Merge pull request #128 from Discngine/issue-127

fixing mmcif writing for db mode

.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/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

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

headers/voronoi.h

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

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

@@ -56,7 +56,7 @@ 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");
@@ -68,8 +68,11 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     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);
@@ -79,15 +82,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     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 == 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 == 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])
@@ -317,7 +313,7 @@ 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);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -342,7 +338,7 @@ 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)
                         {
@@ -354,7 +350,7 @@ 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);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -398,13 +394,10 @@ 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);
-                        // 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);
+
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_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 +427,10 @@ 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 == 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 +438,22 @@ 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])
@@ -472,7 +465,7 @@ 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);
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_id = at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
                         atom->x = ts_in.coords[(3 * i)];
@@ -496,7 +489,7 @@ 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)
@@ -509,7 +502,7 @@ 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);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -538,7 +531,7 @@ 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;
@@ -547,7 +540,7 @@ 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);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -569,7 +562,7 @@ 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++)
@@ -585,7 +578,7 @@ 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);
+                                    strcpy(atom->chain, at_in[i].chain_auth);
                                     atom->res_id = at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
@@ -614,16 +607,18 @@ 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 == 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 +633,9 @@ 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 +649,12 @@ 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])
@@ -1258,8 +1229,10 @@ 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 +1241,25 @@ 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 +1267,7 @@ 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])
@@ -1356,9 +1321,8 @@ 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;
@@ -1380,7 +1344,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 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++)
@@ -1422,7 +1386,9 @@ 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 +1398,7 @@ 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 +1411,8 @@ 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 +1426,16 @@ 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 +1542,49 @@ 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)

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/writepocket.c

@@ -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->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
@@ -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);

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)       : 433.6981
+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_entity_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_asym_id
+ATOM     3335    C  CG2 .  THR   B .  167 ?   23.611  41.302  32.855  0.00  0   B
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     3399    C  CD1 .  ILE   B .  176 ?   22.413  39.457  35.570  0.00  0   B
+ATOM     3397    C  CG1 .  ILE   B .  176 ?   21.483  40.079  36.568  0.00  0   B
+ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
+ATOM     3378    C   CB .  PHE   B .  174 ?   18.390  43.943  35.478  0.00  0   B
+ATOM     3332    O    O .  THR   B .  167 ?   21.633  44.211  32.694 -1.07  0   B
+ATOM     3735    C   CA .  SER   B .  219 ?   24.536  33.701  35.059  0.00  0   B
+ATOM     3729    O    O .  LEU   B .  218 ?   23.720  35.415  36.830  0.00  0   B
+ATOM     1239    C   CB .  ALA   A .  168 ?   21.952  31.542  32.252  0.00  0   A
+ATOM     3454    O    O .  SER   B .  183 ?   12.618  40.049  35.823 -1.07  0   B
+ATOM     3488    O  OD1 .  ASN   B .  187 ?   12.383  40.631  32.241 -1.07  0   B
+ATOM     3380    C  CD1 .  PHE   B .  174 ?   16.492  43.534  33.887  0.00  0   B
+ATOM     3460    O    O .  LEU   B .  184 ?   14.089  37.175  34.255 -3.21  0   B
+ATOM     3458    C   CA .  LEU   B .  184 ?   14.473  38.083  36.400  0.00  0   B
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
+ATOM     3760    C   CB .  TYR   B .  222 ?   18.259  32.959  38.062  0.00  0   B
+ATOM     3756    N    N .  TYR   B .  222 ?   20.251  33.164  39.466 -1.09  0   B
+ATOM     3398    C  CG2 .  ILE   B .  176 ?   21.928  38.594  38.565  0.00  0   B
+ATOM     3463    C  CD1 .  LEU   B .  184 ?   17.369  37.208  38.932  0.00  0   B
+ATOM     3737    O    O .  SER   B .  219 ?   23.395  31.686  35.276 -1.07  0   B
+ATOM     3728    C    C .  LEU   B .  218 ?   24.912  35.395  36.613  0.00  0   B
+ATOM     3730    C   CB .  LEU   B .  218 ?   25.994  37.693  36.437  0.00  0   B
+ATOM     3738    C   CB .  SER   B .  219 ?   25.152  33.376  33.704  0.00  0   B
+ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
+ATOM     3464    C  CD2 .  LEU   B .  184 ?   17.512  38.953  37.066  0.00  0   B
+ATOM     3734    N    N .  SER   B .  219 ?   25.438  34.466  35.848 -1.09  0   B
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     3461    C   CB .  LEU   B .  184 ?   15.552  37.271  37.155  0.00  0   B
+ATOM     1250    N    N .  ALA   A .  170 ?   17.224  33.325  33.516 -4.79  0   A
+ATOM     1255    N    N .  GLY   A .  171 ?   17.151  30.558  34.884 -1.09  0   A
+ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   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_entity_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_asym_id
+ATOM     1236    C   CA .  ALA   A .  168 ?   21.345  31.742  30.855  0.00  0   A
+ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     1239    C   CB .  ALA   A .  168 ?   21.952  31.542  32.252  0.00  0   A
+ATOM     1240    N    N .  HIS   A .  169 ?   19.130  32.633  31.043  0.00  0   A
+ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
+ATOM     1242    C    C .  HIS   A .  169 ?   17.124  32.937  32.241  0.00  0   A
+ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
+ATOM     1245    C   CG .  HIS   A .  169 ?   16.104  34.797  30.229  0.00  0   A
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     1249    N  NE2 .  HIS   A .  169 ?   14.590  36.367  30.529  0.00  0   A
+ATOM     1250    N    N .  ALA   A .  170 ?   17.224  33.325  33.516 -4.79  0   A
+ATOM     1251    C   CA .  ALA   A .  170 ?   16.342  32.830  34.571  0.00  0   A
+ATOM     1252    C    C .  ALA   A .  170 ?   16.105  31.311  34.539  0.00  0   A
+ATOM     1254    C   CB .  ALA   A .  170 ?   15.038  33.564  34.528  0.00  0   A
+ATOM     1255    N    N .  GLY   A .  171 ?   17.151  30.558  34.884 -1.09  0   A
+ATOM     3331    C    C .  THR   B .  167 ?   22.771  43.904  32.327  0.00  0   B
+ATOM     3332    O    O .  THR   B .  167 ?   21.633  44.211  32.694 -1.07  0   B
+ATOM     3333    C   CB .  THR   B .  167 ?   23.958  42.338  33.911  0.00  0   B
+ATOM     3335    C  CG2 .  THR   B .  167 ?   23.611  41.302  32.855  0.00  0   B
+ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     3341    N    N .  HIS   B .  169 ?   19.743  43.280  29.949  0.00  0   B
+ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
+ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
+ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
+ATOM     3347    N  ND1 .  HIS   B .  169 ?   15.399  41.864  29.978 -2.19  0   B
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     3349    C  CE1 .  HIS   B .  169 ?   14.459  40.980  29.690  0.00  0   B
+ATOM     3350    N  NE2 .  HIS   B .  169 ?   14.959  39.769  29.859  0.00  0   B
+ATOM     3374    N    N .  PHE   B .  174 ?   19.806  45.500  34.237  0.00  0   B
+ATOM     3375    C   CA .  PHE   B .  174 ?   19.360  45.109  35.564  0.00  0   B
+ATOM     3377    O    O .  PHE   B .  174 ?   21.500  44.304  36.088  0.00  0   B
+ATOM     3378    C   CB .  PHE   B .  174 ?   18.390  43.943  35.478  0.00  0   B
+ATOM     3379    C   CG .  PHE   B .  174 ?   17.076  44.325  34.855  0.00  0   B
+ATOM     3380    C  CD1 .  PHE   B .  174 ?   16.492  43.534  33.887  0.00  0   B
+ATOM     3382    C  CE1 .  PHE   B .  174 ?   15.273  43.909  33.319  0.00  0   B
+ATOM     3396    C   CB .  ILE   B .  176 ?   21.966  39.989  38.044  0.00  0   B
+ATOM     3397    C  CG1 .  ILE   B .  176 ?   21.483  40.079  36.568  0.00  0   B
+ATOM     3398    C  CG2 .  ILE   B .  176 ?   21.928  38.594  38.565  0.00  0   B
+ATOM     3399    C  CD1 .  ILE   B .  176 ?   22.413  39.457  35.570  0.00  0   B
+ATOM     3453    C    C .  SER   B .  183 ?   12.616  39.571  36.930  0.00  0   B
+ATOM     3454    O    O .  SER   B .  183 ?   12.618  40.049  35.823 -1.07  0   B
+ATOM     3457    N    N .  LEU   B .  184 ?   13.478  38.624  37.304  0.00  0   B
+ATOM     3458    C   CA .  LEU   B .  184 ?   14.473  38.083  36.400  0.00  0   B
+ATOM     3459    C    C .  LEU   B .  184 ?   13.764  37.165  35.433  0.00  0   B
+ATOM     3460    O    O .  LEU   B .  184 ?   14.089  37.175  34.255 -3.21  0   B
+ATOM     3461    C   CB .  LEU   B .  184 ?   15.552  37.271  37.155  0.00  0   B
+ATOM     3462    C   CG .  LEU   B .  184 ?   16.587  38.098  37.951  0.00  0   B
+ATOM     3463    C  CD1 .  LEU   B .  184 ?   17.369  37.208  38.932  0.00  0   B
+ATOM     3464    C  CD2 .  LEU   B .  184 ?   17.512  38.953  37.066  0.00  0   B
+ATOM     3488    O  OD1 .  ASN   B .  187 ?   12.383  40.631  32.241 -1.07  0   B
+ATOM     3727    C   CA .  LEU   B .  218 ?   25.851  36.423  37.264  0.00  0   B
+ATOM     3728    C    C .  LEU   B .  218 ?   24.912  35.395  36.613  0.00  0   B
+ATOM     3729    O    O .  LEU   B .  218 ?   23.720  35.415  36.830  0.00  0   B
+ATOM     3730    C   CB .  LEU   B .  218 ?   25.994  37.693  36.437  0.00  0   B
+ATOM     3734    N    N .  SER   B .  219 ?   25.438  34.466  35.848 -1.09  0   B
+ATOM     3735    C   CA .  SER   B .  219 ?   24.536  33.701  35.059  0.00  0   B
+ATOM     3736    C    C .  SER   B .  219 ?   24.150  32.474  35.811  0.00  0   B
+ATOM     3737    O    O .  SER   B .  219 ?   23.395  31.686  35.276 -1.07  0   B
+ATOM     3738    C   CB .  SER   B .  219 ?   25.152  33.376  33.704  0.00  0   B
+ATOM     3751    C    C .  VAL   B .  221 ?   21.031  32.982  40.538  0.00  0   B
+ATOM     3753    C   CB .  VAL   B .  221 ?   22.559  35.077  40.397  0.00  0   B
+ATOM     3756    N    N .  TYR   B .  222 ?   20.251  33.164  39.466 -1.09  0   B
+ATOM     3757    C   CA .  TYR   B .  222 ?   18.886  32.708  39.432  0.00  0   B
+ATOM     3760    C   CB .  TYR   B .  222 ?   18.259  32.959  38.062  0.00  0   B
+ATOM     3761    C   CG .  TYR   B .  222 ?   16.811  32.522  38.032  0.00  0   B
+ATOM     3762    C  CD1 .  TYR   B .  222 ?   15.795  33.459  38.329  0.00  0   B
+ATOM     3768    N    N .  GLU   B .  223 ?   19.652  30.471  39.123  0.00  0   B
+ATOM     3773    C   CG .  GLU   B .  223 ?   20.865  28.953  37.013  0.00  0   B
+ATOM     3776    O  OE2 .  GLU   B .  223 ?   21.549  28.266  34.820  0.00  0   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)       : 155.2499
+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_entity_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_asym_id
+ATOM     1405    C  CD2 .  PHE   A .  189 ?   10.703  31.452  22.157  0.00  0   A
+ATOM     1435    O    O .  SER   A .  193 ?   11.879  32.960  15.552 -3.21  0   A
+ATOM     1407    C  CE2 .  PHE   A .  189 ?   11.966  31.656  22.739  0.00  0   A
+ATOM      996    O    O .  ARG   A .  135 ?   13.454  28.096  20.320 -4.69  0   A
+ATOM     1436    C   CB .  SER   A .  193 ?    9.997  34.149  17.982  0.00  0   A
+ATOM     1329    N    N .  ALA   A .  180 ?   14.229  35.929  18.757 -1.09  0   A
+ATOM     1327    O  OG1 .  THR   A .  179 ?   17.108  33.330  21.134 -2.14  0   A
+ATOM     1290    C   CD .  PRO   A .  175 ?   18.295  29.738  22.438  0.00  0   A
+ATOM     1323    C   CA .  THR   A .  179 ?   16.193  34.623  19.411  0.00  0   A
+ATOM     1437    O   OG .  SER   A .  193 ?    9.317  33.077  18.605  0.00  0   A
+ATOM     1289    C   CG .  PRO   A .  175 ?   18.737  29.443  21.033  0.00  0   A
+ATOM     1312    C   CB .  TRP   A .  178 ?   18.807  31.481  17.128  0.00  0   A
+ATOM     1005    C   CA .  ASP   A .  136 ?   14.988  26.627  18.681  0.00  0   A
+ATOM     1311    O    O .  TRP   A .  178 ?   16.495  33.261  16.896 -2.14  0   A
+ATOM     1471    C   CB .  ALA   A .  197 ?   14.926  31.065  14.885  0.00  0   A
+ATOM     1355    O   OG .  SER   A .  183 ?   10.954  35.267  20.964  0.00  0   A
+ATOM     1012    N    N .  LEU   A .  137 ?   14.970  26.942  16.300  0.00  0   A
+ATOM     1444    O  OD1 .  ASP   A .  194 ?   10.115  28.834  16.531  0.00  0   A
+ATOM      995    C    C .  ARG   A .  135 ?   12.856  27.406  19.519  0.00  0   A
+ATOM      994    C   CA .  ARG   A .  135 ?   11.309  27.407  19.509  0.00  0   A
+ATOM     1328    C  CG2 .  THR   A .  179 ?   15.235  34.657  21.794  0.00  0   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_entity_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_asym_id
+ATOM      993    N    N .  ARG   A .  135 ?   10.598  26.723  18.417  0.00  0   A
+ATOM      994    C   CA .  ARG   A .  135 ?   11.309  27.407  19.509  0.00  0   A
+ATOM      995    C    C .  ARG   A .  135 ?   12.856  27.406  19.519  0.00  0   A
+ATOM      996    O    O .  ARG   A .  135 ?   13.454  28.096  20.320 -4.69  0   A
+ATOM      997    C   CB .  ARG   A .  135 ?   10.850  26.919  20.881  0.00  0   A
+ATOM     1004    N    N .  ASP   A .  136 ?   13.515  26.641  18.666  0.00  0   A
+ATOM     1005    C   CA .  ASP   A .  136 ?   14.988  26.627  18.681  0.00  0   A
+ATOM     1006    C    C .  ASP   A .  136 ?   15.413  26.185  17.291  0.00  0   A
+ATOM     1008    C   CB .  ASP   A .  136 ?   15.490  25.673  19.755  0.00  0   A
+ATOM     1009    C   CG .  ASP   A .  136 ?   16.996  25.759  19.996  0.00  0   A
+ATOM     1010    O  OD1 .  ASP   A .  136 ?   17.712  26.739  19.639  0.00  0   A
+ATOM     1012    N    N .  LEU   A .  137 ?   14.970  26.942  16.300  0.00  0   A
+ATOM     1014    C    C .  LEU   A .  137 ?   16.652  27.030  14.689  0.00  0   A
+ATOM     1015    O    O .  LEU   A .  137 ?   16.968  28.209  14.932  0.00  0   A
+ATOM     1280    C  CD2 .  PHE   A .  174 ?   15.409  30.643  25.623  0.00  0   A
+ATOM     1287    O    O .  PRO   A .  175 ?   19.472  32.424  20.666  0.00  0   A
+ATOM     1289    C   CG .  PRO   A .  175 ?   18.737  29.443  21.033  0.00  0   A
+ATOM     1290    C   CD .  PRO   A .  175 ?   18.295  29.738  22.438  0.00  0   A
+ATOM     1309    C   CA .  TRP   A .  178 ?   18.854  33.025  17.137  0.00  0   A
+ATOM     1310    C    C .  TRP   A .  178 ?   17.481  33.558  17.564  0.00  0   A
+ATOM     1311    O    O .  TRP   A .  178 ?   16.495  33.261  16.896 -2.14  0   A
+ATOM     1312    C   CB .  TRP   A .  178 ?   18.807  31.481  17.128  0.00  0   A
+ATOM     1322    N    N .  THR   A .  179 ?   17.421  34.347  18.657  0.00  0   A
+ATOM     1323    C   CA .  THR   A .  179 ?   16.193  34.623  19.411  0.00  0   A
+ATOM     1324    C    C .  THR   A .  179 ?   15.545  35.958  19.044  0.00  0   A
+ATOM     1326    C   CB .  THR   A .  179 ?   16.508  34.581  20.893  0.00  0   A
+ATOM     1327    O  OG1 .  THR   A .  179 ?   17.108  33.330  21.134 -2.14  0   A
+ATOM     1328    C  CG2 .  THR   A .  179 ?   15.235  34.657  21.794  0.00  0   A
+ATOM     1329    N    N .  ALA   A .  180 ?   14.229  35.929  18.757 -1.09  0   A
+ATOM     1333    C   CB .  ALA   A .  180 ?   12.155  36.812  17.751  0.00  0   A
+ATOM     1354    C   CB .  SER   A .  183 ?   11.829  35.508  22.060  0.00  0   A
+ATOM     1355    O   OG .  SER   A .  183 ?   10.954  35.267  20.964  0.00  0   A
+ATOM     1405    C  CD2 .  PHE   A .  189 ?   10.703  31.452  22.157  0.00  0   A
+ATOM     1407    C  CE2 .  PHE   A .  189 ?   11.966  31.656  22.739  0.00  0   A
+ATOM     1408    C   CZ .  PHE   A .  189 ?   12.053  32.229  24.016  0.00  0   A
+ATOM     1433    C   CA .  SER   A .  193 ?    9.893  34.090  16.472  0.00  0   A
+ATOM     1434    C    C .  SER   A .  193 ?   10.658  32.899  15.802  0.00  0   A
+ATOM     1435    O    O .  SER   A .  193 ?   11.879  32.960  15.552 -3.21  0   A
+ATOM     1436    C   CB .  SER   A .  193 ?    9.997  34.149  17.982  0.00  0   A
+ATOM     1437    O   OG .  SER   A .  193 ?    9.317  33.077  18.605  0.00  0   A
+ATOM     1438    N    N .  ASP   A .  194 ?    9.907  31.853  15.450  0.00  0   A
+ATOM     1439    C   CA .  ASP   A .  194 ?   10.435  30.800  14.622  0.00  0   A
+ATOM     1444    O  OD1 .  ASP   A .  194 ?   10.115  28.834  16.531  0.00  0   A
+ATOM     1471    C   CB .  ALA   A .  197 ?   14.926  31.065  14.885  0.00  0   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)       : 292.3979
+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_entity_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_asym_id
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     3271    O   OG .  SER   B .  158 ?   19.353  51.914  34.201 -4.02  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     3383    C  CE2 .  PHE   B .  174 ?   15.221  45.900  34.664  0.00  0   B
+ATOM     3094    O    O .  ARG   B .  135 ?   14.784  48.309  40.445 -7.50  0   B
+ATOM     3097    C   CD .  ARG   B .  135 ?   10.822  49.558  37.921  0.00  0   B
+ATOM     3504    C  CE2 .  PHE   B .  189 ?   12.691  45.021  38.263  0.00  0   B
+ATOM     3368    O    O .  LYS   B .  173 ?   18.932  47.542  34.352 -3.62  0   B
+ATOM     3109    O  OD2 .  ASP   B .  136 ?   19.063  51.084  39.753 -0.40  0   B
+ATOM     3258    N    N .  LEU   B .  157 ?   20.869  54.873  37.697  0.00  0   B
+ATOM     3095    C   CB .  ARG   B .  135 ?   12.276  49.729  39.764  0.00  0   B
+ATOM     3084    O    O .  HIS   B .  134 ?   12.372  52.048  41.332 -1.07  0   B
+ATOM     3381    C  CD2 .  PHE   B .  174 ?   16.430  45.506  35.243  0.00  0   B
+ATOM     3270    C   CB .  SER   B .  158 ?   20.116  50.947  34.907  0.00  0   B
+ATOM     3326    C  CE2 .  TYR   B .  166 ?   21.152  49.314  38.053  0.00  0   B
+ATOM     3391    C   CD .  PRO   B .  175 ?   19.172  45.854  38.445  0.00  0   B
+ATOM     3106    C   CB .  ASP   B .  136 ?   17.005  50.806  40.933  0.00  0   B
+ATOM     3107    C   CG .  ASP   B .  136 ?   18.465  50.434  40.626  0.00  0   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_entity_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_asym_id
+ATOM     3084    O    O .  HIS   B .  134 ?   12.372  52.048  41.332 -1.07  0   B
+ATOM     3092    C   CA .  ARG   B .  135 ?   12.705  49.230  41.141  0.00  0   B
+ATOM     3093    C    C .  ARG   B .  135 ?   14.235  49.115  41.170  0.00  0   B
+ATOM     3094    O    O .  ARG   B .  135 ?   14.784  48.309  40.445 -7.50  0   B
+ATOM     3095    C   CB .  ARG   B .  135 ?   12.276  49.729  39.764  0.00  0   B
+ATOM     3096    C   CG .  ARG   B .  135 ?   10.987  49.132  39.313  0.00  0   B
+ATOM     3097    C   CD .  ARG   B .  135 ?   10.822  49.558  37.921  0.00  0   B
+ATOM     3098    N   NE .  ARG   B .  135 ?    9.837  48.697  37.316 -3.28  0   B
+ATOM     3099    C   CZ .  ARG   B .  135 ?    9.680  48.564  36.008  0.00  0   B
+ATOM     3100    N  NH1 .  ARG   B .  135 ?   10.479  49.242  35.166  0.00  0   B
+ATOM     3102    N    N .  ASP   B .  136 ?   14.929  49.943  41.933  0.00  0   B
+ATOM     3103    C   CA .  ASP   B .  136 ?   16.383  49.878  41.974  0.00  0   B
+ATOM     3106    C   CB .  ASP   B .  136 ?   17.005  50.806  40.933  0.00  0   B
+ATOM     3107    C   CG .  ASP   B .  136 ?   18.465  50.434  40.626  0.00  0   B
+ATOM     3108    O  OD1 .  ASP   B .  136 ?   19.011  49.469  41.230 -2.14  0   B
+ATOM     3109    O  OD2 .  ASP   B .  136 ?   19.063  51.084  39.753 -0.40  0   B
+ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM     3256    C    C .  GLY   B .  156 ?   20.360  55.778  36.866  0.00  0   B
+ATOM     3258    N    N .  LEU   B .  157 ?   20.869  54.873  37.697  0.00  0   B
+ATOM     3266    N    N .  SER   B .  158 ?   21.413  52.688  36.129  0.00  0   B
+ATOM     3267    C   CA .  SER   B .  158 ?   21.516  51.514  35.236  0.00  0   B
+ATOM     3270    C   CB .  SER   B .  158 ?   20.116  50.947  34.907  0.00  0   B
+ATOM     3271    O   OG .  SER   B .  158 ?   19.353  51.914  34.201 -4.02  0   B
+ATOM     3324    C  CD2 .  TYR   B .  166 ?   21.644  48.614  37.025  0.00  0   B
+ATOM     3326    C  CE2 .  TYR   B .  166 ?   21.152  49.314  38.053  0.00  0   B
+ATOM     3368    O    O .  LYS   B .  173 ?   18.932  47.542  34.352 -3.62  0   B
+ATOM     3375    C   CA .  PHE   B .  174 ?   19.360  45.109  35.564  0.00  0   B
+ATOM     3381    C  CD2 .  PHE   B .  174 ?   16.430  45.506  35.243  0.00  0   B
+ATOM     3383    C  CE2 .  PHE   B .  174 ?   15.221  45.900  34.664  0.00  0   B
+ATOM     3390    C   CG .  PRO   B .  175 ?   19.698  46.334  39.774  0.00  0   B
+ATOM     3391    C   CD .  PRO   B .  175 ?   19.172  45.854  38.445  0.00  0   B
+ATOM     3502    C  CD2 .  PHE   B .  189 ?   11.410  45.318  38.790  0.00  0   B
+ATOM     3504    C  CE2 .  PHE   B .  189 ?   12.691  45.021  38.263  0.00  0   B
+ATOM     3505    C   CZ .  PHE   B .  189 ?   12.791  44.477  36.970  0.00  0   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)       : 403.2792
+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_entity_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_asym_id
+ATOM     7064    N    N .  VAL   D .  111 ?   48.340  24.744  22.841  0.00  0   D
+ATOM     7069    C  CG1 .  VAL   D .  111 ?   50.065  24.177  20.697  0.00  0   D
+ATOM     7068    C   CB .  VAL   D .  111 ?   49.531  23.019  21.320  0.00  0   D
+ATOM     7063    C   CB .  ALA   D .  110 ?   45.905  26.806  22.761  0.00  0   D
+ATOM     8096    C  CG1 .  VAL   D .  241 ?   40.339  21.749  29.386  0.00  0   D
+ATOM     7780    O    O .  LEU   D .  202 ?   42.550  24.062  33.744  0.00  0   D
+ATOM     7784    C  CD2 .  LEU   D .  202 ?   42.820  19.922  32.429  0.00  0   D
+ATOM     7814    C  CG2 .  ILE   D .  205 ?   46.612  24.182  31.921  0.00  0   D
+ATOM     7081    O    O .  LEU   D .  113 ?   47.597  21.725  29.219 -1.07  0   D
+ATOM     7086    N    N .  LEU   D .  114 ?   47.359  21.989  26.988  0.00  0   D
+ATOM     7087    C   CA .  LEU   D .  114 ?   46.823  20.670  26.737  0.00  0   D
+ATOM     7080    C    C .  LEU   D .  113 ?   47.767  22.386  28.183  0.00  0   D
+ATOM     7062    O    O .  ALA   D .  110 ?   47.080  24.204  24.629 -3.21  0   D
+ATOM     7093    C  CD2 .  LEU   D .  114 ?   45.275  20.097  23.190  0.00  0   D
+ATOM     8079    C   CG .  PRO   D .  238 ?   40.497  24.257  24.472  0.00  0   D
+ATOM     7061    C    C .  ALA   D .  110 ?   47.472  25.051  23.811  0.00  0   D
+ATOM     8080    C   CD .  PRO   D .  238 ?   40.408  25.135  25.676  0.00  0   D
+ATOM     8067    O    O .  GLY   D .  236 ?   40.728  28.470  25.473 -1.21  0   D
+ATOM     7060    C   CA .  ALA   D .  110 ?   46.959  26.484  23.905  0.00  0   D
+ATOM     7084    C  CD1 .  LEU   D .  113 ?   46.418  27.158  28.740  0.00  0   D
+ATOM     7817    C   CA .  ALA   D .  206 ?   43.249  27.236  31.702  0.00  0   D
+ATOM     7819    O    O .  ALA   D .  206 ?   43.166  29.530  31.087 -4.69  0   D
+ATOM     8069    C   CA .  CYS   D .  237 ?   39.173  27.291  27.413  0.00  0   D
+ATOM     7118    C   CB .  ALA   D .  117 ?   45.712  18.926  30.827  0.00  0   D
+ATOM     7820    C   CB .  ALA   D .  206 ?   41.725  26.810  31.590  0.00  0   D
+ATOM     8073    S   SG .  CYS   D .  237 ?   38.662  25.215  29.286  0.00  0   D
+ATOM     7816    N    N .  ALA   D .  206 ?   43.950  26.440  32.723  0.00  0   D
+ATOM     7065    C   CA .  VAL   D .  111 ?   48.863  23.360  22.717  0.00  0   D
+ATOM     7082    C   CB .  LEU   D .  113 ?   47.325  24.825  28.299  0.00  0   D
+ATOM     8097    C  CG2 .  VAL   D .  241 ?   40.590  21.066  26.854  0.00  0   D
+ATOM     7092    C  CD1 .  LEU   D .  114 ?   44.050  19.857  25.449  0.00  0   D
+ATOM     8308    C  CE1 .  PHE   D .  266 ?   42.431  17.800  28.875  0.00  0   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_entity_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_asym_id
+ATOM     7059    N    N .  ALA   D .  110 ?   48.007  27.461  23.893 -1.09  0   D
+ATOM     7060    C   CA .  ALA   D .  110 ?   46.959  26.484  23.905  0.00  0   D
+ATOM     7061    C    C .  ALA   D .  110 ?   47.472  25.051  23.811  0.00  0   D
+ATOM     7062    O    O .  ALA   D .  110 ?   47.080  24.204  24.629 -3.21  0   D
+ATOM     7063    C   CB .  ALA   D .  110 ?   45.905  26.806  22.761  0.00  0   D
+ATOM     7064    N    N .  VAL   D .  111 ?   48.340  24.744  22.841  0.00  0   D
+ATOM     7065    C   CA .  VAL   D .  111 ?   48.863  23.360  22.717  0.00  0   D
+ATOM     7068    C   CB .  VAL   D .  111 ?   49.531  23.019  21.320  0.00  0   D
+ATOM     7069    C  CG1 .  VAL   D .  111 ?   50.065  24.177  20.697  0.00  0   D
+ATOM     7079    C   CA .  LEU   D .  113 ?   48.430  23.739  28.221  0.00  0   D
+ATOM     7080    C    C .  LEU   D .  113 ?   47.767  22.386  28.183  0.00  0   D
+ATOM     7081    O    O .  LEU   D .  113 ?   47.597  21.725  29.219 -1.07  0   D
+ATOM     7082    C   CB .  LEU   D .  113 ?   47.325  24.825  28.299  0.00  0   D
+ATOM     7083    C   CG .  LEU   D .  113 ?   47.664  26.335  28.429  0.00  0   D
+ATOM     7084    C  CD1 .  LEU   D .  113 ?   46.418  27.158  28.740  0.00  0   D
+ATOM     7086    N    N .  LEU   D .  114 ?   47.359  21.989  26.988  0.00  0   D
+ATOM     7087    C   CA .  LEU   D .  114 ?   46.823  20.670  26.737  0.00  0   D
+ATOM     7090    C   CB .  LEU   D .  114 ?   46.375  20.660  25.286  0.00  0   D
+ATOM     7091    C   CG .  LEU   D .  114 ?   45.386  19.662  24.699  0.00  0   D
+ATOM     7092    C  CD1 .  LEU   D .  114 ?   44.050  19.857  25.449  0.00  0   D
+ATOM     7093    C  CD2 .  LEU   D .  114 ?   45.275  20.097  23.190  0.00  0   D
+ATOM     7118    C   CB .  ALA   D .  117 ?   45.712  18.926  30.827  0.00  0   D
+ATOM     7778    C   CA .  LEU   D .  202 ?   42.652  21.867  34.762  0.00  0   D
+ATOM     7779    C    C .  LEU   D .  202 ?   42.175  23.314  34.680  0.00  0   D
+ATOM     7780    O    O .  LEU   D .  202 ?   42.550  24.062  33.744  0.00  0   D
+ATOM     7781    C   CB .  LEU   D .  202 ?   41.521  21.052  34.137  0.00  0   D
+ATOM     7784    C  CD2 .  LEU   D .  202 ?   42.820  19.922  32.429  0.00  0   D
+ATOM     7810    C    C .  ILE   D .  205 ?   45.268  26.571  32.956  0.00  0   D
+ATOM     7812    C   CB .  ILE   D .  205 ?   46.098  24.078  33.335  0.00  0   D
+ATOM     7814    C  CG2 .  ILE   D .  205 ?   46.612  24.182  31.921  0.00  0   D
+ATOM     7816    N    N .  ALA   D .  206 ?   43.950  26.440  32.723  0.00  0   D
+ATOM     7817    C   CA .  ALA   D .  206 ?   43.249  27.236  31.702  0.00  0   D
+ATOM     7818    C    C .  ALA   D .  206 ?   43.351  28.736  31.982  0.00  0   D
+ATOM     7819    O    O .  ALA   D .  206 ?   43.166  29.530  31.087 -4.69  0   D
+ATOM     7820    C   CB .  ALA   D .  206 ?   41.725  26.810  31.590  0.00  0   D
+ATOM     8066    C    C .  GLY   D .  236 ?   39.903  29.189  26.105  0.00  0   D
+ATOM     8067    O    O .  GLY   D .  236 ?   40.728  28.470  25.473 -1.21  0   D
+ATOM     8068    N    N .  CYS   D .  237 ?   39.113  28.714  27.084  0.00  0   D
+ATOM     8069    C   CA .  CYS   D .  237 ?   39.173  27.291  27.413  0.00  0   D
+ATOM     8072    C   CB .  CYS   D .  237 ?   38.727  27.002  28.857  0.00  0   D
+ATOM     8073    S   SG .  CYS   D .  237 ?   38.662  25.215  29.286  0.00  0   D
+ATOM     8074    N    N .  PRO   D .  238 ?   38.989  25.529  25.691  0.00  0   D
+ATOM     8079    C   CG .  PRO   D .  238 ?   40.497  24.257  24.472  0.00  0   D
+ATOM     8080    C   CD .  PRO   D .  238 ?   40.408  25.135  25.676  0.00  0   D
+ATOM     8095    C   CB .  VAL   D .  241 ?   39.605  21.580  27.947  0.00  0   D
+ATOM     8096    C  CG1 .  VAL   D .  241 ?   40.339  21.749  29.386  0.00  0   D
+ATOM     8097    C  CG2 .  VAL   D .  241 ?   40.590  21.066  26.854  0.00  0   D
+ATOM     8306    C  CD1 .  PHE   D .  266 ?   43.156  16.946  28.042  0.00  0   D
+ATOM     8308    C  CE1 .  PHE   D .  266 ?   42.431  17.800  28.875  0.00  0   D
+ATOM     8310    C   CZ .  PHE   D .  266 ?   42.081  17.395  30.126  0.00  0   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)       : 155.2399
+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_entity_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_asym_id
+ATOM     3238    O    O .  ASP   B .  154 ?   17.212  58.730  41.018 -2.14  0   B
+ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     2491    O  OE1 .  GLU   B .   59 ?   14.831  61.607  36.581  0.00  0   B
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     2492    O  OE2 .  GLU   B .   59 ?   15.137  61.777  38.754 -1.07  0   B
+ATOM     2389    N   NZ .  LYS   B .   44 ?   17.801  61.554  36.438 -1.51  0   B
+ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
+ATOM     2489    C   CG .  GLU   B .   59 ?   12.912  61.584  38.000  0.00  0   B
+ATOM     2490    C   CD .  GLU   B .   59 ?   14.404  61.663  37.759  0.00  0   B
+ATOM     3239    C   CB .  ASP   B .  154 ?   15.520  56.620  41.941  0.00  0   B
+ATOM     2488    C   CB .  GLU   B .   59 ?   12.087  61.638  36.697  0.00  0   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_entity_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_asym_id
+ATOM     2389    N   NZ .  LYS   B .   44 ?   17.801  61.554  36.438 -1.51  0   B
+ATOM     2454    O    O .  GLU   B .   55 ?   11.608  61.345  33.284 -1.88  0   B
+ATOM     2485    C   CA .  GLU   B .   59 ?   10.598  61.833  36.936  0.00  0   B
+ATOM     2488    C   CB .  GLU   B .   59 ?   12.087  61.638  36.697  0.00  0   B
+ATOM     2489    C   CG .  GLU   B .   59 ?   12.912  61.584  38.000  0.00  0   B
+ATOM     2490    C   CD .  GLU   B .   59 ?   14.404  61.663  37.759  0.00  0   B
+ATOM     2491    O  OE1 .  GLU   B .   59 ?   14.831  61.607  36.581  0.00  0   B
+ATOM     2492    O  OE2 .  GLU   B .   59 ?   15.137  61.777  38.754 -1.07  0   B
+ATOM     3237    C    C .  ASP   B .  154 ?   17.708  57.721  41.604  0.00  0   B
+ATOM     3238    O    O .  ASP   B .  154 ?   17.212  58.730  41.018 -2.14  0   B
+ATOM     3239    C   CB .  ASP   B .  154 ?   15.520  56.620  41.941  0.00  0   B
+ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     3245    C    C .  PHE   B .  155 ?   19.859  57.712  39.087  0.00  0   B
+ATOM     3246    O    O .  PHE   B .  155 ?   20.558  58.316  38.318 -3.21  0   B
+ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   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)       : 221.5000
+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_entity_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_asym_id
+ATOM     3639    C   CA .  ALA   B .  206 ?   25.485  44.511  57.685  0.00  0   B
+ATOM     2914    C  CD1 .  LEU   B .  113 ?   26.128  47.415  60.882  0.00  0   B
+ATOM     3642    C   CB .  ALA   B .  206 ?   24.633  43.235  57.872  0.00  0   B
+ATOM     3641    O    O .  ALA   B .  206 ?   27.664  43.745  58.449 -4.29  0   B
+ATOM     2922    C  CD1 .  LEU   B .  114 ?   18.369  46.670  63.743  0.00  0   B
+ATOM     3902    C   CD .  PRO   B .  238 ?   22.462  42.067  63.671  0.00  0   B
+ATOM     2892    O    O .  ALA   B .  110 ?   23.079  48.277  64.744 -3.21  0   B
+ATOM     3901    C   CG .  PRO   B .  238 ?   21.818  42.336  65.023  0.00  0   B
+ATOM     3919    C  CG2 .  VAL   B .  241 ?   18.754  43.171  62.407  0.00  0   B
+ATOM     2890    C   CA .  ALA   B .  110 ?   25.351  47.954  65.540  0.00  0   B
+ATOM     3918    C  CG1 .  VAL   B .  241 ?   19.352  42.826  59.944  0.00  0   B
+ATOM     3895    S   SG .  CYS   B .  237 ?   22.468  40.332  60.148  0.00  0   B
+ATOM     2893    C   CB .  ALA   B .  110 ?   25.301  47.008  66.740  0.00  0   B
+ATOM     2916    N    N .  LEU   B .  114 ?   21.229  49.545  62.399 -2.19  0   B
+ATOM     3889    O    O .  GLY   B .  236 ?   25.751  41.531  64.057  0.00  0   B
+ATOM     2912    C   CB .  LEU   B .  113 ?   24.074  48.764  61.348  0.00  0   B
+ATOM     2917    C   CA .  LEU   B .  114 ?   19.825  49.298  62.629  0.00  0   B
+ATOM     4130    C  CE1 .  PHE   B .  266 ?   16.326  46.124  60.459  0.00  0   B
+ATOM     2948    C   CB .  ALA   B .  117 ?   17.953  48.663  58.385  0.00  0   B
+ATOM     2910    C    C .  LEU   B .  113 ?   21.785  49.807  61.241  0.00  0   B
+ATOM     3891    C   CA .  CYS   B .  237 ?   24.487  40.444  62.093  0.00  0   B
+ATOM     2911    O    O .  LEU   B .  113 ?   21.152  49.905  60.239  0.00  0   B
+ATOM     3636    C  CG2 .  ILE   B .  205 ?   23.388  48.453  57.534  0.00  0   B
+ATOM     3602    O    O .  LEU   B .  202 ?   22.353  44.476  55.620 -1.07  0   B
+ATOM     3606    C  CD2 .  LEU   B .  202 ?   18.004  45.680  56.609  0.00  0   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_entity_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_asym_id
+ATOM     2889    N    N .  ALA   B .  110 ?   26.627  48.705  65.568 -4.79  0   B
+ATOM     2890    C   CA .  ALA   B .  110 ?   25.351  47.954  65.540  0.00  0   B
+ATOM     2891    C    C .  ALA   B .  110 ?   24.009  48.706  65.482  0.00  0   B
+ATOM     2892    O    O .  ALA   B .  110 ?   23.079  48.277  64.744 -3.21  0   B
+ATOM     2893    C   CB .  ALA   B .  110 ?   25.301  47.008  66.740  0.00  0   B
+ATOM     2909    C   CA .  LEU   B .  113 ?   23.279  50.062  61.281  0.00  0   B
+ATOM     2910    C    C .  LEU   B .  113 ?   21.785  49.807  61.241  0.00  0   B
+ATOM     2911    O    O .  LEU   B .  113 ?   21.152  49.905  60.239  0.00  0   B
+ATOM     2912    C   CB .  LEU   B .  113 ?   24.074  48.764  61.348  0.00  0   B
+ATOM     2913    C   CG .  LEU   B .  113 ?   25.603  48.823  61.065  0.00  0   B
+ATOM     2914    C  CD1 .  LEU   B .  113 ?   26.128  47.415  60.882  0.00  0   B
+ATOM     2916    N    N .  LEU   B .  114 ?   21.229  49.545  62.399 -2.19  0   B
+ATOM     2917    C   CA .  LEU   B .  114 ?   19.825  49.298  62.629  0.00  0   B
+ATOM     2920    C   CB .  LEU   B .  114 ?   19.727  48.806  64.061  0.00  0   B
+ATOM     2921    C   CG .  LEU   B .  114 ?   18.632  47.903  64.623  0.00  0   B
+ATOM     2922    C  CD1 .  LEU   B .  114 ?   18.369  46.670  63.743  0.00  0   B
+ATOM     2923    C  CD2 .  LEU   B .  114 ?   19.208  47.511  65.968  0.00  0   B
+ATOM     2948    C   CB .  ALA   B .  117 ?   17.953  48.663  58.385  0.00  0   B
+ATOM     3600    C   CA .  LEU   B .  202 ?   20.271  44.948  54.579  0.00  0   B
+ATOM     3601    C    C .  LEU   B .  202 ?   21.600  44.222  54.708  0.00  0   B
+ATOM     3602    O    O .  LEU   B .  202 ?   22.353  44.476  55.620 -1.07  0   B
+ATOM     3603    C   CB .  LEU   B .  202 ?   19.212  44.020  55.190  0.00  0   B
+ATOM     3604    C   CG .  LEU   B .  202 ?   17.876  44.597  55.580  0.00  0   B
+ATOM     3606    C  CD2 .  LEU   B .  202 ?   18.004  45.680  56.609  0.00  0   B
+ATOM     3632    C    C .  ILE   B .  205 ?   25.327  46.616  56.447  0.00  0   B
+ATOM     3634    C   CB .  ILE   B .  205 ?   23.228  47.890  56.077  0.00  0   B
+ATOM     3636    C  CG2 .  ILE   B .  205 ?   23.388  48.453  57.534  0.00  0   B
+ATOM     3638    N    N .  ALA   B .  206 ?   24.907  45.366  56.637  0.00  0   B
+ATOM     3639    C   CA .  ALA   B .  206 ?   25.485  44.511  57.685  0.00  0   B
+ATOM     3640    C    C .  ALA   B .  206 ?   26.979  44.157  57.488  0.00  0   B
+ATOM     3641    O    O .  ALA   B .  206 ?   27.664  43.745  58.449 -4.29  0   B
+ATOM     3642    C   CB .  ALA   B .  206 ?   24.633  43.235  57.872  0.00  0   B
+ATOM     3888    C    C .  GLY   B .  236 ?   26.369  40.695  63.407  0.00  0   B
+ATOM     3889    O    O .  GLY   B .  236 ?   25.751  41.531  64.057  0.00  0   B
+ATOM     3890    N    N .  CYS   B .  237 ?   25.765  39.993  62.462  0.00  0   B
+ATOM     3891    C   CA .  CYS   B .  237 ?   24.487  40.444  62.093  0.00  0   B
+ATOM     3894    C   CB .  CYS   B .  237 ?   24.207  40.164  60.619  0.00  0   B
+ATOM     3895    S   SG .  CYS   B .  237 ?   22.468  40.332  60.148  0.00  0   B
+ATOM     3896    N    N .  PRO   B .  238 ?   22.623  40.597  63.684  0.00  0   B
+ATOM     3901    C   CG .  PRO   B .  238 ?   21.818  42.336  65.023  0.00  0   B
+ATOM     3902    C   CD .  PRO   B .  238 ?   22.462  42.067  63.671  0.00  0   B
+ATOM     3917    C   CB .  VAL   B .  241 ?   19.067  42.132  61.337  0.00  0   B
+ATOM     3918    C  CG1 .  VAL   B .  241 ?   19.352  42.826  59.944  0.00  0   B
+ATOM     3919    C  CG2 .  VAL   B .  241 ?   18.754  43.171  62.407  0.00  0   B
+ATOM     4128    C  CD1 .  PHE   B .  266 ?   15.519  46.953  61.239  0.00  0   B
+ATOM     4130    C  CE1 .  PHE   B .  266 ?   16.326  46.124  60.459  0.00  0   B
+ATOM     4132    C   CZ .  PHE   B .  266 ?   15.850  45.610  59.310  0.00  0   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)       : 380.3267
+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_entity_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_asym_id
+ATOM     7853    C   CA .  SER   D .  211 ?   42.974  31.063  42.423  0.00  0   D
+ATOM     7600    C  CH2 .  TRP   D .  178 ?   43.960  26.363  45.206  0.00  0   D
+ATOM     7847    O    O .  MET   D .  210 ?   44.036  29.741  40.141 -1.07  0   D
+ATOM     7857    O   OG .  SER   D .  211 ?   44.316  32.109  43.942  0.00  0   D
+ATOM     7598    C  CZ2 .  TRP   D .  178 ?   44.202  25.607  44.069  0.00  0   D
+ATOM     7864    C   CD .  PRO   D .  212 ?   41.974  28.366  43.102  0.00  0   D
+ATOM     7302    C   CB .  ARG   D .  140 ?   50.864  24.591  44.728  0.00  0   D
+ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
+ATOM     6936    N  ND2 .  ASN   D .   95 ?   54.321  26.577  41.672  0.00  0   D
+ATOM     6952    C  CD2 .  LEU   D .   97 ?   49.815  28.277  43.031  0.00  0   D
+ATOM     7493    O  OG1 .  THR   D .  165 ?   46.860  28.337  49.111 -0.95  0   D
+ATOM     7307    N  NH1 .  ARG   D .  140 ?   46.275  24.168  46.062  0.00  0   D
+ATOM     7304    C   CD .  ARG   D .  140 ?   49.165  24.333  46.741  0.00  0   D
+ATOM     7468    C   CE .  MET   D .  161 ?   51.743  26.507  49.224  0.00  0   D
+ATOM     6959    O  OD1 .  ASP   D .   98 ?   54.141  30.867  42.252 -4.02  0   D
+ATOM     7806    O  OE1 .  GLU   D .  204 ?   46.278  25.826  41.102 -2.14  0   D
+ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
+ATOM     6991    N  NH2 .  ARG   D .  101 ?   47.806  31.880  42.344 -2.61  0   D
+ATOM     6951    C  CD1 .  LEU   D .   97 ?   48.963  28.362  40.622  0.00  0   D
+ATOM     6990    N  NH1 .  ARG   D .  101 ?   49.983  32.573  42.931 -3.70  0   D
+ATOM     7467    S   SD .  MET   D .  161 ?   50.163  27.152  49.858  0.00  0   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_entity_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_asym_id
+ATOM     6412    C   CG .  GLN   D .   25 ?   57.187  27.871  48.035  0.00  0   D
+ATOM     6413    C   CD .  GLN   D .   25 ?   57.407  27.989  46.515  0.00  0   D
+ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
+ATOM     6934    C   CG .  ASN   D .   95 ?   55.423  26.157  42.216  0.00  0   D
+ATOM     6935    O  OD1 .  ASN   D .   95 ?   56.159  26.889  42.866 -2.14  0   D
+ATOM     6936    N  ND2 .  ASN   D .   95 ?   54.321  26.577  41.672  0.00  0   D
+ATOM     6949    C   CB .  LEU   D .   97 ?   51.235  27.362  41.089  0.00  0   D
+ATOM     6950    C   CG .  LEU   D .   97 ?   50.200  28.423  41.537  0.00  0   D
+ATOM     6951    C  CD1 .  LEU   D .   97 ?   48.963  28.362  40.622  0.00  0   D
+ATOM     6952    C  CD2 .  LEU   D .   97 ?   49.815  28.277  43.031  0.00  0   D
+ATOM     6958    C   CG .  ASP   D .   98 ?   55.143  30.209  41.861  0.00  0   D
+ATOM     6959    O  OD1 .  ASP   D .   98 ?   54.141  30.867  42.252 -4.02  0   D
+ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
+ATOM     6989    C   CZ .  ARG   D .  101 ?   49.039  32.250  41.984  0.00  0   D
+ATOM     6990    N  NH1 .  ARG   D .  101 ?   49.983  32.573  42.931 -3.70  0   D
+ATOM     6991    N  NH2 .  ARG   D .  101 ?   47.806  31.880  42.344 -2.61  0   D
+ATOM     7299    C   CA .  ARG   D .  140 ?   51.455  23.903  43.460  0.00  0   D
+ATOM     7302    C   CB .  ARG   D .  140 ?   50.864  24.591  44.728  0.00  0   D
+ATOM     7303    C   CG .  ARG   D .  140 ?   49.872  23.765  45.486  0.00  0   D
+ATOM     7304    C   CD .  ARG   D .  140 ?   49.165  24.333  46.741  0.00  0   D
+ATOM     7305    N   NE .  ARG   D .  140 ?   48.155  23.363  47.248  0.00  0   D
+ATOM     7306    C   CZ .  ARG   D .  140 ?   46.851  23.301  46.920  0.00  0   D
+ATOM     7307    N  NH1 .  ARG   D .  140 ?   46.275  24.168  46.062  0.00  0   D
+ATOM     7466    C   CG .  MET   D .  161 ?   50.568  27.737  51.524  0.00  0   D
+ATOM     7467    S   SD .  MET   D .  161 ?   50.163  27.152  49.858  0.00  0   D
+ATOM     7468    C   CE .  MET   D .  161 ?   51.743  26.507  49.224  0.00  0   D
+ATOM     7486    O  OD1 .  ASP   D .  164 ?   44.010  31.506  50.068  0.00  0   D
+ATOM     7492    C   CB .  THR   D .  165 ?   46.378  27.253  49.907  0.00  0   D
+ATOM     7493    O  OG1 .  THR   D .  165 ?   46.860  28.337  49.111 -0.95  0   D
+ATOM     7494    C  CG2 .  THR   D .  165 ?   46.295  26.043  49.013  0.00  0   D
+ATOM     7598    C  CZ2 .  TRP   D .  178 ?   44.202  25.607  44.069  0.00  0   D
+ATOM     7599    C  CZ3 .  TRP   D .  178 ?   43.261  25.813  46.311  0.00  0   D
+ATOM     7600    C  CH2 .  TRP   D .  178 ?   43.960  26.363  45.206  0.00  0   D
+ATOM     7805    C   CD .  GLU   D .  204 ?   45.509  25.019  40.553  0.00  0   D
+ATOM     7806    O  OE1 .  GLU   D .  204 ?   46.278  25.826  41.102 -2.14  0   D
+ATOM     7843    O    O .  GLY   D .  209 ?   46.861  31.370  39.639 -1.07  0   D
+ATOM     7846    C    C .  MET   D .  210 ?   43.952  30.964  40.187  0.00  0   D
+ATOM     7847    O    O .  MET   D .  210 ?   44.036  29.741  40.141 -1.07  0   D
+ATOM     7852    N    N .  SER   D .  211 ?   43.574  31.652  41.258 -1.51  0   D
+ATOM     7853    C   CA .  SER   D .  211 ?   42.974  31.063  42.423  0.00  0   D
+ATOM     7854    C    C .  SER   D .  211 ?   41.591  30.664  42.075  0.00  0   D
+ATOM     7856    C   CB .  SER   D .  211 ?   42.985  32.055  43.579  0.00  0   D
+ATOM     7857    O   OG .  SER   D .  211 ?   44.316  32.109  43.942  0.00  0   D
+ATOM     7858    N    N .  PRO   D .  212 ?   41.244  29.428  42.388  0.00  0   D
+ATOM     7864    C   CD .  PRO   D .  212 ?   41.974  28.366  43.102  0.00  0   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)       : 154.0510
+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_entity_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_asym_id
+ATOM     3171    O    O .  GLY   B .  145 ?   24.279  62.076  57.870  0.00  0   B
+ATOM     2751    C  CE1 .  TYR   B .   93 ?   27.916  64.065  57.675  0.00  0   B
+ATOM     3181    N    N .  ASN   B .  147 ?   24.353  63.017  61.460 -3.03  0   B
+ATOM     3189    N    N .  HIS   B .  148 ?   23.808  60.293  60.791  0.00  0   B
+ATOM     2872    O  OE1 .  GLU   B .  107 ?   31.484  58.761  62.681 -0.95  0   B
+ATOM     2752    C  CE2 .  TYR   B .   93 ?   30.166  63.254  57.309  0.00  0   B
+ATOM     2873    O  OE2 .  GLU   B .  107 ?   29.348  59.201  62.656 -7.90  0   B
+ATOM     2754    O   OH .  TYR   B .   93 ?   29.703  64.823  59.044  0.00  0   B
+ATOM     2753    C   CZ .  TYR   B .   93 ?   29.259  64.044  58.017  0.00  0   B
+ATOM     2837    N    N .  ASN   B .  104 ?   33.994  55.404  60.098 -1.09  0   B
+ATOM     2835    C   CB .  CYS   B .  103 ?   31.652  54.686  58.227  0.00  0   B
+ATOM     2832    C   CA .  CYS   B .  103 ?   33.088  55.081  57.860  0.00  0   B
+ATOM     3198    N  NE2 .  HIS   B .  148 ?   27.061  57.958  62.310  0.00  0   B
+ATOM     2802    O   OH .  TYR   B .   99 ?   28.273  57.952  59.075 -7.50  0   B
+ATOM     2799    C  CE1 .  TYR   B .   99 ?   29.022  58.408  56.848  0.00  0   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_entity_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_asym_id
+ATOM     2748    C   CG .  TYR   B .   93 ?   28.347  62.433  55.906  0.00  0   B
+ATOM     2749    C  CD1 .  TYR   B .   93 ?   27.464  63.247  56.634  0.00  0   B
+ATOM     2750    C  CD2 .  TYR   B .   93 ?   29.699  62.458  56.235  0.00  0   B
+ATOM     2751    C  CE1 .  TYR   B .   93 ?   27.916  64.065  57.675  0.00  0   B
+ATOM     2752    C  CE2 .  TYR   B .   93 ?   30.166  63.254  57.309  0.00  0   B
+ATOM     2753    C   CZ .  TYR   B .   93 ?   29.259  64.044  58.017  0.00  0   B
+ATOM     2754    O   OH .  TYR   B .   93 ?   29.703  64.823  59.044  0.00  0   B
+ATOM     2797    C  CD1 .  TYR   B .   99 ?   29.075  58.066  55.512  0.00  0   B
+ATOM     2799    C  CE1 .  TYR   B .   99 ?   29.022  58.408  56.848  0.00  0   B
+ATOM     2801    C   CZ .  TYR   B .   99 ?   28.332  57.583  57.750  0.00  0   B
+ATOM     2802    O   OH .  TYR   B .   99 ?   28.273  57.952  59.075 -7.50  0   B
+ATOM     2832    C   CA .  CYS   B .  103 ?   33.088  55.081  57.860  0.00  0   B
+ATOM     2833    C    C .  CYS   B .  103 ?   34.047  54.644  59.003  0.00  0   B
+ATOM     2835    C   CB .  CYS   B .  103 ?   31.652  54.686  58.227  0.00  0   B
+ATOM     2837    N    N .  ASN   B .  104 ?   33.994  55.404  60.098 -1.09  0   B
+ATOM     2841    C   CB .  ASN   B .  104 ?   34.555  56.312  62.312  0.00  0   B
+ATOM     2871    C   CD .  GLU   B .  107 ?   30.339  58.618  63.162  0.00  0   B
+ATOM     2872    O  OE1 .  GLU   B .  107 ?   31.484  58.761  62.681 -0.95  0   B
+ATOM     2873    O  OE2 .  GLU   B .  107 ?   29.348  59.201  62.656 -7.90  0   B
+ATOM     2880    C  CG2 .  VAL   B .  108 ?   29.169  55.016  60.859  0.00  0   B
+ATOM     3170    C    C .  GLY   B .  145 ?   23.940  63.150  57.410  0.00  0   B
+ATOM     3171    O    O .  GLY   B .  145 ?   24.279  62.076  57.870  0.00  0   B
+ATOM     3173    C   CA .  GLU   B .  146 ?   24.527  64.377  59.465  0.00  0   B
+ATOM     3174    C    C .  GLU   B .  146 ?   23.693  63.539  60.431  0.00  0   B
+ATOM     3181    N    N .  ASN   B .  147 ?   24.353  63.017  61.460 -3.03  0   B
+ATOM     3182    C   CA .  ASN   B .  147 ?   23.727  62.121  62.392  0.00  0   B
+ATOM     3183    C    C .  ASN   B .  147 ?   23.179  60.827  61.846  0.00  0   B
+ATOM     3189    N    N .  HIS   B .  148 ?   23.808  60.293  60.791  0.00  0   B
+ATOM     3190    C   CA .  HIS   B .  148 ?   23.386  59.007  60.237  0.00  0   B
+ATOM     3194    C   CG .  HIS   B .  148 ?   24.910  57.903  61.905  0.00  0   B
+ATOM     3195    N  ND1 .  HIS   B .  148 ?   25.150  58.412  63.173  0.00  0   B
+ATOM     3196    C  CD2 .  HIS   B .  148 ?   26.118  57.632  61.362  0.00  0   B
+ATOM     3197    C  CE1 .  HIS   B .  148 ?   26.449  58.390  63.404  0.00  0   B
+ATOM     3198    N  NE2 .  HIS   B .  148 ?   27.061  57.958  62.310  0.00  0   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)       : 282.0984
+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_entity_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_asym_id
+ATOM     1359    O    O .  LEU   A .  184 ?   14.349  39.319  26.613 -1.07  0   A
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     1363    C  CD2 .  LEU   A .  184 ?   17.375  37.076  23.709  0.00  0   A
+ATOM     3351    N    N .  ALA   B .  170 ?   17.691  42.856  27.354 -6.98  0   B
+ATOM     3340    C   CB .  ALA   B .  168 ?   22.786  43.694  28.595  0.00  0   B
+ATOM     1640    O    O .  SER   A .  219 ?   23.891  43.579  25.385 -1.07  0   A
+ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
+ATOM     1632    O    O .  LEU   A .  218 ?   23.990  39.840  23.886  0.00  0   A
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
+ATOM     1298    C  CD1 .  ILE   A .  176 ?   20.379  35.378  24.896  0.00  0   A
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     1279    C  CD1 .  PHE   A .  174 ?   15.732  32.610  26.953  0.00  0   A
+ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
+ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
+ATOM     1297    C  CG2 .  ILE   A .  176 ?   21.592  37.080  22.335  0.00  0   A
+ATOM     1663    C   CB .  TYR   A .  222 ?   18.792  43.075  23.036  0.00  0   A
+ATOM     1659    N    N .  TYR   A .  222 ?   20.759  42.581  21.578 -1.09  0   A
+ATOM     1362    C  CD1 .  LEU   A .  184 ?   17.407  38.949  21.882  0.00  0   A
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     1357    C   CA .  LEU   A .  184 ?   14.567  38.323  24.463  0.00  0   A
+ATOM     1353    O    O .  SER   A .  183 ?   12.402  36.556  25.117  0.00  0   A
+ATOM     1360    C   CB .  LEU   A .  184 ?   15.704  39.018  23.710  0.00  0   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_entity_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_asym_id
+ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
+ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
+ATOM     1245    C   CG .  HIS   A .  169 ?   16.104  34.797  30.229  0.00  0   A
+ATOM     1246    N  ND1 .  HIS   A .  169 ?   14.891  34.244  30.609  0.00  0   A
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     1248    C  CE1 .  HIS   A .  169 ?   14.000  35.208  30.775  0.00  0   A
+ATOM     1249    N  NE2 .  HIS   A .  169 ?   14.590  36.367  30.529  0.00  0   A
+ATOM     1277    C   CB .  PHE   A .  174 ?   17.509  31.996  25.288  0.00  0   A
+ATOM     1278    C   CG .  PHE   A .  174 ?   16.182  31.763  25.962  0.00  0   A
+ATOM     1279    C  CD1 .  PHE   A .  174 ?   15.732  32.610  26.953  0.00  0   A
+ATOM     1281    C  CE1 .  PHE   A .  174 ?   14.531  32.366  27.594  0.00  0   A
+ATOM     1295    C   CB .  ILE   A .  176 ?   21.717  35.588  22.696  0.00  0   A
+ATOM     1296    C  CG1 .  ILE   A .  176 ?   21.726  35.377  24.235  0.00  0   A
+ATOM     1297    C  CG2 .  ILE   A .  176 ?   21.592  37.080  22.335  0.00  0   A
+ATOM     1298    C  CD1 .  ILE   A .  176 ?   20.379  35.378  24.896  0.00  0   A
+ATOM     1352    C    C .  SER   A .  183 ?   12.496  37.011  23.965  0.00  0   A
+ATOM     1353    O    O .  SER   A .  183 ?   12.402  36.556  25.117  0.00  0   A
+ATOM     1356    N    N .  LEU   A .  184 ?   13.536  37.768  23.548  0.00  0   A
+ATOM     1357    C   CA .  LEU   A .  184 ?   14.567  38.323  24.463  0.00  0   A
+ATOM     1358    C    C .  LEU   A .  184 ?   13.995  39.330  25.444  0.00  0   A
+ATOM     1359    O    O .  LEU   A .  184 ?   14.349  39.319  26.613 -1.07  0   A
+ATOM     1360    C   CB .  LEU   A .  184 ?   15.704  39.018  23.710  0.00  0   A
+ATOM     1361    C   CG .  LEU   A .  184 ?   16.583  38.094  22.866  0.00  0   A
+ATOM     1362    C  CD1 .  LEU   A .  184 ?   17.407  38.949  21.882  0.00  0   A
+ATOM     1363    C  CD2 .  LEU   A .  184 ?   17.375  37.076  23.709  0.00  0   A
+ATOM     1387    O  OD1 .  ASN   A .  187 ?   11.727  35.895  28.835 -1.07  0   A
+ATOM     1631    C    C .  LEU   A .  218 ?   25.155  39.717  24.180  0.00  0   A
+ATOM     1632    O    O .  LEU   A .  218 ?   23.990  39.840  23.886  0.00  0   A
+ATOM     1637    N    N .  SER   A .  219 ?   25.769  40.519  25.023  0.00  0   A
+ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
+ATOM     1639    C    C .  SER   A .  219 ?   24.704  42.744  24.987  0.00  0   A
+ATOM     1640    O    O .  SER   A .  219 ?   23.891  43.579  25.385 -1.07  0   A
+ATOM     1641    C   CB .  SER   A .  219 ?   25.796  41.724  27.105  0.00  0   A
+ATOM     1656    C   CB .  VAL   A .  221 ?   22.834  40.427  20.388  0.00  0   A
+ATOM     1659    N    N .  TYR   A .  222 ?   20.759  42.581  21.578 -1.09  0   A
+ATOM     1660    C   CA .  TYR   A .  222 ?   19.471  43.262  21.673  0.00  0   A
+ATOM     1663    C   CB .  TYR   A .  222 ?   18.792  43.075  23.036  0.00  0   A
+ATOM     1664    C   CG .  TYR   A .  222 ?   17.328  43.572  23.026  0.00  0   A
+ATOM     1665    C  CD1 .  TYR   A .  222 ?   16.254  42.671  22.864  0.00  0   A
+ATOM     3337    C   CA .  ALA   B .  168 ?   22.105  43.779  29.982  0.00  0   B
+ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     3340    C   CB .  ALA   B .  168 ?   22.786  43.694  28.595  0.00  0   B
+ATOM     3341    N    N .  HIS   B .  169 ?   19.743  43.280  29.949  0.00  0   B
+ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
+ATOM     3343    C    C .  HIS   B .  169 ?   17.666  43.282  28.628  0.00  0   B
+ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
+ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     3350    N  NE2 .  HIS   B .  169 ?   14.959  39.769  29.859  0.00  0   B
+ATOM     3351    N    N .  ALA   B .  170 ?   17.691  42.856  27.354 -6.98  0   B
+ATOM     3352    C   CA .  ALA   B .  170 ?   16.780  43.344  26.347  0.00  0   B
+ATOM     3355    C   CB .  ALA   B .  170 ?   15.447  42.648  26.503  0.00  0   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)       : 430.3055
+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_entity_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_asym_id
+ATOM     7944    C   CZ .  TYR   D .  222 ?   28.663  18.750  51.374  0.00  0   D
+ATOM     7943    C  CE2 .  TYR   D .  222 ?   27.884  19.861  51.731  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
+ATOM     7647    C   CB .  ALA   D .  185 ?   30.355  15.757  53.617  0.00  0   D
+ATOM     7644    C   CA .  ALA   D .  185 ?   31.641  16.003  54.405  0.00  0   D
+ATOM     7942    C  CE1 .  TYR   D .  222 ?   29.998  18.906  51.064  0.00  0   D
+ATOM     7940    C  CD1 .  TYR   D .  222 ?   30.563  20.141  51.099  0.00  0   D
+ATOM     7941    C  CD2 .  TYR   D .  222 ?   28.465  21.119  51.770  0.00  0   D
+ATOM     7577    C  CD1 .  ILE   D .  176 ?   37.672  25.382  53.690  0.00  0   D
+ATOM     7576    C  CG2 .  ILE   D .  176 ?   36.592  24.562  50.949  0.00  0   D
+ATOM     7575    C  CG1 .  ILE   D .  176 ?   38.212  24.231  52.898  0.00  0   D
+ATOM     7642    C  CD2 .  LEU   D .  184 ?   36.369  20.233  52.078  0.00  0   D
+ATOM     7641    C  CD1 .  LEU   D .  184 ?   34.448  20.808  50.650  0.00  0   D
+ATOM     7938    C   CB .  TYR   D .  222 ?   30.486  22.638  51.402  0.00  0   D
+ATOM     7934    N    N .  TYR   D .  222 ?   31.202  24.455  49.938 -1.09  0   D
+ATOM     7907    O    O .  LEU   D .  218 ?   34.008  27.525  52.271 -0.40  0   D
+ATOM     7639    C   CB .  LEU   D .  184 ?   34.244  18.838  52.215  0.00  0   D
+ATOM     7939    C   CG .  TYR   D .  222 ?   29.832  21.273  51.448  0.00  0   D
+ATOM     7560    C  CE1 .  PHE   D .  174 ?   39.595  17.433  56.140  0.00  0   D
+ATOM     7638    O    O .  LEU   D .  184 ?   33.870  17.251  55.188  0.00  0   D
+ATOM     7525    N  ND1 .  HIS   D .  169 ?   36.365  20.155  60.429 -1.93  0   D
+ATOM     7558    C  CD1 .  PHE   D .  174 ?   39.696  18.611  55.390  0.00  0   D
+ATOM     7524    C   CG .  HIS   D .  169 ?   36.743  21.442  60.097  0.00  0   D
+ATOM     7527    C  CE1 .  HIS   D .  169 ?   35.170  20.180  60.996  0.00  0   D
+ATOM     7528    N  NE2 .  HIS   D .  169 ?   34.778  21.438  61.089  0.00  0   D
+ATOM     7526    C  CD2 .  HIS   D .  169 ?   35.750  22.249  60.547  0.00  0   D
+ATOM     7637    C    C .  LEU   D .  184 ?   33.727  17.072  53.991  0.00  0   D
+ATOM     7523    C   CB .  HIS   D .  169 ?   38.074  21.770  59.468  0.00  0   D
+ATOM     7556    C   CB .  PHE   D .  174 ?   40.965  20.182  53.857  0.00  0   D
+ATOM     7513    C  CG2 .  THR   D .  167 ?   39.795  26.405  56.782  0.00  0   D
+ATOM     7510    O    O .  THR   D .  167 ?   41.927  23.289  56.784  0.00  0   D
+ATOM     7517    O    O .  ALA   D .  168 ?   40.187  24.764  60.121 -3.35  0   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_entity_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_asym_id
+ATOM     7508    C   CA .  THR   D .  167 ?   42.083  25.551  56.067  0.00  0   D
+ATOM     7509    C    C .  THR   D .  167 ?   42.091  24.462  57.107  0.00  0   D
+ATOM     7510    O    O .  THR   D .  167 ?   41.927  23.289  56.784  0.00  0   D
+ATOM     7511    C   CB .  THR   D .  167 ?   40.671  25.960  55.612  0.00  0   D
+ATOM     7513    C  CG2 .  THR   D .  167 ?   39.795  26.405  56.782  0.00  0   D
+ATOM     7516    C    C .  ALA   D .  168 ?   40.899  23.759  59.909  0.00  0   D
+ATOM     7517    O    O .  ALA   D .  168 ?   40.187  24.764  60.121 -3.35  0   D
+ATOM     7519    N    N .  HIS   D .  169 ?   40.449  22.501  59.939  0.00  0   D
+ATOM     7520    C   CA .  HIS   D .  169 ?   39.141  22.139  60.511  0.00  0   D
+ATOM     7523    C   CB .  HIS   D .  169 ?   38.074  21.770  59.468  0.00  0   D
+ATOM     7524    C   CG .  HIS   D .  169 ?   36.743  21.442  60.097  0.00  0   D
+ATOM     7525    N  ND1 .  HIS   D .  169 ?   36.365  20.155  60.429 -1.93  0   D
+ATOM     7526    C  CD2 .  HIS   D .  169 ?   35.750  22.249  60.547  0.00  0   D
+ATOM     7527    C  CE1 .  HIS   D .  169 ?   35.170  20.180  60.996  0.00  0   D
+ATOM     7528    N  NE2 .  HIS   D .  169 ?   34.778  21.438  61.089  0.00  0   D
+ATOM     7552    N    N .  PHE   D .  174 ?   42.799  21.115  55.259  0.00  0   D
+ATOM     7553    C   CA .  PHE   D .  174 ?   42.370  20.808  53.897  0.00  0   D
+ATOM     7555    O    O .  PHE   D .  174 ?   42.090  23.093  53.386  0.00  0   D
+ATOM     7556    C   CB .  PHE   D .  174 ?   40.965  20.182  53.857  0.00  0   D
+ATOM     7557    C   CG .  PHE   D .  174 ?   40.847  18.885  54.646  0.00  0   D
+ATOM     7558    C  CD1 .  PHE   D .  174 ?   39.696  18.611  55.390  0.00  0   D
+ATOM     7560    C  CE1 .  PHE   D .  174 ?   39.595  17.433  56.140  0.00  0   D
+ATOM     7574    C   CB .  ILE   D .  176 ?   38.063  24.490  51.381  0.00  0   D
+ATOM     7575    C  CG1 .  ILE   D .  176 ?   38.212  24.231  52.898  0.00  0   D
+ATOM     7576    C  CG2 .  ILE   D .  176 ?   36.592  24.562  50.949  0.00  0   D
+ATOM     7577    C  CD1 .  ILE   D .  176 ?   37.672  25.382  53.690  0.00  0   D
+ATOM     7636    C   CA .  LEU   D .  184 ?   34.755  17.589  52.955  0.00  0   D
+ATOM     7637    C    C .  LEU   D .  184 ?   33.727  17.072  53.991  0.00  0   D
+ATOM     7638    O    O .  LEU   D .  184 ?   33.870  17.251  55.188  0.00  0   D
+ATOM     7639    C   CB .  LEU   D .  184 ?   34.244  18.838  52.215  0.00  0   D
+ATOM     7640    C   CG .  LEU   D .  184 ?   35.197  19.678  51.329  0.00  0   D
+ATOM     7641    C  CD1 .  LEU   D .  184 ?   34.448  20.808  50.650  0.00  0   D
+ATOM     7642    C  CD2 .  LEU   D .  184 ?   36.369  20.233  52.078  0.00  0   D
+ATOM     7643    N    N .  ALA   D .  185 ?   32.696  16.403  53.523  0.00  0   D
+ATOM     7644    C   CA .  ALA   D .  185 ?   31.641  16.003  54.405  0.00  0   D
+ATOM     7647    C   CB .  ALA   D .  185 ?   30.355  15.757  53.617  0.00  0   D
+ATOM     7907    O    O .  LEU   D .  218 ?   34.008  27.525  52.271 -0.40  0   D
+ATOM     7929    C    C .  VAL   D .  221 ?   31.195  25.263  48.894  0.00  0   D
+ATOM     7931    C   CB .  VAL   D .  221 ?   33.581  26.362  48.902  0.00  0   D
+ATOM     7934    N    N .  TYR   D .  222 ?   31.202  24.455  49.938 -1.09  0   D
+ATOM     7935    C   CA .  TYR   D .  222 ?   30.407  23.254  49.990  0.00  0   D
+ATOM     7938    C   CB .  TYR   D .  222 ?   30.486  22.638  51.402  0.00  0   D
+ATOM     7939    C   CG .  TYR   D .  222 ?   29.832  21.273  51.448  0.00  0   D
+ATOM     7940    C  CD1 .  TYR   D .  222 ?   30.563  20.141  51.099  0.00  0   D
+ATOM     7941    C  CD2 .  TYR   D .  222 ?   28.465  21.119  51.770  0.00  0   D
+ATOM     7942    C  CE1 .  TYR   D .  222 ?   29.998  18.906  51.064  0.00  0   D
+ATOM     7943    C  CE2 .  TYR   D .  222 ?   27.884  19.861  51.731  0.00  0   D
+ATOM     7944    C   CZ .  TYR   D .  222 ?   28.663  18.750  51.374  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   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)       : 1739.6467
+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_entity_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_asym_id
+ATOM     5124    C  CD1 .  LEU   C .  127 ?   52.412  62.880  19.111  0.00  0   C
+ATOM     5175    O    O .  ILE   C .  133 ?   50.155  63.679  13.849 -1.07  0   C
+ATOM     4642    C  CD1 .  ILE   C .   66 ?   57.564  64.926  16.918  0.00  0   C
+ATOM     5181    C   CA .  HIS   C .  134 ?   49.968  61.358  15.298  0.00  0   C
+ATOM     5168    C  CD2 .  PHE   C .  132 ?   53.775  68.288  14.726  0.00  0   C
+ATOM     5165    C   CB .  PHE   C .  132 ?   52.152  67.148  16.265  0.00  0   C
+ATOM     4607    C  CG1 .  VAL   C .   62 ?   56.843  66.361  13.193  0.00  0   C
+ATOM     5349    C  CD2 .  PHE   C .  155 ?   58.617  52.809  14.766  0.00  0   C
+ATOM     4806    C  CG2 .  THR   C .   88 ?   64.918  58.267  15.934  0.00  0   C
+ATOM     5351    C  CE2 .  PHE   C .  155 ?   58.958  52.743  16.096  0.00  0   C
+ATOM     4805    O  OG1 .  THR   C .   88 ?   65.292  56.165  17.041  0.00  0   C
+ATOM     5166    C   CG .  PHE   C .  132 ?   53.337  68.020  16.020  0.00  0   C
+ATOM     5187    C  CD2 .  HIS   C .  134 ?   52.038  58.986  17.107  0.00  0   C
+ATOM     5125    C  CD2 .  LEU   C .  127 ?   53.933  64.923  19.034  0.00  0   C
+ATOM     4367    C  CG1 .  VAL   C .   29 ?   65.278  51.087  12.687  0.00  0   C
+ATOM     4342    C   CG .  TYR   C .   26 ?   60.508  48.226  13.248  0.00  0   C
+ATOM     4680    C  CD2 .  LEU   C .   71 ?   55.947  61.004  20.573  0.00  0   C
+ATOM     5338    C   CB .  ASP   C .  154 ?   55.209  57.618  13.892  0.00  0   C
+ATOM     4684    O    O .  VAL   C .   72 ?   61.863  60.416  19.355 -5.36  0   C
+ATOM     4640    C  CG1 .  ILE   C .   66 ?   58.912  65.273  17.720  0.00  0   C
+ATOM     4677    C   CB .  LEU   C .   71 ?   58.112  61.528  21.791  0.00  0   C
+ATOM     5341    O  OD2 .  ASP   C .  154 ?   53.714  58.561  12.241 -0.14  0   C
+ATOM     5183    O    O .  HIS   C .  134 ?   50.262  60.307  13.190  0.00  0   C
+ATOM     4608    C  CG2 .  VAL   C .   62 ?   57.086  66.805  10.673  0.00  0   C
+ATOM     4606    C   CB .  VAL   C .   62 ?   57.804  66.325  11.964  0.00  0   C
+ATOM     4849    C  CD2 .  TYR   C .   93 ?   62.771  44.062  27.626  0.00  0   C
+ATOM     4898    C  CE1 .  TYR   C .   99 ?   58.734  44.320  28.340  0.00  0   C
+ATOM     4896    C  CD1 .  TYR   C .   99 ?   58.352  44.217  27.023  0.00  0   C
+ATOM     4924    O    O .  GLU   C .  102 ?   56.618  37.405  27.670 -1.21  0   C
+ATOM     4533    C   CB .  GLU   C .   52 ?   60.007  57.267   0.138  0.00  0   C
+ATOM     4493    N   NZ .  LYS   C .   44 ?   59.948  55.800   8.159  0.00  0   C
+ATOM     4492    C   CE .  LYS   C .   44 ?   61.398  55.419   7.935  0.00  0   C
+ATOM     4565    C  CD1 .  PHE   C .   56 ?   63.711  58.360   4.956  0.00  0   C
+ATOM     4491    C   CD .  LYS   C .   44 ?   62.464  55.863   8.961  0.00  0   C
+ATOM     4591    O  OE2 .  GLU   C .   59 ?   60.141  58.852  10.727 -1.07  0   C
+ATOM     4489    C   CB .  LYS   C .   44 ?   64.904  55.444   9.602  0.00  0   C
+ATOM     4344    C  CD2 .  TYR   C .   26 ?   59.377  48.648  13.987  0.00  0   C
+ATOM     4477    C   CB .  ALA   C .   42 ?   66.815  52.711  16.102  0.00  0   C
+ATOM     4928    O  OE1 .  GLU   C .  102 ?   58.396  38.729  22.754 -0.95  0   C
+ATOM     4845    O    O .  TYR   C .   93 ?   60.677  45.046  23.639 -4.02  0   C
+ATOM     4507    C  CD1 .  LEU   C .   46 ?   63.457  56.650   1.429  0.00  0   C
+ATOM     4614    C   CG .  MET   C .   63 ?   60.952  62.629  14.053  0.00  0   C
+ATOM     4615    S   SD .  MET   C .   63 ?   61.859  61.128  13.673  0.00  0   C
+ATOM     5334    N    N .  ASP   C .  154 ?   56.468  56.249  15.507  0.00  0   C
+ATOM     4854    N    N .  GLY   C .   94 ?   61.926  46.515  22.505 -1.09  0   C
+ATOM     4855    C   CA .  GLY   C .   94 ?   61.148  46.414  21.286  0.00  0   C
+ATOM     4826    C   CZ .  PHE   C .   90 ?   68.029  47.527  20.408  0.00  0   C
+ATOM     4838    O    O .  THR   C .   92 ?   65.169  45.657  23.913  0.00  0   C
+ATOM     4858    N    N .  ASN   C .   95 ?   58.837  46.563  20.532 -2.19  0   C
+ATOM     4864    O  OD1 .  ASN   C .   95 ?   57.197  45.110  18.091 -1.07  0   C
+ATOM     4889    O  OD2 .  ASP   C .   98 ?   56.786  42.248  18.314 -0.81  0   C
+ATOM     4931    C   CA .  CYS   C .  103 ?   55.713  39.474  29.139  0.00  0   C
+ATOM     4923    C    C .  GLU   C .  102 ?   55.803  38.136  27.151  0.00  0   C
+ATOM     5337    O    O .  ASP   C .  154 ?   57.341  56.209  12.768 -1.07  0   C
+ATOM     4891    C   CA .  TYR   C .   99 ?   56.204  43.137  24.766  0.00  0   C
+ATOM     4890    N    N .  TYR   C .   99 ?   55.885  43.129  23.365 -2.19  0   C
+ATOM     4925    C   CB .  GLU   C .  102 ?   56.670  38.222  24.775  0.00  0   C
+ATOM     4341    C   CB .  TYR   C .   26 ?   60.784  48.778  11.861  0.00  0   C
+ATOM     4686    C  CG1 .  VAL   C .   72 ?   60.468  57.953  18.334  0.00  0   C
+ATOM     5333    C   CB .  ALA   C .  153 ?   57.973  55.244  17.737  0.00  0   C
+ATOM     4687    C  CG2 .  VAL   C .   72 ?   62.471  56.742  19.102  0.00  0   C
+ATOM     4314    C  CD1 .  LEU   C .   21 ?   66.372  48.924  15.249  0.00  0   C
+ATOM     4822    C  CD1 .  PHE   C .   90 ?   68.357  49.652  19.357  0.00  0   C
+ATOM     4827    N    N .  MET   C .   91 ?   65.600  51.395  21.975  0.00  0   C
+ATOM     4587    C   CB .  GLU   C .   59 ?   59.660  61.810   8.754  0.00  0   C
+ATOM     4584    C   CA .  GLU   C .   59 ?   59.760  63.312   8.983  0.00  0   C
+ATOM     4348    O   OH .  TYR   C .   26 ?   59.736  46.661  17.066 -2.14  0   C
+ATOM     4335    O  OE1 .  GLN   C .   25 ?   58.998  43.247  14.898 -4.69  0   C
+ATOM     4886    C   CB .  ASP   C .   98 ?   56.203  41.956  20.500  0.00  0   C
+ATOM     4929    O  OE2 .  GLU   C .  102 ?   57.083  38.222  21.105 -0.54  0   C
+ATOM     4316    N    N .  GLY   C .   22 ?   64.012  43.884  14.345 -6.98  0   C
+ATOM     4315    C  CD2 .  LEU   C .   21 ?   67.339  46.763  16.058  0.00  0   C
+ATOM     4312    C   CB .  LEU   C .   21 ?   65.502  46.661  14.421  0.00  0   C
+ATOM     4893    O    O .  TYR   C .   99 ?   55.173  41.873  26.595  0.00  0   C
+ATOM     5331    C    C .  ALA   C .  153 ?   55.953  56.313  16.712  0.00  0   C
+ATOM     5332    O    O .  ALA   C .  153 ?   54.761  56.347  16.907  0.00  0   C
+ATOM     4485    N    N .  LYS   C .   44 ?   66.985  54.643  10.662  0.00  0   C
+ATOM     4317    C   CA .  GLY   C .   22 ?   62.747  43.150  14.231  0.00  0   C
+ATOM     4343    C  CD1 .  TYR   C .   26 ?   61.357  47.296  13.808  0.00  0   C
+ATOM     4830    O    O .  MET   C .   91 ?   64.488  48.834  22.426  0.00  0   C
+ATOM     4824    C  CE1 .  PHE   C .   90 ?   68.165  48.287  19.279  0.00  0   C
+ATOM     5258    C  CD1 .  LEU   C .  143 ?   60.801  52.853  19.522  0.00  0   C
+ATOM     4810    O    O .  GLU   C .   89 ?   66.226  54.641  19.567  0.00  0   C
+ATOM     4590    O  OE1 .  GLU   C .   59 ?   60.143  59.180   8.562  0.00  0   C
+ATOM     4560    C   CA .  PHE   C .   56 ?   61.727  61.139   4.612  0.00  0   C
+ATOM     4552    C    C .  GLU   C .   55 ?   59.443  61.938   4.041  0.00  0   C
+ATOM     4553    O    O .  GLU   C .   55 ?   59.074  62.152   5.210 -0.40  0   C
+ATOM     4559    N    N .  PHE   C .   56 ?   60.677  61.556   3.690  0.00  0   C
+ATOM     5354    C   CA .  GLY   C .  156 ?   55.185  54.289   9.070  0.00  0   C
+ATOM     5340    O  OD1 .  ASP   C .  154 ?   54.160  56.484  12.072 -0.40  0   C
+ATOM     4588    C   CG .  GLU   C .   59 ?   59.879  61.018  10.009  0.00  0   C
+ATOM     4586    O    O .  GLU   C .   59 ?   60.890  64.044  10.965  0.00  0   C
+ATOM     4554    C   CB .  GLU   C .   55 ?   57.705  60.840   2.562  0.00  0   C
+ATOM     5356    O    O .  GLY   C .  156 ?   55.311  52.499   7.563 -3.62  0   C
+ATOM     5376    C   CG .  ARG   C .  159 ?   54.486  53.056   3.655  0.00  0   C
+ATOM     5259    C  CD2 .  LEU   C .  143 ?   60.391  50.436  19.544  0.00  0   C
+ATOM     4346    C  CE2 .  TYR   C .   26 ?   59.090  48.126  15.277  0.00  0   C
+ATOM     4347    C   CZ .  TYR   C .   26 ?   59.971  47.200  15.806  0.00  0   C
+ATOM     4345    C  CE1 .  TYR   C .   26 ?   61.109  46.769  15.049  0.00  0   C
+ATOM     4790    C  CG2 .  ILE   C .   86 ?   65.267  59.719  11.684  0.00  0   C
+ATOM     5343    C   CA .  PHE   C .  155 ?   57.162  53.520  12.244  0.00  0   C
+ATOM     5345    O    O .  PHE   C .  155 ?   57.545  52.974   9.992 -1.07  0   C
+ATOM     4476    O    O .  ALA   C .   42 ?   68.283  54.987  14.590  0.00  0   C
+ATOM     4497    O    O .  THR   C .   45 ?   65.625  53.907   4.664 -2.55  0   C
+ATOM     4368    C  CG2 .  VAL   C .   29 ?   63.667  51.380  10.691  0.00  0   C
+ATOM     5346    C   CB .  PHE   C .  155 ?   57.304  52.068  12.736  0.00  0   C
+ATOM     5353    N    N .  GLY   C .  156 ?   55.685  54.235  10.437  0.00  0   C
+ATOM     5330    C   CA .  ALA   C .  153 ?   56.928  56.348  17.874  0.00  0   C
+ATOM     5325    O    O .  VAL   C .  152 ?   57.290  57.718  20.233  0.00  0   C
+ATOM     4589    C   CD .  GLU   C .   59 ?   60.082  59.588   9.746  0.00  0   C
+ATOM     5339    C   CG .  ASP   C .  154 ?   54.313  57.558  12.649  0.00  0   C
+ATOM     4787    O    O .  ILE   C .   86 ?   67.579  57.024  11.540  0.00  0   C
+ATOM     4532    O    O .  GLU   C .   52 ?   60.629  60.058   1.220 -1.07  0   C
+ATOM     4563    C   CB .  PHE   C .   56 ?   62.803  60.407   3.827  0.00  0   C
+ATOM     4555    C   CG .  GLU   C .   55 ?   56.341  60.714   3.218  0.00  0   C
+ATOM     4557    O  OE1 .  GLU   C .   55 ?   54.968  62.335   4.361  0.00  0   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_entity_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_asym_id
+ATOM     4309    C   CA .  LEU   C .   21 ?   65.825  45.363  13.662  0.00  0   C
+ATOM     4310    C    C .  LEU   C .   21 ?   64.536  44.614  13.361  0.00  0   C
+ATOM     4312    C   CB .  LEU   C .   21 ?   65.502  46.661  14.421  0.00  0   C
+ATOM     4313    C   CG .  LEU   C .   21 ?   66.698  47.490  14.883  0.00  0   C
+ATOM     4314    C  CD1 .  LEU   C .   21 ?   66.372  48.924  15.249  0.00  0   C
+ATOM     4315    C  CD2 .  LEU   C .   21 ?   67.339  46.763  16.058  0.00  0   C
+ATOM     4316    N    N .  GLY   C .   22 ?   64.012  43.884  14.345 -6.98  0   C
+ATOM     4317    C   CA .  GLY   C .   22 ?   62.747  43.150  14.231  0.00  0   C
+ATOM     4334    C   CD .  GLN   C .   25 ?   58.140  44.074  14.570  0.00  0   C
+ATOM     4335    O  OE1 .  GLN   C .   25 ?   58.998  43.247  14.898 -4.69  0   C
+ATOM     4336    N  NE2 .  GLN   C .   25 ?   57.317  44.634  15.447 -3.70  0   C
+ATOM     4338    C   CA .  TYR   C .   26 ?   60.002  48.078  10.730  0.00  0   C
+ATOM     4340    O    O .  TYR   C .   26 ?   60.592  49.665   9.045 -3.21  0   C
+ATOM     4341    C   CB .  TYR   C .   26 ?   60.784  48.778  11.861  0.00  0   C
+ATOM     4342    C   CG .  TYR   C .   26 ?   60.508  48.226  13.248  0.00  0   C
+ATOM     4343    C  CD1 .  TYR   C .   26 ?   61.357  47.296  13.808  0.00  0   C
+ATOM     4344    C  CD2 .  TYR   C .   26 ?   59.377  48.648  13.987  0.00  0   C
+ATOM     4345    C  CE1 .  TYR   C .   26 ?   61.109  46.769  15.049  0.00  0   C
+ATOM     4346    C  CE2 .  TYR   C .   26 ?   59.090  48.126  15.277  0.00  0   C
+ATOM     4347    C   CZ .  TYR   C .   26 ?   59.971  47.200  15.806  0.00  0   C
+ATOM     4348    O   OH .  TYR   C .   26 ?   59.736  46.661  17.066 -2.14  0   C
+ATOM     4366    C   CB .  VAL   C .   29 ?   64.687  50.461  11.321  0.00  0   C
+ATOM     4367    C  CG1 .  VAL   C .   29 ?   65.278  51.087  12.687  0.00  0   C
+ATOM     4368    C  CG2 .  VAL   C .   29 ?   63.667  51.380  10.691  0.00  0   C
+ATOM     4474    C   CA .  ALA   C .   42 ?   68.331  52.880  15.676  0.00  0   C
+ATOM     4475    C    C .  ALA   C .   42 ?   68.451  53.776  14.487  0.00  0   C
+ATOM     4476    O    O .  ALA   C .   42 ?   68.283  54.987  14.590  0.00  0   C
+ATOM     4477    C   CB .  ALA   C .   42 ?   66.815  52.711  16.102  0.00  0   C
+ATOM     4478    N    N .  VAL   C .   43 ?   68.686  53.184  13.337  0.00  0   C
+ATOM     4479    C   CA .  VAL   C .   43 ?   68.854  53.984  12.121  0.00  0   C
+ATOM     4480    C    C .  VAL   C .   43 ?   67.829  53.673  11.024  0.00  0   C
+ATOM     4485    N    N .  LYS   C .   44 ?   66.985  54.643  10.662  0.00  0   C
+ATOM     4486    C   CA .  LYS   C .   44 ?   66.141  54.548   9.456  0.00  0   C
+ATOM     4489    C   CB .  LYS   C .   44 ?   64.904  55.444   9.602  0.00  0   C
+ATOM     4490    C   CG .  LYS   C .   44 ?   63.734  55.094   8.667  0.00  0   C
+ATOM     4491    C   CD .  LYS   C .   44 ?   62.464  55.863   8.961  0.00  0   C
+ATOM     4492    C   CE .  LYS   C .   44 ?   61.398  55.419   7.935  0.00  0   C
+ATOM     4493    N   NZ .  LYS   C .   44 ?   59.948  55.800   8.159  0.00  0   C
+ATOM     4496    C    C .  THR   C .   45 ?   66.704  54.505   4.719  0.00  0   C
+ATOM     4497    O    O .  THR   C .   45 ?   65.625  53.907   4.664 -2.55  0   C
+ATOM     4505    C   CB .  LEU   C .   46 ?   65.738  56.785   2.407  0.00  0   C
+ATOM     4507    C  CD1 .  LEU   C .   46 ?   63.457  56.650   1.429  0.00  0   C
+ATOM     4530    C   CA .  GLU   C .   52 ?   59.974  58.619  -0.607  0.00  0   C
+ATOM     4531    C    C .  GLU   C .   52 ?   60.889  59.675   0.070  0.00  0   C
+ATOM     4532    O    O .  GLU   C .   52 ?   60.629  60.058   1.220 -1.07  0   C
+ATOM     4533    C   CB .  GLU   C .   52 ?   60.007  57.267   0.138  0.00  0   C
+ATOM     4551    C   CA .  GLU   C .   55 ?   58.464  62.142   2.868  0.00  0   C
+ATOM     4552    C    C .  GLU   C .   55 ?   59.443  61.938   4.041  0.00  0   C
+ATOM     4553    O    O .  GLU   C .   55 ?   59.074  62.152   5.210 -0.40  0   C
+ATOM     4554    C   CB .  GLU   C .   55 ?   57.705  60.840   2.562  0.00  0   C
+ATOM     4555    C   CG .  GLU   C .   55 ?   56.341  60.714   3.218  0.00  0   C
+ATOM     4556    C   CD .  GLU   C .   55 ?   55.575  62.043   3.296  0.00  0   C
+ATOM     4557    O  OE1 .  GLU   C .   55 ?   54.968  62.335   4.361  0.00  0   C
+ATOM     4559    N    N .  PHE   C .   56 ?   60.677  61.556   3.690  0.00  0   C
+ATOM     4560    C   CA .  PHE   C .   56 ?   61.727  61.139   4.612  0.00  0   C
+ATOM     4563    C   CB .  PHE   C .   56 ?   62.803  60.407   3.827  0.00  0   C
+ATOM     4564    C   CG .  PHE   C .   56 ?   63.829  59.722   4.676  0.00  0   C
+ATOM     4565    C  CD1 .  PHE   C .   56 ?   63.711  58.360   4.956  0.00  0   C
+ATOM     4567    C  CE1 .  PHE   C .   56 ?   64.665  57.708   5.732  0.00  0   C
+ATOM     4581    O    O .  LYS   C .   58 ?   59.033  65.956   8.597  0.00  0   C
+ATOM     4583    N    N .  GLU   C .   59 ?   59.754  64.014   7.713 -1.09  0   C
+ATOM     4584    C   CA .  GLU   C .   59 ?   59.760  63.312   8.983  0.00  0   C
+ATOM     4585    C    C .  GLU   C .   59 ?   61.012  63.718   9.801  0.00  0   C
+ATOM     4586    O    O .  GLU   C .   59 ?   60.890  64.044  10.965  0.00  0   C
+ATOM     4587    C   CB .  GLU   C .   59 ?   59.660  61.810   8.754  0.00  0   C
+ATOM     4588    C   CG .  GLU   C .   59 ?   59.879  61.018  10.009  0.00  0   C
+ATOM     4589    C   CD .  GLU   C .   59 ?   60.082  59.588   9.746  0.00  0   C
+ATOM     4590    O  OE1 .  GLU   C .   59 ?   60.143  59.180   8.562  0.00  0   C
+ATOM     4591    O  OE2 .  GLU   C .   59 ?   60.141  58.852  10.727 -1.07  0   C
+ATOM     4604    C    C .  VAL   C .   62 ?   59.706  66.684  13.538  0.00  0   C
+ATOM     4606    C   CB .  VAL   C .   62 ?   57.804  66.325  11.964  0.00  0   C
+ATOM     4607    C  CG1 .  VAL   C .   62 ?   56.843  66.361  13.193  0.00  0   C
+ATOM     4608    C  CG2 .  VAL   C .   62 ?   57.086  66.805  10.673  0.00  0   C
+ATOM     4609    N    N .  MET   C .   63 ?   60.563  65.681  13.428  0.00  0   C
+ATOM     4613    C   CB .  MET   C .   63 ?   61.901  63.786  14.236  0.00  0   C
+ATOM     4614    C   CG .  MET   C .   63 ?   60.952  62.629  14.053  0.00  0   C
+ATOM     4615    S   SD .  MET   C .   63 ?   61.859  61.128  13.673  0.00  0   C
+ATOM     4616    C   CE .  MET   C .   63 ?   61.818  61.384  11.995  0.00  0   C
+ATOM     4639    C   CB .  ILE   C .   66 ?   58.639  66.208  18.869  0.00  0   C
+ATOM     4640    C  CG1 .  ILE   C .   66 ?   58.912  65.273  17.720  0.00  0   C
+ATOM     4642    C  CD1 .  ILE   C .   66 ?   57.564  64.926  16.918  0.00  0   C
+ATOM     4674    C   CA .  LEU   C .   71 ?   58.528  60.228  22.492  0.00  0   C
+ATOM     4675    C    C .  LEU   C .   71 ?   59.922  59.793  22.078  0.00  0   C
+ATOM     4677    C   CB .  LEU   C .   71 ?   58.112  61.528  21.791  0.00  0   C
+ATOM     4678    C   CG .  LEU   C .   71 ?   56.577  61.697  21.797  0.00  0   C
+ATOM     4680    C  CD2 .  LEU   C .   71 ?   55.947  61.004  20.573  0.00  0   C
+ATOM     4681    N    N .  VAL   C .   72 ?   60.009  58.893  21.100  0.00  0   C
+ATOM     4683    C    C .  VAL   C .   72 ?   62.252  59.595  20.196  0.00  0   C
+ATOM     4684    O    O .  VAL   C .   72 ?   61.863  60.416  19.355 -5.36  0   C
+ATOM     4685    C   CB .  VAL   C .   72 ?   61.147  57.312  19.529  0.00  0   C
+ATOM     4686    C  CG1 .  VAL   C .   72 ?   60.468  57.953  18.334  0.00  0   C
+ATOM     4687    C  CG2 .  VAL   C .   72 ?   62.471  56.742  19.102  0.00  0   C
+ATOM     4786    C    C .  ILE   C .   86 ?   67.749  58.236  11.640  0.00  0   C
+ATOM     4787    O    O .  ILE   C .   86 ?   67.579  57.024  11.540  0.00  0   C
+ATOM     4788    C   CB .  ILE   C .   86 ?   65.914  59.237  10.348  0.00  0   C
+ATOM     4790    C  CG2 .  ILE   C .   86 ?   65.267  59.719  11.684  0.00  0   C
+ATOM     4800    N    N .  THR   C .   88 ?   67.723  57.504  15.818  0.00  0   C
+ATOM     4804    C   CB .  THR   C .   88 ?   65.559  57.569  17.104  0.00  0   C
+ATOM     4805    O  OG1 .  THR   C .   88 ?   65.292  56.165  17.041  0.00  0   C
+ATOM     4806    C  CG2 .  THR   C .   88 ?   64.918  58.267  15.934  0.00  0   C
+ATOM     4809    C    C .  GLU   C .   89 ?   67.131  54.920  20.346  0.00  0   C
+ATOM     4810    O    O .  GLU   C .   89 ?   66.226  54.641  19.567  0.00  0   C
+ATOM     4817    C   CA .  PHE   C .   90 ?   67.450  52.586  20.886  0.00  0   C
+ATOM     4818    C    C .  PHE   C .   90 ?   66.693  52.151  22.165  0.00  0   C
+ATOM     4820    C   CB .  PHE   C .   90 ?   68.719  51.763  20.661  0.00  0   C
+ATOM     4821    C   CG .  PHE   C .   90 ?   68.478  50.271  20.568  0.00  0   C
+ATOM     4822    C  CD1 .  PHE   C .   90 ?   68.357  49.652  19.357  0.00  0   C
+ATOM     4824    C  CE1 .  PHE   C .   90 ?   68.165  48.287  19.279  0.00  0   C
+ATOM     4825    C  CE2 .  PHE   C .   90 ?   68.168  48.136  21.643  0.00  0   C
+ATOM     4826    C   CZ .  PHE   C .   90 ?   68.029  47.527  20.408  0.00  0   C
+ATOM     4827    N    N .  MET   C .   91 ?   65.600  51.395  21.975  0.00  0   C
+ATOM     4828    C   CA .  MET   C .   91 ?   64.687  51.072  23.087  0.00  0   C
+ATOM     4829    C    C .  MET   C .   91 ?   64.825  49.585  23.311  0.00  0   C
+ATOM     4830    O    O .  MET   C .   91 ?   64.488  48.834  22.426  0.00  0   C
+ATOM     4831    C   CB .  MET   C .   91 ?   63.247  51.450  22.726  0.00  0   C
+ATOM     4832    C   CG .  MET   C .   91 ?   63.058  52.948  22.613  0.00  0   C
+ATOM     4837    C    C .  THR   C .   92 ?   64.810  46.729  24.429  0.00  0   C
+ATOM     4838    O    O .  THR   C .   92 ?   65.169  45.657  23.913  0.00  0   C
+ATOM     4843    C   CA .  TYR   C .   93 ?   62.583  45.894  24.767  0.00  0   C
+ATOM     4844    C    C .  TYR   C .   93 ?   61.651  45.780  23.573  0.00  0   C
+ATOM     4845    O    O .  TYR   C .   93 ?   60.677  45.046  23.639 -4.02  0   C
+ATOM     4846    C   CB .  TYR   C .   93 ?   61.822  45.842  26.120  0.00  0   C
+ATOM     4847    C   CG .  TYR   C .   93 ?   62.708  45.399  27.251  0.00  0   C
+ATOM     4849    C  CD2 .  TYR   C .   93 ?   62.771  44.062  27.626  0.00  0   C
+ATOM     4851    C  CE2 .  TYR   C .   93 ?   63.623  43.640  28.650  0.00  0   C
+ATOM     4854    N    N .  GLY   C .   94 ?   61.926  46.515  22.505 -1.09  0   C
+ATOM     4855    C   CA .  GLY   C .   94 ?   61.148  46.414  21.286  0.00  0   C
+ATOM     4856    C    C .  GLY   C .   94 ?   59.784  47.035  21.343  0.00  0   C
+ATOM     4858    N    N .  ASN   C .   95 ?   58.837  46.563  20.532 -2.19  0   C
+ATOM     4861    O    O .  ASN   C .   95 ?   56.724  45.626  22.065  0.00  0   C
+ATOM     4863    C   CG .  ASN   C .   95 ?   56.450  45.916  18.682  0.00  0   C
+ATOM     4864    O  OD1 .  ASN   C .   95 ?   57.197  45.110  18.091 -1.07  0   C
+ATOM     4883    C   CA .  ASP   C .   98 ?   54.984  42.071  21.363  0.00  0   C
+ATOM     4884    C    C .  ASP   C .   98 ?   55.443  42.017  22.812  0.00  0   C
+ATOM     4885    O    O .  ASP   C .   98 ?   55.375  40.977  23.443  0.00  0   C
+ATOM     4886    C   CB .  ASP   C .   98 ?   56.203  41.956  20.500  0.00  0   C
+ATOM     4887    C   CG .  ASP   C .   98 ?   55.860  41.893  19.062  0.00  0   C
+ATOM     4889    O  OD2 .  ASP   C .   98 ?   56.786  42.248  18.314 -0.81  0   C
+ATOM     4890    N    N .  TYR   C .   99 ?   55.885  43.129  23.365 -2.19  0   C
+ATOM     4891    C   CA .  TYR   C .   99 ?   56.204  43.137  24.766  0.00  0   C
+ATOM     4892    C    C .  TYR   C .   99 ?   55.017  42.706  25.685  0.00  0   C
+ATOM     4893    O    O .  TYR   C .   99 ?   55.173  41.873  26.595  0.00  0   C
+ATOM     4894    C   CB .  TYR   C .   99 ?   56.726  44.500  25.132  0.00  0   C
+ATOM     4895    C   CG .  TYR   C .   99 ?   57.096  44.639  26.581  0.00  0   C
+ATOM     4896    C  CD1 .  TYR   C .   99 ?   58.352  44.217  27.023  0.00  0   C
+ATOM     4898    C  CE1 .  TYR   C .   99 ?   58.734  44.320  28.340  0.00  0   C
+ATOM     4900    C   CZ .  TYR   C .   99 ?   57.871  44.894  29.252  0.00  0   C
+ATOM     4922    C   CA .  GLU   C .  102 ?   55.431  37.971  25.671  0.00  0   C
+ATOM     4923    C    C .  GLU   C .  102 ?   55.803  38.136  27.151  0.00  0   C
+ATOM     4924    O    O .  GLU   C .  102 ?   56.618  37.405  27.670 -1.21  0   C
+ATOM     4925    C   CB .  GLU   C .  102 ?   56.670  38.222  24.775  0.00  0   C
+ATOM     4927    C   CD .  GLU   C .  102 ?   57.337  38.298  22.330  0.00  0   C
+ATOM     4928    O  OE1 .  GLU   C .  102 ?   58.396  38.729  22.754 -0.95  0   C
+ATOM     4929    O  OE2 .  GLU   C .  102 ?   57.083  38.222  21.105 -0.54  0   C
+ATOM     4930    N    N .  CYS   C .  103 ?   55.219  39.097  27.827  0.00  0   C
+ATOM     4931    C   CA .  CYS   C .  103 ?   55.713  39.474  29.139  0.00  0   C
+ATOM     4934    C   CB .  CYS   C .  103 ?   55.275  40.917  29.497  0.00  0   C
+ATOM     5123    C   CG .  LEU   C .  127 ?   52.817  64.233  19.845  0.00  0   C
+ATOM     5124    C  CD1 .  LEU   C .  127 ?   52.412  62.880  19.111  0.00  0   C
+ATOM     5125    C  CD2 .  LEU   C .  127 ?   53.933  64.923  19.034  0.00  0   C
+ATOM     5162    C   CA .  PHE   C .  132 ?   50.825  67.783  15.847  0.00  0   C
+ATOM     5165    C   CB .  PHE   C .  132 ?   52.152  67.148  16.265  0.00  0   C
+ATOM     5166    C   CG .  PHE   C .  132 ?   53.337  68.020  16.020  0.00  0   C
+ATOM     5167    C  CD1 .  PHE   C .  132 ?   54.011  68.601  17.071  0.00  0   C
+ATOM     5168    C  CD2 .  PHE   C .  132 ?   53.775  68.288  14.726  0.00  0   C
+ATOM     5170    C  CE2 .  PHE   C .  132 ?   54.886  69.135  14.503  0.00  0   C
+ATOM     5172    N    N .  ILE   C .  133 ?   49.469  65.974  14.990 -3.28  0   C
+ATOM     5174    C    C .  ILE   C .  133 ?   49.338  63.641  14.747  0.00  0   C
+ATOM     5175    O    O .  ILE   C .  133 ?   50.155  63.679  13.849 -1.07  0   C
+ATOM     5180    N    N .  HIS   C .  134 ?   49.159  62.560  15.511  0.00  0   C
+ATOM     5181    C   CA .  HIS   C .  134 ?   49.968  61.358  15.298  0.00  0   C
+ATOM     5182    C    C .  HIS   C .  134 ?   49.471  60.618  14.035  0.00  0   C
+ATOM     5183    O    O .  HIS   C .  134 ?   50.262  60.307  13.190  0.00  0   C
+ATOM     5184    C   CB .  HIS   C .  134 ?   49.966  60.452  16.557  0.00  0   C
+ATOM     5185    C   CG .  HIS   C .  134 ?   50.894  59.284  16.450  0.00  0   C
+ATOM     5186    N  ND1 .  HIS   C .  134 ?   50.716  58.287  15.523  0.00  0   C
+ATOM     5187    C  CD2 .  HIS   C .  134 ?   52.038  58.986  17.107  0.00  0   C
+ATOM     5188    C  CE1 .  HIS   C .  134 ?   51.679  57.389  15.644  0.00  0   C
+ATOM     5189    N  NE2 .  HIS   C .  134 ?   52.489  57.786  16.607  0.00  0   C
+ATOM     5257    C   CG .  LEU   C .  143 ?   59.891  51.727  20.024  0.00  0   C
+ATOM     5258    C  CD1 .  LEU   C .  143 ?   60.801  52.853  19.522  0.00  0   C
+ATOM     5259    C  CD2 .  LEU   C .  143 ?   60.391  50.436  19.544  0.00  0   C
+ATOM     5324    C    C .  VAL   C .  152 ?   56.357  56.927  20.160  0.00  0   C
+ATOM     5325    O    O .  VAL   C .  152 ?   57.290  57.718  20.233  0.00  0   C
+ATOM     5327    C  CG1 .  VAL   C .  152 ?   53.471  58.150  20.325  0.00  0   C
+ATOM     5329    N    N .  ALA   C .  153 ?   56.140  56.186  19.075  0.00  0   C
+ATOM     5330    C   CA .  ALA   C .  153 ?   56.928  56.348  17.874  0.00  0   C
+ATOM     5331    C    C .  ALA   C .  153 ?   55.953  56.313  16.712  0.00  0   C
+ATOM     5332    O    O .  ALA   C .  153 ?   54.761  56.347  16.907  0.00  0   C
+ATOM     5333    C   CB .  ALA   C .  153 ?   57.973  55.244  17.737  0.00  0   C
+ATOM     5334    N    N .  ASP   C .  154 ?   56.468  56.249  15.507  0.00  0   C
+ATOM     5335    C   CA .  ASP   C .  154 ?   55.632  56.206  14.371  0.00  0   C
+ATOM     5336    C    C .  ASP   C .  154 ?   56.487  55.557  13.330  0.00  0   C
+ATOM     5337    O    O .  ASP   C .  154 ?   57.341  56.209  12.768 -1.07  0   C
+ATOM     5338    C   CB .  ASP   C .  154 ?   55.209  57.618  13.892  0.00  0   C
+ATOM     5339    C   CG .  ASP   C .  154 ?   54.313  57.558  12.649  0.00  0   C
+ATOM     5340    O  OD1 .  ASP   C .  154 ?   54.160  56.484  12.072 -0.40  0   C
+ATOM     5341    O  OD2 .  ASP   C .  154 ?   53.714  58.561  12.241 -0.14  0   C
+ATOM     5342    N    N .  PHE   C .  155 ?   56.245  54.285  13.069  0.00  0   C
+ATOM     5343    C   CA .  PHE   C .  155 ?   57.162  53.520  12.244  0.00  0   C
+ATOM     5344    C    C .  PHE   C .  155 ?   56.801  53.559  10.785  0.00  0   C
+ATOM     5345    O    O .  PHE   C .  155 ?   57.545  52.974   9.992 -1.07  0   C
+ATOM     5346    C   CB .  PHE   C .  155 ?   57.304  52.068  12.736  0.00  0   C
+ATOM     5347    C   CG .  PHE   C .  155 ?   57.674  51.960  14.215  0.00  0   C
+ATOM     5349    C  CD2 .  PHE   C .  155 ?   58.617  52.809  14.766  0.00  0   C
+ATOM     5350    C  CE1 .  PHE   C .  155 ?   57.402  50.907  16.384  0.00  0   C
+ATOM     5351    C  CE2 .  PHE   C .  155 ?   58.958  52.743  16.096  0.00  0   C
+ATOM     5352    C   CZ .  PHE   C .  155 ?   58.346  51.781  16.925  0.00  0   C
+ATOM     5353    N    N .  GLY   C .  156 ?   55.685  54.235  10.437  0.00  0   C
+ATOM     5354    C   CA .  GLY   C .  156 ?   55.185  54.289   9.070  0.00  0   C
+ATOM     5355    C    C .  GLY   C .  156 ?   54.848  52.901   8.598  0.00  0   C
+ATOM     5356    O    O .  GLY   C .  156 ?   55.311  52.499   7.563 -3.62  0   C
+ATOM     5376    C   CG .  ARG   C .  159 ?   54.486  53.056   3.655  0.00  0   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)       : 418.3302
+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_entity_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_asym_id
+ATOM     1578    C   CA .  SER   A .  211 ?   28.519  31.580  13.536  0.00  0   A
+ATOM      729    N  NH2 .  ARG   A .  101 ?   29.744  27.079  13.417 -2.19  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1531    O  OE1 .  GLU   A .  204 ?   23.660  27.646  12.432 -1.07  0   A
+ATOM     1572    O    O .  MET   A .  210 ?   27.392  30.484  11.286 -2.14  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1192    C   CE .  MET   A .  161 ?   25.473  22.258  20.061  0.00  0   A
+ATOM     1193    N    N .  THR   A .  162 ?   27.717  23.001  24.543 -3.28  0   A
+ATOM     1196    O    O .  THR   A .  162 ?   30.318  24.681  23.653 -0.54  0   A
+ATOM     1190    C   CG .  MET   A .  161 ?   25.693  23.794  22.437  0.00  0   A
+ATOM     1191    S   SD .  MET   A .  161 ?   25.108  23.914  20.726  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1197    C   CB .  THR   A .  162 ?   30.043  22.165  24.907  0.00  0   A
+ATOM      728    N  NH1 .  ARG   A .  101 ?   30.641  25.059  14.054  0.00  0   A
+ATOM     1319    C  CZ2 .  TRP   A .  178 ?   23.312  29.778  15.389  0.00  0   A
+ATOM      690    C  CD2 .  LEU   A .   97 ?   26.615  24.712  14.130  0.00  0   A
+ATOM     1039    N  NH1 .  ARG   A .  140 ?   22.161  27.219  17.402 -2.19  0   A
+ATOM     1036    C   CD .  ARG   A .  140 ?   22.384  24.464  18.025  0.00  0   A
+ATOM      697    O  OD1 .  ASP   A .   98 ?   29.383  20.437  13.443  0.00  0   A
+ATOM      136    N  NE2 .  GLN   A .   25 ?   26.655  17.754  17.106 -1.51  0   A
+ATOM     1034    C   CB .  ARG   A .  140 ?   22.854  23.046  15.953  0.00  0   A
+ATOM      674    N  ND2 .  ASN   A .   95 ?   25.138  19.957  12.965 -2.19  0   A
+ATOM     1198    O  OG1 .  THR   A .  162 ?   29.373  20.894  24.874 -2.55  0   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_entity_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_asym_id
+ATOM      136    N  NE2 .  GLN   A .   25 ?   26.655  17.754  17.106 -1.51  0   A
+ATOM      672    C   CG .  ASN   A .   95 ?   24.977  18.738  13.399  0.00  0   A
+ATOM      673    O  OD1 .  ASN   A .   95 ?   25.880  18.114  13.960 -2.14  0   A
+ATOM      674    N  ND2 .  ASN   A .   95 ?   25.138  19.957  12.965 -2.19  0   A
+ATOM      687    C   CB .  LEU   A .   97 ?   25.726  23.134  12.371  0.00  0   A
+ATOM      688    C   CG .  LEU   A .   97 ?   26.663  24.325  12.667  0.00  0   A
+ATOM      689    C  CD1 .  LEU   A .   97 ?   26.439  25.580  11.708  0.00  0   A
+ATOM      690    C  CD2 .  LEU   A .   97 ?   26.615  24.712  14.130  0.00  0   A
+ATOM      696    C   CG .  ASP   A .   98 ?   28.941  19.302  13.063  0.00  0   A
+ATOM      697    O  OD1 .  ASP   A .   98 ?   29.383  20.437  13.443  0.00  0   A
+ATOM      698    O  OD2 .  ASP   A .   98 ?   28.581  18.421  13.874  0.00  0   A
+ATOM      727    C   CZ .  ARG   A .  101 ?   30.221  25.880  13.100  0.00  0   A
+ATOM      728    N  NH1 .  ARG   A .  101 ?   30.641  25.059  14.054  0.00  0   A
+ATOM      729    N  NH2 .  ARG   A .  101 ?   29.744  27.079  13.417 -2.19  0   A
+ATOM     1031    C   CA .  ARG   A .  140 ?   22.308  22.460  14.667  0.00  0   A
+ATOM     1034    C   CB .  ARG   A .  140 ?   22.854  23.046  15.953  0.00  0   A
+ATOM     1035    C   CG .  ARG   A .  140 ?   21.827  23.818  16.751  0.00  0   A
+ATOM     1036    C   CD .  ARG   A .  140 ?   22.384  24.464  18.025  0.00  0   A
+ATOM     1037    N   NE .  ARG   A .  140 ?   21.358  25.394  18.567  0.00  0   A
+ATOM     1038    C   CZ .  ARG   A .  140 ?   21.285  26.690  18.242  0.00  0   A
+ATOM     1039    N  NH1 .  ARG   A .  140 ?   22.161  27.219  17.402 -2.19  0   A
+ATOM     1190    C   CG .  MET   A .  161 ?   25.693  23.794  22.437  0.00  0   A
+ATOM     1191    S   SD .  MET   A .  161 ?   25.108  23.914  20.726  0.00  0   A
+ATOM     1192    C   CE .  MET   A .  161 ?   25.473  22.258  20.061  0.00  0   A
+ATOM     1193    N    N .  THR   A .  162 ?   27.717  23.001  24.543 -3.28  0   A
+ATOM     1194    C   CA .  THR   A .  162 ?   28.998  23.321  25.160  0.00  0   A
+ATOM     1195    C    C .  THR   A .  162 ?   29.554  24.650  24.630  0.00  0   A
+ATOM     1196    O    O .  THR   A .  162 ?   30.318  24.681  23.653 -0.54  0   A
+ATOM     1197    C   CB .  THR   A .  162 ?   30.043  22.165  24.907  0.00  0   A
+ATOM     1198    O  OG1 .  THR   A .  162 ?   29.373  20.894  24.874 -2.55  0   A
+ATOM     1213    C   CB .  THR   A .  165 ?   25.536  27.768  21.247  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1215    C  CG2 .  THR   A .  165 ?   24.206  27.716  20.463  0.00  0   A
+ATOM     1319    C  CZ2 .  TRP   A .  178 ?   23.312  29.778  15.389  0.00  0   A
+ATOM     1320    C  CZ3 .  TRP   A .  178 ?   23.462  30.785  17.625  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1530    C   CD .  GLU   A .  204 ?   22.806  28.372  11.796  0.00  0   A
+ATOM     1531    O  OE1 .  GLU   A .  204 ?   23.660  27.646  12.432 -1.07  0   A
+ATOM     1571    C    C .  MET   A .  210 ?   28.632  30.657  11.307  0.00  0   A
+ATOM     1572    O    O .  MET   A .  210 ?   27.392  30.484  11.286 -2.14  0   A
+ATOM     1577    N    N .  SER   A .  211 ?   29.277  31.096  12.377 -1.51  0   A
+ATOM     1578    C   CA .  SER   A .  211 ?   28.519  31.580  13.536  0.00  0   A
+ATOM     1581    C   CB .  SER   A .  211 ?   29.357  31.629  14.802  0.00  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1588    C   CG .  PRO   A .  212 ?   24.603  32.718  14.282  0.00  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     8085    C   CB .  GLU   D .  239 ?   33.579  23.349  24.058  0.00  0   D
+ATOM     8118    O  OE2 .  GLU   D .  243 ?   31.919  19.332  25.048  0.00  0   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)       : 338.1321
+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_entity_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_asym_id
+ATOM     5013    C  CD1 .  LEU   C .  113 ?   47.637  45.537  32.420  0.00  0   C
+ATOM     5969    O    O .  GLY   C .  236 ?   41.436  44.926  35.683 -1.88  0   C
+ATOM     5742    C  CE2 .  TYR   C .  208 ?   47.578  41.887  31.506  0.00  0   C
+ATOM     5744    O   OH .  TYR   C .  208 ?   49.149  42.483  33.247  0.00  0   C
+ATOM     5967    C   CA .  GLY   C .  236 ?   40.408  42.885  35.092  0.00  0   C
+ATOM     5960    O    O .  GLU   C .  235 ?   40.959  41.746  32.508 -6.17  0   C
+ATOM     5724    O    O .  ALA   C .  206 ?   44.035  43.617  29.804 -4.29  0   C
+ATOM     4992    C   CB .  ALA   C .  110 ?   46.896  45.998  37.907  0.00  0   C
+ATOM     4989    C   CA .  ALA   C .  110 ?   48.023  46.286  36.893  0.00  0   C
+ATOM     4988    N    N .  ALA   C .  110 ?   49.019  45.250  37.006 -1.09  0   C
+ATOM     5722    C   CA .  ALA   C .  206 ?   44.400  45.936  29.263  0.00  0   C
+ATOM     5011    C   CB .  LEU   C .  113 ?   48.507  47.814  32.706  0.00  0   C
+ATOM     5725    C   CB .  ALA   C .  206 ?   43.007  46.611  29.412  0.00  0   C
+ATOM     5971    C   CA .  CYS   C .  237 ?   40.269  46.381  33.554  0.00  0   C
+ATOM     5968    C    C .  GLY   C .  236 ?   40.655  44.362  34.916  0.00  0   C
+ATOM     5009    C    C .  LEU   C .  113 ?   49.262  50.208  32.866  0.00  0   C
+ATOM     6002    C  CG1 .  VAL   C .  241 ?   41.927  51.680  31.567  0.00  0   C
+ATOM     5010    O    O .  LEU   C .  113 ?   49.304  50.941  31.905  0.00  0   C
+ATOM     5982    C   CD .  PRO   C .  238 ?   41.741  48.427  35.286  0.00  0   C
+ATOM     5975    S   SG .  CYS   C .  237 ?   39.866  48.440  31.675  0.00  0   C
+ATOM     4991    O    O .  ALA   C .  110 ?   48.119  48.581  36.365 -4.29  0   C
+ATOM     5021    C  CD1 .  LEU   C .  114 ?   45.548  52.723  35.306  0.00  0   C
+ATOM     6003    C  CG2 .  VAL   C .  241 ?   42.161  52.318  34.092  0.00  0   C
+ATOM     5981    C   CG .  PRO   C .  238 ?   41.902  49.346  36.487  0.00  0   C
+ATOM     5015    N    N .  LEU   C .  114 ?   48.853  50.629  34.038 -1.09  0   C
+ATOM     5016    C   CA .  LEU   C .  114 ?   48.437  52.025  34.290  0.00  0   C
+ATOM     5047    C   CB .  ALA   C .  117 ?   47.619  53.976  30.267  0.00  0   C
+ATOM     5689    C  CD2 .  LEU   C .  202 ?   44.675  53.384  28.357  0.00  0   C
+ATOM     6210    C  CE1 .  PHE   C .  266 ?   44.724  55.322  32.190  0.00  0   C
+ATOM     5719    C  CG2 .  ILE   C .  205 ?   48.010  48.643  29.034  0.00  0   C
+ATOM     5685    O    O .  LEU   C .  202 ?   43.911  49.067  27.179 -2.14  0   C
+ATOM     5721    N    N .  ALA   C .  206 ?   45.181  46.650  28.250  0.00  0   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_entity_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_asym_id
+ATOM     4981    C   CA .  ASN   C .  109 ?   50.825  43.818  36.384  0.00  0   C
+ATOM     4982    C    C .  ASN   C .  109 ?   50.104  45.124  36.248  0.00  0   C
+ATOM     4988    N    N .  ALA   C .  110 ?   49.019  45.250  37.006 -1.09  0   C
+ATOM     4989    C   CA .  ALA   C .  110 ?   48.023  46.286  36.893  0.00  0   C
+ATOM     4990    C    C .  ALA   C .  110 ?   48.553  47.694  37.074  0.00  0   C
+ATOM     4991    O    O .  ALA   C .  110 ?   48.119  48.581  36.365 -4.29  0   C
+ATOM     4992    C   CB .  ALA   C .  110 ?   46.896  45.998  37.907  0.00  0   C
+ATOM     5008    C   CA .  LEU   C .  113 ?   49.712  48.768  32.777  0.00  0   C
+ATOM     5009    C    C .  LEU   C .  113 ?   49.262  50.208  32.866  0.00  0   C
+ATOM     5010    O    O .  LEU   C .  113 ?   49.304  50.941  31.905  0.00  0   C
+ATOM     5011    C   CB .  LEU   C .  113 ?   48.507  47.814  32.706  0.00  0   C
+ATOM     5012    C   CG .  LEU   C .  113 ?   48.922  46.332  32.524  0.00  0   C
+ATOM     5013    C  CD1 .  LEU   C .  113 ?   47.637  45.537  32.420  0.00  0   C
+ATOM     5015    N    N .  LEU   C .  114 ?   48.853  50.629  34.038 -1.09  0   C
+ATOM     5016    C   CA .  LEU   C .  114 ?   48.437  52.025  34.290  0.00  0   C
+ATOM     5019    C   CB .  LEU   C .  114 ?   47.935  52.152  35.736  0.00  0   C
+ATOM     5020    C   CG .  LEU   C .  114 ?   46.796  53.097  36.098  0.00  0   C
+ATOM     5021    C  CD1 .  LEU   C .  114 ?   45.548  52.723  35.306  0.00  0   C
+ATOM     5047    C   CB .  ALA   C .  117 ?   47.619  53.976  30.267  0.00  0   C
+ATOM     5683    C   CA .  LEU   C .  202 ?   44.169  51.283  26.225  0.00  0   C
+ATOM     5684    C    C .  LEU   C .  202 ?   43.587  49.854  26.305  0.00  0   C
+ATOM     5685    O    O .  LEU   C .  202 ?   43.911  49.067  27.179 -2.14  0   C
+ATOM     5686    C   CB .  LEU   C .  202 ?   43.118  52.210  26.812  0.00  0   C
+ATOM     5689    C  CD2 .  LEU   C .  202 ?   44.675  53.384  28.357  0.00  0   C
+ATOM     5715    C    C .  ILE   C .  205 ?   46.474  46.377  28.013  0.00  0   C
+ATOM     5717    C   CB .  ILE   C .  205 ?   47.488  48.723  27.607  0.00  0   C
+ATOM     5719    C  CG2 .  ILE   C .  205 ?   48.010  48.643  29.034  0.00  0   C
+ATOM     5721    N    N .  ALA   C .  206 ?   45.181  46.650  28.250  0.00  0   C
+ATOM     5722    C   CA .  ALA   C .  206 ?   44.400  45.936  29.263  0.00  0   C
+ATOM     5723    C    C .  ALA   C .  206 ?   44.262  44.467  28.933  0.00  0   C
+ATOM     5724    O    O .  ALA   C .  206 ?   44.035  43.617  29.804 -4.29  0   C
+ATOM     5725    C   CB .  ALA   C .  206 ?   43.007  46.611  29.412  0.00  0   C
+ATOM     5740    C  CD2 .  TYR   C .  208 ?   47.363  41.572  30.167  0.00  0   C
+ATOM     5742    C  CE2 .  TYR   C .  208 ?   47.578  41.887  31.506  0.00  0   C
+ATOM     5743    C   CZ .  TYR   C .  208 ?   48.869  42.193  31.926  0.00  0   C
+ATOM     5744    O   OH .  TYR   C .  208 ?   49.149  42.483  33.247  0.00  0   C
+ATOM     5959    C    C .  GLU   C .  235 ?   39.827  41.766  32.965  0.00  0   C
+ATOM     5960    O    O .  GLU   C .  235 ?   40.959  41.746  32.508 -6.17  0   C
+ATOM     5966    N    N .  GLY   C .  236 ?   39.492  42.242  34.155 -2.61  0   C
+ATOM     5967    C   CA .  GLY   C .  236 ?   40.408  42.885  35.092  0.00  0   C
+ATOM     5968    C    C .  GLY   C .  236 ?   40.655  44.362  34.916  0.00  0   C
+ATOM     5969    O    O .  GLY   C .  236 ?   41.436  44.926  35.683 -1.88  0   C
+ATOM     5970    N    N .  CYS   C .  237 ?   39.998  45.000  33.919  0.00  0   C
+ATOM     5971    C   CA .  CYS   C .  237 ?   40.269  46.381  33.554  0.00  0   C
+ATOM     5972    C    C .  CYS   C .  237 ?   39.560  47.241  34.572  0.00  0   C
+ATOM     5974    C   CB .  CYS   C .  237 ?   39.767  46.673  32.160  0.00  0   C
+ATOM     5975    S   SG .  CYS   C .  237 ?   39.866  48.440  31.675  0.00  0   C
+ATOM     5976    N    N .  PRO   C .  238 ?   40.288  48.167  35.270  0.00  0   C
+ATOM     5981    C   CG .  PRO   C .  238 ?   41.902  49.346  36.487  0.00  0   C
+ATOM     5982    C   CD .  PRO   C .  238 ?   41.741  48.427  35.286  0.00  0   C
+ATOM     6001    C   CB .  VAL   C .  241 ?   41.221  51.947  32.945  0.00  0   C
+ATOM     6002    C  CG1 .  VAL   C .  241 ?   41.927  51.680  31.567  0.00  0   C
+ATOM     6003    C  CG2 .  VAL   C .  241 ?   42.161  52.318  34.092  0.00  0   C
+ATOM     6208    C  CD1 .  PHE   C .  266 ?   45.432  56.220  32.964  0.00  0   C
+ATOM     6210    C  CE1 .  PHE   C .  266 ?   44.724  55.322  32.190  0.00  0   C
+ATOM     6212    C   CZ .  PHE   C .  266 ?   44.262  55.693  30.950  0.00  0   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)       : 668.7173
+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_entity_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_asym_id
+ATOM     4048    O    O .  ARG   B .  256 ?    5.584  39.776  52.007 -0.40  0   B
+ATOM     4034    O    O .  SER   B .  254 ?    3.034  36.722  50.663 -3.35  0   B
+ATOM     4092    O  OE1 .  GLU   B .  261 ?    4.400  40.941  57.227  0.00  0   B
+ATOM     4093    O  OE2 .  GLU   B .  261 ?    2.933  42.122  56.184  0.00  0   B
+ATOM     4040    O    O .  ASP   B .  255 ?    6.559  36.007  52.815  0.00  0   B
+ATOM     4057    C   CA .  PRO   B .  257 ?    6.624  40.819  54.353  0.00  0   B
+ATOM     4143    C   CB .  THR   B .  268 ?   10.227  46.401  67.772  0.00  0   B
+ATOM     4118    C   CA .  ALA   B .  265 ?    9.929  45.031  63.065  0.00  0   B
+ATOM     4145    C  CG2 .  THR   B .  268 ?   10.384  45.639  69.065  0.00  0   B
+ATOM     4144    O  OG1 .  THR   B .  268 ?    8.840  46.564  67.429  0.00  0   B
+ATOM     4120    O    O .  ALA   B .  265 ?   11.641  45.676  64.603 -1.48  0   B
+ATOM     4089    C   CB .  GLU   B .  261 ?    5.421  43.577  58.123  0.00  0   B
+ATOM     4060    C   CB .  PRO   B .  257 ?    7.583  41.016  55.523  0.00  0   B
+ATOM     3947    C  CD1 .  LEU   B .  244 ?   11.916  41.124  59.300  0.00  0   B
+ATOM     4047    C    C .  ARG   B .  256 ?    6.658  39.348  52.433  0.00  0   B
+ATOM     3972    C   CB .  ALA   B .  247 ?   11.015  37.196  55.846  0.00  0   B
+ATOM     3937    C   CG .  GLU   B .  243 ?   13.561  35.641  61.217  0.00  0   B
+ATOM     3940    O  OE2 .  GLU   B .  243 ?   11.836  34.934  62.719  0.00  0   B
+ATOM     3935    O    O .  GLU   B .  243 ?   13.956  36.736  57.962 -1.48  0   B
+ATOM     4062    C   CD .  PRO   B .  257 ?    8.652  39.555  53.954  0.00  0   B
+ATOM     3938    C   CD .  GLU   B .  243 ?   12.975  35.501  62.669  0.00  0   B
+ATOM     3911    O    O .  LYS   B .  240 ?   15.567  39.731  61.909 -3.21  0   B
+ATOM     3939    O  OE1 .  GLU   B .  243 ?   13.626  35.936  63.713  0.00  0   B
+ATOM     4152    S   SD .  MET   B .  269 ?   15.508  43.520  64.899  0.00  0   B
+ATOM     4153    C   CE .  MET   B .  269 ?   14.440  43.776  63.513  0.00  0   B
+ATOM     3912    C   CB .  LYS   B .  240 ?   15.915  39.653  65.197  0.00  0   B
+ATOM     4151    C   CG .  MET   B .  269 ?   14.602  44.443  66.216  0.00  0   B
+ATOM     4121    C   CB .  ALA   B .  265 ?   10.310  43.906  62.117  0.00  0   B
+ATOM     4088    O    O .  GLU   B .  261 ?    7.481  45.179  60.241 -3.62  0   B
+ATOM     3528    N   NZ .  LYS   B .  192 ?    4.513  41.805  50.925  0.00  0   B
+ATOM     4056    N    N .  PRO   B .  257 ?    7.275  39.856  53.515 -1.09  0   B
+ATOM     4061    C   CG .  PRO   B .  257 ?    8.908  40.517  55.032  0.00  0   B
+ATOM     3948    C  CD2 .  LEU   B .  244 ?   13.574  42.584  60.502  0.00  0   B
+ATOM     4087    C    C .  GLU   B .  261 ?    7.103  45.132  59.045  0.00  0   B
+ATOM     4094    N    N .  ILE   B .  262 ?    7.932  45.257  57.985  0.00  0   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_entity_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_asym_id
+ATOM     3527    C   CE .  LYS   B .  192 ?    4.230  41.475  49.521  0.00  0   B
+ATOM     3528    N   NZ .  LYS   B .  192 ?    4.513  41.805  50.925  0.00  0   B
+ATOM     3909    C   CA .  LYS   B .  240 ?   16.489  38.866  63.991  0.00  0   B
+ATOM     3910    C    C .  LYS   B .  240 ?   16.549  39.699  62.695  0.00  0   B
+ATOM     3911    O    O .  LYS   B .  240 ?   15.567  39.731  61.909 -3.21  0   B
+ATOM     3912    C   CB .  LYS   B .  240 ?   15.915  39.653  65.197  0.00  0   B
+ATOM     3934    C    C .  GLU   B .  243 ?   14.663  37.242  58.823  0.00  0   B
+ATOM     3935    O    O .  GLU   B .  243 ?   13.956  36.736  57.962 -1.48  0   B
+ATOM     3936    C   CB .  GLU   B .  243 ?   14.951  36.297  61.139  0.00  0   B
+ATOM     3937    C   CG .  GLU   B .  243 ?   13.561  35.641  61.217  0.00  0   B
+ATOM     3938    C   CD .  GLU   B .  243 ?   12.975  35.501  62.669  0.00  0   B
+ATOM     3939    O  OE1 .  GLU   B .  243 ?   13.626  35.936  63.713  0.00  0   B
+ATOM     3940    O  OE2 .  GLU   B .  243 ?   11.836  34.934  62.719  0.00  0   B
+ATOM     3941    N    N .  LEU   B .  244 ?   14.719  38.538  59.058  0.00  0   B
+ATOM     3942    C   CA .  LEU   B .  244 ?   14.186  39.576  58.225  0.00  0   B
+ATOM     3945    C   CB .  LEU   B .  244 ?   14.468  40.916  58.905  0.00  0   B
+ATOM     3946    C   CG .  LEU   B .  244 ?   13.279  41.832  59.221  0.00  0   B
+ATOM     3947    C  CD1 .  LEU   B .  244 ?   11.916  41.124  59.300  0.00  0   B
+ATOM     3948    C  CD2 .  LEU   B .  244 ?   13.574  42.584  60.502  0.00  0   B
+ATOM     3972    C   CB .  ALA   B .  247 ?   11.015  37.196  55.846  0.00  0   B
+ATOM     4034    O    O .  SER   B .  254 ?    3.034  36.722  50.663 -3.35  0   B
+ATOM     4038    C   CA .  ASP   B .  255 ?    5.252  35.220  50.980  0.00  0   B
+ATOM     4039    C    C .  ASP   B .  255 ?    6.138  36.234  51.683  0.00  0   B
+ATOM     4040    O    O .  ASP   B .  255 ?    6.559  36.007  52.815  0.00  0   B
+ATOM     4045    N    N .  ARG   B .  256 ?    6.452  37.343  51.021  0.00  0   B
+ATOM     4046    C   CA .  ARG   B .  256 ?    7.422  38.306  51.602  0.00  0   B
+ATOM     4047    C    C .  ARG   B .  256 ?    6.658  39.348  52.433  0.00  0   B
+ATOM     4048    O    O .  ARG   B .  256 ?    5.584  39.776  52.007 -0.40  0   B
+ATOM     4056    N    N .  PRO   B .  257 ?    7.275  39.856  53.515 -1.09  0   B
+ATOM     4057    C   CA .  PRO   B .  257 ?    6.624  40.819  54.353  0.00  0   B
+ATOM     4060    C   CB .  PRO   B .  257 ?    7.583  41.016  55.523  0.00  0   B
+ATOM     4061    C   CG .  PRO   B .  257 ?    8.908  40.517  55.032  0.00  0   B
+ATOM     4062    C   CD .  PRO   B .  257 ?    8.652  39.555  53.954  0.00  0   B
+ATOM     4086    C   CA .  GLU   B .  261 ?    5.633  44.949  58.707  0.00  0   B
+ATOM     4087    C    C .  GLU   B .  261 ?    7.103  45.132  59.045  0.00  0   B
+ATOM     4088    O    O .  GLU   B .  261 ?    7.481  45.179  60.241 -3.62  0   B
+ATOM     4089    C   CB .  GLU   B .  261 ?    5.421  43.577  58.123  0.00  0   B
+ATOM     4090    C   CG .  GLU   B .  261 ?    3.980  43.147  58.071  0.00  0   B
+ATOM     4091    C   CD .  GLU   B .  261 ?    3.752  41.985  57.107  0.00  0   B
+ATOM     4092    O  OE1 .  GLU   B .  261 ?    4.400  40.941  57.227  0.00  0   B
+ATOM     4093    O  OE2 .  GLU   B .  261 ?    2.933  42.122  56.184  0.00  0   B
+ATOM     4094    N    N .  ILE   B .  262 ?    7.932  45.257  57.985  0.00  0   B
+ATOM     4095    C   CA .  ILE   B .  262 ?    9.374  45.475  58.093  0.00  0   B
+ATOM     4099    C  CG1 .  ILE   B .  262 ?   10.102  44.158  56.052  0.00  0   B
+ATOM     4117    N    N .  ALA   B .  265 ?    8.883  45.921  62.496 -1.09  0   B
+ATOM     4118    C   CA .  ALA   B .  265 ?    9.929  45.031  63.065  0.00  0   B
+ATOM     4119    C    C .  ALA   B .  265 ?   11.159  45.807  63.476  0.00  0   B
+ATOM     4120    O    O .  ALA   B .  265 ?   11.641  45.676  64.603 -1.48  0   B
+ATOM     4121    C   CB .  ALA   B .  265 ?   10.310  43.906  62.117  0.00  0   B
+ATOM     4143    C   CB .  THR   B .  268 ?   10.227  46.401  67.772  0.00  0   B
+ATOM     4144    O  OG1 .  THR   B .  268 ?    8.840  46.564  67.429  0.00  0   B
+ATOM     4145    C  CG2 .  THR   B .  268 ?   10.384  45.639  69.065  0.00  0   B
+ATOM     4151    C   CG .  MET   B .  269 ?   14.602  44.443  66.216  0.00  0   B
+ATOM     4152    S   SD .  MET   B .  269 ?   15.508  43.520  64.899  0.00  0   B
+ATOM     4153    C   CE .  MET   B .  269 ?   14.440  43.776  63.513  0.00  0   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)       : 245.5694
+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_entity_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_asym_id
+ATOM     8199    C   CG .  ASN   D .  252 ?   27.586   9.214  42.829  0.00  0   D
+ATOM     8186    C  CD1 .  TRP   D .  251 ?   26.276  14.665  45.063  0.00  0   D
+ATOM     8201    N  ND2 .  ASN   D .  252 ?   28.367   8.903  43.871  0.00  0   D
+ATOM     8198    C   CB .  ASN   D .  252 ?   27.436  10.710  42.437  0.00  0   D
+ATOM     8195    C   CA .  ASN   D .  252 ?   28.576  11.606  42.953  0.00  0   D
+ATOM     8188    N  NE1 .  TRP   D .  251 ?   26.256  14.921  46.406 -0.17  0   D
+ATOM     8183    O    O .  TRP   D .  251 ?   29.606  13.897  44.157 -1.07  0   D
+ATOM     8208    C   CD .  PRO   D .  253 ?   30.672  10.672  44.713  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
+ATOM     8191    C  CZ2 .  TRP   D .  251 ?   27.038  16.816  47.830  0.00  0   D
+ATOM     7656    C  CE1 .  TYR   D .  186 ?   28.922  12.123  52.576  0.00  0   D
+ATOM     7659    O   OH .  TYR   D .  186 ?   26.735  12.867  53.246  0.00  0   D
+ATOM     7620    N    N .  GLU   D .  182 ?   32.487  14.873  49.114  0.00  0   D
+ATOM     8189    C  CE2 .  TRP   D .  251 ?   26.844  16.141  46.643  0.00  0   D
+ATOM     7617    C   CB .  PRO   D .  181 ?   30.988  17.092  47.631  0.00  0   D
+ATOM     7624    C   CB .  GLU   D .  182 ?   32.311  12.417  49.315  0.00  0   D
+ATOM     7621    C   CA .  GLU   D .  182 ?   32.543  13.747  50.045  0.00  0   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_entity_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_asym_id
+ATOM     7614    C   CA .  PRO   D .  181 ?   32.231  17.243  48.469  0.00  0   D
+ATOM     7615    C    C .  PRO   D .  181 ?   32.350  16.130  49.537  0.00  0   D
+ATOM     7616    O    O .  PRO   D .  181 ?   32.388  16.443  50.725  0.00  0   D
+ATOM     7617    C   CB .  PRO   D .  181 ?   30.988  17.092  47.631  0.00  0   D
+ATOM     7618    C   CG .  PRO   D .  181 ?   31.356  17.693  46.325  0.00  0   D
+ATOM     7620    N    N .  GLU   D .  182 ?   32.487  14.873  49.114  0.00  0   D
+ATOM     7621    C   CA .  GLU   D .  182 ?   32.543  13.747  50.045  0.00  0   D
+ATOM     7624    C   CB .  GLU   D .  182 ?   32.311  12.417  49.315  0.00  0   D
+ATOM     7625    C   CG .  GLU   D .  182 ?   33.511  11.813  48.605  0.00  0   D
+ATOM     7627    O  OE1 .  GLU   D .  182 ?   33.039  13.333  46.837  0.00  0   D
+ATOM     7647    C   CB .  ALA   D .  185 ?   30.355  15.757  53.617  0.00  0   D
+ATOM     7654    C  CD1 .  TYR   D .  186 ?   30.228  11.746  52.896  0.00  0   D
+ATOM     7656    C  CE1 .  TYR   D .  186 ?   28.922  12.123  52.576  0.00  0   D
+ATOM     7658    C   CZ .  TYR   D .  186 ?   28.026  12.495  53.587  0.00  0   D
+ATOM     7659    O   OH .  TYR   D .  186 ?   26.735  12.867  53.246  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
+ATOM     8182    C    C .  TRP   D .  251 ?   28.907  14.027  43.133  0.00  0   D
+ATOM     8183    O    O .  TRP   D .  251 ?   29.606  13.897  44.157 -1.07  0   D
+ATOM     8185    C   CG .  TRP   D .  251 ?   26.880  15.703  44.398  0.00  0   D
+ATOM     8186    C  CD1 .  TRP   D .  251 ?   26.276  14.665  45.063  0.00  0   D
+ATOM     8187    C  CD2 .  TRP   D .  251 ?   27.270  16.654  45.395  0.00  0   D
+ATOM     8188    N  NE1 .  TRP   D .  251 ?   26.256  14.921  46.406 -0.17  0   D
+ATOM     8189    C  CE2 .  TRP   D .  251 ?   26.844  16.141  46.643  0.00  0   D
+ATOM     8191    C  CZ2 .  TRP   D .  251 ?   27.038  16.816  47.830  0.00  0   D
+ATOM     8193    C  CH2 .  TRP   D .  251 ?   27.687  18.028  47.774  0.00  0   D
+ATOM     8194    N    N .  ASN   D .  252 ?   28.369  12.984  42.500 -2.19  0   D
+ATOM     8195    C   CA .  ASN   D .  252 ?   28.576  11.606  42.953  0.00  0   D
+ATOM     8198    C   CB .  ASN   D .  252 ?   27.436  10.710  42.437  0.00  0   D
+ATOM     8199    C   CG .  ASN   D .  252 ?   27.586   9.214  42.829  0.00  0   D
+ATOM     8200    O  OD1 .  ASN   D .  252 ?   26.967   8.353  42.186  0.00  0   D
+ATOM     8201    N  ND2 .  ASN   D .  252 ?   28.367   8.903  43.871  0.00  0   D
+ATOM     8202    N    N .  PRO   D .  253 ?   30.848  10.724  43.243  0.00  0   D
+ATOM     8207    C   CG .  PRO   D .  253 ?   31.809   9.793  45.177  0.00  0   D
+ATOM     8208    C   CD .  PRO   D .  253 ?   30.672  10.672  44.713  0.00  0   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)       : 470.3947
+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_entity_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_asym_id
+ATOM     1634    C   CG .  LEU   A .  218 ?   26.546  36.235  23.630  0.00  0   A
+ATOM     1635    C  CD1 .  LEU   A .  218 ?   26.663  34.961  24.461  0.00  0   A
+ATOM     1625    C   CB .  ASP   A .  217 ?   29.707  40.718  23.735  0.00  0   A
+ATOM     1633    C   CB .  LEU   A .  218 ?   25.982  37.405  24.438  0.00  0   A
+ATOM     1616    O    O .  ILE   A .  216 ?   28.714  38.833  20.120 -0.40  0   A
+ATOM     1208    C   CB .  ASP   A .  164 ?   29.178  31.688  24.167  0.00  0   A
+ATOM     1307    N   NZ .  LYS   A .  177 ?   28.045  36.395  18.402 -5.21  0   A
+ATOM     1636    C  CD2 .  LEU   A .  218 ?   25.660  35.987  22.435  0.00  0   A
+ATOM     1207    O    O .  ASP   A .  164 ?   26.463  31.466  23.365 -2.55  0   A
+ATOM     1306    C   CE .  LYS   A .  177 ?   26.638  36.392  18.974  0.00  0   A
+ATOM     1305    C   CD .  LYS   A .  177 ?   25.713  35.218  18.453  0.00  0   A
+ATOM     1212    O    O .  THR   A .  165 ?   23.541  30.232  22.305 -2.14  0   A
+ATOM     1299    N    N .  LYS   A .  177 ?   21.604  34.670  19.815  0.00  0   A
+ATOM     1586    O    O .  PRO   A .  212 ?   27.163  35.309  15.349 -2.14  0   A
+ATOM     1581    C   CB .  SER   A .  211 ?   29.357  31.629  14.802  0.00  0   A
+ATOM     1320    C  CZ3 .  TRP   A .  178 ?   23.462  30.785  17.625  0.00  0   A
+ATOM     1637    N    N .  SER   A .  219 ?   25.769  40.519  25.023  0.00  0   A
+ATOM     1642    O   OG .  SER   A .  219 ?   26.959  42.469  26.857  0.00  0   A
+ATOM     1641    C   CB .  SER   A .  219 ?   25.796  41.724  27.105  0.00  0   A
+ATOM     1629    N    N .  LEU   A .  218 ?   27.266  38.964  23.188  0.00  0   A
+ATOM     1622    C   CA .  ASP   A .  217 ?   29.148  40.081  22.440  0.00  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1206    C    C .  ASP   A .  164 ?   27.100  30.422  23.545  0.00  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     1204    N    N .  ASP   A .  164 ?   29.062  29.235  24.428 -0.84  0   A
+ATOM     1209    N    N .  THR   A .  165 ?   26.804  29.250  22.931  0.00  0   A
+ATOM     1210    C   CA .  THR   A .  165 ?   25.644  29.125  21.999  0.00  0   A
+ATOM     1611    C    C .  GLY   A .  215 ?   31.790  39.345  18.361  0.00  0   A
+ATOM     1610    C   CA .  GLY   A .  215 ?   32.619  38.349  17.567  0.00  0   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_entity_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_asym_id
+ATOM     1204    N    N .  ASP   A .  164 ?   29.062  29.235  24.428 -0.84  0   A
+ATOM     1205    C   CA .  ASP   A .  164 ?   28.289  30.466  24.504  0.00  0   A
+ATOM     1206    C    C .  ASP   A .  164 ?   27.100  30.422  23.545  0.00  0   A
+ATOM     1207    O    O .  ASP   A .  164 ?   26.463  31.466  23.365 -2.55  0   A
+ATOM     1208    C   CB .  ASP   A .  164 ?   29.178  31.688  24.167  0.00  0   A
+ATOM     1209    N    N .  THR   A .  165 ?   26.804  29.250  22.931  0.00  0   A
+ATOM     1210    C   CA .  THR   A .  165 ?   25.644  29.125  21.999  0.00  0   A
+ATOM     1211    C    C .  THR   A .  165 ?   24.326  29.397  22.732  0.00  0   A
+ATOM     1212    O    O .  THR   A .  165 ?   23.541  30.232  22.305 -2.14  0   A
+ATOM     1213    C   CB .  THR   A .  165 ?   25.536  27.768  21.247  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1215    C  CG2 .  THR   A .  165 ?   24.206  27.716  20.463  0.00  0   A
+ATOM     1286    C    C .  PRO   A .  175 ?   20.244  32.256  21.608  0.00  0   A
+ATOM     1291    N    N .  ILE   A .  176 ?   20.859  33.260  22.267  0.00  0   A
+ATOM     1292    C   CA .  ILE   A .  176 ?   20.637  34.711  22.002  0.00  0   A
+ATOM     1293    C    C .  ILE   A .  176 ?   20.604  35.150  20.552  0.00  0   A
+ATOM     1295    C   CB .  ILE   A .  176 ?   21.717  35.588  22.696  0.00  0   A
+ATOM     1299    N    N .  LYS   A .  177 ?   21.604  34.670  19.815  0.00  0   A
+ATOM     1300    C   CA .  LYS   A .  177 ?   21.829  35.087  18.428  0.00  0   A
+ATOM     1303    C   CB .  LYS   A .  177 ?   23.257  34.714  18.002  0.00  0   A
+ATOM     1304    C   CG .  LYS   A .  177 ?   24.269  35.792  18.311  0.00  0   A
+ATOM     1305    C   CD .  LYS   A .  177 ?   25.713  35.218  18.453  0.00  0   A
+ATOM     1306    C   CE .  LYS   A .  177 ?   26.638  36.392  18.974  0.00  0   A
+ATOM     1307    N   NZ .  LYS   A .  177 ?   28.045  36.395  18.402 -5.21  0   A
+ATOM     1318    C  CE3 .  TRP   A .  178 ?   22.147  31.051  17.645  0.00  0   A
+ATOM     1320    C  CZ3 .  TRP   A .  178 ?   23.462  30.785  17.625  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1578    C   CA .  SER   A .  211 ?   28.519  31.580  13.536  0.00  0   A
+ATOM     1581    C   CB .  SER   A .  211 ?   29.357  31.629  14.802  0.00  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1583    N    N .  PRO   A .  212 ?   26.749  33.241  13.625  0.00  0   A
+ATOM     1586    O    O .  PRO   A .  212 ?   27.163  35.309  15.349 -2.14  0   A
+ATOM     1588    C   CG .  PRO   A .  212 ?   24.603  32.718  14.282  0.00  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     1609    N    N .  GLY   A .  215 ?   31.958  37.588  16.536 -2.35  0   A
+ATOM     1610    C   CA .  GLY   A .  215 ?   32.619  38.349  17.567  0.00  0   A
+ATOM     1611    C    C .  GLY   A .  215 ?   31.790  39.345  18.361  0.00  0   A
+ATOM     1612    O    O .  GLY   A .  215 ?   32.322  40.025  19.268  0.00  0   A
+ATOM     1613    N    N .  ILE   A .  216 ?   30.504  39.488  18.032  0.00  0   A
+ATOM     1615    C    C .  ILE   A .  216 ?   29.274  39.951  20.050  0.00  0   A
+ATOM     1616    O    O .  ILE   A .  216 ?   28.714  38.833  20.120 -0.40  0   A
+ATOM     1621    N    N .  ASP   A .  217 ?   29.581  40.653  21.147  0.00  0   A
+ATOM     1622    C   CA .  ASP   A .  217 ?   29.148  40.081  22.440  0.00  0   A
+ATOM     1623    C    C .  ASP   A .  217 ?   27.658  40.069  22.573  0.00  0   A
+ATOM     1625    C   CB .  ASP   A .  217 ?   29.707  40.718  23.735  0.00  0   A
+ATOM     1626    C   CG .  ASP   A .  217 ?   29.495  42.204  23.817  0.00  0   A
+ATOM     1628    O  OD2 .  ASP   A .  217 ?   29.236  42.748  24.938 -5.36  0   A
+ATOM     1629    N    N .  LEU   A .  218 ?   27.266  38.964  23.188  0.00  0   A
+ATOM     1630    C   CA .  LEU   A .  218 ?   25.952  38.629  23.546  0.00  0   A
+ATOM     1631    C    C .  LEU   A .  218 ?   25.155  39.717  24.180  0.00  0   A
+ATOM     1633    C   CB .  LEU   A .  218 ?   25.982  37.405  24.438  0.00  0   A
+ATOM     1634    C   CG .  LEU   A .  218 ?   26.546  36.235  23.630  0.00  0   A
+ATOM     1635    C  CD1 .  LEU   A .  218 ?   26.663  34.961  24.461  0.00  0   A
+ATOM     1636    C  CD2 .  LEU   A .  218 ?   25.660  35.987  22.435  0.00  0   A
+ATOM     1637    N    N .  SER   A .  219 ?   25.769  40.519  25.023  0.00  0   A
+ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
+ATOM     1641    C   CB .  SER   A .  219 ?   25.796  41.724  27.105  0.00  0   A
+ATOM     1642    O   OG .  SER   A .  219 ?   26.959  42.469  26.857  0.00  0   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)       : 276.7805
+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_entity_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_asym_id
+ATOM     6291    O    O .  GLU   D .    9 ?   72.604   3.890  48.729  0.00  0   D
+ATOM     6300    O    O .  MET   D .   10 ?   74.107   7.374  51.316 -2.14  0   D
+ATOM     6293    C   CG .  GLU   D .    9 ?   71.423   4.039  52.375  0.00  0   D
+ATOM     6312    O  OE1 .  GLU   D .   11 ?   77.808   6.551  52.358  0.00  0   D
+ATOM     6299    C    C .  MET   D .   10 ?   74.371   7.293  50.096  0.00  0   D
+ATOM     6305    N    N .  GLU   D .   11 ?   75.439   7.869  49.548 -2.19  0   D
+ATOM     6309    C   CB .  GLU   D .   11 ?   77.861   8.128  49.916  0.00  0   D
+ATOM     6510    C   CE .  LYS   D .   36 ?   78.782   6.894  42.671  0.00  0   D
+ATOM     6511    N   NZ .  LYS   D .   36 ?   78.219   5.612  42.198  0.00  0   D
+ATOM     6301    C   CB .  MET   D .   10 ?   73.225   7.186  47.771  0.00  0   D
+ATOM     6335    O  OD2 .  ASP   D .   14 ?   78.726   9.496  45.541 -2.55  0   D
+ATOM     6298    C   CA .  MET   D .   10 ?   73.486   6.472  49.131  0.00  0   D
+ATOM     6491    C  CZ2 .  TRP   D .   34 ?   73.535   8.757  43.118  0.00  0   D
+ATOM     6488    N  NE1 .  TRP   D .   34 ?   75.151  10.418  44.105 -1.09  0   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_entity_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_asym_id
+ATOM     6290    C    C .  GLU   D .    9 ?   71.915   4.628  49.430  0.00  0   D
+ATOM     6291    O    O .  GLU   D .    9 ?   72.604   3.890  48.729  0.00  0   D
+ATOM     6292    C   CB .  GLU   D .    9 ?   70.763   3.288  51.242  0.00  0   D
+ATOM     6293    C   CG .  GLU   D .    9 ?   71.423   4.039  52.375  0.00  0   D
+ATOM     6297    N    N .  MET   D .   10 ?   72.265   5.885  49.709  0.00  0   D
+ATOM     6298    C   CA .  MET   D .   10 ?   73.486   6.472  49.131  0.00  0   D
+ATOM     6299    C    C .  MET   D .   10 ?   74.371   7.293  50.096  0.00  0   D
+ATOM     6300    O    O .  MET   D .   10 ?   74.107   7.374  51.316 -2.14  0   D
+ATOM     6301    C   CB .  MET   D .   10 ?   73.225   7.186  47.771  0.00  0   D
+ATOM     6303    S   SD .  MET   D .   10 ?   72.034   9.214  46.200  0.00  0   D
+ATOM     6304    C   CE .  MET   D .   10 ?   73.478  10.172  46.696  0.00  0   D
+ATOM     6305    N    N .  GLU   D .   11 ?   75.439   7.869  49.548 -2.19  0   D
+ATOM     6306    C   CA .  GLU   D .   11 ?   76.441   8.484  50.396  0.00  0   D
+ATOM     6309    C   CB .  GLU   D .   11 ?   77.861   8.128  49.916  0.00  0   D
+ATOM     6310    C   CG .  GLU   D .   11 ?   78.934   8.247  51.025  0.00  0   D
+ATOM     6311    C   CD .  GLU   D .   11 ?   78.901   7.095  52.047  0.00  0   D
+ATOM     6312    O  OE1 .  GLU   D .   11 ?   77.808   6.551  52.358  0.00  0   D
+ATOM     6313    O  OE2 .  GLU   D .   11 ?   79.993   6.732  52.542  0.00  0   D
+ATOM     6333    C   CG .  ASP   D .   14 ?   78.386  10.697  45.659  0.00  0   D
+ATOM     6335    O  OD2 .  ASP   D .   14 ?   78.726   9.496  45.541 -2.55  0   D
+ATOM     6488    N  NE1 .  TRP   D .   34 ?   75.151  10.418  44.105 -1.09  0   D
+ATOM     6489    C  CE2 .  TRP   D .   34 ?   74.096  10.029  43.321  0.00  0   D
+ATOM     6491    C  CZ2 .  TRP   D .   34 ?   73.535   8.757  43.118  0.00  0   D
+ATOM     6509    C   CD .  LYS   D .   36 ?   78.417   8.015  41.707  0.00  0   D
+ATOM     6510    C   CE .  LYS   D .   36 ?   78.782   6.894  42.671  0.00  0   D
+ATOM     6511    N   NZ .  LYS   D .   36 ?   78.219   5.612  42.198  0.00  0   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)       : 227.3031
+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_entity_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_asym_id
+ATOM     1821    C  CG1 .  VAL   A .  241 ?   18.722  33.273   0.801  0.00  0   A
+ATOM      824    N    N .  LEU   A .  114 ?   19.877  26.311  -1.669  0.00  0   A
+ATOM      818    C    C .  LEU   A .  113 ?   20.351  26.072  -0.464  0.00  0   A
+ATOM      825    C   CA .  LEU   A .  114 ?   18.529  26.785  -1.887  0.00  0   A
+ATOM      798    C   CA .  ALA   A .  110 ?   24.131  27.516  -4.659  0.00  0   A
+ATOM     1805    C   CD .  PRO   A .  238 ?   21.822  33.590  -2.836  0.00  0   A
+ATOM     1792    O    O .  GLY   A .  236 ?   25.501  33.661  -3.290 -6.17  0   A
+ATOM      801    C   CB .  ALA   A .  110 ?   24.277  28.499  -5.862  0.00  0   A
+ATOM      819    O    O .  LEU   A .  113 ?   19.663  26.116   0.542 -1.07  0   A
+ATOM      856    C   CB .  ALA   A .  117 ?   16.641  27.654   2.208  0.00  0   A
+ATOM     1539    C  CG2 .  ILE   A .  205 ?   21.953  27.141   3.249  0.00  0   A
+ATOM     1509    C  CD2 .  LEU   A .  202 ?   16.995  30.754   4.286  0.00  0   A
+ATOM     1505    O    O .  LEU   A .  202 ?   21.436  31.217   5.146 -3.21  0   A
+ATOM      820    C   CB .  LEU   A .  113 ?   22.728  26.946  -0.496  0.00  0   A
+ATOM      830    C  CD1 .  LEU   A .  114 ?   17.000  29.244  -2.786  0.00  0   A
+ATOM     2030    C  CE1 .  PHE   A .  266 ?   15.255  30.669   0.284  0.00  0   A
+ATOM      828    C   CB .  LEU   A .  114 ?   18.476  27.301  -3.305  0.00  0   A
+ATOM     1804    C   CG .  PRO   A .  238 ?   21.078  33.317  -4.111  0.00  0   A
+ATOM     1822    C  CG2 .  VAL   A .  241 ?   17.795  32.913  -1.514  0.00  0   A
+ATOM      800    O    O .  ALA   A .  110 ?   21.862  27.166  -3.931 -1.07  0   A
+ATOM     1545    C   CB .  ALA   A .  206 ?   24.087  32.253   2.900  0.00  0   A
+ATOM     1541    N    N .  ALA   A .  206 ?   24.014  29.985   3.998  0.00  0   A
+ATOM     1798    S   SG .  CYS   A .  237 ?   22.030  35.316   0.634  0.00  0   A
+ATOM     1794    C   CA .  CYS   A .  237 ?   24.026  34.922  -1.329  0.00  0   A
+ATOM     1544    O    O .  ALA   A .  206 ?   26.983  31.382   2.492 -3.21  0   A
+ATOM     1542    C   CA .  ALA   A .  206 ?   24.748  30.821   3.023  0.00  0   A
+ATOM      822    C  CD1 .  LEU   A .  113 ?   25.012  27.872  -0.209  0.00  0   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_entity_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_asym_id
+ATOM      797    N    N .  ALA   A .  110 ?   25.276  26.616  -4.638 -1.51  0   A
+ATOM      798    C   CA .  ALA   A .  110 ?   24.131  27.516  -4.659  0.00  0   A
+ATOM      799    C    C .  ALA   A .  110 ?   22.743  26.831  -4.716  0.00  0   A
+ATOM      800    O    O .  ALA   A .  110 ?   21.862  27.166  -3.931 -1.07  0   A
+ATOM      801    C   CB .  ALA   A .  110 ?   24.277  28.499  -5.862  0.00  0   A
+ATOM      817    C   CA .  LEU   A .  113 ?   21.830  25.699  -0.438  0.00  0   A
+ATOM      818    C    C .  LEU   A .  113 ?   20.351  26.072  -0.464  0.00  0   A
+ATOM      819    O    O .  LEU   A .  113 ?   19.663  26.116   0.542 -1.07  0   A
+ATOM      820    C   CB .  LEU   A .  113 ?   22.728  26.946  -0.496  0.00  0   A
+ATOM      821    C   CG .  LEU   A .  113 ?   24.241  26.609  -0.297  0.00  0   A
+ATOM      822    C  CD1 .  LEU   A .  113 ?   25.012  27.872  -0.209  0.00  0   A
+ATOM      824    N    N .  LEU   A .  114 ?   19.877  26.311  -1.669  0.00  0   A
+ATOM      825    C   CA .  LEU   A .  114 ?   18.529  26.785  -1.887  0.00  0   A
+ATOM      827    O    O .  LEU   A .  114 ?   16.580  25.881  -0.904  0.00  0   A
+ATOM      828    C   CB .  LEU   A .  114 ?   18.476  27.301  -3.305  0.00  0   A
+ATOM      829    C   CG .  LEU   A .  114 ?   17.265  28.058  -3.739  0.00  0   A
+ATOM      830    C  CD1 .  LEU   A .  114 ?   17.000  29.244  -2.786  0.00  0   A
+ATOM      831    C  CD2 .  LEU   A .  114 ?   17.621  28.502  -5.177  0.00  0   A
+ATOM      856    C   CB .  ALA   A .  117 ?   16.641  27.654   2.208  0.00  0   A
+ATOM     1503    C   CA .  LEU   A .  202 ?   19.270  31.160   6.206  0.00  0   A
+ATOM     1504    C    C .  LEU   A .  202 ?   20.726  31.628   6.075  0.00  0   A
+ATOM     1505    O    O .  LEU   A .  202 ?   21.436  31.217   5.146 -3.21  0   A
+ATOM     1506    C   CB .  LEU   A .  202 ?   18.358  32.297   5.678  0.00  0   A
+ATOM     1509    C  CD2 .  LEU   A .  202 ?   16.995  30.754   4.286  0.00  0   A
+ATOM     1535    C    C .  ILE   A .  205 ?   24.224  28.698   4.198  0.00  0   A
+ATOM     1537    C   CB .  ILE   A .  205 ?   21.844  27.691   4.617  0.00  0   A
+ATOM     1539    C  CG2 .  ILE   A .  205 ?   21.953  27.141   3.249  0.00  0   A
+ATOM     1540    C  CD1 .  ILE   A .  205 ?   19.543  26.545   5.231  0.00  0   A
+ATOM     1541    N    N .  ALA   A .  206 ?   24.014  29.985   3.998  0.00  0   A
+ATOM     1542    C   CA .  ALA   A .  206 ?   24.748  30.821   3.023  0.00  0   A
+ATOM     1543    C    C .  ALA   A .  206 ?   26.201  31.004   3.353  0.00  0   A
+ATOM     1544    O    O .  ALA   A .  206 ?   26.983  31.382   2.492 -3.21  0   A
+ATOM     1545    C   CB .  ALA   A .  206 ?   24.087  32.253   2.900  0.00  0   A
+ATOM     1783    O    O .  GLU   A .  235 ?   28.595  34.381  -0.451 -0.95  0   A
+ATOM     1791    C    C .  GLY   A .  236 ?   26.040  34.560  -2.661  0.00  0   A
+ATOM     1792    O    O .  GLY   A .  236 ?   25.501  33.661  -3.290 -6.17  0   A
+ATOM     1793    N    N .  CYS   A .  237 ?   25.399  35.253  -1.728  0.00  0   A
+ATOM     1794    C   CA .  CYS   A .  237 ?   24.026  34.922  -1.329  0.00  0   A
+ATOM     1797    C   CB .  CYS   A .  237 ?   23.762  35.291   0.152  0.00  0   A
+ATOM     1798    S   SG .  CYS   A .  237 ?   22.030  35.316   0.634  0.00  0   A
+ATOM     1799    N    N .  PRO   A .  238 ?   22.157  35.032  -2.930  0.00  0   A
+ATOM     1804    C   CG .  PRO   A .  238 ?   21.078  33.317  -4.111  0.00  0   A
+ATOM     1805    C   CD .  PRO   A .  238 ?   21.822  33.590  -2.836  0.00  0   A
+ATOM     1820    C   CB .  VAL   A .  241 ?   18.354  33.953  -0.560  0.00  0   A
+ATOM     1821    C  CG1 .  VAL   A .  241 ?   18.722  33.273   0.801  0.00  0   A
+ATOM     1822    C  CG2 .  VAL   A .  241 ?   17.795  32.913  -1.514  0.00  0   A
+ATOM     2028    C  CD1 .  PHE   A .  266 ?   14.325  29.916  -0.423  0.00  0   A
+ATOM     2030    C  CE1 .  PHE   A .  266 ?   15.255  30.669   0.284  0.00  0   A
+ATOM     2032    C   CZ .  PHE   A .  266 ?   14.987  31.067   1.550  0.00  0   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)       : 244.3582
+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_entity_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_asym_id
+ATOM     1256    C   CA .  GLY   A .  171 ?   17.074  29.084  34.902  0.00  0   A
+ATOM     3772    C   CB .  GLU   B .  223 ?   20.899  28.443  38.451  0.00  0   B
+ATOM     3769    C   CA .  GLU   B .  223 ?   19.756  29.026  39.321  0.00  0   B
+ATOM     3800    O  OE1 .  GLU   B .  226 ?   14.870  27.408  38.360 -0.81  0   B
+ATOM     1258    O    O .  GLY   A .  171 ?   17.211  27.237  33.384  0.00  0   A
+ATOM     3810    N   NZ .  LYS   B .  227 ?   18.871  22.046  40.724  0.00  0   B
+ATOM     3799    C   CD .  GLU   B .  226 ?   13.993  27.306  39.282  0.00  0   B
+ATOM     3798    C   CG .  GLU   B .  226 ?   14.425  27.213  40.755  0.00  0   B
+ATOM     3809    C   CE .  LYS   B .  227 ?   19.628  23.270  41.089  0.00  0   B
+ATOM     3774    C   CD .  GLU   B .  223 ?   21.775  28.184  36.070  0.00  0   B
+ATOM     3775    O  OE1 .  GLU   B .  223 ?   22.737  27.521  36.550  0.00  0   B
+ATOM     3771    O    O .  GLU   B .  223 ?   19.336  27.833  41.335  0.00  0   B
+ATOM     3797    C   CB .  GLU   B .  226 ?   15.576  28.210  41.069  0.00  0   B
+ATOM     3773    C   CG .  GLU   B .  223 ?   20.865  28.953  37.013  0.00  0   B
+ATOM     3808    C   CD .  LYS   B .  227 ?   19.254  23.527  42.569  0.00  0   B
+ATOM     3796    O    O .  GLU   B .  226 ?   15.035  26.681  43.850  0.00  0   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_entity_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_asym_id
+ATOM     1256    C   CA .  GLY   A .  171 ?   17.074  29.084  34.902  0.00  0   A
+ATOM     1257    C    C .  GLY   A .  171 ?   16.881  28.422  33.539  0.00  0   A
+ATOM     1258    O    O .  GLY   A .  171 ?   17.211  27.237  33.384  0.00  0   A
+ATOM     3768    N    N .  GLU   B .  223 ?   19.652  30.471  39.123  0.00  0   B
+ATOM     3769    C   CA .  GLU   B .  223 ?   19.756  29.026  39.321  0.00  0   B
+ATOM     3770    C    C .  GLU   B .  223 ?   19.994  28.706  40.771  0.00  0   B
+ATOM     3771    O    O .  GLU   B .  223 ?   19.336  27.833  41.335  0.00  0   B
+ATOM     3772    C   CB .  GLU   B .  223 ?   20.899  28.443  38.451  0.00  0   B
+ATOM     3773    C   CG .  GLU   B .  223 ?   20.865  28.953  37.013  0.00  0   B
+ATOM     3774    C   CD .  GLU   B .  223 ?   21.775  28.184  36.070  0.00  0   B
+ATOM     3775    O  OE1 .  GLU   B .  223 ?   22.737  27.521  36.550  0.00  0   B
+ATOM     3776    O  OE2 .  GLU   B .  223 ?   21.549  28.266  34.820  0.00  0   B
+ATOM     3794    C   CA .  GLU   B .  226 ?   15.782  28.535  42.552  0.00  0   B
+ATOM     3795    C    C .  GLU   B .  226 ?   16.011  27.275  43.405  0.00  0   B
+ATOM     3796    O    O .  GLU   B .  226 ?   15.035  26.681  43.850  0.00  0   B
+ATOM     3797    C   CB .  GLU   B .  226 ?   15.576  28.210  41.069  0.00  0   B
+ATOM     3798    C   CG .  GLU   B .  226 ?   14.425  27.213  40.755  0.00  0   B
+ATOM     3799    C   CD .  GLU   B .  226 ?   13.993  27.306  39.282  0.00  0   B
+ATOM     3800    O  OE1 .  GLU   B .  226 ?   14.870  27.408  38.360 -0.81  0   B
+ATOM     3801    O  OE2 .  GLU   B .  226 ?   12.770  27.280  39.032 -3.35  0   B
+ATOM     3802    N    N .  LYS   B .  227 ?   17.281  26.917  43.674  0.00  0   B
+ATOM     3803    C   CA .  LYS   B .  227 ?   17.638  25.810  44.612  0.00  0   B
+ATOM     3806    C   CB .  LYS   B .  227 ?   19.009  25.214  44.314  0.00  0   B
+ATOM     3807    C   CG .  LYS   B .  227 ?   19.331  24.982  42.891  0.00  0   B
+ATOM     3808    C   CD .  LYS   B .  227 ?   19.254  23.527  42.569  0.00  0   B
+ATOM     3809    C   CE .  LYS   B .  227 ?   19.628  23.270  41.089  0.00  0   B
+ATOM     3810    N   NZ .  LYS   B .  227 ?   18.871  22.046  40.724  0.00  0   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)       : 153.5727
+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_entity_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_asym_id
+ATOM     5155    C    C .  ASN   C .  131 ?   49.791  69.967  16.216  0.00  0   C
+ATOM     5164    O    O .  PHE   C .  132 ?   48.967  66.829  17.018  0.00  0   C
+ATOM     5154    C   CA .  ASN   C .  131 ?   49.335  70.969  17.293  0.00  0   C
+ATOM     5156    O    O .  ASN   C .  131 ?   49.458  70.110  15.000 -2.55  0   C
+ATOM     5177    C  CG1 .  ILE   C .  133 ?   46.547  66.252  14.171  0.00  0   C
+ATOM     5179    C  CD1 .  ILE   C .  133 ?   45.747  66.718  12.918  0.00  0   C
+ATOM     5159    O  OD1 .  ASN   C .  131 ?   46.848  72.862  17.330  0.00  0   C
+ATOM     5600    C  CG1 .  ILE   C .  191 ?   45.611  66.019  19.250  0.00  0   C
+ATOM     5129    O    O .  GLU   C .  128 ?   48.054  70.332  20.849 -1.48  0   C
+ATOM     5595    N    N .  ILE   C .  191 ?   43.539  65.578  16.244  0.00  0   C
+ATOM     5599    C   CB .  ILE   C .  191 ?   44.408  66.418  18.397  0.00  0   C
+ATOM     5601    C  CG2 .  ILE   C .  191 ?   43.280  67.132  19.172  0.00  0   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_entity_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_asym_id
+ATOM     5121    O    O .  LEU   C .  127 ?   50.397  68.122  19.530  0.00  0   C
+ATOM     5127    C   CA .  GLU   C .  128 ?   48.268  67.988  21.395  0.00  0   C
+ATOM     5128    C    C .  GLU   C .  128 ?   48.593  69.482  21.560  0.00  0   C
+ATOM     5129    O    O .  GLU   C .  128 ?   48.054  70.332  20.849 -1.48  0   C
+ATOM     5153    N    N .  ASN   C .  131 ?   50.135  71.066  18.529  0.00  0   C
+ATOM     5154    C   CA .  ASN   C .  131 ?   49.335  70.969  17.293  0.00  0   C
+ATOM     5155    C    C .  ASN   C .  131 ?   49.791  69.967  16.216  0.00  0   C
+ATOM     5156    O    O .  ASN   C .  131 ?   49.458  70.110  15.000 -2.55  0   C
+ATOM     5157    C   CB .  ASN   C .  131 ?   49.099  72.344  16.675  0.00  0   C
+ATOM     5158    C   CG .  ASN   C .  131 ?   48.068  73.136  17.435  0.00  0   C
+ATOM     5159    O  OD1 .  ASN   C .  131 ?   46.848  72.862  17.330  0.00  0   C
+ATOM     5161    N    N .  PHE   C .  132 ?   50.528  68.950  16.668  0.00  0   C
+ATOM     5163    C    C .  PHE   C .  132 ?   49.677  66.798  16.013  0.00  0   C
+ATOM     5164    O    O .  PHE   C .  132 ?   48.967  66.829  17.018  0.00  0   C
+ATOM     5177    C  CG1 .  ILE   C .  133 ?   46.547  66.252  14.171  0.00  0   C
+ATOM     5179    C  CD1 .  ILE   C .  133 ?   45.747  66.718  12.918  0.00  0   C
+ATOM     5590    C   CA .  SER   C .  190 ?   42.695  65.333  13.987  0.00  0   C
+ATOM     5591    C    C .  SER   C .  190 ?   43.234  64.721  15.300  0.00  0   C
+ATOM     5593    C   CB .  SER   C .  190 ?   41.413  66.119  14.252  0.00  0   C
+ATOM     5595    N    N .  ILE   C .  191 ?   43.539  65.578  16.244  0.00  0   C
+ATOM     5596    C   CA .  ILE   C .  191 ?   43.914  65.163  17.570  0.00  0   C
+ATOM     5599    C   CB .  ILE   C .  191 ?   44.408  66.418  18.397  0.00  0   C
+ATOM     5600    C  CG1 .  ILE   C .  191 ?   45.611  66.019  19.250  0.00  0   C
+ATOM     5601    C  CG2 .  ILE   C .  191 ?   43.280  67.132  19.172  0.00  0   C
+#

tests/reference_output/123abc_out/pocket28_vert.pqr

@@ -0,0 +1,17 @@
+ATOM      1    O STP    28      46.129  69.213  16.468    0.00     3.75
+ATOM      2    O STP    28      45.578  69.884  15.172    0.00     3.89
+ATOM      3    O STP    28      46.095  69.217  16.465    0.00     3.78
+ATOM      4    O STP    28      46.052  69.252  16.449    0.00     3.80
+ATOM      5    O STP    28      46.578  69.070  18.026    0.00     3.43
+ATOM      6    O STP    28      43.837  69.980  15.822    0.00     4.43
+ATOM      7    O STP    28      45.514  69.780  18.447    0.00     3.54
+ATOM      8    C STP    28      44.607  69.670  15.712    0.00     4.22
+ATOM      9    O STP    28      44.445  69.726  15.676    0.00     4.28
+ATOM     10    C STP    28      44.564  69.552  15.695    0.00     4.14
+ATOM     11    O STP    28      46.213  69.434  17.959    0.00     3.54
+ATOM     12    C STP    28      46.537  69.097  18.016    0.00     3.44
+ATOM     13    C STP    28      46.081  69.217  16.476    0.00     3.78
+ATOM     14    C STP    28      46.049  69.248  16.459    0.00     3.80
+ATOM     15    C STP    28      46.551  69.075  17.986    0.00     3.44
+TER
+END

tests/reference_output/123abc_out/pocket29_atm.cif

@@ -0,0 +1,60 @@
+data_pocket29_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    29:
+0  - Pocket Score                      : -0.0486
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    18
+3  - Mean alpha-sphere radius          : 4.0946
+4  - Mean alpha-sphere Solvent Acc.    : 0.6067
+5  - Mean B-factor of pocket residues  : 0.3394
+6  - Hydrophobicity Score              : 23.8333
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.0833
+9  - Pocket volume (Monte Carlo)       : 280.7122
+10  -Pocket volume (convex hull)       : 12.3014
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 4.0000
+13 - Number of apolar alpha sphere     :     5
+14 - Proportion of apolar alpha sphere : 0.2778
+# 
+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_entity_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_asym_id
+ATOM      633    C  CE1 .  PHE   A .   90 ?   23.219   7.620  12.523  0.00  0   A
+ATOM      115    C  CD2 .  LEU   A .   21 ?   23.833   8.296  15.998  0.00  0   A
+ATOM      116    N    N .  GLY   A .   22 ?   26.977  10.989  17.772  0.00  0   A
+ATOM      664    C   CA .  GLY   A .   94 ?   24.159  13.940  10.732  0.00  0   A
+ATOM      148    O   OH .  TYR   A .   26 ?   24.138  15.654  15.314  0.00  0   A
+ATOM      667    N    N .  ASN   A .   95 ?   23.996  16.143  11.694  0.00  0   A
+ATOM      673    O  OD1 .  ASN   A .   95 ?   25.880  18.114  13.960 -2.14  0   A
+ATOM      135    O  OE1 .  GLN   A .   25 ?   27.558  15.740  17.545 -2.14  0   A
+ATOM      117    C   CA .  GLY   A .   22 ?   27.711  12.259  17.704  0.00  0   A
+ATOM      635    C   CZ .  PHE   A .   90 ?   23.754   7.359  11.279  0.00  0   A
+ATOM      639    O    O .  MET   A .   91 ?   22.317  10.826   9.705  0.00  0   A
+ATOM      647    O    O .  THR   A .   92 ?   25.377  10.176   8.230  0.00  0   A
+ATOM      698    O  OD2 .  ASP   A .   98 ?   28.581  18.421  13.874  0.00  0   A
+ATOM      695    C   CB .  ASP   A .   98 ?   28.818  18.983  11.564  0.00  0   A
+ATOM      654    O    O .  TYR   A .   93 ?   25.886  14.436   8.543 -2.95  0   A
+ATOM      737    O  OE1 .  GLU   A .  102 ?   31.683  16.733   9.180  0.00  0   A
+ATOM      738    O  OE2 .  GLU   A .  102 ?   32.646  17.951  10.762 -1.88  0   A
+ATOM      145    C  CE1 .  TYR   A .   26 ?   24.215  14.118  17.108  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket29_env_atm.cif

@@ -0,0 +1,55 @@
+data_pocket29_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_entity_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_asym_id
+ATOM      109    C   CA .  LEU   A .   21 ?   25.411   9.365  18.618  0.00  0   A
+ATOM      110    C    C .  LEU   A .   21 ?   26.217  10.637  18.809  0.00  0   A
+ATOM      112    C   CB .  LEU   A .   21 ?   24.055   9.763  18.043  0.00  0   A
+ATOM      113    C   CG .  LEU   A .   21 ?   23.240   8.692  17.348  0.00  0   A
+ATOM      115    C  CD2 .  LEU   A .   21 ?   23.833   8.296  15.998  0.00  0   A
+ATOM      116    N    N .  GLY   A .   22 ?   26.977  10.989  17.772  0.00  0   A
+ATOM      117    C   CA .  GLY   A .   22 ?   27.711  12.259  17.704  0.00  0   A
+ATOM      134    C   CD .  GLN   A .   25 ?   26.983  16.776  17.929  0.00  0   A
+ATOM      135    O  OE1 .  GLN   A .   25 ?   27.558  15.740  17.545 -2.14  0   A
+ATOM      136    N  NE2 .  GLN   A .   25 ?   26.655  17.754  17.106 -1.51  0   A
+ATOM      143    C  CD1 .  TYR   A .   26 ?   23.817  13.724  18.368  0.00  0   A
+ATOM      145    C  CE1 .  TYR   A .   26 ?   24.215  14.118  17.108  0.00  0   A
+ATOM      147    C   CZ .  TYR   A .   26 ?   23.727  15.310  16.576  0.00  0   A
+ATOM      148    O   OH .  TYR   A .   26 ?   24.138  15.654  15.314  0.00  0   A
+ATOM      633    C  CE1 .  PHE   A .   90 ?   23.219   7.620  12.523  0.00  0   A
+ATOM      635    C   CZ .  PHE   A .   90 ?   23.754   7.359  11.279  0.00  0   A
+ATOM      639    O    O .  MET   A .   91 ?   22.317  10.826   9.705  0.00  0   A
+ATOM      646    C    C .  THR   A .   92 ?   24.325  10.445   7.647  0.00  0   A
+ATOM      647    O    O .  THR   A .   92 ?   25.377  10.176   8.230  0.00  0   A
+ATOM      653    C    C .  TYR   A .   93 ?   25.046  13.581   8.441  0.00  0   A
+ATOM      654    O    O .  TYR   A .   93 ?   25.886  14.436   8.543 -2.95  0   A
+ATOM      663    N    N .  GLY   A .   94 ?   24.175  13.288   9.414  0.00  0   A
+ATOM      664    C   CA .  GLY   A .   94 ?   24.159  13.940  10.732  0.00  0   A
+ATOM      665    C    C .  GLY   A .   94 ?   23.592  15.331  10.711  0.00  0   A
+ATOM      667    N    N .  ASN   A .   95 ?   23.996  16.143  11.694  0.00  0   A
+ATOM      668    C   CA .  ASN   A .   95 ?   23.482  17.523  11.792  0.00  0   A
+ATOM      670    O    O .  ASN   A .   95 ?   25.129  18.291  10.166  0.00  0   A
+ATOM      672    C   CG .  ASN   A .   95 ?   24.977  18.738  13.399  0.00  0   A
+ATOM      673    O  OD1 .  ASN   A .   95 ?   25.880  18.114  13.960 -2.14  0   A
+ATOM      695    C   CB .  ASP   A .   98 ?   28.818  18.983  11.564  0.00  0   A
+ATOM      696    C   CG .  ASP   A .   98 ?   28.941  19.302  13.063  0.00  0   A
+ATOM      698    O  OD2 .  ASP   A .   98 ?   28.581  18.421  13.874  0.00  0   A
+ATOM      736    C   CD .  GLU   A .  102 ?   32.361  17.729   9.573  0.00  0   A
+ATOM      737    O  OE1 .  GLU   A .  102 ?   31.683  16.733   9.180  0.00  0   A
+ATOM      738    O  OE2 .  GLU   A .  102 ?   32.646  17.951  10.762 -1.88  0   A
+#