIS    Dxp 169 ?   35.170   20.180   60.996   0.00  0 396 D
+ATOM     7528    N  NE2 ?  HIS    Dxp 169 ?   34.778   21.438   61.089   0.00  0 396 D
+ATOM     7552    N    N ?  PHE    Dxp 174 ?   42.799   21.115   55.259   0.00  0 401 D
+ATOM     7553    C   CA ?  PHE    Dxp 174 ?   42.370   20.808   53.897   0.00  0 401 D
+ATOM     7555    O    O ?  PHE    Dxp 174 ?   42.090   23.093   53.386   0.00  0 401 D
+ATOM     7556    C   CB ?  PHE    Dxp 174 ?   40.965   20.182   53.857   0.00  0 401 D
+ATOM     7557    C   CG ?  PHE    Dxp 174 ?   40.847   18.885   54.646   0.00  0 401 D
+ATOM     7558    C  CD1 ?  PHE    Dxp 174 ?   39.696   18.611   55.390   0.00  0 401 D
+ATOM     7560    C  CE1 ?  PHE    Dxp 174 ?   39.595   17.433   56.140   0.00  0 401 D
+ATOM     7574    C   CB ?  ILE    Dxp 176 ?   38.063   24.490   51.381   0.00  0 403 D
+ATOM     7575    C  CG1 ?  ILE    Dxp 176 ?   38.212   24.231   52.898   0.00  0 403 D
+ATOM     7576    C  CG2 ?  ILE    Dxp 176 ?   36.592   24.562   50.949   0.00  0 403 D
+ATOM     7577    C  CD1 ?  ILE    Dxp 176 ?   37.672   25.382   53.690   0.00  0 403 D
+ATOM     7636    C   CA ?  LEU    Dxp 184 ?   34.755   17.589   52.955   0.00  0 411 D
+ATOM     7637    C    C ?  LEU    Dxp 184 ?   33.727   17.072   53.991   0.00  0 411 D
+ATOM     7638    O    O ?  LEU    Dxp 184 ?   33.870   17.251   55.188   0.00  0 411 D
+ATOM     7639    C   CB ?  LEU    Dxp 184 ?   34.244   18.838   52.215   0.00  0 411 D
+ATOM     7640    C   CG ?  LEU    Dxp 184 ?   35.197   19.678   51.329   0.00  0 411 D
+ATOM     7641    C  CD1 ?  LEU    Dxp 184 ?   34.448   20.808   50.650   0.00  0 411 D
+ATOM     7642    C  CD2 ?  LEU    Dxp 184 ?   36.369   20.233   52.078   0.00  0 411 D
+ATOM     7643    N    N ?  ALA    Dxp 185 ?   32.696   16.403   53.523   0.00  0 412 D
+ATOM     7644    C   CA ?  ALA    Dxp 185 ?   31.641   16.003   54.405   0.00  0 412 D
+ATOM     7647    C   CB ?  ALA    Dxp 185 ?   30.355   15.757   53.617   0.00  0 412 D
+ATOM     7907    O    O ?  LEU    Dxp 218 ?   34.008   27.525   52.271  -0.40  0 445 D
+ATOM     7929    C    C ?  VAL    Dxp 221 ?   31.195   25.263   48.894   0.00  0 448 D
+ATOM     7931    C   CB ?  VAL    Dxp 221 ?   33.581   26.362   48.902   0.00  0 448 D
+ATOM     7934    N    N ?  TYR    Dxp 222 ?   31.202   24.455   49.938  -1.09  0 449 D
+ATOM     7935    C   CA ?  TYR    Dxp 222 ?   30.407   23.254   49.990   0.00  0 449 D
+ATOM     7938    C   CB ?  TYR    Dxp 222 ?   30.486   22.638   51.402   0.00  0 449 D
+ATOM     7939    C   CG ?  TYR    Dxp 222 ?   29.832   21.273   51.448   0.00  0 449 D
+ATOM     7940    C  CD1 ?  TYR    Dxp 222 ?   30.563   20.141   51.099   0.00  0 449 D
+ATOM     7941    C  CD2 ?  TYR    Dxp 222 ?   28.465   21.119   51.770   0.00  0 449 D
+ATOM     7942    C  CE1 ?  TYR    Dxp 222 ?   29.998   18.906   51.064   0.00  0 449 D
+ATOM     7943    C  CE2 ?  TYR    Dxp 222 ?   27.884   19.861   51.731   0.00  0 449 D
+ATOM     7944    C   CZ ?  TYR    Dxp 222 ?   28.663   18.750   51.374   0.00  0 449 D
+ATOM     7945    O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+#

tests/reference_output/123abc_out/pocket19_vert.pqr

@@ -0,0 +1,42 @@
+ATOM      1    C STP    19      28.124  18.169  54.762    0.00     3.48
+ATOM      2    C STP    19      30.068  19.091  54.527    0.00     3.47
+ATOM      3    C STP    19      29.765  19.253  54.970    0.00     3.79
+ATOM      4    C STP    19      30.099  19.499  54.866    0.00     3.85
+ATOM      5    C STP    19      30.094  19.509  54.880    0.00     3.86
+ATOM      6    C STP    19      30.089  19.508  54.883    0.00     3.86
+ATOM      7    C STP    19      34.917  23.065  53.763    0.00     3.60
+ATOM      8    C STP    19      34.239  23.162  54.001    0.00     4.10
+ATOM      9    O STP    19      33.504  24.042  52.586    0.00     3.53
+ATOM     10    C STP    19      33.753  23.601  54.061    0.00     4.32
+ATOM     11    C STP    19      33.821  23.393  54.097    0.00     4.35
+ATOM     12    C STP    19      33.777  23.093  54.595    0.00     4.61
+ATOM     13    C STP    19      33.524  22.502  54.697    0.00     4.48
+ATOM     14    C STP    19      32.186  21.079  54.231    0.00     3.65
+ATOM     15    C STP    19      30.112  19.533  54.903    0.00     3.88
+ATOM     16    O STP    19      36.461  19.062  56.970    0.00     3.63
+ATOM     17    O STP    19      36.271  19.931  56.579    0.00     3.86
+ATOM     18    O STP    19      34.100  20.722  57.174    0.00     4.01
+ATOM     19    O STP    19      34.024  20.801  57.151    0.00     4.06
+ATOM     20    O STP    19      33.999  20.876  57.102    0.00     4.10
+ATOM     21    C STP    19      31.217  19.533  54.543    0.00     3.56
+ATOM     22    C STP    19      30.800  19.903  55.142    0.00     4.06
+ATOM     23    C STP    19      31.726  19.942  54.421    0.00     3.53
+ATOM     24    C STP    19      31.863  20.685  54.835    0.00     3.99
+ATOM     25    C STP    19      32.077  21.161  55.116    0.00     4.30
+ATOM     26    C STP    19      36.327  19.925  56.617    0.00     3.82
+ATOM     27    C STP    19      38.506  22.053  55.836    0.00     3.67
+ATOM     28    C STP    19      37.201  21.625  55.648    0.00     3.92
+ATOM     29    C STP    19      35.985  22.151  55.819    0.00     4.22
+ATOM     30    C STP    19      35.425  22.259  55.926    0.00     4.45
+ATOM     31    C STP    19      36.161  20.471  56.128    0.00     4.06
+ATOM     32    C STP    19      35.912  20.692  56.139    0.00     4.11
+ATOM     33    C STP    19      36.252  20.024  56.510    0.00     3.89
+ATOM     34    C STP    19      36.230  24.652  57.366    0.00     4.02
+ATOM     35    C STP    19      35.463  23.056  56.422    0.00     4.21
+ATOM     36    C STP    19      38.680  22.011  55.937    0.00     3.59
+ATOM     37    C STP    19      38.586  22.113  55.860    0.00     3.66
+ATOM     38    C STP    19      38.460  23.045  56.206    0.00     3.52
+ATOM     39    C STP    19      38.466  23.208  56.308    0.00     3.49
+ATOM     40    C STP    19      36.890  25.112  58.583    0.00     3.65
+TER
+END

tests/reference_output/123abc_out/pocket1_atm.cif

@@ -0,0 +1,158 @@
+data_pocket1_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket     1:
+0  - Pocket Score                      : 1.0099
+1  - Drug Score                        : 0.9898
+2  - Number of alpha spheres           :   213
+3  - Mean alpha-sphere radius          : 4.0060
+4  - Mean alpha-sphere Solvent Acc.    : 0.5026
+5  - Mean B-factor of pocket residues  : 0.1858
+6  - Hydrophobicity Score              : 39.5476
+7  - Polarity Score                    :    18
+8  - Amino Acid based volume Score     : 4.2857
+9  - Pocket volume (Monte Carlo)       : 1714.9120
+10  -Pocket volume (convex hull)       : 1610.3746
+11 - Charge Score                      :    -4
+12 - Local hydrophobic density Score   : 53.0308
+13 - Number of apolar alpha sphere     :   130
+14 - Proportion of apolar alpha sphere : 0.6103
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     5124    C  CD1 ?  LEU    Cxp 127 ?   52.412   62.880   19.111   0.00  0 354 C
+ATOM     5175    O    O ?  ILE    Cxp 133 ?   50.155   63.679   13.849  -1.07  0 360 C
+ATOM     4642    C  CD1 ?  ILE    Cxp 66 ?   57.564   64.926   16.918   0.00  0 293 C
+ATOM     5181    C   CA ?  HIS    Cxp 134 ?   49.968   61.358   15.298   0.00  0 361 C
+ATOM     5168    C  CD2 ?  PHE    Cxp 132 ?   53.775   68.288   14.726   0.00  0 359 C
+ATOM     5165    C   CB ?  PHE    Cxp 132 ?   52.152   67.148   16.265   0.00  0 359 C
+ATOM     4607    C  CG1 ?  VAL    Cxp 62 ?   56.843   66.361   13.193   0.00  0 289 C
+ATOM     5349    C  CD2 ?  PHE    Cxp 155 ?   58.617   52.809   14.766   0.00  0 382 C
+ATOM     4806    C  CG2 ?  THR    Cxp 88 ?   64.918   58.267   15.934   0.00  0 315 C
+ATOM     5351    C  CE2 ?  PHE    Cxp 155 ?   58.958   52.743   16.096   0.00  0 382 C
+ATOM     4805    O  OG1 ?  THR    Cxp 88 ?   65.292   56.165   17.041   0.00  0 315 C
+ATOM     5166    C   CG ?  PHE    Cxp 132 ?   53.337   68.020   16.020   0.00  0 359 C
+ATOM     5187    C  CD2 ?  HIS    Cxp 134 ?   52.038   58.986   17.107   0.00  0 361 C
+ATOM     5125    C  CD2 ?  LEU    Cxp 127 ?   53.933   64.923   19.034   0.00  0 354 C
+ATOM     4367    C  CG1 ?  VAL    Cxp 29 ?   65.278   51.087   12.687   0.00  0 256 C
+ATOM     4342    C   CG ?  TYR    Cxp 26 ?   60.508   48.226   13.248   0.00  0 253 C
+ATOM     4680    C  CD2 ?  LEU    Cxp 71 ?   55.947   61.004   20.573   0.00  0 298 C
+ATOM     5338    C   CB ?  ASP    Cxp 154 ?   55.209   57.618   13.892   0.00  0 381 C
+ATOM     4684    O    O ?  VAL    Cxp 72 ?   61.863   60.416   19.355  -5.36  0 299 C
+ATOM     4640    C  CG1 ?  ILE    Cxp 66 ?   58.912   65.273   17.720   0.00  0 293 C
+ATOM     4677    C   CB ?  LEU    Cxp 71 ?   58.112   61.528   21.791   0.00  0 298 C
+ATOM     5341    O  OD2 ?  ASP    Cxp 154 ?   53.714   58.561   12.241  -0.14  0 381 C
+ATOM     5183    O    O ?  HIS    Cxp 134 ?   50.262   60.307   13.190   0.00  0 361 C
+ATOM     4608    C  CG2 ?  VAL    Cxp 62 ?   57.086   66.805   10.673   0.00  0 289 C
+ATOM     4606    C   CB ?  VAL    Cxp 62 ?   57.804   66.325   11.964   0.00  0 289 C
+ATOM     4849    C  CD2 ?  TYR    Cxp 93 ?   62.771   44.062   27.626   0.00  0 320 C
+ATOM     4898    C  CE1 ?  TYR    Cxp 99 ?   58.734   44.320   28.340   0.00  0 326 C
+ATOM     4896    C  CD1 ?  TYR    Cxp 99 ?   58.352   44.217   27.023   0.00  0 326 C
+ATOM     4924    O    O ?  GLU    Cxp 102 ?   56.618   37.405   27.670  -1.21  0 329 C
+ATOM     4533    C   CB ?  GLU    Cxp 52 ?   60.007   57.267    0.138   0.00  0 279 C
+ATOM     4493    N   NZ ?  LYS    Cxp 44 ?   59.948   55.800    8.159   0.00  0 271 C
+ATOM     4492    C   CE ?  LYS    Cxp 44 ?   61.398   55.419    7.935   0.00  0 271 C
+ATOM     4565    C  CD1 ?  PHE    Cxp 56 ?   63.711   58.360    4.956   0.00  0 283 C
+ATOM     4491    C   CD ?  LYS    Cxp 44 ?   62.464   55.863    8.961   0.00  0 271 C
+ATOM     4591    O  OE2 ?  GLU    Cxp 59 ?   60.141   58.852   10.727  -1.07  0 286 C
+ATOM     4489    C   CB ?  LYS    Cxp 44 ?   64.904   55.444    9.602   0.00  0 271 C
+ATOM     4344    C  CD2 ?  TYR    Cxp 26 ?   59.377   48.648   13.987   0.00  0 253 C
+ATOM     4477    C   CB ?  ALA    Cxp 42 ?   66.815   52.711   16.102   0.00  0 269 C
+ATOM     4928    O  OE1 ?  GLU    Cxp 102 ?   58.396   38.729   22.754  -0.95  0 329 C
+ATOM     4845    O    O ?  TYR    Cxp 93 ?   60.677   45.046   23.639  -4.02  0 320 C
+ATOM     4507    C  CD1 ?  LEU    Cxp 46 ?   63.457   56.650    1.429   0.00  0 273 C
+ATOM     4614    C   CG ?  MET    Cxp 63 ?   60.952   62.629   14.053   0.00  0 290 C
+ATOM     4615    S   SD ?  MET    Cxp 63 ?   61.859   61.128   13.673   0.00  0 290 C
+ATOM     5334    N    N ?  ASP    Cxp 154 ?   56.468   56.249   15.507   0.00  0 381 C
+ATOM     4854    N    N ?  GLY    Cxp 94 ?   61.926   46.515   22.505  -1.09  0 321 C
+ATOM     4855    C   CA ?  GLY    Cxp 94 ?   61.148   46.414   21.286   0.00  0 321 C
+ATOM     4826    C   CZ ?  PHE    Cxp 90 ?   68.029   47.527   20.408   0.00  0 317 C
+ATOM     4838    O    O ?  THR    Cxp 92 ?   65.169   45.657   23.913   0.00  0 319 C
+ATOM     4858    N    N ?  ASN    Cxp 95 ?   58.837   46.563   20.532  -2.19  0 322 C
+ATOM     4864    O  OD1 ?  ASN    Cxp 95 ?   57.197   45.110   18.091  -1.07  0 322 C
+ATOM     4889    O  OD2 ?  ASP    Cxp 98 ?   56.786   42.248   18.314  -0.81  0 325 C
+ATOM     4931    C   CA ?  CYS    Cxp 103 ?   55.713   39.474   29.139   0.00  0 330 C
+ATOM     4923    C    C ?  GLU    Cxp 102 ?   55.803   38.136   27.151   0.00  0 329 C
+ATOM     5337    O    O ?  ASP    Cxp 154 ?   57.341   56.209   12.768  -1.07  0 381 C
+ATOM     4891    C   CA ?  TYR    Cxp 99 ?   56.204   43.137   24.766   0.00  0 326 C
+ATOM     4890    N    N ?  TYR    Cxp 99 ?   55.885   43.129   23.365  -2.19  0 326 C
+ATOM     4925    C   CB ?  GLU    Cxp 102 ?   56.670   38.222   24.775   0.00  0 329 C
+ATOM     4341    C   CB ?  TYR    Cxp 26 ?   60.784   48.778   11.861   0.00  0 253 C
+ATOM     4686    C  CG1 ?  VAL    Cxp 72 ?   60.468   57.953   18.334   0.00  0 299 C
+ATOM     5333    C   CB ?  ALA    Cxp 153 ?   57.973   55.244   17.737   0.00  0 380 C
+ATOM     4687    C  CG2 ?  VAL    Cxp 72 ?   62.471   56.742   19.102   0.00  0 299 C
+ATOM     4314    C  CD1 ?  LEU    Cxp 21 ?   66.372   48.924   15.249   0.00  0 248 C
+ATOM     4822    C  CD1 ?  PHE    Cxp 90 ?   68.357   49.652   19.357   0.00  0 317 C
+ATOM     4827    N    N ?  MET    Cxp 91 ?   65.600   51.395   21.975   0.00  0 318 C
+ATOM     4587    C   CB ?  GLU    Cxp 59 ?   59.660   61.810    8.754   0.00  0 286 C
+ATOM     4584    C   CA ?  GLU    Cxp 59 ?   59.760   63.312    8.983   0.00  0 286 C
+ATOM     4348    O   OH ?  TYR    Cxp 26 ?   59.736   46.661   17.066  -2.14  0 253 C
+ATOM     4335    O  OE1 ?  GLN    Cxp 25 ?   58.998   43.247   14.898  -4.69  0 252 C
+ATOM     4886    C   CB ?  ASP    Cxp 98 ?   56.203   41.956   20.500   0.00  0 325 C
+ATOM     4929    O  OE2 ?  GLU    Cxp 102 ?   57.083   38.222   21.105  -0.54  0 329 C
+ATOM     4316    N    N ?  GLY    Cxp 22 ?   64.012   43.884   14.345  -6.98  0 249 C
+ATOM     4315    C  CD2 ?  LEU    Cxp 21 ?   67.339   46.763   16.058   0.00  0 248 C
+ATOM     4312    C   CB ?  LEU    Cxp 21 ?   65.502   46.661   14.421   0.00  0 248 C
+ATOM     4893    O    O ?  TYR    Cxp 99 ?   55.173   41.873   26.595   0.00  0 326 C
+ATOM     5331    C    C ?  ALA    Cxp 153 ?   55.953   56.313   16.712   0.00  0 380 C
+ATOM     5332    O    O ?  ALA    Cxp 153 ?   54.761   56.347   16.907   0.00  0 380 C
+ATOM     4485    N    N ?  LYS    Cxp 44 ?   66.985   54.643   10.662   0.00  0 271 C
+ATOM     4317    C   CA ?  GLY    Cxp 22 ?   62.747   43.150   14.231   0.00  0 249 C
+ATOM     4343    C  CD1 ?  TYR    Cxp 26 ?   61.357   47.296   13.808   0.00  0 253 C
+ATOM     4830    O    O ?  MET    Cxp 91 ?   64.488   48.834   22.426   0.00  0 318 C
+ATOM     4824    C  CE1 ?  PHE    Cxp 90 ?   68.165   48.287   19.279   0.00  0 317 C
+ATOM     5258    C  CD1 ?  LEU    Cxp 143 ?   60.801   52.853   19.522   0.00  0 370 C
+ATOM     4810    O    O ?  GLU    Cxp 89 ?   66.226   54.641   19.567   0.00  0 316 C
+ATOM     4590    O  OE1 ?  GLU    Cxp 59 ?   60.143   59.180    8.562   0.00  0 286 C
+ATOM     4560    C   CA ?  PHE    Cxp 56 ?   61.727   61.139    4.612   0.00  0 283 C
+ATOM     4552    C    C ?  GLU    Cxp 55 ?   59.443   61.938    4.041   0.00  0 282 C
+ATOM     4553    O    O ?  GLU    Cxp 55 ?   59.074   62.152    5.210  -0.40  0 282 C
+ATOM     4559    N    N ?  PHE    Cxp 56 ?   60.677   61.556    3.690   0.00  0 283 C
+ATOM     5354    C   CA ?  GLY    Cxp 156 ?   55.185   54.289    9.070   0.00  0 383 C
+ATOM     5340    O  OD1 ?  ASP    Cxp 154 ?   54.160   56.484   12.072  -0.40  0 381 C
+ATOM     4588    C   CG ?  GLU    Cxp 59 ?   59.879   61.018   10.009   0.00  0 286 C
+ATOM     4586    O    O ?  GLU    Cxp 59 ?   60.890   64.044   10.965   0.00  0 286 C
+ATOM     4554    C   CB ?  GLU    Cxp 55 ?   57.705   60.840    2.562   0.00  0 282 C
+ATOM     5356    O    O ?  GLY    Cxp 156 ?   55.311   52.499    7.563  -3.62  0 383 C
+ATOM     5376    C   CG ?  ARG    Cxp 159 ?   54.486   53.056    3.655   0.00  0 386 C
+ATOM     5259    C  CD2 ?  LEU    Cxp 143 ?   60.391   50.436   19.544   0.00  0 370 C
+ATOM     4346    C  CE2 ?  TYR    Cxp 26 ?   59.090   48.126   15.277   0.00  0 253 C
+ATOM     4347    C   CZ ?  TYR    Cxp 26 ?   59.971   47.200   15.806   0.00  0 253 C
+ATOM     4345    C  CE1 ?  TYR    Cxp 26 ?   61.109   46.769   15.049   0.00  0 253 C
+ATOM     4790    C  CG2 ?  ILE    Cxp 86 ?   65.267   59.719   11.684   0.00  0 313 C
+ATOM     5343    C   CA ?  PHE    Cxp 155 ?   57.162   53.520   12.244   0.00  0 382 C
+ATOM     5345    O    O ?  PHE    Cxp 155 ?   57.545   52.974    9.992  -1.07  0 382 C
+ATOM     4476    O    O ?  ALA    Cxp 42 ?   68.283   54.987   14.590   0.00  0 269 C
+ATOM     4497    O    O ?  THR    Cxp 45 ?   65.625   53.907    4.664  -2.55  0 272 C
+ATOM     4368    C  CG2 ?  VAL    Cxp 29 ?   63.667   51.380   10.691   0.00  0 256 C
+ATOM     5346    C   CB ?  PHE    Cxp 155 ?   57.304   52.068   12.736   0.00  0 382 C
+ATOM     5353    N    N ?  GLY    Cxp 156 ?   55.685   54.235   10.437   0.00  0 383 C
+ATOM     5330    C   CA ?  ALA    Cxp 153 ?   56.928   56.348   17.874   0.00  0 380 C
+ATOM     5325    O    O ?  VAL    Cxp 152 ?   57.290   57.718   20.233   0.00  0 379 C
+ATOM     4589    C   CD ?  GLU    Cxp 59 ?   60.082   59.588    9.746   0.00  0 286 C
+ATOM     5339    C   CG ?  ASP    Cxp 154 ?   54.313   57.558   12.649   0.00  0 381 C
+ATOM     4787    O    O ?  ILE    Cxp 86 ?   67.579   57.024   11.540   0.00  0 313 C
+ATOM     4532    O    O ?  GLU    Cxp 52 ?   60.629   60.058    1.220  -1.07  0 279 C
+ATOM     4563    C   CB ?  PHE    Cxp 56 ?   62.803   60.407    3.827   0.00  0 283 C
+ATOM     4555    C   CG ?  GLU    Cxp 55 ?   56.341   60.714    3.218   0.00  0 282 C
+ATOM     4557    O  OE1 ?  GLU    Cxp 55 ?   54.968   62.335    4.361   0.00  0 282 C
+# 

tests/reference_output/123abc_out/pocket1_env_atm.cif

@@ -0,0 +1,233 @@
+data_pocket1_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     4309    C   CA ?  LEU    Cxp 21 ?   65.825   45.363   13.662   0.00  0 248 C
+ATOM     4310    C    C ?  LEU    Cxp 21 ?   64.536   44.614   13.361   0.00  0 248 C
+ATOM     4312    C   CB ?  LEU    Cxp 21 ?   65.502   46.661   14.421   0.00  0 248 C
+ATOM     4313    C   CG ?  LEU    Cxp 21 ?   66.698   47.490   14.883   0.00  0 248 C
+ATOM     4314    C  CD1 ?  LEU    Cxp 21 ?   66.372   48.924   15.249   0.00  0 248 C
+ATOM     4315    C  CD2 ?  LEU    Cxp 21 ?   67.339   46.763   16.058   0.00  0 248 C
+ATOM     4316    N    N ?  GLY    Cxp 22 ?   64.012   43.884   14.345  -6.98  0 249 C
+ATOM     4317    C   CA ?  GLY    Cxp 22 ?   62.747   43.150   14.231   0.00  0 249 C
+ATOM     4334    C   CD ?  GLN    Cxp 25 ?   58.140   44.074   14.570   0.00  0 252 C
+ATOM     4335    O  OE1 ?  GLN    Cxp 25 ?   58.998   43.247   14.898  -4.69  0 252 C
+ATOM     4336    N  NE2 ?  GLN    Cxp 25 ?   57.317   44.634   15.447  -3.70  0 252 C
+ATOM     4338    C   CA ?  TYR    Cxp 26 ?   60.002   48.078   10.730   0.00  0 253 C
+ATOM     4340    O    O ?  TYR    Cxp 26 ?   60.592   49.665    9.045  -3.21  0 253 C
+ATOM     4341    C   CB ?  TYR    Cxp 26 ?   60.784   48.778   11.861   0.00  0 253 C
+ATOM     4342    C   CG ?  TYR    Cxp 26 ?   60.508   48.226   13.248   0.00  0 253 C
+ATOM     4343    C  CD1 ?  TYR    Cxp 26 ?   61.357   47.296   13.808   0.00  0 253 C
+ATOM     4344    C  CD2 ?  TYR    Cxp 26 ?   59.377   48.648   13.987   0.00  0 253 C
+ATOM     4345    C  CE1 ?  TYR    Cxp 26 ?   61.109   46.769   15.049   0.00  0 253 C
+ATOM     4346    C  CE2 ?  TYR    Cxp 26 ?   59.090   48.126   15.277   0.00  0 253 C
+ATOM     4347    C   CZ ?  TYR    Cxp 26 ?   59.971   47.200   15.806   0.00  0 253 C
+ATOM     4348    O   OH ?  TYR    Cxp 26 ?   59.736   46.661   17.066  -2.14  0 253 C
+ATOM     4366    C   CB ?  VAL    Cxp 29 ?   64.687   50.461   11.321   0.00  0 256 C
+ATOM     4367    C  CG1 ?  VAL    Cxp 29 ?   65.278   51.087   12.687   0.00  0 256 C
+ATOM     4368    C  CG2 ?  VAL    Cxp 29 ?   63.667   51.380   10.691   0.00  0 256 C
+ATOM     4474    C   CA ?  ALA    Cxp 42 ?   68.331   52.880   15.676   0.00  0 269 C
+ATOM     4475    C    C ?  ALA    Cxp 42 ?   68.451   53.776   14.487   0.00  0 269 C
+ATOM     4476    O    O ?  ALA    Cxp 42 ?   68.283   54.987   14.590   0.00  0 269 C
+ATOM     4477    C   CB ?  ALA    Cxp 42 ?   66.815   52.711   16.102   0.00  0 269 C
+ATOM     4478    N    N ?  VAL    Cxp 43 ?   68.686   53.184   13.337   0.00  0 270 C
+ATOM     4479    C   CA ?  VAL    Cxp 43 ?   68.854   53.984   12.121   0.00  0 270 C
+ATOM     4480    C    C ?  VAL    Cxp 43 ?   67.829   53.673   11.024   0.00  0 270 C
+ATOM     4485    N    N ?  LYS    Cxp 44 ?   66.985   54.643   10.662   0.00  0 271 C
+ATOM     4486    C   CA ?  LYS    Cxp 44 ?   66.141   54.548    9.456   0.00  0 271 C
+ATOM     4489    C   CB ?  LYS    Cxp 44 ?   64.904   55.444    9.602   0.00  0 271 C
+ATOM     4490    C   CG ?  LYS    Cxp 44 ?   63.734   55.094    8.667   0.00  0 271 C
+ATOM     4491    C   CD ?  LYS    Cxp 44 ?   62.464   55.863    8.961   0.00  0 271 C
+ATOM     4492    C   CE ?  LYS    Cxp 44 ?   61.398   55.419    7.935   0.00  0 271 C
+ATOM     4493    N   NZ ?  LYS    Cxp 44 ?   59.948   55.800    8.159   0.00  0 271 C
+ATOM     4496    C    C ?  THR    Cxp 45 ?   66.704   54.505    4.719   0.00  0 272 C
+ATOM     4497    O    O ?  THR    Cxp 45 ?   65.625   53.907    4.664  -2.55  0 272 C
+ATOM     4505    C   CB ?  LEU    Cxp 46 ?   65.738   56.785    2.407   0.00  0 273 C
+ATOM     4507    C  CD1 ?  LEU    Cxp 46 ?   63.457   56.650    1.429   0.00  0 273 C
+ATOM     4530    C   CA ?  GLU    Cxp 52 ?   59.974   58.619   -0.607   0.00  0 279 C
+ATOM     4531    C    C ?  GLU    Cxp 52 ?   60.889   59.675    0.070   0.00  0 279 C
+ATOM     4532    O    O ?  GLU    Cxp 52 ?   60.629   60.058    1.220  -1.07  0 279 C
+ATOM     4533    C   CB ?  GLU    Cxp 52 ?   60.007   57.267    0.138   0.00  0 279 C
+ATOM     4551    C   CA ?  GLU    Cxp 55 ?   58.464   62.142    2.868   0.00  0 282 C
+ATOM     4552    C    C ?  GLU    Cxp 55 ?   59.443   61.938    4.041   0.00  0 282 C
+ATOM     4553    O    O ?  GLU    Cxp 55 ?   59.074   62.152    5.210  -0.40  0 282 C
+ATOM     4554    C   CB ?  GLU    Cxp 55 ?   57.705   60.840    2.562   0.00  0 282 C
+ATOM     4555    C   CG ?  GLU    Cxp 55 ?   56.341   60.714    3.218   0.00  0 282 C
+ATOM     4556    C   CD ?  GLU    Cxp 55 ?   55.575   62.043    3.296   0.00  0 282 C
+ATOM     4557    O  OE1 ?  GLU    Cxp 55 ?   54.968   62.335    4.361   0.00  0 282 C
+ATOM     4559    N    N ?  PHE    Cxp 56 ?   60.677   61.556    3.690   0.00  0 283 C
+ATOM     4560    C   CA ?  PHE    Cxp 56 ?   61.727   61.139    4.612   0.00  0 283 C
+ATOM     4563    C   CB ?  PHE    Cxp 56 ?   62.803   60.407    3.827   0.00  0 283 C
+ATOM     4564    C   CG ?  PHE    Cxp 56 ?   63.829   59.722    4.676   0.00  0 283 C
+ATOM     4565    C  CD1 ?  PHE    Cxp 56 ?   63.711   58.360    4.956   0.00  0 283 C
+ATOM     4567    C  CE1 ?  PHE    Cxp 56 ?   64.665   57.708    5.732   0.00  0 283 C
+ATOM     4581    O    O ?  LYS    Cxp 58 ?   59.033   65.956    8.597   0.00  0 285 C
+ATOM     4583    N    N ?  GLU    Cxp 59 ?   59.754   64.014    7.713  -1.09  0 286 C
+ATOM     4584    C   CA ?  GLU    Cxp 59 ?   59.760   63.312    8.983   0.00  0 286 C
+ATOM     4585    C    C ?  GLU    Cxp 59 ?   61.012   63.718    9.801   0.00  0 286 C
+ATOM     4586    O    O ?  GLU    Cxp 59 ?   60.890   64.044   10.965   0.00  0 286 C
+ATOM     4587    C   CB ?  GLU    Cxp 59 ?   59.660   61.810    8.754   0.00  0 286 C
+ATOM     4588    C   CG ?  GLU    Cxp 59 ?   59.879   61.018   10.009   0.00  0 286 C
+ATOM     4589    C   CD ?  GLU    Cxp 59 ?   60.082   59.588    9.746   0.00  0 286 C
+ATOM     4590    O  OE1 ?  GLU    Cxp 59 ?   60.143   59.180    8.562   0.00  0 286 C
+ATOM     4591    O  OE2 ?  GLU    Cxp 59 ?   60.141   58.852   10.727  -1.07  0 286 C
+ATOM     4604    C    C ?  VAL    Cxp 62 ?   59.706   66.684   13.538   0.00  0 289 C
+ATOM     4606    C   CB ?  VAL    Cxp 62 ?   57.804   66.325   11.964   0.00  0 289 C
+ATOM     4607    C  CG1 ?  VAL    Cxp 62 ?   56.843   66.361   13.193   0.00  0 289 C
+ATOM     4608    C  CG2 ?  VAL    Cxp 62 ?   57.086   66.805   10.673   0.00  0 289 C
+ATOM     4609    N    N ?  MET    Cxp 63 ?   60.563   65.681   13.428   0.00  0 290 C
+ATOM     4613    C   CB ?  MET    Cxp 63 ?   61.901   63.786   14.236   0.00  0 290 C
+ATOM     4614    C   CG ?  MET    Cxp 63 ?   60.952   62.629   14.053   0.00  0 290 C
+ATOM     4615    S   SD ?  MET    Cxp 63 ?   61.859   61.128   13.673   0.00  0 290 C
+ATOM     4616    C   CE ?  MET    Cxp 63 ?   61.818   61.384   11.995   0.00  0 290 C
+ATOM     4639    C   CB ?  ILE    Cxp 66 ?   58.639   66.208   18.869   0.00  0 293 C
+ATOM     4640    C  CG1 ?  ILE    Cxp 66 ?   58.912   65.273   17.720   0.00  0 293 C
+ATOM     4642    C  CD1 ?  ILE    Cxp 66 ?   57.564   64.926   16.918   0.00  0 293 C
+ATOM     4674    C   CA ?  LEU    Cxp 71 ?   58.528   60.228   22.492   0.00  0 298 C
+ATOM     4675    C    C ?  LEU    Cxp 71 ?   59.922   59.793   22.078   0.00  0 298 C
+ATOM     4677    C   CB ?  LEU    Cxp 71 ?   58.112   61.528   21.791   0.00  0 298 C
+ATOM     4678    C   CG ?  LEU    Cxp 71 ?   56.577   61.697   21.797   0.00  0 298 C
+ATOM     4680    C  CD2 ?  LEU    Cxp 71 ?   55.947   61.004   20.573   0.00  0 298 C
+ATOM     4681    N    N ?  VAL    Cxp 72 ?   60.009   58.893   21.100   0.00  0 299 C
+ATOM     4683    C    C ?  VAL    Cxp 72 ?   62.252   59.595   20.196   0.00  0 299 C
+ATOM     4684    O    O ?  VAL    Cxp 72 ?   61.863   60.416   19.355  -5.36  0 299 C
+ATOM     4685    C   CB ?  VAL    Cxp 72 ?   61.147   57.312   19.529   0.00  0 299 C
+ATOM     4686    C  CG1 ?  VAL    Cxp 72 ?   60.468   57.953   18.334   0.00  0 299 C
+ATOM     4687    C  CG2 ?  VAL    Cxp 72 ?   62.471   56.742   19.102   0.00  0 299 C
+ATOM     4786    C    C ?  ILE    Cxp 86 ?   67.749   58.236   11.640   0.00  0 313 C
+ATOM     4787    O    O ?  ILE    Cxp 86 ?   67.579   57.024   11.540   0.00  0 313 C
+ATOM     4788    C   CB ?  ILE    Cxp 86 ?   65.914   59.237   10.348   0.00  0 313 C
+ATOM     4790    C  CG2 ?  ILE    Cxp 86 ?   65.267   59.719   11.684   0.00  0 313 C
+ATOM     4800    N    N ?  THR    Cxp 88 ?   67.723   57.504   15.818   0.00  0 315 C
+ATOM     4804    C   CB ?  THR    Cxp 88 ?   65.559   57.569   17.104   0.00  0 315 C
+ATOM     4805    O  OG1 ?  THR    Cxp 88 ?   65.292   56.165   17.041   0.00  0 315 C
+ATOM     4806    C  CG2 ?  THR    Cxp 88 ?   64.918   58.267   15.934   0.00  0 315 C
+ATOM     4809    C    C ?  GLU    Cxp 89 ?   67.131   54.920   20.346   0.00  0 316 C
+ATOM     4810    O    O ?  GLU    Cxp 89 ?   66.226   54.641   19.567   0.00  0 316 C
+ATOM     4817    C   CA ?  PHE    Cxp 90 ?   67.450   52.586   20.886   0.00  0 317 C
+ATOM     4818    C    C ?  PHE    Cxp 90 ?   66.693   52.151   22.165   0.00  0 317 C
+ATOM     4820    C   CB ?  PHE    Cxp 90 ?   68.719   51.763   20.661   0.00  0 317 C
+ATOM     4821    C   CG ?  PHE    Cxp 90 ?   68.478   50.271   20.568   0.00  0 317 C
+ATOM     4822    C  CD1 ?  PHE    Cxp 90 ?   68.357   49.652   19.357   0.00  0 317 C
+ATOM     4824    C  CE1 ?  PHE    Cxp 90 ?   68.165   48.287   19.279   0.00  0 317 C
+ATOM     4825    C  CE2 ?  PHE    Cxp 90 ?   68.168   48.136   21.643   0.00  0 317 C
+ATOM     4826    C   CZ ?  PHE    Cxp 90 ?   68.029   47.527   20.408   0.00  0 317 C
+ATOM     4827    N    N ?  MET    Cxp 91 ?   65.600   51.395   21.975   0.00  0 318 C
+ATOM     4828    C   CA ?  MET    Cxp 91 ?   64.687   51.072   23.087   0.00  0 318 C
+ATOM     4829    C    C ?  MET    Cxp 91 ?   64.825   49.585   23.311   0.00  0 318 C
+ATOM     4830    O    O ?  MET    Cxp 91 ?   64.488   48.834   22.426   0.00  0 318 C
+ATOM     4831    C   CB ?  MET    Cxp 91 ?   63.247   51.450   22.726   0.00  0 318 C
+ATOM     4832    C   CG ?  MET    Cxp 91 ?   63.058   52.948   22.613   0.00  0 318 C
+ATOM     4837    C    C ?  THR    Cxp 92 ?   64.810   46.729   24.429   0.00  0 319 C
+ATOM     4838    O    O ?  THR    Cxp 92 ?   65.169   45.657   23.913   0.00  0 319 C
+ATOM     4843    C   CA ?  TYR    Cxp 93 ?   62.583   45.894   24.767   0.00  0 320 C
+ATOM     4844    C    C ?  TYR    Cxp 93 ?   61.651   45.780   23.573   0.00  0 320 C
+ATOM     4845    O    O ?  TYR    Cxp 93 ?   60.677   45.046   23.639  -4.02  0 320 C
+ATOM     4846    C   CB ?  TYR    Cxp 93 ?   61.822   45.842   26.120   0.00  0 320 C
+ATOM     4847    C   CG ?  TYR    Cxp 93 ?   62.708   45.399   27.251   0.00  0 320 C
+ATOM     4849    C  CD2 ?  TYR    Cxp 93 ?   62.771   44.062   27.626   0.00  0 320 C
+ATOM     4851    C  CE2 ?  TYR    Cxp 93 ?   63.623   43.640   28.650   0.00  0 320 C
+ATOM     4854    N    N ?  GLY    Cxp 94 ?   61.926   46.515   22.505  -1.09  0 321 C
+ATOM     4855    C   CA ?  GLY    Cxp 94 ?   61.148   46.414   21.286   0.00  0 321 C
+ATOM     4856    C    C ?  GLY    Cxp 94 ?   59.784   47.035   21.343   0.00  0 321 C
+ATOM     4858    N    N ?  ASN    Cxp 95 ?   58.837   46.563   20.532  -2.19  0 322 C
+ATOM     4861    O    O ?  ASN    Cxp 95 ?   56.724   45.626   22.065   0.00  0 322 C
+ATOM     4863    C   CG ?  ASN    Cxp 95 ?   56.450   45.916   18.682   0.00  0 322 C
+ATOM     4864    O  OD1 ?  ASN    Cxp 95 ?   57.197   45.110   18.091  -1.07  0 322 C
+ATOM     4883    C   CA ?  ASP    Cxp 98 ?   54.984   42.071   21.363   0.00  0 325 C
+ATOM     4884    C    C ?  ASP    Cxp 98 ?   55.443   42.017   22.812   0.00  0 325 C
+ATOM     4885    O    O ?  ASP    Cxp 98 ?   55.375   40.977   23.443   0.00  0 325 C
+ATOM     4886    C   CB ?  ASP    Cxp 98 ?   56.203   41.956   20.500   0.00  0 325 C
+ATOM     4887    C   CG ?  ASP    Cxp 98 ?   55.860   41.893   19.062   0.00  0 325 C
+ATOM     4889    O  OD2 ?  ASP    Cxp 98 ?   56.786   42.248   18.314  -0.81  0 325 C
+ATOM     4890    N    N ?  TYR    Cxp 99 ?   55.885   43.129   23.365  -2.19  0 326 C
+ATOM     4891    C   CA ?  TYR    Cxp 99 ?   56.204   43.137   24.766   0.00  0 326 C
+ATOM     4892    C    C ?  TYR    Cxp 99 ?   55.017   42.706   25.685   0.00  0 326 C
+ATOM     4893    O    O ?  TYR    Cxp 99 ?   55.173   41.873   26.595   0.00  0 326 C
+ATOM     4894    C   CB ?  TYR    Cxp 99 ?   56.726   44.500   25.132   0.00  0 326 C
+ATOM     4895    C   CG ?  TYR    Cxp 99 ?   57.096   44.639   26.581   0.00  0 326 C
+ATOM     4896    C  CD1 ?  TYR    Cxp 99 ?   58.352   44.217   27.023   0.00  0 326 C
+ATOM     4898    C  CE1 ?  TYR    Cxp 99 ?   58.734   44.320   28.340   0.00  0 326 C
+ATOM     4900    C   CZ ?  TYR    Cxp 99 ?   57.871   44.894   29.252   0.00  0 326 C
+ATOM     4922    C   CA ?  GLU    Cxp 102 ?   55.431   37.971   25.671   0.00  0 329 C
+ATOM     4923    C    C ?  GLU    Cxp 102 ?   55.803   38.136   27.151   0.00  0 329 C
+ATOM     4924    O    O ?  GLU    Cxp 102 ?   56.618   37.405   27.670  -1.21  0 329 C
+ATOM     4925    C   CB ?  GLU    Cxp 102 ?   56.670   38.222   24.775   0.00  0 329 C
+ATOM     4927    C   CD ?  GLU    Cxp 102 ?   57.337   38.298   22.330   0.00  0 329 C
+ATOM     4928    O  OE1 ?  GLU    Cxp 102 ?   58.396   38.729   22.754  -0.95  0 329 C
+ATOM     4929    O  OE2 ?  GLU    Cxp 102 ?   57.083   38.222   21.105  -0.54  0 329 C
+ATOM     4930    N    N ?  CYS    Cxp 103 ?   55.219   39.097   27.827   0.00  0 330 C
+ATOM     4931    C   CA ?  CYS    Cxp 103 ?   55.713   39.474   29.139   0.00  0 330 C
+ATOM     4934    C   CB ?  CYS    Cxp 103 ?   55.275   40.917   29.497   0.00  0 330 C
+ATOM     5123    C   CG ?  LEU    Cxp 127 ?   52.817   64.233   19.845   0.00  0 354 C
+ATOM     5124    C  CD1 ?  LEU    Cxp 127 ?   52.412   62.880   19.111   0.00  0 354 C
+ATOM     5125    C  CD2 ?  LEU    Cxp 127 ?   53.933   64.923   19.034   0.00  0 354 C
+ATOM     5162    C   CA ?  PHE    Cxp 132 ?   50.825   67.783   15.847   0.00  0 359 C
+ATOM     5165    C   CB ?  PHE    Cxp 132 ?   52.152   67.148   16.265   0.00  0 359 C
+ATOM     5166    C   CG ?  PHE    Cxp 132 ?   53.337   68.020   16.020   0.00  0 359 C
+ATOM     5167    C  CD1 ?  PHE    Cxp 132 ?   54.011   68.601   17.071   0.00  0 359 C
+ATOM     5168    C  CD2 ?  PHE    Cxp 132 ?   53.775   68.288   14.726   0.00  0 359 C
+ATOM     5170    C  CE2 ?  PHE    Cxp 132 ?   54.886   69.135   14.503   0.00  0 359 C
+ATOM     5172    N    N ?  ILE    Cxp 133 ?   49.469   65.974   14.990  -3.28  0 360 C
+ATOM     5174    C    C ?  ILE    Cxp 133 ?   49.338   63.641   14.747   0.00  0 360 C
+ATOM     5175    O    O ?  ILE    Cxp 133 ?   50.155   63.679   13.849  -1.07  0 360 C
+ATOM     5180    N    N ?  HIS    Cxp 134 ?   49.159   62.560   15.511   0.00  0 361 C
+ATOM     5181    C   CA ?  HIS    Cxp 134 ?   49.968   61.358   15.298   0.00  0 361 C
+ATOM     5182    C    C ?  HIS    Cxp 134 ?   49.471   60.618   14.035   0.00  0 361 C
+ATOM     5183    O    O ?  HIS    Cxp 134 ?   50.262   60.307   13.190   0.00  0 361 C
+ATOM     5184    C   CB ?  HIS    Cxp 134 ?   49.966   60.452   16.557   0.00  0 361 C
+ATOM     5185    C   CG ?  HIS    Cxp 134 ?   50.894   59.284   16.450   0.00  0 361 C
+ATOM     5186    N  ND1 ?  HIS    Cxp 134 ?   50.716   58.287   15.523   0.00  0 361 C
+ATOM     5187    C  CD2 ?  HIS    Cxp 134 ?   52.038   58.986   17.107   0.00  0 361 C
+ATOM     5188    C  CE1 ?  HIS    Cxp 134 ?   51.679   57.389   15.644   0.00  0 361 C
+ATOM     5189    N  NE2 ?  HIS    Cxp 134 ?   52.489   57.786   16.607   0.00  0 361 C
+ATOM     5257    C   CG ?  LEU    Cxp 143 ?   59.891   51.727   20.024   0.00  0 370 C
+ATOM     5258    C  CD1 ?  LEU    Cxp 143 ?   60.801   52.853   19.522   0.00  0 370 C
+ATOM     5259    C  CD2 ?  LEU    Cxp 143 ?   60.391   50.436   19.544   0.00  0 370 C
+ATOM     5324    C    C ?  VAL    Cxp 152 ?   56.357   56.927   20.160   0.00  0 379 C
+ATOM     5325    O    O ?  VAL    Cxp 152 ?   57.290   57.718   20.233   0.00  0 379 C
+ATOM     5327    C  CG1 ?  VAL    Cxp 152 ?   53.471   58.150   20.325   0.00  0 379 C
+ATOM     5329    N    N ?  ALA    Cxp 153 ?   56.140   56.186   19.075   0.00  0 380 C
+ATOM     5330    C   CA ?  ALA    Cxp 153 ?   56.928   56.348   17.874   0.00  0 380 C
+ATOM     5331    C    C ?  ALA    Cxp 153 ?   55.953   56.313   16.712   0.00  0 380 C
+ATOM     5332    O    O ?  ALA    Cxp 153 ?   54.761   56.347   16.907   0.00  0 380 C
+ATOM     5333    C   CB ?  ALA    Cxp 153 ?   57.973   55.244   17.737   0.00  0 380 C
+ATOM     5334    N    N ?  ASP    Cxp 154 ?   56.468   56.249   15.507   0.00  0 381 C
+ATOM     5335    C   CA ?  ASP    Cxp 154 ?   55.632   56.206   14.371   0.00  0 381 C
+ATOM     5336    C    C ?  ASP    Cxp 154 ?   56.487   55.557   13.330   0.00  0 381 C
+ATOM     5337    O    O ?  ASP    Cxp 154 ?   57.341   56.209   12.768  -1.07  0 381 C
+ATOM     5338    C   CB ?  ASP    Cxp 154 ?   55.209   57.618   13.892   0.00  0 381 C
+ATOM     5339    C   CG ?  ASP    Cxp 154 ?   54.313   57.558   12.649   0.00  0 381 C
+ATOM     5340    O  OD1 ?  ASP    Cxp 154 ?   54.160   56.484   12.072  -0.40  0 381 C
+ATOM     5341    O  OD2 ?  ASP    Cxp 154 ?   53.714   58.561   12.241  -0.14  0 381 C
+ATOM     5342    N    N ?  PHE    Cxp 155 ?   56.245   54.285   13.069   0.00  0 382 C
+ATOM     5343    C   CA ?  PHE    Cxp 155 ?   57.162   53.520   12.244   0.00  0 382 C
+ATOM     5344    C    C ?  PHE    Cxp 155 ?   56.801   53.559   10.785   0.00  0 382 C
+ATOM     5345    O    O ?  PHE    Cxp 155 ?   57.545   52.974    9.992  -1.07  0 382 C
+ATOM     5346    C   CB ?  PHE    Cxp 155 ?   57.304   52.068   12.736   0.00  0 382 C
+ATOM     5347    C   CG ?  PHE    Cxp 155 ?   57.674   51.960   14.215   0.00  0 382 C
+ATOM     5349    C  CD2 ?  PHE    Cxp 155 ?   58.617   52.809   14.766   0.00  0 382 C
+ATOM     5350    C  CE1 ?  PHE    Cxp 155 ?   57.402   50.907   16.384   0.00  0 382 C
+ATOM     5351    C  CE2 ?  PHE    Cxp 155 ?   58.958   52.743   16.096   0.00  0 382 C
+ATOM     5352    C   CZ ?  PHE    Cxp 155 ?   58.346   51.781   16.925   0.00  0 382 C
+ATOM     5353    N    N ?  GLY    Cxp 156 ?   55.685   54.235   10.437   0.00  0 383 C
+ATOM     5354    C   CA ?  GLY    Cxp 156 ?   55.185   54.289    9.070   0.00  0 383 C
+ATOM     5355    C    C ?  GLY    Cxp 156 ?   54.848   52.901    8.598   0.00  0 383 C
+ATOM     5356    O    O ?  GLY    Cxp 156 ?   55.311   52.499    7.563  -3.62  0 383 C
+ATOM     5376    C   CG ?  ARG    Cxp 159 ?   54.486   53.056    3.655   0.00  0 386 C
+#

tests/reference_output/123abc_out/pocket1_vert.pqr

@@ -0,0 +1,215 @@
+ATOM      1    C STP     1      54.296  62.485  15.067    0.00     4.48
+ATOM      2    C STP     1      53.679  64.691  14.007    0.00     3.67
+ATOM      3    C STP     1      54.133  63.784  14.934    0.00     4.12
+ATOM      4    C STP     1      61.690  55.737  14.834    0.00     4.25
+ATOM      5    C STP     1      54.546  64.893  15.281    0.00     3.43
+ATOM      6    C STP     1      54.389  62.279  15.091    0.00     4.52
+ATOM      7    C STP     1      54.077  63.697  15.105    0.00     4.12
+ATOM      8    C STP     1      53.180  63.771  15.741    0.00     3.57
+ATOM      9    C STP     1      54.142  63.034  15.217    0.00     4.26
+ATOM     10    C STP     1      62.704  53.958  14.486    0.00     4.25
+ATOM     11    C STP     1      62.048  51.371  14.525    0.00     3.73
+ATOM     12    C STP     1      55.310  61.466  16.498    0.00     4.15
+ATOM     13    C STP     1      55.656  61.137  16.298    0.00     4.29
+ATOM     14    C STP     1      55.364  62.203  17.313    0.00     3.52
+ATOM     15    C STP     1      58.627  61.647  18.159    0.00     3.66
+ATOM     16    C STP     1      58.630  61.653  18.171    0.00     3.66
+ATOM     17    O STP     1      53.674  61.976  14.170    0.00     3.92
+ATOM     18    O STP     1      53.283  60.958  14.623    0.00     3.41
+ATOM     19    O STP     1      54.436  62.308  14.801    0.00     4.60
+ATOM     20    C STP     1      54.458  62.208  14.919    0.00     4.59
+ATOM     21    C STP     1      54.730  61.959  15.034    0.00     4.51
+ATOM     22    C STP     1      56.035  62.015  13.884    0.00     4.47
+ATOM     23    O STP     1      54.576  62.541  14.369    0.00     4.59
+ATOM     24    C STP     1      55.268  62.665  11.079    0.00     4.54
+ATOM     25    C STP     1      60.399  40.081  27.471    0.00     4.64
+ATOM     26    C STP     1      60.256  56.336   4.114    0.00     4.09
+ATOM     27    C STP     1      61.967  55.699  13.525    0.00     4.59
+ATOM     28    C STP     1      62.491  55.187  13.517    0.00     4.61
+ATOM     29    C STP     1      62.469  55.074  13.529    0.00     4.64
+ATOM     30    C STP     1      62.405  55.187  13.547    0.00     4.64
+ATOM     31    C STP     1      61.617  51.160  14.625    0.00     3.43
+ATOM     32    C STP     1      62.890  53.449  15.078    0.00     4.12
+ATOM     33    O STP     1      60.731  41.159  25.316    0.00     4.23
+ATOM     34    C STP     1      60.369  56.193   4.060    0.00     4.08
+ATOM     35    C STP     1      56.526  61.913  13.749    0.00     4.49
+ATOM     36    C STP     1      59.228  61.669  17.140    0.00     3.66
+ATOM     37    C STP     1      58.225  59.962  13.840    0.00     3.82
+ATOM     38    C STP     1      58.383  59.740  15.095    0.00     4.00
+ATOM     39    C STP     1      56.577  61.868  13.309    0.00     4.50
+ATOM     40    O STP     1      64.749  45.269  19.945    0.00     4.01
+ATOM     41    O STP     1      60.316  43.286  19.285    0.00     3.81
+ATOM     42    C STP     1      59.437  40.350  27.729    0.00     4.08
+ATOM     43    C STP     1      58.782  40.464  27.166    0.00     3.78
+ATOM     44    O STP     1      58.413  59.616  13.998    0.00     3.78
+ATOM     45    O STP     1      58.571  59.356  14.623    0.00     3.85
+ATOM     46    O STP     1      61.734  55.916  13.763    0.00     4.51
+ATOM     47    O STP     1      61.673  55.612  13.285    0.00     4.40
+ATOM     48    O STP     1      59.591  41.663  24.657    0.00     3.70
+ATOM     49    O STP     1      59.118  42.014  23.372    0.00     3.42
+ATOM     50    C STP     1      58.856  40.429  27.000    0.00     3.82
+ATOM     51    C STP     1      58.969  40.921  25.604    0.00     3.64
+ATOM     52    C STP     1      60.504  40.078  26.704    0.00     4.68
+ATOM     53    C STP     1      61.914  51.491  13.996    0.00     3.63
+ATOM     54    C STP     1      58.474  61.214  17.627    0.00     3.89
+ATOM     55    C STP     1      58.849  61.249  17.029    0.00     3.90
+ATOM     56    C STP     1      58.470  59.733  15.331    0.00     4.02
+ATOM     57    C STP     1      57.409  60.524  16.415    0.00     4.43
+ATOM     58    C STP     1      57.636  60.564  16.144    0.00     4.43
+ATOM     59    C STP     1      58.009  60.149  15.733    0.00     4.20
+ATOM     60    O STP     1      59.256  58.684  14.851    0.00     3.76
+ATOM     61    O STP     1      59.984  56.539  15.114    0.00     3.55
+ATOM     62    C STP     1      61.255  57.042  14.329    0.00     4.18
+ATOM     63    O STP     1      60.920  57.245  14.367    0.00     4.05
+ATOM     64    O STP     1      61.257  56.840  14.305    0.00     4.25
+ATOM     65    C STP     1      61.378  56.182  14.443    0.00     4.37
+ATOM     66    C STP     1      60.443  56.146  14.980    0.00     3.81
+ATOM     67    C STP     1      61.626  55.808  14.854    0.00     4.25
+ATOM     68    C STP     1      60.572  55.993  15.133    0.00     3.75
+ATOM     69    C STP     1      61.659  55.773  14.912    0.00     4.23
+ATOM     70    C STP     1      61.701  55.581  15.331    0.00     4.02
+ATOM     71    C STP     1      61.970  56.158  15.538    0.00     3.65
+ATOM     72    C STP     1      62.880  51.138  16.182    0.00     4.24
+ATOM     73    C STP     1      64.738  50.428  18.370    0.00     3.83
+ATOM     74    C STP     1      55.726  62.535  10.776    0.00     4.48
+ATOM     75    O STP     1      60.427  43.622  19.010    0.00     3.67
+ATOM     76    O STP     1      60.640  43.211  18.915    0.00     4.02
+ATOM     77    O STP     1      60.432  43.199  18.383    0.00     3.77
+ATOM     78    O STP     1      61.132  42.829  18.728    0.00     4.40
+ATOM     79    O STP     1      59.375  40.599  19.974    0.00     3.49
+ATOM     80    O STP     1      60.687  41.851  20.492    0.00     4.48
+ATOM     81    O STP     1      59.119  42.145  22.437    0.00     3.51
+ATOM     82    O STP     1      60.244  42.521  20.463    0.00     4.08
+ATOM     83    O STP     1      59.918  42.889  20.425    0.00     3.83
+ATOM     84    O STP     1      59.857  42.923  20.619    0.00     3.78
+ATOM     85    C STP     1      63.871  45.645  18.167    0.00     4.21
+ATOM     86    C STP     1      58.457  40.874  26.114    0.00     3.47
+ATOM     87    C STP     1      58.560  40.555  27.094    0.00     3.67
+ATOM     88    C STP     1      58.600  40.535  26.911    0.00     3.69
+ATOM     89    C STP     1      55.726  60.205  16.763    0.00     3.90
+ATOM     90    C STP     1      55.429  59.788  16.648    0.00     3.51
+ATOM     91    C STP     1      55.522  59.841  17.205    0.00     3.59
+ATOM     92    O STP     1      64.164  54.829  13.465    0.00     3.98
+ATOM     93    O STP     1      64.449  55.467  13.388    0.00     3.81
+ATOM     94    O STP     1      61.577  42.827  18.579    0.00     4.51
+ATOM     95    O STP     1      62.712  44.049  18.271    0.00     4.14
+ATOM     96    C STP     1      62.606  50.707  15.883    0.00     4.18
+ATOM     97    C STP     1      62.624  50.699  15.920    0.00     4.20
+ATOM     98    C STP     1      64.183  47.712  18.496    0.00     4.10
+ATOM     99    C STP     1      63.994  47.608  18.445    0.00     4.20
+ATOM    100    C STP     1      64.557  49.531  18.617    0.00     3.87
+ATOM    101    O STP     1      64.511  49.713  18.607    0.00     3.92
+ATOM    102    C STP     1      64.330  47.013  18.788    0.00     4.07
+ATOM    103    C STP     1      64.324  46.989  18.793    0.00     4.08
+ATOM    104    O STP     1      64.629  46.018  19.959    0.00     3.75
+ATOM    105    O STP     1      64.763  45.881  20.283    0.00     3.66
+ATOM    106    O STP     1      64.198  51.696  18.543    0.00     3.72
+ATOM    107    O STP     1      63.737  53.117  17.673    0.00     3.48
+ATOM    108    C STP     1      62.888  53.149  16.179    0.00     3.95
+ATOM    109    C STP     1      62.263  54.222  16.481    0.00     3.64
+ATOM    110    O STP     1      60.044  57.879   5.099    0.00     3.70
+ATOM    111    O STP     1      59.376  58.754   5.265    0.00     3.41
+ATOM    112    O STP     1      57.036  57.538   9.418    0.00     3.62
+ATOM    113    O STP     1      59.258  58.177   4.931    0.00     3.87
+ATOM    114    O STP     1      56.555  57.916   9.364    0.00     3.89
+ATOM    115    O STP     1      56.175  58.261   8.982    0.00     4.09
+ATOM    116    O STP     1      56.971  60.087  11.935    0.00     3.61
+ATOM    117    C STP     1      57.680  60.606  13.242    0.00     3.93
+ATOM    118    C STP     1      56.740  61.689  13.060    0.00     4.43
+ATOM    119    C STP     1      57.859  62.795  12.322    0.00     3.55
+ATOM    120    C STP     1      55.742  62.532  10.790    0.00     4.47
+ATOM    121    C STP     1      55.981  62.310  11.647    0.00     4.42
+ATOM    122    C STP     1      57.240  62.441  12.628    0.00     3.98
+ATOM    123    C STP     1      56.647  61.876  13.010    0.00     4.49
+ATOM    124    C STP     1      55.615  62.473  10.815    0.00     4.58
+ATOM    125    C STP     1      55.692  62.514  10.787    0.00     4.51
+ATOM    126    C STP     1      55.601  62.471  10.776    0.00     4.58
+ATOM    127    O STP     1      58.855  58.445   5.157    0.00     3.71
+ATOM    128    O STP     1      59.246  58.150   4.917    0.00     3.89
+ATOM    129    O STP     1      59.260  58.116   4.902    0.00     3.91
+ATOM    130    O STP     1      59.304  57.953   4.838    0.00     4.01
+ATOM    131    O STP     1      56.771  55.756   5.638    0.00     4.06
+ATOM    132    C STP     1      62.014  50.449  16.085    0.00     3.82
+ATOM    133    C STP     1      62.089  50.407  16.085    0.00     3.85
+ATOM    134    C STP     1      62.238  50.427  16.051    0.00     3.95
+ATOM    135    C STP     1      62.284  50.513  16.015    0.00     4.01
+ATOM    136    C STP     1      62.334  50.534  16.009    0.00     4.04
+ATOM    137    C STP     1      62.281  50.494  16.022    0.00     4.00
+ATOM    138    C STP     1      62.616  50.670  15.982    0.00     4.21
+ATOM    139    C STP     1      62.880  51.137  16.185    0.00     4.24
+ATOM    140    C STP     1      62.880  51.227  16.245    0.00     4.21
+ATOM    141    C STP     1      64.227  50.507  18.282    0.00     4.04
+ATOM    142    C STP     1      64.086  51.042  18.373    0.00     3.92
+ATOM    143    C STP     1      63.675  48.085  18.367    0.00     4.21
+ATOM    144    O STP     1      64.235  49.820  18.536    0.00     4.02
+ATOM    145    C STP     1      62.602  48.545  17.639    0.00     3.48
+ATOM    146    C STP     1      62.261  50.406  16.067    0.00     3.95
+ATOM    147    C STP     1      62.660  50.393  16.141    0.00     4.09
+ATOM    148    O STP     1      62.477  44.597  17.343    0.00     3.44
+ATOM    149    C STP     1      63.762  45.705  18.101    0.00     4.18
+ATOM    150    O STP     1      63.504  45.449  18.088    0.00     4.09
+ATOM    151    C STP     1      63.559  48.005  18.233    0.00     4.20
+ATOM    152    C STP     1      63.517  47.997  18.233    0.00     4.18
+ATOM    153    C STP     1      63.801  46.894  18.168    0.00     4.12
+ATOM    154    C STP     1      63.796  47.427  18.198    0.00     4.19
+ATOM    155    C STP     1      63.808  47.406  18.128    0.00     4.14
+ATOM    156    C STP     1      62.638  57.564  13.119    0.00     3.69
+ATOM    157    C STP     1      62.823  56.758  12.859    0.00     4.02
+ATOM    158    C STP     1      62.926  56.692  12.845    0.00     4.00
+ATOM    159    C STP     1      60.830  54.679  12.236    0.00     3.85
+ATOM    160    O STP     1      60.357  54.480  11.330    0.00     3.46
+ATOM    161    O STP     1      60.294  54.858  11.498    0.00     3.49
+ATOM    162    O STP     1      64.687  54.612  13.716    0.00     3.72
+ATOM    163    O STP     1      64.644  54.690  13.625    0.00     3.78
+ATOM    164    C STP     1      62.240  55.114   4.449    0.00     3.60
+ATOM    165    C STP     1      60.989  53.871  11.916    0.00     3.86
+ATOM    166    C STP     1      60.863  53.715  11.601    0.00     3.76
+ATOM    167    C STP     1      61.889  51.599  13.828    0.00     3.61
+ATOM    168    C STP     1      62.462  54.839  13.402    0.00     4.56
+ATOM    169    C STP     1      60.659  52.184  12.098    0.00     3.42
+ATOM    170    C STP     1      60.653  52.908  11.838    0.00     3.57
+ATOM    171    C STP     1      60.627  52.880  11.764    0.00     3.56
+ATOM    172    C STP     1      62.579  54.842  13.546    0.00     4.62
+ATOM    173    C STP     1      62.821  54.767  13.541    0.00     4.51
+ATOM    174    C STP     1      62.631  54.651  13.677    0.00     4.55
+ATOM    175    O STP     1      56.911  57.553   9.345    0.00     3.70
+ATOM    176    O STP     1      56.910  57.554   9.344    0.00     3.70
+ATOM    177    O STP     1      56.907  57.557   9.345    0.00     3.70
+ATOM    178    O STP     1      56.508  57.712   9.497    0.00     3.69
+ATOM    179    C STP     1      57.497  60.047  17.244    0.00     3.79
+ATOM    180    C STP     1      57.398  60.498  16.430    0.00     4.42
+ATOM    181    C STP     1      57.277  60.450  16.467    0.00     4.35
+ATOM    182    C STP     1      57.453  60.392  16.373    0.00     4.35
+ATOM    183    C STP     1      57.372  60.339  16.390    0.00     4.28
+ATOM    184    O STP     1      56.718  59.674  10.781    0.00     3.52
+ATOM    185    O STP     1      56.577  58.585   9.972    0.00     3.65
+ATOM    186    O STP     1      55.933  59.755   8.811    0.00     4.26
+ATOM    187    C STP     1      56.015  59.888   9.074    0.00     4.13
+ATOM    188    O STP     1      56.420  58.276   9.445    0.00     3.90
+ATOM    189    O STP     1      56.380  58.276   9.344    0.00     3.95
+ATOM    190    O STP     1      56.570  58.289   9.751    0.00     3.74
+ATOM    191    O STP     1      56.528  58.182   9.593    0.00     3.83
+ATOM    192    O STP     1      56.704  57.935   9.478    0.00     3.77
+ATOM    193    O STP     1      56.548  58.027   9.438    0.00     3.88
+ATOM    194    O STP     1      64.829  55.574  13.463    0.00     3.66
+ATOM    195    O STP     1      64.899  55.604  13.497    0.00     3.61
+ATOM    196    O STP     1      64.864  55.561  13.476    0.00     3.64
+ATOM    197    O STP     1      64.592  55.700  13.284    0.00     3.70
+ATOM    198    C STP     1      64.367  56.538  12.911    0.00     3.53
+ATOM    199    O STP     1      59.565  57.695   4.363    0.00     4.07
+ATOM    200    C STP     1      60.203  57.869   4.101    0.00     3.64
+ATOM    201    O STP     1      59.474  57.443   4.311    0.00     4.21
+ATOM    202    O STP     1      59.553  57.581   4.404    0.00     4.17
+ATOM    203    O STP     1      59.697  57.396   4.304    0.00     4.18
+ATOM    204    O STP     1      59.674  57.526   4.382    0.00     4.16
+ATOM    205    C STP     1      57.736  56.360   4.100    0.00     4.66
+ATOM    206    C STP     1      58.013  56.612   4.148    0.00     4.53
+ATOM    207    C STP     1      56.419  56.757   5.456    0.00     4.55
+ATOM    208    O STP     1      56.291  57.906   6.692    0.00     4.47
+ATOM    209    O STP     1      58.398  57.961   5.209    0.00     3.97
+ATOM    210    O STP     1      58.417  58.508   5.352    0.00     3.71
+ATOM    211    O STP     1      55.559  59.734   8.153    0.00     4.64
+ATOM    212    O STP     1      56.404  59.954   7.276    0.00     4.03
+ATOM    213    O STP     1      56.425  59.812   7.144    0.00     4.03
+TER
+END

tests/reference_output/123abc_out/pocket20_atm.cif

@@ -0,0 +1,66 @@
+data_pocket20_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    20:
+0  - Pocket Score                      : -0.0058
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    37
+3  - Mean alpha-sphere radius          : 3.7789
+4  - Mean alpha-sphere Solvent Acc.    : 0.4544
+5  - Mean B-factor of pocket residues  : 0.2229
+6  - Hydrophobicity Score              : 11.7857
+7  - Polarity Score                    :    10
+8  - Amino Acid based volume Score     : 4.4286
+9  - Pocket volume (Monte Carlo)       : 424.2686
+10  -Pocket volume (convex hull)       : 54.0760
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 7.4000
+13 - Number of apolar alpha sphere     :    10
+14 - Proportion of apolar alpha sphere : 0.2703
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1578    C   CA ?  SER    Axp 211 ?   28.519   31.580   13.536   0.00  0 438 A
+ATOM      729    N  NH2 ?  ARG    Axp 101 ?   29.744   27.079   13.417  -2.19  0 328 A
+ATOM     1582    O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM     1531    O  OE1 ?  GLU    Axp 204 ?   23.660   27.646   12.432  -1.07  0 431 A
+ATOM     1572    O    O ?  MET    Axp 210 ?   27.392   30.484   11.286  -2.14  0 437 A
+ATOM     1589    C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM     1321    C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM     1192    C   CE ?  MET    Axp 161 ?   25.473   22.258   20.061   0.00  0 388 A
+ATOM     1193    N    N ?  THR    Axp 162 ?   27.717   23.001   24.543  -3.28  0 389 A
+ATOM     1196    O    O ?  THR    Axp 162 ?   30.318   24.681   23.653  -0.54  0 389 A
+ATOM     1190    C   CG ?  MET    Axp 161 ?   25.693   23.794   22.437   0.00  0 388 A
+ATOM     1191    S   SD ?  MET    Axp 161 ?   25.108   23.914   20.726   0.00  0 388 A
+ATOM     1214    O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM     1197    C   CB ?  THR    Axp 162 ?   30.043   22.165   24.907   0.00  0 389 A
+ATOM      728    N  NH1 ?  ARG    Axp 101 ?   30.641   25.059   14.054   0.00  0 328 A
+ATOM     1319    C  CZ2 ?  TRP    Axp 178 ?   23.312   29.778   15.389   0.00  0 405 A
+ATOM      690    C  CD2 ?  LEU    Axp 97 ?   26.615   24.712   14.130   0.00  0 324 A
+ATOM     1039    N  NH1 ?  ARG    Axp 140 ?   22.161   27.219   17.402  -2.19  0 367 A
+ATOM     1036    C   CD ?  ARG    Axp 140 ?   22.384   24.464   18.025   0.00  0 367 A
+ATOM      697    O  OD1 ?  ASP    Axp 98 ?   29.383   20.437   13.443   0.00  0 325 A
+ATOM      136    N  NE2 ?  GLN    Axp 25 ?   26.655   17.754   17.106  -1.51  0 252 A
+ATOM     1034    C   CB ?  ARG    Axp 140 ?   22.854   23.046   15.953   0.00  0 367 A
+ATOM      674    N  ND2 ?  ASN    Axp 95 ?   25.138   19.957   12.965  -2.19  0 322 A
+ATOM     1198    O  OG1 ?  THR    Axp 162 ?   29.373   20.894   24.874  -2.55  0 389 A
+# 

tests/reference_output/123abc_out/pocket20_env_atm.cif

@@ -0,0 +1,68 @@
+data_pocket20_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM      136    N  NE2 ?  GLN    Axp 25 ?   26.655   17.754   17.106  -1.51  0 252 A
+ATOM      672    C   CG ?  ASN    Axp 95 ?   24.977   18.738   13.399   0.00  0 322 A
+ATOM      673    O  OD1 ?  ASN    Axp 95 ?   25.880   18.114   13.960  -2.14  0 322 A
+ATOM      674    N  ND2 ?  ASN    Axp 95 ?   25.138   19.957   12.965  -2.19  0 322 A
+ATOM      687    C   CB ?  LEU    Axp 97 ?   25.726   23.134   12.371   0.00  0 324 A
+ATOM      688    C   CG ?  LEU    Axp 97 ?   26.663   24.325   12.667   0.00  0 324 A
+ATOM      689    C  CD1 ?  LEU    Axp 97 ?   26.439   25.580   11.708   0.00  0 324 A
+ATOM      690    C  CD2 ?  LEU    Axp 97 ?   26.615   24.712   14.130   0.00  0 324 A
+ATOM      696    C   CG ?  ASP    Axp 98 ?   28.941   19.302   13.063   0.00  0 325 A
+ATOM      697    O  OD1 ?  ASP    Axp 98 ?   29.383   20.437   13.443   0.00  0 325 A
+ATOM      698    O  OD2 ?  ASP    Axp 98 ?   28.581   18.421   13.874   0.00  0 325 A
+ATOM      727    C   CZ ?  ARG    Axp 101 ?   30.221   25.880   13.100   0.00  0 328 A
+ATOM      728    N  NH1 ?  ARG    Axp 101 ?   30.641   25.059   14.054   0.00  0 328 A
+ATOM      729    N  NH2 ?  ARG    Axp 101 ?   29.744   27.079   13.417  -2.19  0 328 A
+ATOM     1031    C   CA ?  ARG    Axp 140 ?   22.308   22.460   14.667   0.00  0 367 A
+ATOM     1034    C   CB ?  ARG    Axp 140 ?   22.854   23.046   15.953   0.00  0 367 A
+ATOM     1035    C   CG ?  ARG    Axp 140 ?   21.827   23.818   16.751   0.00  0 367 A
+ATOM     1036    C   CD ?  ARG    Axp 140 ?   22.384   24.464   18.025   0.00  0 367 A
+ATOM     1037    N   NE ?  ARG    Axp 140 ?   21.358   25.394   18.567   0.00  0 367 A
+ATOM     1038    C   CZ ?  ARG    Axp 140 ?   21.285   26.690   18.242   0.00  0 367 A
+ATOM     1039    N  NH1 ?  ARG    Axp 140 ?   22.161   27.219   17.402  -2.19  0 367 A
+ATOM     1190    C   CG ?  MET    Axp 161 ?   25.693   23.794   22.437   0.00  0 388 A
+ATOM     1191    S   SD ?  MET    Axp 161 ?   25.108   23.914   20.726   0.00  0 388 A
+ATOM     1192    C   CE ?  MET    Axp 161 ?   25.473   22.258   20.061   0.00  0 388 A
+ATOM     1193    N    N ?  THR    Axp 162 ?   27.717   23.001   24.543  -3.28  0 389 A
+ATOM     1194    C   CA ?  THR    Axp 162 ?   28.998   23.321   25.160   0.00  0 389 A
+ATOM     1195    C    C ?  THR    Axp 162 ?   29.554   24.650   24.630   0.00  0 389 A
+ATOM     1196    O    O ?  THR    Axp 162 ?   30.318   24.681   23.653  -0.54  0 389 A
+ATOM     1197    C   CB ?  THR    Axp 162 ?   30.043   22.165   24.907   0.00  0 389 A
+ATOM     1198    O  OG1 ?  THR    Axp 162 ?   29.373   20.894   24.874  -2.55  0 389 A
+ATOM     1213    C   CB ?  THR    Axp 165 ?   25.536   27.768   21.247   0.00  0 392 A
+ATOM     1214    O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM     1215    C  CG2 ?  THR    Axp 165 ?   24.206   27.716   20.463   0.00  0 392 A
+ATOM     1319    C  CZ2 ?  TRP    Axp 178 ?   23.312   29.778   15.389   0.00  0 405 A
+ATOM     1320    C  CZ3 ?  TRP    Axp 178 ?   23.462   30.785   17.625   0.00  0 405 A
+ATOM     1321    C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM     1530    C   CD ?  GLU    Axp 204 ?   22.806   28.372   11.796   0.00  0 431 A
+ATOM     1531    O  OE1 ?  GLU    Axp 204 ?   23.660   27.646   12.432  -1.07  0 431 A
+ATOM     1571    C    C ?  MET    Axp 210 ?   28.632   30.657   11.307   0.00  0 437 A
+ATOM     1572    O    O ?  MET    Axp 210 ?   27.392   30.484   11.286  -2.14  0 437 A
+ATOM     1577    N    N ?  SER    Axp 211 ?   29.277   31.096   12.377  -1.51  0 438 A
+ATOM     1578    C   CA ?  SER    Axp 211 ?   28.519   31.580   13.536   0.00  0 438 A
+ATOM     1581    C   CB ?  SER    Axp 211 ?   29.357   31.629   14.802   0.00  0 438 A
+ATOM     1582    O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM     1588    C   CG ?  PRO    Axp 212 ?   24.603   32.718   14.282   0.00  0 439 A
+ATOM     1589    C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM     8085    C   CB ?  GLU    Dxp 239 ?   33.579   23.349   24.058   0.00  0 466 D
+ATOM     8118    O  OE2 ?  GLU    Dxp 243 ?   31.919   19.332   25.048   0.00  0 470 D
+#

tests/reference_output/123abc_out/pocket20_vert.pqr

@@ -0,0 +1,39 @@
+ATOM      1    O STP    20      26.589  28.615  14.344    0.00     3.63
+ATOM      2    O STP    20      26.602  28.620  14.263    0.00     3.60
+ATOM      3    C STP    20      26.598  28.788  14.467    0.00     3.51
+ATOM      4    O STP    20      28.797  22.646  21.197    0.00     3.53
+ATOM      5    O STP    20      28.563  24.733  20.562    0.00     3.55
+ATOM      6    O STP    20      29.250  24.340  19.443    0.00     4.36
+ATOM      7    C STP    20      28.770  23.839  20.428    0.00     3.67
+ATOM      8    O STP    20      29.217  21.945  21.103    0.00     3.90
+ATOM      9    O STP    20      29.451  26.924  17.490    0.00     4.09
+ATOM     10    O STP    20      26.588  28.615  14.345    0.00     3.63
+ATOM     11    C STP    20      26.584  28.672  14.389    0.00     3.60
+ATOM     12    O STP    20      26.529  28.328  14.546    0.00     3.63
+ATOM     13    O STP    20      26.588  28.613  14.347    0.00     3.63
+ATOM     14    O STP    20      26.593  28.574  14.417    0.00     3.63
+ATOM     15    C STP    20      26.558  28.741  14.384    0.00     3.55
+ATOM     16    O STP    20      26.501  28.745  14.241    0.00     3.54
+ATOM     17    O STP    20      26.515  28.731  14.253    0.00     3.56
+ATOM     18    C STP    20      26.513  28.737  14.252    0.00     3.55
+ATOM     19    O STP    20      26.527  28.315  14.554    0.00     3.63
+ATOM     20    C STP    20      26.522  28.312  14.557    0.00     3.63
+ATOM     21    O STP    20      27.081  27.741  16.482    0.00     3.86
+ATOM     22    O STP    20      27.750  27.338  16.678    0.00     3.83
+ATOM     23    O STP    20      26.767  28.174  15.140    0.00     3.61
+ATOM     24    O STP    20      25.746  26.954  16.857    0.00     3.64
+ATOM     25    O STP    20      28.554  26.410  17.126    0.00     3.95
+ATOM     26    O STP    20      25.549  26.015  17.308    0.00     3.60
+ATOM     27    O STP    20      28.735  24.513  18.039    0.00     4.45
+ATOM     28    C STP    20      28.023  24.664  17.964    0.00     4.09
+ATOM     29    O STP    20      28.886  22.589  17.272    0.00     4.42
+ATOM     30    C STP    20      25.810  25.494  17.559    0.00     3.61
+ATOM     31    C STP    20      25.736  24.383  17.408    0.00     3.41
+ATOM     32    C STP    20      26.407  21.551  16.365    0.00     3.88
+ATOM     33    O STP    20      26.380  21.511  16.271    0.00     3.86
+ATOM     34    O STP    20      27.247  21.641  16.564    0.00     3.97
+ATOM     35    O STP    20      26.798  21.429  16.074    0.00     3.82
+ATOM     36    O STP    20      29.197  21.897  21.121    0.00     3.89
+ATOM     37    O STP    20      29.922  21.533  20.430    0.00     4.52
+TER
+END

tests/reference_output/123abc_out/pocket21_atm.cif

@@ -0,0 +1,74 @@
+data_pocket21_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    21:
+0  - Pocket Score                      : -0.0129
+1  - Drug Score                        : 0.0844
+2  - Number of alpha spheres           :    48
+3  - Mean alpha-sphere radius          : 3.7739
+4  - Mean alpha-sphere Solvent Acc.    : 0.4618
+5  - Mean B-factor of pocket residues  : 0.0755
+6  - Hydrophobicity Score              : 51.7143
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 3.8571
+9  - Pocket volume (Monte Carlo)       : 336.8528
+10  -Pocket volume (convex hull)       : 33.9441
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 32.5294
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.7083
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     5013    C  CD1 ?  LEU    Cxp 113 ?   47.637   45.537   32.420   0.00  0 340 C
+ATOM     5969    O    O ?  GLY    Cxp 236 ?   41.436   44.926   35.683  -1.88  0 463 C
+ATOM     5742    C  CE2 ?  TYR    Cxp 208 ?   47.578   41.887   31.506   0.00  0 435 C
+ATOM     5744    O   OH ?  TYR    Cxp 208 ?   49.149   42.483   33.247   0.00  0 435 C
+ATOM     5967    C   CA ?  GLY    Cxp 236 ?   40.408   42.885   35.092   0.00  0 463 C
+ATOM     5960    O    O ?  GLU    Cxp 235 ?   40.959   41.746   32.508  -6.17  0 462 C
+ATOM     5724    O    O ?  ALA    Cxp 206 ?   44.035   43.617   29.804  -4.29  0 433 C
+ATOM     4992    C   CB ?  ALA    Cxp 110 ?   46.896   45.998   37.907   0.00  0 337 C
+ATOM     4989    C   CA ?  ALA    Cxp 110 ?   48.023   46.286   36.893   0.00  0 337 C
+ATOM     4988    N    N ?  ALA    Cxp 110 ?   49.019   45.250   37.006  -1.09  0 337 C
+ATOM     5722    C   CA ?  ALA    Cxp 206 ?   44.400   45.936   29.263   0.00  0 433 C
+ATOM     5011    C   CB ?  LEU    Cxp 113 ?   48.507   47.814   32.706   0.00  0 340 C
+ATOM     5725    C   CB ?  ALA    Cxp 206 ?   43.007   46.611   29.412   0.00  0 433 C
+ATOM     5971    C   CA ?  CYS    Cxp 237 ?   40.269   46.381   33.554   0.00  0 464 C
+ATOM     5968    C    C ?  GLY    Cxp 236 ?   40.655   44.362   34.916   0.00  0 463 C
+ATOM     5009    C    C ?  LEU    Cxp 113 ?   49.262   50.208   32.866   0.00  0 340 C
+ATOM     6002    C  CG1 ?  VAL    Cxp 241 ?   41.927   51.680   31.567   0.00  0 468 C
+ATOM     5010    O    O ?  LEU    Cxp 113 ?   49.304   50.941   31.905   0.00  0 340 C
+ATOM     5982    C   CD ?  PRO    Cxp 238 ?   41.741   48.427   35.286   0.00  0 465 C
+ATOM     5975    S   SG ?  CYS    Cxp 237 ?   39.866   48.440   31.675   0.00  0 464 C
+ATOM     4991    O    O ?  ALA    Cxp 110 ?   48.119   48.581   36.365  -4.29  0 337 C
+ATOM     5021    C  CD1 ?  LEU    Cxp 114 ?   45.548   52.723   35.306   0.00  0 341 C
+ATOM     6003    C  CG2 ?  VAL    Cxp 241 ?   42.161   52.318   34.092   0.00  0 468 C
+ATOM     5981    C   CG ?  PRO    Cxp 238 ?   41.902   49.346   36.487   0.00  0 465 C
+ATOM     5015    N    N ?  LEU    Cxp 114 ?   48.853   50.629   34.038  -1.09  0 341 C
+ATOM     5016    C   CA ?  LEU    Cxp 114 ?   48.437   52.025   34.290   0.00  0 341 C
+ATOM     5047    C   CB ?  ALA    Cxp 117 ?   47.619   53.976   30.267   0.00  0 344 C
+ATOM     5689    C  CD2 ?  LEU    Cxp 202 ?   44.675   53.384   28.357   0.00  0 429 C
+ATOM     6210    C  CE1 ?  PHE    Cxp 266 ?   44.724   55.322   32.190   0.00  0 493 C
+ATOM     5719    C  CG2 ?  ILE    Cxp 205 ?   48.010   48.643   29.034   0.00  0 432 C
+ATOM     5685    O    O ?  LEU    Cxp 202 ?   43.911   49.067   27.179  -2.14  0 429 C
+ATOM     5721    N    N ?  ALA    Cxp 206 ?   45.181   46.650   28.250   0.00  0 433 C
+# 

tests/reference_output/123abc_out/pocket21_env_atm.cif

@@ -0,0 +1,76 @@
+data_pocket21_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     4981    C   CA ?  ASN    Cxp 109 ?   50.825   43.818   36.384   0.00  0 336 C
+ATOM     4982    C    C ?  ASN    Cxp 109 ?   50.104   45.124   36.248   0.00  0 336 C
+ATOM     4988    N    N ?  ALA    Cxp 110 ?   49.019   45.250   37.006  -1.09  0 337 C
+ATOM     4989    C   CA ?  ALA    Cxp 110 ?   48.023   46.286   36.893   0.00  0 337 C
+ATOM     4990    C    C ?  ALA    Cxp 110 ?   48.553   47.694   37.074   0.00  0 337 C
+ATOM     4991    O    O ?  ALA    Cxp 110 ?   48.119   48.581   36.365  -4.29  0 337 C
+ATOM     4992    C   CB ?  ALA    Cxp 110 ?   46.896   45.998   37.907   0.00  0 337 C
+ATOM     5008    C   CA ?  LEU    Cxp 113 ?   49.712   48.768   32.777   0.00  0 340 C
+ATOM     5009    C    C ?  LEU    Cxp 113 ?   49.262   50.208   32.866   0.00  0 340 C
+ATOM     5010    O    O ?  LEU    Cxp 113 ?   49.304   50.941   31.905   0.00  0 340 C
+ATOM     5011    C   CB ?  LEU    Cxp 113 ?   48.507   47.814   32.706   0.00  0 340 C
+ATOM     5012    C   CG ?  LEU    Cxp 113 ?   48.922   46.332   32.524   0.00  0 340 C
+ATOM     5013    C  CD1 ?  LEU    Cxp 113 ?   47.637   45.537   32.420   0.00  0 340 C
+ATOM     5015    N    N ?  LEU    Cxp 114 ?   48.853   50.629   34.038  -1.09  0 341 C
+ATOM     5016    C   CA ?  LEU    Cxp 114 ?   48.437   52.025   34.290   0.00  0 341 C
+ATOM     5019    C   CB ?  LEU    Cxp 114 ?   47.935   52.152   35.736   0.00  0 341 C
+ATOM     5020    C   CG ?  LEU    Cxp 114 ?   46.796   53.097   36.098   0.00  0 341 C
+ATOM     5021    C  CD1 ?  LEU    Cxp 114 ?   45.548   52.723   35.306   0.00  0 341 C
+ATOM     5047    C   CB ?  ALA    Cxp 117 ?   47.619   53.976   30.267   0.00  0 344 C
+ATOM     5683    C   CA ?  LEU    Cxp 202 ?   44.169   51.283   26.225   0.00  0 429 C
+ATOM     5684    C    C ?  LEU    Cxp 202 ?   43.587   49.854   26.305   0.00  0 429 C
+ATOM     5685    O    O ?  LEU    Cxp 202 ?   43.911   49.067   27.179  -2.14  0 429 C
+ATOM     5686    C   CB ?  LEU    Cxp 202 ?   43.118   52.210   26.812   0.00  0 429 C
+ATOM     5689    C  CD2 ?  LEU    Cxp 202 ?   44.675   53.384   28.357   0.00  0 429 C
+ATOM     5715    C    C ?  ILE    Cxp 205 ?   46.474   46.377   28.013   0.00  0 432 C
+ATOM     5717    C   CB ?  ILE    Cxp 205 ?   47.488   48.723   27.607   0.00  0 432 C
+ATOM     5719    C  CG2 ?  ILE    Cxp 205 ?   48.010   48.643   29.034   0.00  0 432 C
+ATOM     5721    N    N ?  ALA    Cxp 206 ?   45.181   46.650   28.250   0.00  0 433 C
+ATOM     5722    C   CA ?  ALA    Cxp 206 ?   44.400   45.936   29.263   0.00  0 433 C
+ATOM     5723    C    C ?  ALA    Cxp 206 ?   44.262   44.467   28.933   0.00  0 433 C
+ATOM     5724    O    O ?  ALA    Cxp 206 ?   44.035   43.617   29.804  -4.29  0 433 C
+ATOM     5725    C   CB ?  ALA    Cxp 206 ?   43.007   46.611   29.412   0.00  0 433 C
+ATOM     5740    C  CD2 ?  TYR    Cxp 208 ?   47.363   41.572   30.167   0.00  0 435 C
+ATOM     5742    C  CE2 ?  TYR    Cxp 208 ?   47.578   41.887   31.506   0.00  0 435 C
+ATOM     5743    C   CZ ?  TYR    Cxp 208 ?   48.869   42.193   31.926   0.00  0 435 C
+ATOM     5744    O   OH ?  TYR    Cxp 208 ?   49.149   42.483   33.247   0.00  0 435 C
+ATOM     5959    C    C ?  GLU    Cxp 235 ?   39.827   41.766   32.965   0.00  0 462 C
+ATOM     5960    O    O ?  GLU    Cxp 235 ?   40.959   41.746   32.508  -6.17  0 462 C
+ATOM     5966    N    N ?  GLY    Cxp 236 ?   39.492   42.242   34.155  -2.61  0 463 C
+ATOM     5967    C   CA ?  GLY    Cxp 236 ?   40.408   42.885   35.092   0.00  0 463 C
+ATOM     5968    C    C ?  GLY    Cxp 236 ?   40.655   44.362   34.916   0.00  0 463 C
+ATOM     5969    O    O ?  GLY    Cxp 236 ?   41.436   44.926   35.683  -1.88  0 463 C
+ATOM     5970    N    N ?  CYS    Cxp 237 ?   39.998   45.000   33.919   0.00  0 464 C
+ATOM     5971    C   CA ?  CYS    Cxp 237 ?   40.269   46.381   33.554   0.00  0 464 C
+ATOM     5972    C    C ?  CYS    Cxp 237 ?   39.560   47.241   34.572   0.00  0 464 C
+ATOM     5974    C   CB ?  CYS    Cxp 237 ?   39.767   46.673   32.160   0.00  0 464 C
+ATOM     5975    S   SG ?  CYS    Cxp 237 ?   39.866   48.440   31.675   0.00  0 464 C
+ATOM     5976    N    N ?  PRO    Cxp 238 ?   40.288   48.167   35.270   0.00  0 465 C
+ATOM     5981    C   CG ?  PRO    Cxp 238 ?   41.902   49.346   36.487   0.00  0 465 C
+ATOM     5982    C   CD ?  PRO    Cxp 238 ?   41.741   48.427   35.286   0.00  0 465 C
+ATOM     6001    C   CB ?  VAL    Cxp 241 ?   41.221   51.947   32.945   0.00  0 468 C
+ATOM     6002    C  CG1 ?  VAL    Cxp 241 ?   41.927   51.680   31.567   0.00  0 468 C
+ATOM     6003    C  CG2 ?  VAL    Cxp 241 ?   42.161   52.318   34.092   0.00  0 468 C
+ATOM     6208    C  CD1 ?  PHE    Cxp 266 ?   45.432   56.220   32.964   0.00  0 493 C
+ATOM     6210    C  CE1 ?  PHE    Cxp 266 ?   44.724   55.322   32.190   0.00  0 493 C
+ATOM     6212    C   CZ ?  PHE    Cxp 266 ?   44.262   55.693   30.950   0.00  0 493 C
+#

tests/reference_output/123abc_out/pocket21_vert.pqr

@@ -0,0 +1,50 @@
+ATOM      1    O STP    21      45.219  43.007  34.932    0.00     4.31
+ATOM      2    O STP    21      44.666  42.221  34.691    0.00     4.33
+ATOM      3    O STP    21      44.507  43.160  33.774    0.00     4.02
+ATOM      4    O STP    21      44.580  43.308  33.773    0.00     4.02
+ATOM      5    C STP    21      46.145  43.538  35.199    0.00     3.73
+ATOM      6    O STP    21      45.310  43.104  35.123    0.00     4.32
+ATOM      7    O STP    21      46.292  43.449  35.337    0.00     3.67
+ATOM      8    C STP    21      44.833  47.942  32.336    0.00     3.70
+ATOM      9    O STP    21      43.929  45.624  32.970    0.00     3.75
+ATOM     10    C STP    21      43.957  45.990  32.988    0.00     3.75
+ATOM     11    C STP    21      43.927  45.730  32.986    0.00     3.76
+ATOM     12    C STP    21      43.761  45.619  32.838    0.00     3.65
+ATOM     13    O STP    21      43.873  45.627  32.945    0.00     3.73
+ATOM     14    O STP    21      43.658  43.806  33.255    0.00     3.48
+ATOM     15    C STP    21      45.491  50.141  31.889    0.00     3.90
+ATOM     16    C STP    21      44.024  46.212  33.262    0.00     3.77
+ATOM     17    C STP    21      43.252  48.581  32.210    0.00     3.43
+ATOM     18    C STP    21      44.816  46.316  34.787    0.00     3.76
+ATOM     19    C STP    21      44.013  46.402  33.048    0.00     3.78
+ATOM     20    C STP    21      44.589  48.768  32.440    0.00     4.04
+ATOM     21    C STP    21      44.613  47.981  32.689    0.00     3.90
+ATOM     22    C STP    21      45.204  47.548  34.342    0.00     3.70
+ATOM     23    C STP    21      45.156  47.109  34.687    0.00     3.71
+ATOM     24    C STP    21      44.974  46.644  34.780    0.00     3.73
+ATOM     25    C STP    21      45.090  47.199  35.066    0.00     3.57
+ATOM     26    C STP    21      44.746  49.609  33.183    0.00     3.85
+ATOM     27    C STP    21      44.896  49.477  33.075    0.00     3.99
+ATOM     28    C STP    21      45.032  49.347  35.104    0.00     3.42
+ATOM     29    C STP    21      45.222  49.183  34.001    0.00     3.79
+ATOM     30    O STP    21      45.450  49.323  33.996    0.00     3.64
+ATOM     31    C STP    21      45.333  50.050  32.491    0.00     3.89
+ATOM     32    C STP    21      45.421  50.137  32.284    0.00     3.89
+ATOM     33    O STP    21      45.721  50.799  32.263    0.00     3.60
+ATOM     34    O STP    21      45.517  50.527  32.181    0.00     3.82
+ATOM     35    O STP    21      45.516  50.520  32.180    0.00     3.82
+ATOM     36    C STP    21      45.782  51.457  31.987    0.00     3.56
+ATOM     37    C STP    21      45.608  51.301  31.876    0.00     3.71
+ATOM     38    C STP    21      45.601  50.842  31.034    0.00     3.81
+ATOM     39    C STP    21      45.371  51.921  31.933    0.00     3.47
+ATOM     40    C STP    21      45.496  50.082  31.662    0.00     3.91
+ATOM     41    C STP    21      45.623  50.837  31.001    0.00     3.79
+ATOM     42    C STP    21      45.599  50.823  31.022    0.00     3.81
+ATOM     43    C STP    21      45.026  49.245  31.537    0.00     3.94
+ATOM     44    C STP    21      45.099  50.376  30.357    0.00     3.64
+ATOM     45    C STP    21      45.177  48.853  31.428    0.00     3.71
+ATOM     46    C STP    21      45.124  48.874  30.833    0.00     3.41
+ATOM     47    C STP    21      44.843  49.547  30.735    0.00     3.71
+ATOM     48    O STP    21      44.930  49.287  30.483    0.00     3.46
+TER
+END

tests/reference_output/123abc_out/pocket22_atm.cif

@@ -0,0 +1,77 @@
+data_pocket22_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    22:
+0  - Pocket Score                      : -0.0139
+1  - Drug Score                        : 0.0034
+2  - Number of alpha spheres           :    36
+3  - Mean alpha-sphere radius          : 3.9913
+4  - Mean alpha-sphere Solvent Acc.    : 0.6555
+5  - Mean B-factor of pocket residues  : 0.2200
+6  - Hydrophobicity Score              : 9.7857
+7  - Polarity Score                    :     8
+8  - Amino Acid based volume Score     : 4.0714
+9  - Pocket volume (Monte Carlo)       : 694.6691
+10  -Pocket volume (convex hull)       : 117.8604
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 17.8095
+13 - Number of apolar alpha sphere     :    21
+14 - Proportion of apolar alpha sphere : 0.5833
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     4048    O    O ?  ARG    Bxp 256 ?    5.584   39.776   52.007  -0.40  0 483 B
+ATOM     4034    O    O ?  SER    Bxp 254 ?    3.034   36.722   50.663  -3.35  0 481 B
+ATOM     4092    O  OE1 ?  GLU    Bxp 261 ?    4.400   40.941   57.227   0.00  0 488 B
+ATOM     4093    O  OE2 ?  GLU    Bxp 261 ?    2.933   42.122   56.184   0.00  0 488 B
+ATOM     4040    O    O ?  ASP    Bxp 255 ?    6.559   36.007   52.815   0.00  0 482 B
+ATOM     4057    C   CA ?  PRO    Bxp 257 ?    6.624   40.819   54.353   0.00  0 484 B
+ATOM     4143    C   CB ?  THR    Bxp 268 ?   10.227   46.401   67.772   0.00  0 495 B
+ATOM     4118    C   CA ?  ALA    Bxp 265 ?    9.929   45.031   63.065   0.00  0 492 B
+ATOM     4145    C  CG2 ?  THR    Bxp 268 ?   10.384   45.639   69.065   0.00  0 495 B
+ATOM     4144    O  OG1 ?  THR    Bxp 268 ?    8.840   46.564   67.429   0.00  0 495 B
+ATOM     4120    O    O ?  ALA    Bxp 265 ?   11.641   45.676   64.603  -1.48  0 492 B
+ATOM     4089    C   CB ?  GLU    Bxp 261 ?    5.421   43.577   58.123   0.00  0 488 B
+ATOM     4060    C   CB ?  PRO    Bxp 257 ?    7.583   41.016   55.523   0.00  0 484 B
+ATOM     3947    C  CD1 ?  LEU    Bxp 244 ?   11.916   41.124   59.300   0.00  0 471 B
+ATOM     4047    C    C ?  ARG    Bxp 256 ?    6.658   39.348   52.433   0.00  0 483 B
+ATOM     3972    C   CB ?  ALA    Bxp 247 ?   11.015   37.196   55.846   0.00  0 474 B
+ATOM     3937    C   CG ?  GLU    Bxp 243 ?   13.561   35.641   61.217   0.00  0 470 B
+ATOM     3940    O  OE2 ?  GLU    Bxp 243 ?   11.836   34.934   62.719   0.00  0 470 B
+ATOM     3935    O    O ?  GLU    Bxp 243 ?   13.956   36.736   57.962  -1.48  0 470 B
+ATOM     4062    C   CD ?  PRO    Bxp 257 ?    8.652   39.555   53.954   0.00  0 484 B
+ATOM     3938    C   CD ?  GLU    Bxp 243 ?   12.975   35.501   62.669   0.00  0 470 B
+ATOM     3911    O    O ?  LYS    Bxp 240 ?   15.567   39.731   61.909  -3.21  0 467 B
+ATOM     3939    O  OE1 ?  GLU    Bxp 243 ?   13.626   35.936   63.713   0.00  0 470 B
+ATOM     4152    S   SD ?  MET    Bxp 269 ?   15.508   43.520   64.899   0.00  0 496 B
+ATOM     4153    C   CE ?  MET    Bxp 269 ?   14.440   43.776   63.513   0.00  0 496 B
+ATOM     3912    C   CB ?  LYS    Bxp 240 ?   15.915   39.653   65.197   0.00  0 467 B
+ATOM     4151    C   CG ?  MET    Bxp 269 ?   14.602   44.443   66.216   0.00  0 496 B
+ATOM     4121    C   CB ?  ALA    Bxp 265 ?   10.310   43.906   62.117   0.00  0 492 B
+ATOM     4088    O    O ?  GLU    Bxp 261 ?    7.481   45.179   60.241  -3.62  0 488 B
+ATOM     3528    N   NZ ?  LYS    Bxp 192 ?    4.513   41.805   50.925   0.00  0 419 B
+ATOM     4056    N    N ?  PRO    Bxp 257 ?    7.275   39.856   53.515  -1.09  0 484 B
+ATOM     4061    C   CG ?  PRO    Bxp 257 ?    8.908   40.517   55.032   0.00  0 484 B
+ATOM     3948    C  CD2 ?  LEU    Bxp 244 ?   13.574   42.584   60.502   0.00  0 471 B
+ATOM     4087    C    C ?  GLU    Bxp 261 ?    7.103   45.132   59.045   0.00  0 488 B
+ATOM     4094    N    N ?  ILE    Bxp 262 ?    7.932   45.257   57.985   0.00  0 489 B
+# 

tests/reference_output/123abc_out/pocket22_env_atm.cif

@@ -0,0 +1,75 @@
+data_pocket22_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     3527    C   CE ?  LYS    Bxp 192 ?    4.230   41.475   49.521   0.00  0 419 B
+ATOM     3528    N   NZ ?  LYS    Bxp 192 ?    4.513   41.805   50.925   0.00  0 419 B
+ATOM     3909    C   CA ?  LYS    Bxp 240 ?   16.489   38.866   63.991   0.00  0 467 B
+ATOM     3910    C    C ?  LYS    Bxp 240 ?   16.549   39.699   62.695   0.00  0 467 B
+ATOM     3911    O    O ?  LYS    Bxp 240 ?   15.567   39.731   61.909  -3.21  0 467 B
+ATOM     3912    C   CB ?  LYS    Bxp 240 ?   15.915   39.653   65.197   0.00  0 467 B
+ATOM     3934    C    C ?  GLU    Bxp 243 ?   14.663   37.242   58.823   0.00  0 470 B
+ATOM     3935    O    O ?  GLU    Bxp 243 ?   13.956   36.736   57.962  -1.48  0 470 B
+ATOM     3936    C   CB ?  GLU    Bxp 243 ?   14.951   36.297   61.139   0.00  0 470 B
+ATOM     3937    C   CG ?  GLU    Bxp 243 ?   13.561   35.641   61.217   0.00  0 470 B
+ATOM     3938    C   CD ?  GLU    Bxp 243 ?   12.975   35.501   62.669   0.00  0 470 B
+ATOM     3939    O  OE1 ?  GLU    Bxp 243 ?   13.626   35.936   63.713   0.00  0 470 B
+ATOM     3940    O  OE2 ?  GLU    Bxp 243 ?   11.836   34.934   62.719   0.00  0 470 B
+ATOM     3941    N    N ?  LEU    Bxp 244 ?   14.719   38.538   59.058   0.00  0 471 B
+ATOM     3942    C   CA ?  LEU    Bxp 244 ?   14.186   39.576   58.225   0.00  0 471 B
+ATOM     3945    C   CB ?  LEU    Bxp 244 ?   14.468   40.916   58.905   0.00  0 471 B
+ATOM     3946    C   CG ?  LEU    Bxp 244 ?   13.279   41.832   59.221   0.00  0 471 B
+ATOM     3947    C  CD1 ?  LEU    Bxp 244 ?   11.916   41.124   59.300   0.00  0 471 B
+ATOM     3948    C  CD2 ?  LEU    Bxp 244 ?   13.574   42.584   60.502   0.00  0 471 B
+ATOM     3972    C   CB ?  ALA    Bxp 247 ?   11.015   37.196   55.846   0.00  0 474 B
+ATOM     4034    O    O ?  SER    Bxp 254 ?    3.034   36.722   50.663  -3.35  0 481 B
+ATOM     4038    C   CA ?  ASP    Bxp 255 ?    5.252   35.220   50.980   0.00  0 482 B
+ATOM     4039    C    C ?  ASP    Bxp 255 ?    6.138   36.234   51.683   0.00  0 482 B
+ATOM     4040    O    O ?  ASP    Bxp 255 ?    6.559   36.007   52.815   0.00  0 482 B
+ATOM     4045    N    N ?  ARG    Bxp 256 ?    6.452   37.343   51.021   0.00  0 483 B
+ATOM     4046    C   CA ?  ARG    Bxp 256 ?    7.422   38.306   51.602   0.00  0 483 B
+ATOM     4047    C    C ?  ARG    Bxp 256 ?    6.658   39.348   52.433   0.00  0 483 B
+ATOM     4048    O    O ?  ARG    Bxp 256 ?    5.584   39.776   52.007  -0.40  0 483 B
+ATOM     4056    N    N ?  PRO    Bxp 257 ?    7.275   39.856   53.515  -1.09  0 484 B
+ATOM     4057    C   CA ?  PRO    Bxp 257 ?    6.624   40.819   54.353   0.00  0 484 B
+ATOM     4060    C   CB ?  PRO    Bxp 257 ?    7.583   41.016   55.523   0.00  0 484 B
+ATOM     4061    C   CG ?  PRO    Bxp 257 ?    8.908   40.517   55.032   0.00  0 484 B
+ATOM     4062    C   CD ?  PRO    Bxp 257 ?    8.652   39.555   53.954   0.00  0 484 B
+ATOM     4086    C   CA ?  GLU    Bxp 261 ?    5.633   44.949   58.707   0.00  0 488 B
+ATOM     4087    C    C ?  GLU    Bxp 261 ?    7.103   45.132   59.045   0.00  0 488 B
+ATOM     4088    O    O ?  GLU    Bxp 261 ?    7.481   45.179   60.241  -3.62  0 488 B
+ATOM     4089    C   CB ?  GLU    Bxp 261 ?    5.421   43.577   58.123   0.00  0 488 B
+ATOM     4090    C   CG ?  GLU    Bxp 261 ?    3.980   43.147   58.071   0.00  0 488 B
+ATOM     4091    C   CD ?  GLU    Bxp 261 ?    3.752   41.985   57.107   0.00  0 488 B
+ATOM     4092    O  OE1 ?  GLU    Bxp 261 ?    4.400   40.941   57.227   0.00  0 488 B
+ATOM     4093    O  OE2 ?  GLU    Bxp 261 ?    2.933   42.122   56.184   0.00  0 488 B
+ATOM     4094    N    N ?  ILE    Bxp 262 ?    7.932   45.257   57.985   0.00  0 489 B
+ATOM     4095    C   CA ?  ILE    Bxp 262 ?    9.374   45.475   58.093   0.00  0 489 B
+ATOM     4099    C  CG1 ?  ILE    Bxp 262 ?   10.102   44.158   56.052   0.00  0 489 B
+ATOM     4117    N    N ?  ALA    Bxp 265 ?    8.883   45.921   62.496  -1.09  0 492 B
+ATOM     4118    C   CA ?  ALA    Bxp 265 ?    9.929   45.031   63.065   0.00  0 492 B
+ATOM     4119    C    C ?  ALA    Bxp 265 ?   11.159   45.807   63.476   0.00  0 492 B
+ATOM     4120    O    O ?  ALA    Bxp 265 ?   11.641   45.676   64.603  -1.48  0 492 B
+ATOM     4121    C   CB ?  ALA    Bxp 265 ?   10.310   43.906   62.117   0.00  0 492 B
+ATOM     4143    C   CB ?  THR    Bxp 268 ?   10.227   46.401   67.772   0.00  0 495 B
+ATOM     4144    O  OG1 ?  THR    Bxp 268 ?    8.840   46.564   67.429   0.00  0 495 B
+ATOM     4145    C  CG2 ?  THR    Bxp 268 ?   10.384   45.639   69.065   0.00  0 495 B
+ATOM     4151    C   CG ?  MET    Bxp 269 ?   14.602   44.443   66.216   0.00  0 496 B
+ATOM     4152    S   SD ?  MET    Bxp 269 ?   15.508   43.520   64.899   0.00  0 496 B
+ATOM     4153    C   CE ?  MET    Bxp 269 ?   14.440   43.776   63.513   0.00  0 496 B
+#

tests/reference_output/123abc_out/pocket22_vert.pqr

@@ -0,0 +1,38 @@
+ATOM      1    O STP    22       2.588  38.277  54.536    0.00     4.20
+ATOM      2    O STP    22       3.184  37.659  54.810    0.00     4.25
+ATOM      3    O STP    22       4.324  37.993  54.993    0.00     3.70
+ATOM      4    C STP    22       9.349  42.432  66.420    0.00     4.28
+ATOM      5    O STP    22       9.487  43.149  66.203    0.00     3.69
+ATOM      6    C STP    22       9.573  42.447  66.402    0.00     4.24
+ATOM      7    C STP    22       7.778  40.463  59.690    0.00     4.21
+ATOM      8    O STP    22       4.421  38.008  54.944    0.00     3.62
+ATOM      9    O STP    22       6.635  36.857  57.395    0.00     4.66
+ATOM     10    C STP    22      10.018  37.442  59.904    0.00     4.19
+ATOM     11    C STP    22      10.593  37.528  59.656    0.00     3.85
+ATOM     12    C STP    22       6.906  37.060  56.916    0.00     4.25
+ATOM     13    C STP    22      10.875  38.162  61.227    0.00     3.68
+ATOM     14    O STP    22      11.793  39.205  62.679    0.00     3.89
+ATOM     15    C STP    22      12.234  38.783  61.835    0.00     3.47
+ATOM     16    C STP    22      12.498  41.297  65.680    0.00     3.82
+ATOM     17    C STP    22      11.285  41.146  65.790    0.00     4.70
+ATOM     18    O STP    22      11.543  39.962  64.004    0.00     4.54
+ATOM     19    C STP    22      11.873  40.379  63.979    0.00     4.28
+ATOM     20    O STP    22      11.407  39.813  63.544    0.00     4.47
+ATOM     21    C STP    22      10.473  39.400  63.420    0.00     4.69
+ATOM     22    C STP    22       7.875  41.026  60.332    0.00     4.17
+ATOM     23    O STP    22       1.566  39.790  53.037    0.00     4.15
+ATOM     24    O STP    22       6.610  37.401  56.398    0.00     3.84
+ATOM     25    O STP    22       5.693  37.631  56.068    0.00     3.74
+ATOM     26    O STP    22       6.100  37.491  56.424    0.00     3.93
+ATOM     27    O STP    22       6.057  37.632  56.349    0.00     3.80
+ATOM     28    O STP    22       4.807  37.998  54.958    0.00     3.41
+ATOM     29    C STP    22       8.765  38.873  58.604    0.00     3.93
+ATOM     30    C STP    22       7.672  37.739  56.806    0.00     3.52
+ATOM     31    C STP    22      11.711  40.207  63.329    0.00     4.14
+ATOM     32    C STP    22      11.998  40.554  63.625    0.00     4.04
+ATOM     33    C STP    22       8.269  41.657  59.472    0.00     3.69
+ATOM     34    C STP    22       8.433  41.818  58.900    0.00     3.57
+ATOM     35    C STP    22       8.465  41.854  58.862    0.00     3.55
+ATOM     36    C STP    22       8.418  41.878  58.828    0.00     3.52
+TER
+END

tests/reference_output/123abc_out/pocket23_atm.cif

@@ -0,0 +1,59 @@
+data_pocket23_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    23:
+0  - Pocket Score                      : -0.0164
+1  - Drug Score                        : 0.0005
+2  - Number of alpha spheres           :    21
+3  - Mean alpha-sphere radius          : 3.6900
+4  - Mean alpha-sphere Solvent Acc.    : 0.4917
+5  - Mean B-factor of pocket residues  : 0.2299
+6  - Hydrophobicity Score              : 10.2857
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 244.5305
+10  -Pocket volume (convex hull)       : 9.4367
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 6.0000
+13 - Number of apolar alpha sphere     :     7
+14 - Proportion of apolar alpha sphere : 0.3333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     8199    C   CG ?  ASN    Dxp 252 ?   27.586    9.214   42.829   0.00  0 479 D
+ATOM     8186    C  CD1 ?  TRP    Dxp 251 ?   26.276   14.665   45.063   0.00  0 478 D
+ATOM     8201    N  ND2 ?  ASN    Dxp 252 ?   28.367    8.903   43.871   0.00  0 479 D
+ATOM     8198    C   CB ?  ASN    Dxp 252 ?   27.436   10.710   42.437   0.00  0 479 D
+ATOM     8195    C   CA ?  ASN    Dxp 252 ?   28.576   11.606   42.953   0.00  0 479 D
+ATOM     8188    N  NE1 ?  TRP    Dxp 251 ?   26.256   14.921   46.406  -0.17  0 478 D
+ATOM     8183    O    O ?  TRP    Dxp 251 ?   29.606   13.897   44.157  -1.07  0 478 D
+ATOM     8208    C   CD ?  PRO    Dxp 253 ?   30.672   10.672   44.713   0.00  0 480 D
+ATOM     7945    O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM     8191    C  CZ2 ?  TRP    Dxp 251 ?   27.038   16.816   47.830   0.00  0 478 D
+ATOM     7656    C  CE1 ?  TYR    Dxp 186 ?   28.922   12.123   52.576   0.00  0 413 D
+ATOM     7659    O   OH ?  TYR    Dxp 186 ?   26.735   12.867   53.246   0.00  0 413 D
+ATOM     7620    N    N ?  GLU    Dxp 182 ?   32.487   14.873   49.114   0.00  0 409 D
+ATOM     8189    C  CE2 ?  TRP    Dxp 251 ?   26.844   16.141   46.643   0.00  0 478 D
+ATOM     7617    C   CB ?  PRO    Dxp 181 ?   30.988   17.092   47.631   0.00  0 408 D
+ATOM     7624    C   CB ?  GLU    Dxp 182 ?   32.311   12.417   49.315   0.00  0 409 D
+ATOM     7621    C   CA ?  GLU    Dxp 182 ?   32.543   13.747   50.045   0.00  0 409 D
+# 

tests/reference_output/123abc_out/pocket23_env_atm.cif

@@ -0,0 +1,54 @@
+data_pocket23_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     7614    C   CA ?  PRO    Dxp 181 ?   32.231   17.243   48.469   0.00  0 408 D
+ATOM     7615    C    C ?  PRO    Dxp 181 ?   32.350   16.130   49.537   0.00  0 408 D
+ATOM     7616    O    O ?  PRO    Dxp 181 ?   32.388   16.443   50.725   0.00  0 408 D
+ATOM     7617    C   CB ?  PRO    Dxp 181 ?   30.988   17.092   47.631   0.00  0 408 D
+ATOM     7618    C   CG ?  PRO    Dxp 181 ?   31.356   17.693   46.325   0.00  0 408 D
+ATOM     7620    N    N ?  GLU    Dxp 182 ?   32.487   14.873   49.114   0.00  0 409 D
+ATOM     7621    C   CA ?  GLU    Dxp 182 ?   32.543   13.747   50.045   0.00  0 409 D
+ATOM     7624    C   CB ?  GLU    Dxp 182 ?   32.311   12.417   49.315   0.00  0 409 D
+ATOM     7625    C   CG ?  GLU    Dxp 182 ?   33.511   11.813   48.605   0.00  0 409 D
+ATOM     7627    O  OE1 ?  GLU    Dxp 182 ?   33.039   13.333   46.837   0.00  0 409 D
+ATOM     7647    C   CB ?  ALA    Dxp 185 ?   30.355   15.757   53.617   0.00  0 412 D
+ATOM     7654    C  CD1 ?  TYR    Dxp 186 ?   30.228   11.746   52.896   0.00  0 413 D
+ATOM     7656    C  CE1 ?  TYR    Dxp 186 ?   28.922   12.123   52.576   0.00  0 413 D
+ATOM     7658    C   CZ ?  TYR    Dxp 186 ?   28.026   12.495   53.587   0.00  0 413 D
+ATOM     7659    O   OH ?  TYR    Dxp 186 ?   26.735   12.867   53.246   0.00  0 413 D
+ATOM     7945    O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM     8182    C    C ?  TRP    Dxp 251 ?   28.907   14.027   43.133   0.00  0 478 D
+ATOM     8183    O    O ?  TRP    Dxp 251 ?   29.606   13.897   44.157  -1.07  0 478 D
+ATOM     8185    C   CG ?  TRP    Dxp 251 ?   26.880   15.703   44.398   0.00  0 478 D
+ATOM     8186    C  CD1 ?  TRP    Dxp 251 ?   26.276   14.665   45.063   0.00  0 478 D
+ATOM     8187    C  CD2 ?  TRP    Dxp 251 ?   27.270   16.654   45.395   0.00  0 478 D
+ATOM     8188    N  NE1 ?  TRP    Dxp 251 ?   26.256   14.921   46.406  -0.17  0 478 D
+ATOM     8189    C  CE2 ?  TRP    Dxp 251 ?   26.844   16.141   46.643   0.00  0 478 D
+ATOM     8191    C  CZ2 ?  TRP    Dxp 251 ?   27.038   16.816   47.830   0.00  0 478 D
+ATOM     8193    C  CH2 ?  TRP    Dxp 251 ?   27.687   18.028   47.774   0.00  0 478 D
+ATOM     8194    N    N ?  ASN    Dxp 252 ?   28.369   12.984   42.500  -2.19  0 479 D
+ATOM     8195    C   CA ?  ASN    Dxp 252 ?   28.576   11.606   42.953   0.00  0 479 D
+ATOM     8198    C   CB ?  ASN    Dxp 252 ?   27.436   10.710   42.437   0.00  0 479 D
+ATOM     8199    C   CG ?  ASN    Dxp 252 ?   27.586    9.214   42.829   0.00  0 479 D
+ATOM     8200    O  OD1 ?  ASN    Dxp 252 ?   26.967    8.353   42.186   0.00  0 479 D
+ATOM     8201    N  ND2 ?  ASN    Dxp 252 ?   28.367    8.903   43.871   0.00  0 479 D
+ATOM     8202    N    N ?  PRO    Dxp 253 ?   30.848   10.724   43.243   0.00  0 480 D
+ATOM     8207    C   CG ?  PRO    Dxp 253 ?   31.809    9.793   45.177   0.00  0 480 D
+ATOM     8208    C   CD ?  PRO    Dxp 253 ?   30.672   10.672   44.713   0.00  0 480 D
+#

tests/reference_output/123abc_out/pocket23_vert.pqr

@@ -0,0 +1,23 @@
+ATOM      1    C STP    23      24.981  10.606  46.057    0.00     4.38
+ATOM      2    C STP    23      26.542  11.221  45.819    0.00     3.54
+ATOM      3    O STP    23      27.850  11.854  46.325    0.00     3.46
+ATOM      4    O STP    23      27.847  11.859  46.317    0.00     3.45
+ATOM      5    O STP    23      27.477  11.387  46.522    0.00     3.74
+ATOM      6    O STP    23      27.267  11.364  46.403    0.00     3.70
+ATOM      7    O STP    23      27.563  14.223  50.125    0.00     3.50
+ATOM      8    O STP    23      27.248  13.675  49.707    0.00     3.67
+ATOM      9    O STP    23      28.935  14.321  49.677    0.00     3.64
+ATOM     10    O STP    23      29.401  13.941  47.679    0.00     3.53
+ATOM     11    O STP    23      29.398  13.934  47.683    0.00     3.53
+ATOM     12    C STP    23      29.231  14.161  48.180    0.00     3.46
+ATOM     13    O STP    23      29.120  13.943  48.322    0.00     3.58
+ATOM     14    C STP    23      28.130  11.365  48.279    0.00     4.43
+ATOM     15    O STP    23      28.886  12.418  47.611    0.00     3.83
+ATOM     16    O STP    23      29.374  13.741  47.735    0.00     3.59
+ATOM     17    C STP    23      28.677  13.581  49.048    0.00     3.83
+ATOM     18    C STP    23      28.878  13.903  49.286    0.00     3.74
+ATOM     19    O STP    23      29.032  13.830  48.521    0.00     3.66
+ATOM     20    C STP    23      28.897  13.903  49.305    0.00     3.72
+ATOM     21    O STP    23      29.082  14.390  49.883    0.00     3.52
+TER
+END

tests/reference_output/123abc_out/pocket24_atm.cif

@@ -0,0 +1,73 @@
+data_pocket24_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    24:
+0  - Pocket Score                      : -0.0278
+1  - Drug Score                        : 0.0029
+2  - Number of alpha spheres           :    41
+3  - Mean alpha-sphere radius          : 3.9593
+4  - Mean alpha-sphere Solvent Acc.    : 0.5927
+5  - Mean B-factor of pocket residues  : 0.1915
+6  - Hydrophobicity Score              : 10.6364
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.7273
+9  - Pocket volume (Monte Carlo)       : 474.0035
+10  -Pocket volume (convex hull)       : 89.6285
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 10.0000
+13 - Number of apolar alpha sphere     :    14
+14 - Proportion of apolar alpha sphere : 0.3415
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1634    C   CG ?  LEU    Axp 218 ?   26.546   36.235   23.630   0.00  0 445 A
+ATOM     1635    C  CD1 ?  LEU    Axp 218 ?   26.663   34.961   24.461   0.00  0 445 A
+ATOM     1625    C   CB ?  ASP    Axp 217 ?   29.707   40.718   23.735   0.00  0 444 A
+ATOM     1633    C   CB ?  LEU    Axp 218 ?   25.982   37.405   24.438   0.00  0 445 A
+ATOM     1616    O    O ?  ILE    Axp 216 ?   28.714   38.833   20.120  -0.40  0 443 A
+ATOM     1208    C   CB ?  ASP    Axp 164 ?   29.178   31.688   24.167   0.00  0 391 A
+ATOM     1307    N   NZ ?  LYS    Axp 177 ?   28.045   36.395   18.402  -5.21  0 404 A
+ATOM     1636    C  CD2 ?  LEU    Axp 218 ?   25.660   35.987   22.435   0.00  0 445 A
+ATOM     1207    O    O ?  ASP    Axp 164 ?   26.463   31.466   23.365  -2.55  0 391 A
+ATOM     1306    C   CE ?  LYS    Axp 177 ?   26.638   36.392   18.974   0.00  0 404 A
+ATOM     1305    C   CD ?  LYS    Axp 177 ?   25.713   35.218   18.453   0.00  0 404 A
+ATOM     1212    O    O ?  THR    Axp 165 ?   23.541   30.232   22.305  -2.14  0 392 A
+ATOM     1299    N    N ?  LYS    Axp 177 ?   21.604   34.670   19.815   0.00  0 404 A
+ATOM     1586    O    O ?  PRO    Axp 212 ?   27.163   35.309   15.349  -2.14  0 439 A
+ATOM     1581    C   CB ?  SER    Axp 211 ?   29.357   31.629   14.802   0.00  0 438 A
+ATOM     1320    C  CZ3 ?  TRP    Axp 178 ?   23.462   30.785   17.625   0.00  0 405 A
+ATOM     1637    N    N ?  SER    Axp 219 ?   25.769   40.519   25.023   0.00  0 446 A
+ATOM     1642    O   OG ?  SER    Axp 219 ?   26.959   42.469   26.857   0.00  0 446 A
+ATOM     1641    C   CB ?  SER    Axp 219 ?   25.796   41.724   27.105   0.00  0 446 A
+ATOM     1629    N    N ?  LEU    Axp 218 ?   27.266   38.964   23.188   0.00  0 445 A
+ATOM     1622    C   CA ?  ASP    Axp 217 ?   29.148   40.081   22.440   0.00  0 444 A
+ATOM     1582    O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM     1321    C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM     1214    O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM     1206    C    C ?  ASP    Axp 164 ?   27.100   30.422   23.545   0.00  0 391 A
+ATOM     1589    C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM     1204    N    N ?  ASP    Axp 164 ?   29.062   29.235   24.428  -0.84  0 391 A
+ATOM     1209    N    N ?  THR    Axp 165 ?   26.804   29.250   22.931   0.00  0 392 A
+ATOM     1210    C   CA ?  THR    Axp 165 ?   25.644   29.125   21.999   0.00  0 392 A
+ATOM     1611    C    C ?  GLY    Axp 215 ?   31.790   39.345   18.361   0.00  0 442 A
+ATOM     1610    C   CA ?  GLY    Axp 215 ?   32.619   38.349   17.567   0.00  0 442 A
+# 

tests/reference_output/123abc_out/pocket24_env_atm.cif

@@ -0,0 +1,78 @@
+data_pocket24_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1204    N    N ?  ASP    Axp 164 ?   29.062   29.235   24.428  -0.84  0 391 A
+ATOM     1205    C   CA ?  ASP    Axp 164 ?   28.289   30.466   24.504   0.00  0 391 A
+ATOM     1206    C    C ?  ASP    Axp 164 ?   27.100   30.422   23.545   0.00  0 391 A
+ATOM     1207    O    O ?  ASP    Axp 164 ?   26.463   31.466   23.365  -2.55  0 391 A
+ATOM     1208    C   CB ?  ASP    Axp 164 ?   29.178   31.688   24.167   0.00  0 391 A
+ATOM     1209    N    N ?  THR    Axp 165 ?   26.804   29.250   22.931   0.00  0 392 A
+ATOM     1210    C   CA ?  THR    Axp 165 ?   25.644   29.125   21.999   0.00  0 392 A
+ATOM     1211    C    C ?  THR    Axp 165 ?   24.326   29.397   22.732   0.00  0 392 A
+ATOM     1212    O    O ?  THR    Axp 165 ?   23.541   30.232   22.305  -2.14  0 392 A
+ATOM     1213    C   CB ?  THR    Axp 165 ?   25.536   27.768   21.247   0.00  0 392 A
+ATOM     1214    O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM     1215    C  CG2 ?  THR    Axp 165 ?   24.206   27.716   20.463   0.00  0 392 A
+ATOM     1286    C    C ?  PRO    Axp 175 ?   20.244   32.256   21.608   0.00  0 402 A
+ATOM     1291    N    N ?  ILE    Axp 176 ?   20.859   33.260   22.267   0.00  0 403 A
+ATOM     1292    C   CA ?  ILE    Axp 176 ?   20.637   34.711   22.002   0.00  0 403 A
+ATOM     1293    C    C ?  ILE    Axp 176 ?   20.604   35.150   20.552   0.00  0 403 A
+ATOM     1295    C   CB ?  ILE    Axp 176 ?   21.717   35.588   22.696   0.00  0 403 A
+ATOM     1299    N    N ?  LYS    Axp 177 ?   21.604   34.670   19.815   0.00  0 404 A
+ATOM     1300    C   CA ?  LYS    Axp 177 ?   21.829   35.087   18.428   0.00  0 404 A
+ATOM     1303    C   CB ?  LYS    Axp 177 ?   23.257   34.714   18.002   0.00  0 404 A
+ATOM     1304    C   CG ?  LYS    Axp 177 ?   24.269   35.792   18.311   0.00  0 404 A
+ATOM     1305    C   CD ?  LYS    Axp 177 ?   25.713   35.218   18.453   0.00  0 404 A
+ATOM     1306    C   CE ?  LYS    Axp 177 ?   26.638   36.392   18.974   0.00  0 404 A
+ATOM     1307    N   NZ ?  LYS    Axp 177 ?   28.045   36.395   18.402  -5.21  0 404 A
+ATOM     1318    C  CE3 ?  TRP    Axp 178 ?   22.147   31.051   17.645   0.00  0 405 A
+ATOM     1320    C  CZ3 ?  TRP    Axp 178 ?   23.462   30.785   17.625   0.00  0 405 A
+ATOM     1321    C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM     1578    C   CA ?  SER    Axp 211 ?   28.519   31.580   13.536   0.00  0 438 A
+ATOM     1581    C   CB ?  SER    Axp 211 ?   29.357   31.629   14.802   0.00  0 438 A
+ATOM     1582    O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM     1583    N    N ?  PRO    Axp 212 ?   26.749   33.241   13.625   0.00  0 439 A
+ATOM     1586    O    O ?  PRO    Axp 212 ?   27.163   35.309   15.349  -2.14  0 439 A
+ATOM     1588    C   CG ?  PRO    Axp 212 ?   24.603   32.718   14.282   0.00  0 439 A
+ATOM     1589    C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM     1609    N    N ?  GLY    Axp 215 ?   31.958   37.588   16.536  -2.35  0 442 A
+ATOM     1610    C   CA ?  GLY    Axp 215 ?   32.619   38.349   17.567   0.00  0 442 A
+ATOM     1611    C    C ?  GLY    Axp 215 ?   31.790   39.345   18.361   0.00  0 442 A
+ATOM     1612    O    O ?  GLY    Axp 215 ?   32.322   40.025   19.268   0.00  0 442 A
+ATOM     1613    N    N ?  ILE    Axp 216 ?   30.504   39.488   18.032   0.00  0 443 A
+ATOM     1615    C    C ?  ILE    Axp 216 ?   29.274   39.951   20.050   0.00  0 443 A
+ATOM     1616    O    O ?  ILE    Axp 216 ?   28.714   38.833   20.120  -0.40  0 443 A
+ATOM     1621    N    N ?  ASP    Axp 217 ?   29.581   40.653   21.147   0.00  0 444 A
+ATOM     1622    C   CA ?  ASP    Axp 217 ?   29.148   40.081   22.440   0.00  0 444 A
+ATOM     1623    C    C ?  ASP    Axp 217 ?   27.658   40.069   22.573   0.00  0 444 A
+ATOM     1625    C   CB ?  ASP    Axp 217 ?   29.707   40.718   23.735   0.00  0 444 A
+ATOM     1626    C   CG ?  ASP    Axp 217 ?   29.495   42.204   23.817   0.00  0 444 A
+ATOM     1628    O  OD2 ?  ASP    Axp 217 ?   29.236   42.748   24.938  -5.36  0 444 A
+ATOM     1629    N    N ?  LEU    Axp 218 ?   27.266   38.964   23.188   0.00  0 445 A
+ATOM     1630    C   CA ?  LEU    Axp 218 ?   25.952   38.629   23.546   0.00  0 445 A
+ATOM     1631    C    C ?  LEU    Axp 218 ?   25.155   39.717   24.180   0.00  0 445 A
+ATOM     1633    C   CB ?  LEU    Axp 218 ?   25.982   37.405   24.438   0.00  0 445 A
+ATOM     1634    C   CG ?  LEU    Axp 218 ?   26.546   36.235   23.630   0.00  0 445 A
+ATOM     1635    C  CD1 ?  LEU    Axp 218 ?   26.663   34.961   24.461   0.00  0 445 A
+ATOM     1636    C  CD2 ?  LEU    Axp 218 ?   25.660   35.987   22.435   0.00  0 445 A
+ATOM     1637    N    N ?  SER    Axp 219 ?   25.769   40.519   25.023   0.00  0 446 A
+ATOM     1638    C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM     1641    C   CB ?  SER    Axp 219 ?   25.796   41.724   27.105   0.00  0 446 A
+ATOM     1642    O   OG ?  SER    Axp 219 ?   26.959   42.469   26.857   0.00  0 446 A
+#

tests/reference_output/123abc_out/pocket24_vert.pqr

@@ -0,0 +1,43 @@
+ATOM      1    C STP    24      29.876  37.188  26.022    0.00     4.21
+ATOM      2    O STP    24      30.426  35.207  21.880    0.00     4.38
+ATOM      3    C STP    24      28.282  33.848  21.575    0.00     3.49
+ATOM      4    C STP    24      28.671  34.151  21.536    0.00     3.64
+ATOM      5    O STP    24      28.427  33.777  21.105    0.00     3.78
+ATOM      6    O STP    24      28.297  33.738  21.025    0.00     3.74
+ATOM      7    C STP    24      28.838  34.231  21.395    0.00     3.78
+ATOM      8    C STP    24      27.757  33.607  20.857    0.00     3.54
+ATOM      9    O STP    24      24.476  33.189  20.894    0.00     3.41
+ATOM     10    O STP    24      28.142  33.401  20.640    0.00     3.74
+ATOM     11    O STP    24      28.243  33.072  17.680    0.00     3.41
+ATOM     12    O STP    24      25.417  32.190  20.131    0.00     3.47
+ATOM     13    O STP    24      28.693  38.642  27.462    0.00     4.25
+ATOM     14    O STP    24      28.810  38.670  27.356    0.00     4.26
+ATOM     15    C STP    24      29.810  37.238  25.904    0.00     4.10
+ATOM     16    C STP    24      30.439  36.829  24.407    0.00     4.01
+ATOM     17    O STP    24      29.793  36.707  22.598    0.00     3.44
+ATOM     18    O STP    24      28.540  38.802  26.552    0.00     3.60
+ATOM     19    O STP    24      27.437  31.294  18.535    0.00     4.11
+ATOM     20    O STP    24      27.483  31.421  18.628    0.00     4.19
+ATOM     21    C STP    24      27.385  31.536  18.333    0.00     4.05
+ATOM     22    C STP    24      27.401  31.506  18.399    0.00     4.08
+ATOM     23    O STP    24      28.366  31.691  19.300    0.00     4.49
+ATOM     24    O STP    24      29.238  31.324  19.637    0.00     4.55
+ATOM     25    O STP    24      28.861  31.534  19.517    0.00     4.53
+ATOM     26    O STP    24      28.755  32.120  19.127    0.00     4.39
+ATOM     27    O STP    24      28.835  31.975  19.445    0.00     4.61
+ATOM     28    O STP    24      29.040  31.988  19.524    0.00     4.65
+ATOM     29    O STP    24      29.052  31.660  19.575    0.00     4.59
+ATOM     30    C STP    24      27.218  31.730  17.975    0.00     3.83
+ATOM     31    C STP    24      27.188  31.191  17.407    0.00     3.42
+ATOM     32    C STP    24      26.680  31.993  17.751    0.00     3.44
+ATOM     33    O STP    24      30.087  30.005  20.439    0.00     4.19
+ATOM     34    O STP    24      29.373  30.961  19.923    0.00     4.31
+ATOM     35    O STP    24      28.353  31.275  19.815    0.00     4.03
+ATOM     36    O STP    24      28.093  31.226  19.865    0.00     3.87
+ATOM     37    O STP    24      25.511  31.989  20.106    0.00     3.44
+ATOM     38    O STP    24      27.792  31.635  19.345    0.00     4.24
+ATOM     39    C STP    24      27.156  31.499  19.100    0.00     4.04
+ATOM     40    C STP    24      25.946  31.968  19.881    0.00     3.56
+ATOM     41    O STP    24      31.137  36.344  19.989    0.00     3.48
+TER
+END

tests/reference_output/123abc_out/pocket25_atm.cif

@@ -0,0 +1,56 @@
+data_pocket25_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    25:
+0  - Pocket Score                      : -0.0372
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 4.0910
+4  - Mean alpha-sphere Solvent Acc.    : 0.5844
+5  - Mean B-factor of pocket residues  : 0.6654
+6  - Hydrophobicity Score              : 5.1667
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 272.2723
+10  -Pocket volume (convex hull)       : 4.5972
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.1333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     6291    O    O ?  GLU    Dxp 9 ?   72.604    3.890   48.729   0.00  0 236 D
+ATOM     6300    O    O ?  MET    Dxp 10 ?   74.107    7.374   51.316  -2.14  0 237 D
+ATOM     6293    C   CG ?  GLU    Dxp 9 ?   71.423    4.039   52.375   0.00  0 236 D
+ATOM     6312    O  OE1 ?  GLU    Dxp 11 ?   77.808    6.551   52.358   0.00  0 238 D
+ATOM     6299    C    C ?  MET    Dxp 10 ?   74.371    7.293   50.096   0.00  0 237 D
+ATOM     6305    N    N ?  GLU    Dxp 11 ?   75.439    7.869   49.548  -2.19  0 238 D
+ATOM     6309    C   CB ?  GLU    Dxp 11 ?   77.861    8.128   49.916   0.00  0 238 D
+ATOM     6510    C   CE ?  LYS    Dxp 36 ?   78.782    6.894   42.671   0.00  0 263 D
+ATOM     6511    N   NZ ?  LYS    Dxp 36 ?   78.219    5.612   42.198   0.00  0 263 D
+ATOM     6301    C   CB ?  MET    Dxp 10 ?   73.225    7.186   47.771   0.00  0 237 D
+ATOM     6335    O  OD2 ?  ASP    Dxp 14 ?   78.726    9.496   45.541  -2.55  0 241 D
+ATOM     6298    C   CA ?  MET    Dxp 10 ?   73.486    6.472   49.131   0.00  0 237 D
+ATOM     6491    C  CZ2 ?  TRP    Dxp 34 ?   73.535    8.757   43.118   0.00  0 261 D
+ATOM     6488    N  NE1 ?  TRP    Dxp 34 ?   75.151   10.418   44.105  -1.09  0 261 D
+# 

tests/reference_output/123abc_out/pocket25_env_atm.cif

@@ -0,0 +1,46 @@
+data_pocket25_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     6290    C    C ?  GLU    Dxp 9 ?   71.915    4.628   49.430   0.00  0 236 D
+ATOM     6291    O    O ?  GLU    Dxp 9 ?   72.604    3.890   48.729   0.00  0 236 D
+ATOM     6292    C   CB ?  GLU    Dxp 9 ?   70.763    3.288   51.242   0.00  0 236 D
+ATOM     6293    C   CG ?  GLU    Dxp 9 ?   71.423    4.039   52.375   0.00  0 236 D
+ATOM     6297    N    N ?  MET    Dxp 10 ?   72.265    5.885   49.709   0.00  0 237 D
+ATOM     6298    C   CA ?  MET    Dxp 10 ?   73.486    6.472   49.131   0.00  0 237 D
+ATOM     6299    C    C ?  MET    Dxp 10 ?   74.371    7.293   50.096   0.00  0 237 D
+ATOM     6300    O    O ?  MET    Dxp 10 ?   74.107    7.374   51.316  -2.14  0 237 D
+ATOM     6301    C   CB ?  MET    Dxp 10 ?   73.225    7.186   47.771   0.00  0 237 D
+ATOM     6303    S   SD ?  MET    Dxp 10 ?   72.034    9.214   46.200   0.00  0 237 D
+ATOM     6304    C   CE ?  MET    Dxp 10 ?   73.478   10.172   46.696   0.00  0 237 D
+ATOM     6305    N    N ?  GLU    Dxp 11 ?   75.439    7.869   49.548  -2.19  0 238 D
+ATOM     6306    C   CA ?  GLU    Dxp 11 ?   76.441    8.484   50.396   0.00  0 238 D
+ATOM     6309    C   CB ?  GLU    Dxp 11 ?   77.861    8.128   49.916   0.00  0 238 D
+ATOM     6310    C   CG ?  GLU    Dxp 11 ?   78.934    8.247   51.025   0.00  0 238 D
+ATOM     6311    C   CD ?  GLU    Dxp 11 ?   78.901    7.095   52.047   0.00  0 238 D
+ATOM     6312    O  OE1 ?  GLU    Dxp 11 ?   77.808    6.551   52.358   0.00  0 238 D
+ATOM     6313    O  OE2 ?  GLU    Dxp 11 ?   79.993    6.732   52.542   0.00  0 238 D
+ATOM     6333    C   CG ?  ASP    Dxp 14 ?   78.386   10.697   45.659   0.00  0 241 D
+ATOM     6335    O  OD2 ?  ASP    Dxp 14 ?   78.726    9.496   45.541  -2.55  0 241 D
+ATOM     6488    N  NE1 ?  TRP    Dxp 34 ?   75.151   10.418   44.105  -1.09  0 261 D
+ATOM     6489    C  CE2 ?  TRP    Dxp 34 ?   74.096   10.029   43.321   0.00  0 261 D
+ATOM     6491    C  CZ2 ?  TRP    Dxp 34 ?   73.535    8.757   43.118   0.00  0 261 D
+ATOM     6509    C   CD ?  LYS    Dxp 36 ?   78.417    8.015   41.707   0.00  0 263 D
+ATOM     6510    C   CE ?  LYS    Dxp 36 ?   78.782    6.894   42.671   0.00  0 263 D
+ATOM     6511    N   NZ ?  LYS    Dxp 36 ?   78.219    5.612   42.198   0.00  0 263 D
+#

tests/reference_output/123abc_out/pocket25_vert.pqr

@@ -0,0 +1,17 @@
+ATOM      1    O STP    25      75.274   3.616  51.622    0.00     3.95
+ATOM      2    O STP    25      75.447   3.857  51.198    0.00     3.77
+ATOM      3    O STP    25      77.265   3.650  48.742    0.00     4.67
+ATOM      4    O STP    25      77.429   5.196  46.574    0.00     4.47
+ATOM      5    O STP    25      76.872   5.560  46.252    0.00     4.27
+ATOM      6    O STP    25      77.405   5.505  46.519    0.00     4.32
+ATOM      7    O STP    25      76.830   5.855  46.190    0.00     4.16
+ATOM      8    O STP    25      76.241   3.921  50.013    0.00     3.86
+ATOM      9    O STP    25      76.891   3.834  49.144    0.00     4.31
+ATOM     10    O STP    25      76.615   4.112  49.507    0.00     3.94
+ATOM     11    O STP    25      76.919   4.561  46.576    0.00     4.69
+ATOM     12    C STP    25      75.852   6.436  45.091    0.00     3.83
+ATOM     13    C STP    25      76.021   6.874  45.250    0.00     3.78
+ATOM     14    O STP    25      76.062   7.019  45.119    0.00     3.66
+ATOM     15    O STP    25      75.987   6.992  45.287    0.00     3.72
+TER
+END

tests/reference_output/123abc_out/pocket26_atm.cif

@@ -0,0 +1,69 @@
+data_pocket26_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    26:
+0  - Pocket Score                      : -0.0384
+1  - Drug Score                        : 0.0846
+2  - Number of alpha spheres           :    45
+3  - Mean alpha-sphere radius          : 3.7304
+4  - Mean alpha-sphere Solvent Acc.    : 0.4267
+5  - Mean B-factor of pocket residues  : 0.1353
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 231.5366
+10  -Pocket volume (convex hull)       : 15.0678
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 38.0000
+13 - Number of apolar alpha sphere     :    39
+14 - Proportion of apolar alpha sphere : 0.8667
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1821    C  CG1 ?  VAL    Axp 241 ?   18.722   33.273    0.801   0.00  0 468 A
+ATOM      824    N    N ?  LEU    Axp 114 ?   19.877   26.311   -1.669   0.00  0 341 A
+ATOM      818    C    C ?  LEU    Axp 113 ?   20.351   26.072   -0.464   0.00  0 340 A
+ATOM      825    C   CA ?  LEU    Axp 114 ?   18.529   26.785   -1.887   0.00  0 341 A
+ATOM      798    C   CA ?  ALA    Axp 110 ?   24.131   27.516   -4.659   0.00  0 337 A
+ATOM     1805    C   CD ?  PRO    Axp 238 ?   21.822   33.590   -2.836   0.00  0 465 A
+ATOM     1792    O    O ?  GLY    Axp 236 ?   25.501   33.661   -3.290  -6.17  0 463 A
+ATOM      801    C   CB ?  ALA    Axp 110 ?   24.277   28.499   -5.862   0.00  0 337 A
+ATOM      819    O    O ?  LEU    Axp 113 ?   19.663   26.116    0.542  -1.07  0 340 A
+ATOM      856    C   CB ?  ALA    Axp 117 ?   16.641   27.654    2.208   0.00  0 344 A
+ATOM     1539    C  CG2 ?  ILE    Axp 205 ?   21.953   27.141    3.249   0.00  0 432 A
+ATOM     1509    C  CD2 ?  LEU    Axp 202 ?   16.995   30.754    4.286   0.00  0 429 A
+ATOM     1505    O    O ?  LEU    Axp 202 ?   21.436   31.217    5.146  -3.21  0 429 A
+ATOM      820    C   CB ?  LEU    Axp 113 ?   22.728   26.946   -0.496   0.00  0 340 A
+ATOM      830    C  CD1 ?  LEU    Axp 114 ?   17.000   29.244   -2.786   0.00  0 341 A
+ATOM     2030    C  CE1 ?  PHE    Axp 266 ?   15.255   30.669    0.284   0.00  0 493 A
+ATOM      828    C   CB ?  LEU    Axp 114 ?   18.476   27.301   -3.305   0.00  0 341 A
+ATOM     1804    C   CG ?  PRO    Axp 238 ?   21.078   33.317   -4.111   0.00  0 465 A
+ATOM     1822    C  CG2 ?  VAL    Axp 241 ?   17.795   32.913   -1.514   0.00  0 468 A
+ATOM      800    O    O ?  ALA    Axp 110 ?   21.862   27.166   -3.931  -1.07  0 337 A
+ATOM     1545    C   CB ?  ALA    Axp 206 ?   24.087   32.253    2.900   0.00  0 433 A
+ATOM     1541    N    N ?  ALA    Axp 206 ?   24.014   29.985    3.998   0.00  0 433 A
+ATOM     1798    S   SG ?  CYS    Axp 237 ?   22.030   35.316    0.634   0.00  0 464 A
+ATOM     1794    C   CA ?  CYS    Axp 237 ?   24.026   34.922   -1.329   0.00  0 464 A
+ATOM     1544    O    O ?  ALA    Axp 206 ?   26.983   31.382    2.492  -3.21  0 433 A
+ATOM     1542    C   CA ?  ALA    Axp 206 ?   24.748   30.821    3.023   0.00  0 433 A
+ATOM      822    C  CD1 ?  LEU    Axp 113 ?   25.012   27.872   -0.209   0.00  0 340 A
+# 

tests/reference_output/123abc_out/pocket26_env_atm.cif

@@ -0,0 +1,69 @@
+data_pocket26_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM      797    N    N ?  ALA    Axp 110 ?   25.276   26.616   -4.638  -1.51  0 337 A
+ATOM      798    C   CA ?  ALA    Axp 110 ?   24.131   27.516   -4.659   0.00  0 337 A
+ATOM      799    C    C ?  ALA    Axp 110 ?   22.743   26.831   -4.716   0.00  0 337 A
+ATOM      800    O    O ?  ALA    Axp 110 ?   21.862   27.166   -3.931  -1.07  0 337 A
+ATOM      801    C   CB ?  ALA    Axp 110 ?   24.277   28.499   -5.862   0.00  0 337 A
+ATOM      817    C   CA ?  LEU    Axp 113 ?   21.830   25.699   -0.438   0.00  0 340 A
+ATOM      818    C    C ?  LEU    Axp 113 ?   20.351   26.072   -0.464   0.00  0 340 A
+ATOM      819    O    O ?  LEU    Axp 113 ?   19.663   26.116    0.542  -1.07  0 340 A
+ATOM      820    C   CB ?  LEU    Axp 113 ?   22.728   26.946   -0.496   0.00  0 340 A
+ATOM      821    C   CG ?  LEU    Axp 113 ?   24.241   26.609   -0.297   0.00  0 340 A
+ATOM      822    C  CD1 ?  LEU    Axp 113 ?   25.012   27.872   -0.209   0.00  0 340 A
+ATOM      824    N    N ?  LEU    Axp 114 ?   19.877   26.311   -1.669   0.00  0 341 A
+ATOM      825    C   CA ?  LEU    Axp 114 ?   18.529   26.785   -1.887   0.00  0 341 A
+ATOM      827    O    O ?  LEU    Axp 114 ?   16.580   25.881   -0.904   0.00  0 341 A
+ATOM      828    C   CB ?  LEU    Axp 114 ?   18.476   27.301   -3.305   0.00  0 341 A
+ATOM      829    C   CG ?  LEU    Axp 114 ?   17.265   28.058   -3.739   0.00  0 341 A
+ATOM      830    C  CD1 ?  LEU    Axp 114 ?   17.000   29.244   -2.786   0.00  0 341 A
+ATOM      831    C  CD2 ?  LEU    Axp 114 ?   17.621   28.502   -5.177   0.00  0 341 A
+ATOM      856    C   CB ?  ALA    Axp 117 ?   16.641   27.654    2.208   0.00  0 344 A
+ATOM     1503    C   CA ?  LEU    Axp 202 ?   19.270   31.160    6.206   0.00  0 429 A
+ATOM     1504    C    C ?  LEU    Axp 202 ?   20.726   31.628    6.075   0.00  0 429 A
+ATOM     1505    O    O ?  LEU    Axp 202 ?   21.436   31.217    5.146  -3.21  0 429 A
+ATOM     1506    C   CB ?  LEU    Axp 202 ?   18.358   32.297    5.678   0.00  0 429 A
+ATOM     1509    C  CD2 ?  LEU    Axp 202 ?   16.995   30.754    4.286   0.00  0 429 A
+ATOM     1535    C    C ?  ILE    Axp 205 ?   24.224   28.698    4.198   0.00  0 432 A
+ATOM     1537    C   CB ?  ILE    Axp 205 ?   21.844   27.691    4.617   0.00  0 432 A
+ATOM     1539    C  CG2 ?  ILE    Axp 205 ?   21.953   27.141    3.249   0.00  0 432 A
+ATOM     1540    C  CD1 ?  ILE    Axp 205 ?   19.543   26.545    5.231   0.00  0 432 A
+ATOM     1541    N    N ?  ALA    Axp 206 ?   24.014   29.985    3.998   0.00  0 433 A
+ATOM     1542    C   CA ?  ALA    Axp 206 ?   24.748   30.821    3.023   0.00  0 433 A
+ATOM     1543    C    C ?  ALA    Axp 206 ?   26.201   31.004    3.353   0.00  0 433 A
+ATOM     1544    O    O ?  ALA    Axp 206 ?   26.983   31.382    2.492  -3.21  0 433 A
+ATOM     1545    C   CB ?  ALA    Axp 206 ?   24.087   32.253    2.900   0.00  0 433 A
+ATOM     1783    O    O ?  GLU    Axp 235 ?   28.595   34.381   -0.451  -0.95  0 462 A
+ATOM     1791    C    C ?  GLY    Axp 236 ?   26.040   34.560   -2.661   0.00  0 463 A
+ATOM     1792    O    O ?  GLY    Axp 236 ?   25.501   33.661   -3.290  -6.17  0 463 A
+ATOM     1793    N    N ?  CYS    Axp 237 ?   25.399   35.253   -1.728   0.00  0 464 A
+ATOM     1794    C   CA ?  CYS    Axp 237 ?   24.026   34.922   -1.329   0.00  0 464 A
+ATOM     1797    C   CB ?  CYS    Axp 237 ?   23.762   35.291    0.152   0.00  0 464 A
+ATOM     1798    S   SG ?  CYS    Axp 237 ?   22.030   35.316    0.634   0.00  0 464 A
+ATOM     1799    N    N ?  PRO    Axp 238 ?   22.157   35.032   -2.930   0.00  0 465 A
+ATOM     1804    C   CG ?  PRO    Axp 238 ?   21.078   33.317   -4.111   0.00  0 465 A
+ATOM     1805    C   CD ?  PRO    Axp 238 ?   21.822   33.590   -2.836   0.00  0 465 A
+ATOM     1820    C   CB ?  VAL    Axp 241 ?   18.354   33.953   -0.560   0.00  0 468 A
+ATOM     1821    C  CG1 ?  VAL    Axp 241 ?   18.722   33.273    0.801   0.00  0 468 A
+ATOM     1822    C  CG2 ?  VAL    Axp 241 ?   17.795   32.913   -1.514   0.00  0 468 A
+ATOM     2028    C  CD1 ?  PHE    Axp 266 ?   14.325   29.916   -0.423   0.00  0 493 A
+ATOM     2030    C  CE1 ?  PHE    Axp 266 ?   15.255   30.669    0.284   0.00  0 493 A
+ATOM     2032    C   CZ ?  PHE    Axp 266 ?   14.987   31.067    1.550   0.00  0 493 A
+#

tests/reference_output/123abc_out/pocket26_vert.pqr

@@ -0,0 +1,47 @@
+ATOM      1    C STP    26      20.150  29.902  -0.345    0.00     3.84
+ATOM      2    C STP    26      23.707  30.654  -3.158    0.00     3.50
+ATOM      3    C STP    26      18.968  29.679   0.276    0.00     3.64
+ATOM      4    C STP    26      19.969  29.826  -0.150    0.00     3.79
+ATOM      5    C STP    26      19.700  29.805   1.860    0.00     3.76
+ATOM      6    C STP    26      19.843  29.950   2.035    0.00     3.72
+ATOM      7    C STP    26      19.739  29.732   1.625    0.00     3.78
+ATOM      8    C STP    26      20.314  29.863   0.084    0.00     3.83
+ATOM      9    C STP    26      20.576  29.869   0.864    0.00     3.88
+ATOM     10    C STP    26      20.280  29.938  -0.389    0.00     3.87
+ATOM     11    C STP    26      18.931  29.688   0.257    0.00     3.63
+ATOM     12    C STP    26      18.668  29.789   0.271    0.00     3.52
+ATOM     13    C STP    26      20.351  29.880  -1.633    0.00     3.60
+ATOM     14    C STP    26      20.609  30.100  -1.721    0.00     3.86
+ATOM     15    C STP    26      20.532  30.179  -2.237    0.00     3.70
+ATOM     16    C STP    26      20.286  30.453  -2.152    0.00     3.56
+ATOM     17    C STP    26      20.564  30.154  -1.461    0.00     3.91
+ATOM     18    C STP    26      20.394  30.083  -0.743    0.00     3.92
+ATOM     19    C STP    26      20.716  30.322  -0.910    0.00     3.95
+ATOM     20    C STP    26      20.610  30.165  -1.314    0.00     3.94
+ATOM     21    C STP    26      20.252  30.037  -0.680    0.00     3.87
+ATOM     22    C STP    26      19.848  29.978  -0.509    0.00     3.72
+ATOM     23    C STP    26      20.327  30.070  -1.073    0.00     3.83
+ATOM     24    O STP    26      20.629  30.091  -1.743    0.00     3.85
+ATOM     25    O STP    26      20.762  30.073  -1.634    0.00     3.86
+ATOM     26    C STP    26      20.541  30.175  -2.241    0.00     3.70
+ATOM     27    C STP    26      21.109  30.384   1.449    0.00     3.80
+ATOM     28    O STP    26      21.280  30.324   1.623    0.00     3.64
+ATOM     29    C STP    26      21.871  31.832   0.206    0.00     3.51
+ATOM     30    C STP    26      21.749  30.787   0.011    0.00     4.00
+ATOM     31    C STP    26      21.271  30.284   0.986    0.00     3.93
+ATOM     32    O STP    26      25.061  31.701  -0.420    0.00     3.50
+ATOM     33    O STP    26      24.995  31.508  -0.479    0.00     3.58
+ATOM     34    C STP    26      21.690  30.116   1.082    0.00     3.69
+ATOM     35    C STP    26      21.686  30.129   1.247    0.00     3.61
+ATOM     36    O STP    26      25.003  31.451  -0.503    0.00     3.59
+ATOM     37    C STP    26      23.791  30.489  -2.503    0.00     3.69
+ATOM     38    C STP    26      24.886  31.454  -0.516    0.00     3.60
+ATOM     39    C STP    26      22.493  30.785  -0.284    0.00     3.85
+ATOM     40    C STP    26      22.567  30.447   0.214    0.00     3.58
+ATOM     41    C STP    26      23.175  30.212  -2.359    0.00     3.67
+ATOM     42    C STP    26      22.977  30.181  -2.185    0.00     3.66
+ATOM     43    C STP    26      23.964  31.286  -0.978    0.00     3.65
+ATOM     44    C STP    26      24.634  31.444  -0.576    0.00     3.61
+ATOM     45    C STP    26      23.728  31.305  -0.650    0.00     3.69
+TER
+END

tests/reference_output/123abc_out/pocket27_atm.cif

@@ -0,0 +1,58 @@
+data_pocket27_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    27:
+0  - Pocket Score                      : -0.0425
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    17
+3  - Mean alpha-sphere radius          : 3.8983
+4  - Mean alpha-sphere Solvent Acc.    : 0.5210
+5  - Mean B-factor of pocket residues  : 0.3129
+6  - Hydrophobicity Score              : -21.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.7500
+9  - Pocket volume (Monte Carlo)       : 231.2226
+10  -Pocket volume (convex hull)       : 8.0231
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 8.0000
+13 - Number of apolar alpha sphere     :     9
+14 - Proportion of apolar alpha sphere : 0.5294
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1256    C   CA ?  GLY    Axp 171 ?   17.074   29.084   34.902   0.00  0 398 A
+ATOM     3772    C   CB ?  GLU    Bxp 223 ?   20.899   28.443   38.451   0.00  0 450 B
+ATOM     3769    C   CA ?  GLU    Bxp 223 ?   19.756   29.026   39.321   0.00  0 450 B
+ATOM     3800    O  OE1 ?  GLU    Bxp 226 ?   14.870   27.408   38.360  -0.81  0 453 B
+ATOM     1258    O    O ?  GLY    Axp 171 ?   17.211   27.237   33.384   0.00  0 398 A
+ATOM     3810    N   NZ ?  LYS    Bxp 227 ?   18.871   22.046   40.724   0.00  0 454 B
+ATOM     3799    C   CD ?  GLU    Bxp 226 ?   13.993   27.306   39.282   0.00  0 453 B
+ATOM     3798    C   CG ?  GLU    Bxp 226 ?   14.425   27.213   40.755   0.00  0 453 B
+ATOM     3809    C   CE ?  LYS    Bxp 227 ?   19.628   23.270   41.089   0.00  0 454 B
+ATOM     3774    C   CD ?  GLU    Bxp 223 ?   21.775   28.184   36.070   0.00  0 450 B
+ATOM     3775    O  OE1 ?  GLU    Bxp 223 ?   22.737   27.521   36.550   0.00  0 450 B
+ATOM     3771    O    O ?  GLU    Bxp 223 ?   19.336   27.833   41.335   0.00  0 450 B
+ATOM     3797    C   CB ?  GLU    Bxp 226 ?   15.576   28.210   41.069   0.00  0 453 B
+ATOM     3773    C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM     3808    C   CD ?  LYS    Bxp 227 ?   19.254   23.527   42.569   0.00  0 454 B
+ATOM     3796    O    O ?  GLU    Bxp 226 ?   15.035   26.681   43.850   0.00  0 453 B
+# 

tests/reference_output/123abc_out/pocket27_env_atm.cif

@@ -0,0 +1,47 @@
+data_pocket27_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     1256    C   CA ?  GLY    Axp 171 ?   17.074   29.084   34.902   0.00  0 398 A
+ATOM     1257    C    C ?  GLY    Axp 171 ?   16.881   28.422   33.539   0.00  0 398 A
+ATOM     1258    O    O ?  GLY    Axp 171 ?   17.211   27.237   33.384   0.00  0 398 A
+ATOM     3768    N    N ?  GLU    Bxp 223 ?   19.652   30.471   39.123   0.00  0 450 B
+ATOM     3769    C   CA ?  GLU    Bxp 223 ?   19.756   29.026   39.321   0.00  0 450 B
+ATOM     3770    C    C ?  GLU    Bxp 223 ?   19.994   28.706   40.771   0.00  0 450 B
+ATOM     3771    O    O ?  GLU    Bxp 223 ?   19.336   27.833   41.335   0.00  0 450 B
+ATOM     3772    C   CB ?  GLU    Bxp 223 ?   20.899   28.443   38.451   0.00  0 450 B
+ATOM     3773    C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM     3774    C   CD ?  GLU    Bxp 223 ?   21.775   28.184   36.070   0.00  0 450 B
+ATOM     3775    O  OE1 ?  GLU    Bxp 223 ?   22.737   27.521   36.550   0.00  0 450 B
+ATOM     3776    O  OE2 ?  GLU    Bxp 223 ?   21.549   28.266   34.820   0.00  0 450 B
+ATOM     3794    C   CA ?  GLU    Bxp 226 ?   15.782   28.535   42.552   0.00  0 453 B
+ATOM     3795    C    C ?  GLU    Bxp 226 ?   16.011   27.275   43.405   0.00  0 453 B
+ATOM     3796    O    O ?  GLU    Bxp 226 ?   15.035   26.681   43.850   0.00  0 453 B
+ATOM     3797    C   CB ?  GLU    Bxp 226 ?   15.576   28.210   41.069   0.00  0 453 B
+ATOM     3798    C   CG ?  GLU    Bxp 226 ?   14.425   27.213   40.755   0.00  0 453 B
+ATOM     3799    C   CD ?  GLU    Bxp 226 ?   13.993   27.306   39.282   0.00  0 453 B
+ATOM     3800    O  OE1 ?  GLU    Bxp 226 ?   14.870   27.408   38.360  -0.81  0 453 B
+ATOM     3801    O  OE2 ?  GLU    Bxp 226 ?   12.770   27.280   39.032  -3.35  0 453 B
+ATOM     3802    N    N ?  LYS    Bxp 227 ?   17.281   26.917   43.674   0.00  0 454 B
+ATOM     3803    C   CA ?  LYS    Bxp 227 ?   17.638   25.810   44.612   0.00  0 454 B
+ATOM     3806    C   CB ?  LYS    Bxp 227 ?   19.009   25.214   44.314   0.00  0 454 B
+ATOM     3807    C   CG ?  LYS    Bxp 227 ?   19.331   24.982   42.891   0.00  0 454 B
+ATOM     3808    C   CD ?  LYS    Bxp 227 ?   19.254   23.527   42.569   0.00  0 454 B
+ATOM     3809    C   CE ?  LYS    Bxp 227 ?   19.628   23.270   41.089   0.00  0 454 B
+ATOM     3810    N   NZ ?  LYS    Bxp 227 ?   18.871   22.046   40.724   0.00  0 454 B
+#

tests/reference_output/123abc_out/pocket27_vert.pqr

@@ -0,0 +1,19 @@
+ATOM      1    C STP    27      18.099  26.773  37.273    0.00     3.47
+ATOM      2    O STP    27      18.249  25.928  36.959    0.00     3.95
+ATOM      3    O STP    27      15.488  23.639  39.415    0.00     3.96
+ATOM      4    C STP    27      19.658  24.616  37.045    0.00     4.26
+ATOM      5    O STP    27      16.640  24.629  39.709    0.00     3.56
+ATOM      6    O STP    27      18.258  25.625  38.398    0.00     3.83
+ATOM      7    C STP    27      18.286  25.596  38.307    0.00     3.87
+ATOM      8    C STP    27      18.399  25.632  38.432    0.00     3.76
+ATOM      9    O STP    27      18.418  24.934  37.073    0.00     4.51
+ATOM     10    O STP    27      18.133  24.528  36.953    0.00     4.57
+ATOM     11    C STP    27      18.924  24.656  36.771    0.00     4.59
+ATOM     12    O STP    27      17.296  25.484  39.862    0.00     3.44
+ATOM     13    C STP    27      17.245  25.443  39.888    0.00     3.44
+ATOM     14    C STP    27      18.372  26.031  36.845    0.00     3.84
+ATOM     15    C STP    27      18.826  25.492  36.643    0.00     4.03
+ATOM     16    C STP    27      16.408  24.422  40.885    0.00     3.43
+ATOM     17    O STP    27      15.644  23.760  41.575    0.00     3.75
+TER
+END

tests/reference_output/123abc_out/pocket28_atm.cif

@@ -0,0 +1,54 @@
+data_pocket28_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    28:
+0  - Pocket Score                      : -0.0435
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 3.8178
+4  - Mean alpha-sphere Solvent Acc.    : 0.5111
+5  - Mean B-factor of pocket residues  : 0.2583
+6  - Hydrophobicity Score              : 47.8000
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 4.6000
+9  - Pocket volume (Monte Carlo)       : 150.8492
+10  -Pocket volume (convex hull)       : 1.1933
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.4000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     5155    C    C ?  ASN    Cxp 131 ?   49.791   69.967   16.216   0.00  0 358 C
+ATOM     5164    O    O ?  PHE    Cxp 132 ?   48.967   66.829   17.018   0.00  0 359 C
+ATOM     5154    C   CA ?  ASN    Cxp 131 ?   49.335   70.969   17.293   0.00  0 358 C
+ATOM     5156    O    O ?  ASN    Cxp 131 ?   49.458   70.110   15.000  -2.55  0 358 C
+ATOM     5177    C  CG1 ?  ILE    Cxp 133 ?   46.547   66.252   14.171   0.00  0 360 C
+ATOM     5179    C  CD1 ?  ILE    Cxp 133 ?   45.747   66.718   12.918   0.00  0 360 C
+ATOM     5159    O  OD1 ?  ASN    Cxp 131 ?   46.848   72.862   17.330   0.00  0 358 C
+ATOM     5600    C  CG1 ?  ILE    Cxp 191 ?   45.611   66.019   19.250   0.00  0 418 C
+ATOM     5129    O    O ?  GLU    Cxp 128 ?   48.054   70.332   20.849  -1.48  0 355 C
+ATOM     5595    N    N ?  ILE    Cxp 191 ?   43.539   65.578   16.244   0.00  0 418 C
+ATOM     5599    C   CB ?  ILE    Cxp 191 ?   44.408   66.418   18.397   0.00  0 418 C
+ATOM     5601    C  CG2 ?  ILE    Cxp 191 ?   43.280   67.132   19.172   0.00  0 418 C
+# 

tests/reference_output/123abc_out/pocket28_env_atm.cif

@@ -0,0 +1,44 @@
+data_pocket28_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM     5121    O    O ?  LEU    Cxp 127 ?   50.397   68.122   19.530   0.00  0 354 C
+ATOM     5127    C   CA ?  GLU    Cxp 128 ?   48.268   67.988   21.395   0.00  0 355 C
+ATOM     5128    C    C ?  GLU    Cxp 128 ?   48.593   69.482   21.560   0.00  0 355 C
+ATOM     5129    O    O ?  GLU    Cxp 128 ?   48.054   70.332   20.849  -1.48  0 355 C
+ATOM     5153    N    N ?  ASN    Cxp 131 ?   50.135   71.066   18.529   0.00  0 358 C
+ATOM     5154    C   CA ?  ASN    Cxp 131 ?   49.335   70.969   17.293   0.00  0 358 C
+ATOM     5155    C    C ?  ASN    Cxp 131 ?   49.791   69.967   16.216   0.00  0 358 C
+ATOM     5156    O    O ?  ASN    Cxp 131 ?   49.458   70.110   15.000  -2.55  0 358 C
+ATOM     5157    C   CB ?  ASN    Cxp 131 ?   49.099   72.344   16.675   0.00  0 358 C
+ATOM     5158    C   CG ?  ASN    Cxp 131 ?   48.068   73.136   17.435   0.00  0 358 C
+ATOM     5159    O  OD1 ?  ASN    Cxp 131 ?   46.848   72.862   17.330   0.00  0 358 C
+ATOM     5161    N    N ?  PHE    Cxp 132 ?   50.528   68.950   16.668   0.00  0 359 C
+ATOM     5163    C    C ?  PHE    Cxp 132 ?   49.677   66.798   16.013   0.00  0 359 C
+ATOM     5164    O    O ?  PHE    Cxp 132 ?   48.967   66.829   17.018   0.00  0 359 C
+ATOM     5177    C  CG1 ?  ILE    Cxp 133 ?   46.547   66.252   14.171   0.00  0 360 C
+ATOM     5179    C  CD1 ?  ILE    Cxp 133 ?   45.747   66.718   12.918   0.00  0 360 C
+ATOM     5590    C   CA ?  SER    Cxp 190 ?   42.695   65.333   13.987   0.00  0 417 C
+ATOM     5591    C    C ?  SER    Cxp 190 ?   43.234   64.721   15.300   0.00  0 417 C
+ATOM     5593    C   CB ?  SER    Cxp 190 ?   41.413   66.119   14.252   0.00  0 417 C
+ATOM     5595    N    N ?  ILE    Cxp 191 ?   43.539   65.578   16.244   0.00  0 418 C
+ATOM     5596    C   CA ?  ILE    Cxp 191 ?   43.914   65.163   17.570   0.00  0 418 C
+ATOM     5599    C   CB ?  ILE    Cxp 191 ?   44.408   66.418   18.397   0.00  0 418 C
+ATOM     5600    C  CG1 ?  ILE    Cxp 191 ?   45.611   66.019   19.250   0.00  0 418 C
+ATOM     5601    C  CG2 ?  ILE    Cxp 191 ?   43.280   67.132   19.172   0.00  0 418 C
+#