Merge branch 'issue-107' of https://github.com/Discngine/fpocket into issue-107

Issue 119

.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/*
 

headers/fparams.h

@@ -55,6 +55,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #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_CHAIN_NAME_LENGTH 20
+#define M_MAX_LIG_RESNAME_LENGTH 20
 
 #define M_MIN_AS_DENSITY 0.7
 
@@ -121,7 +123,7 @@ 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'
@@ -182,10 +184,10 @@ 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 custom_pocket_arg[M_MAX_CUSTOM_PÖCKET_LEN];
+	char custom_pocket_arg[M_MAX_CUSTOM_POCKET_LEN];
 	char **pdb_lst;
-	char xlig_chain_code[3];
-	char xlig_resname[3];
+	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;
@@ -204,7 +206,8 @@ typedef struct s_fparams
 												 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 */
+		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 */
@@ -214,8 +217,10 @@ typedef struct s_fparams
 		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];
+	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*/
 

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_PÖCKET_LEN 8000 /** maximum length for a custom pocket string*/
+#define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
 #define M_SIGN 1
 #define M_NO_SIGN 0
 

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

@@ -89,6 +89,8 @@ s_fparams *init_def_fparams(void)
     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;
 }
 
@@ -120,9 +122,9 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     opterr = 0;
     char *pt;
     char *apt;
-    char *residue_string[M_MAX_CUSTOM_PÖCKET_LEN];
+    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},
@@ -185,54 +187,53 @@ s_fparams *get_fpocket_args(int nargs, char **args)
         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;
 
         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);
             }
+            par->n_chains_to_delete=nk;
             // printf("%s\n",par->chain_delete);
             par->chain_is_kept = 1;
             status++;
@@ -246,26 +247,29 @@ s_fparams *get_fpocket_args(int nargs, char **args)
 
             status++;
 
-            strcpy(par->custom_ligand, optarg);
+            // strcpy(par->custom_ligand, optarg);
             // printf("%s and %s",par->custom_ligand,optarg);
-            pt = strtok(par->custom_ligand, ":");
+            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
@@ -292,7 +296,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                 strcpy(&residue_string, pt);
                 rest2 = residue_string;
                 apti = 0;
-                while (apt = strtok_r(rest2, ":", &rest2))
+                while ((apt = strtok_r(rest2, ":", &rest2)))
                 {
                     switch (apti)
                     {
@@ -971,18 +975,18 @@ void print_pocket_usage(FILE *f)
     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\ 
+    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\ 
+    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\

src/fpmain.c

@@ -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);
@@ -222,8 +222,10 @@ 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)

src/fpocket.c

@@ -165,7 +165,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
         fflush(DEBUG_STREAM);
     }
 
-    apply_clustering(pockets, params);
+    apply_clustering(pockets);
     if (DEBUG)
     {
         fprintf(DEBUG_STREAM, "applied clustering to pockets");
@@ -216,7 +216,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
             print_number_of_objects_in_memory();
         //        int i;
 
-        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path)
+        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path[0])
             calculate_pocket_energy_grids(pockets, params, pdb);
         // params->fpocket_running &&
     }

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])
@@ -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)
                         {
@@ -356,7 +352,6 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->res_name, at_in[i].resname);
                             strncpy(atom->chain, at_in[i].chain, 2);
                             atom->res_id = at_in[i].resid;
-                            // fprintf(stdout, " here : %c\n", at_in[i].insertion[0]);
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -399,13 +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);
                         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];
@@ -435,9 +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];
@@ -445,23 +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])
@@ -497,7 +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)
@@ -539,7 +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;
@@ -570,7 +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++)
@@ -615,16 +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++;
                 }
             }
@@ -639,6 +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;
@@ -652,6 +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

@@ -978,11 +978,13 @@ float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
           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;
 
     short unsigned int cur_atom_index = 0;
     int n_explicit_atoms_ok = 0;
+    int vidx;
 
     if (params->xpocket_n > 0)
     {
@@ -1063,7 +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))
@@ -1427,37 +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

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

tests/environment.yml

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

tests/reference_output/1ATP_out/1ATP_info.txt

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

tests/reference_output/1ATP_out/1ATP_pockets.pqr

@@ -107,405 +107,432 @@ ATOM    103    C STP     1       8.025   9.593   3.157    0.00     4.18
 ATOM    104    C STP     1       9.377   9.170   3.567    0.00     4.51
 ATOM    105    O STP     1       9.399   8.934   3.561    0.00     4.38
 ATOM    106    O STP     1       9.649   9.131   3.392    0.00     4.48
-ATOM    107    O STP     2      17.904  16.846   2.034    0.00     4.00
-ATOM    108    C STP     2      13.212  24.010  -0.223    0.00     3.56
-ATOM    109    O STP     2      13.590  24.333  -0.124    0.00     3.66
-ATOM    110    C STP     2      16.767  18.684   1.078    0.00     4.22
-ATOM    111    C STP     2      16.715  18.704   1.057    0.00     4.20
-ATOM    112    O STP     2      17.342  17.855   1.830    0.00     4.24
-ATOM    113    O STP     2      17.041  17.846   1.980    0.00     4.08
-ATOM    114    O STP     2      16.580  19.060   0.747    0.00     4.27
-ATOM    115    O STP     2      17.635  17.024   1.403    0.00     3.80
-ATOM    116    O STP     2      17.395  17.419   1.401    0.00     3.89
-ATOM    117    C STP     2      16.900  18.376   1.091    0.00     4.07
-ATOM    118    O STP     2      17.782  16.444   1.256    0.00     3.57
-ATOM    119    O STP     2      14.632  22.244  -1.461    0.00     3.60
-ATOM    120    O STP     2      14.379  23.675  -0.187    0.00     4.18
-ATOM    121    O STP     2      14.950  20.959  -0.498    0.00     4.03
-ATOM    122    O STP     2      16.062  19.544  -0.072    0.00     4.25
-ATOM    123    O STP     2      16.188  19.842  -0.177    0.00     4.42
-ATOM    124    C STP     2      16.044  18.633   0.739    0.00     3.73
-ATOM    125    O STP     2      15.502  19.054  -0.011    0.00     3.68
-ATOM    126    C STP     3       5.666  -2.347   9.650    0.00     3.64
-ATOM    127    C STP     3       5.663  -2.342   9.659    0.00     3.64
-ATOM    128    C STP     3       4.857  -3.237  11.687    0.00     3.51
-ATOM    129    C STP     3       4.909  -3.421  12.179    0.00     3.52
-ATOM    130    C STP     3       4.463  -1.923  10.602    0.00     3.52
-ATOM    131    C STP     3       4.751  -3.640  11.929    0.00     3.49
-ATOM    132    C STP     3       4.816  -3.657  12.202    0.00     3.51
-ATOM    133    C STP     3       5.643  -2.334   9.598    0.00     3.62
-ATOM    134    C STP     3       5.573  -2.273   9.693    0.00     3.63
-ATOM    135    C STP     3       5.625  -2.300   9.658    0.00     3.64
-ATOM    136    C STP     3       5.618  -2.250   9.664    0.00     3.62
-ATOM    137    C STP     3       4.669  -1.977  10.488    0.00     3.53
-ATOM    138    C STP     3       4.819  -1.860  10.403    0.00     3.43
-ATOM    139    C STP     3       4.472  -1.924  10.605    0.00     3.53
-ATOM    140    C STP     3       4.423  -1.750  10.637    0.00     3.43
-ATOM    141    C STP     3       4.474  -1.928  10.609    0.00     3.53
-ATOM    142    C STP     3       4.552  -2.069  10.740    0.00     3.51
-ATOM    143    C STP     3       4.780  -3.687  12.261    0.00     3.48
-ATOM    144    O STP     4      10.707   8.465   9.562    0.00     3.56
-ATOM    145    O STP     4      11.897   7.600  10.387    0.00     3.53
-ATOM    146    O STP     4      11.713   7.651  10.429    0.00     3.61
-ATOM    147    O STP     4      11.722   7.673  10.440    0.00     3.59
-ATOM    148    O STP     4      11.706   7.635  10.442    0.00     3.60
-ATOM    149    O STP     4      13.057   5.577  11.209    0.00     3.45
-ATOM    150    C STP     4      13.599   4.782  12.622    0.00     3.56
-ATOM    151    O STP     4      12.926   5.521  11.298    0.00     3.49
-ATOM    152    O STP     4      11.593   6.620  11.138    0.00     3.56
-ATOM    153    O STP     4      11.150   6.837  11.229    0.00     3.58
-ATOM    154    O STP     4      11.203   6.847  11.061    0.00     3.66
-ATOM    155    O STP     4      10.100   6.854  10.639    0.00     3.72
-ATOM    156    O STP     4      10.043   6.829  10.609    0.00     3.72
-ATOM    157    O STP     4      10.008   6.832  11.002    0.00     3.55
-ATOM    158    O STP     4       9.996   6.814  10.721    0.00     3.65
-ATOM    159    O STP     4      14.136   3.921  15.176    0.00     4.64
-ATOM    160    O STP     4      13.450   4.065  15.198    0.00     4.27
-ATOM    161    O STP     4      14.349   4.009  14.805    0.00     4.61
-ATOM    162    O STP     4      13.844   4.358  14.153    0.00     4.07
-ATOM    163    C STP     4      14.400   4.002  14.664    0.00     4.57
-ATOM    164    C STP     4      13.873   4.433  13.491    0.00     3.88
-ATOM    165    C STP     4      13.578   4.355  12.749    0.00     3.43
-ATOM    166    O STP     4       9.524   6.563  10.325    0.00     3.47
-ATOM    167    C STP     4       9.327   7.050  10.077    0.00     3.46
-ATOM    168    O STP     4      10.903   8.245   9.723    0.00     3.55
-ATOM    169    O STP     4      11.424   7.798  10.169    0.00     3.58
-ATOM    170    O STP     4      10.102   6.908  10.584    0.00     3.71
-ATOM    171    O STP     4      10.425   8.337   9.557    0.00     3.58
-ATOM    172    O STP     4      10.324   8.322   9.469    0.00     3.54
-ATOM    173    O STP     4      10.351   8.314   9.560    0.00     3.59
-ATOM    174    C STP     4      10.082   7.855   9.856    0.00     3.56
-ATOM    175    C STP     4       9.763   7.428   9.952    0.00     3.52
-ATOM    176    C STP     4       9.808   6.869  10.405    0.00     3.64
-ATOM    177    O STP     4      10.016   6.824  10.586    0.00     3.71
-ATOM    178    O STP     4       9.960   6.815  10.553    0.00     3.70
-ATOM    179    O STP     4       9.895   6.462  10.350    0.00     3.45
-ATOM    180    O STP     4       9.826   6.743  10.451    0.00     3.64
-ATOM    181    O STP     5      -3.903   9.091  -8.804    0.00     4.57
-ATOM    182    O STP     5      -3.754   8.992  -8.593    0.00     4.51
-ATOM    183    O STP     5      -2.044   6.009  -7.092    0.00     3.61
-ATOM    184    O STP     5      -2.612   5.104  -6.282    0.00     3.41
-ATOM    185    O STP     5      -2.076   5.517  -6.742    0.00     3.61
-ATOM    186    O STP     5      -1.785   5.216  -7.035    0.00     3.65
-ATOM    187    O STP     5      -3.701   8.983  -8.573    0.00     4.49
-ATOM    188    O STP     5      -3.246   8.932  -8.467    0.00     4.30
-ATOM    189    O STP     5      -1.423   9.628  -8.928    0.00     3.47
-ATOM    190    O STP     5      -2.819   9.025  -8.670    0.00     4.13
-ATOM    191    O STP     5      -1.924   8.885  -8.753    0.00     3.78
-ATOM    192    O STP     5      -1.997   4.980  -6.859    0.00     3.52
-ATOM    193    O STP     5      -1.773   5.141  -7.052    0.00     3.64
-ATOM    194    O STP     5      -1.816   5.091  -7.152    0.00     3.55
-ATOM    195    O STP     5      -1.491   5.021  -7.121    0.00     3.59
-ATOM    196    O STP     5      -1.417   4.986  -7.145    0.00     3.57
-ATOM    197    O STP     5      -1.425   4.982  -7.131    0.00     3.57
-ATOM    198    O STP     5      -2.908   8.645  -8.261    0.00     4.08
-ATOM    199    O STP     5      -1.967   6.532  -7.237    0.00     3.55
-ATOM    200    C STP     5      -2.911   8.402  -8.137    0.00     3.98
-ATOM    201    O STP     5      -1.038   7.720  -7.892    0.00     3.49
-ATOM    202    O STP     5      -1.266   8.004  -8.024    0.00     3.55
-ATOM    203    C STP     6      17.284  -3.003  -7.392    0.00     3.79
-ATOM    204    C STP     6      17.140  -3.037  -7.495    0.00     3.70
-ATOM    205    C STP     6      17.287  -2.942  -7.558    0.00     3.71
-ATOM    206    O STP     6      15.862  -3.114  -6.582    0.00     3.49
-ATOM    207    O STP     6      18.410  -1.869  -6.831    0.00     3.46
-ATOM    208    O STP     6      18.093  -1.568  -4.665    0.00     3.47
-ATOM    209    O STP     6      18.176  -2.391  -6.545    0.00     3.68
-ATOM    210    O STP     6      18.178  -1.260  -4.556    0.00     3.40
-ATOM    211    O STP     6      18.146  -1.324  -4.503    0.00     3.45
-ATOM    212    O STP     6      17.446  -3.009  -6.936    0.00     3.90
-ATOM    213    O STP     6      17.338  -2.967  -7.164    0.00     3.86
-ATOM    214    O STP     6      16.971  -3.071  -6.456    0.00     3.78
-ATOM    215    O STP     6      16.372  -3.033  -6.540    0.00     3.63
-ATOM    216    O STP     6      16.616  -2.342  -4.591    0.00     3.50
-ATOM    217    O STP     6      16.735  -2.388  -4.679    0.00     3.51
-ATOM    218    C STP     6      16.003  -2.925  -6.361    0.00     3.50
-ATOM    219    C STP     6      15.537  -2.940  -6.326    0.00     3.41
-ATOM    220    O STP     7      -1.389 -15.808   4.608    0.00     3.81
-ATOM    221    O STP     7      -1.682 -16.022   4.590    0.00     3.66
-ATOM    222    O STP     7      -1.648 -15.823   4.692    0.00     3.85
-ATOM    223    C STP     7      -5.623 -13.895   2.816    0.00     3.42
-ATOM    224    C STP     7      -7.247 -14.004   3.331    0.00     3.65
-ATOM    225    C STP     7      -8.747 -13.072   4.181    0.00     3.82
-ATOM    226    C STP     7      -3.506 -14.247   3.643    0.00     3.79
-ATOM    227    O STP     7      -3.650 -14.469   3.805    0.00     3.84
-ATOM    228    O STP     7      -5.817 -14.938   3.693    0.00     3.87
-ATOM    229    C STP     7      -2.262 -14.253   4.649    0.00     4.35
-ATOM    230    O STP     7      -8.823 -12.829   5.969    0.00     3.78
-ATOM    231    C STP     7      -8.681 -12.900   4.221    0.00     3.68
-ATOM    232    O STP     7      -1.409 -15.542   5.914    0.00     4.33
-ATOM    233    O STP     7      -1.417 -15.715   4.699    0.00     3.91
-ATOM    234    O STP     7      -1.682 -15.399   5.074    0.00     4.31
-ATOM    235    C STP     7      -1.560 -13.587   5.226    0.00     4.51
-ATOM    236    C STP     7      -1.567 -13.472   5.345    0.00     4.45
-ATOM    237    O STP     7      -1.180 -15.075   6.105    0.00     4.34
-ATOM    238    O STP     7      -1.076 -15.289   7.116    0.00     4.14
-ATOM    239    O STP     7      -1.505 -13.532   5.394    0.00     4.46
-ATOM    240    O STP     7      -0.289 -13.357   5.212    0.00     3.55
-ATOM    241    C STP     7      -0.289 -13.067   3.400    0.00     3.46
-ATOM    242    O STP     7      -1.253 -14.770   5.826    0.00     4.37
-ATOM    243    C STP     7      -1.525 -13.665   5.202    0.00     4.54
-ATOM    244    O STP     7      -1.488 -13.667   5.270    0.00     4.52
-ATOM    245    C STP     7      -1.739 -14.231   4.832    0.00     4.53
-ATOM    246    C STP     7      -1.647 -14.742   4.977    0.00     4.44
-ATOM    247    C STP     7      -1.682 -14.732   5.030    0.00     4.49
-ATOM    248    C STP     7      -1.616 -13.199   5.185    0.00     4.27
-ATOM    249    C STP     7      -1.612 -13.209   5.227    0.00     4.28
-ATOM    250    C STP     7      -1.726 -13.041   5.798    0.00     4.17
-ATOM    251    O STP     8      15.640  11.395  -7.384    0.00     3.87
-ATOM    252    O STP     8      14.547  11.507  -5.506    0.00     3.47
-ATOM    253    C STP     8      15.133  11.716  -6.441    0.00     3.54
-ATOM    254    O STP     8      14.464  10.763  -5.571    0.00     3.51
-ATOM    255    O STP     8      14.467  10.370  -5.296    0.00     3.44
-ATOM    256    O STP     8      14.848  13.223  -6.639    0.00     3.50
-ATOM    257    O STP     8      15.418  12.203  -7.050    0.00     3.68
-ATOM    258    O STP     8      15.660  11.576  -7.445    0.00     3.87
-ATOM    259    O STP     8      16.047  11.948  -7.515    0.00     3.67
-ATOM    260    O STP     8      15.521  11.388  -7.841    0.00     3.75
-ATOM    261    O STP     8      15.570  11.317  -8.748    0.00     3.41
-ATOM    262    O STP     8      15.604  11.206  -7.376    0.00     3.86
-ATOM    263    O STP     8      15.544  11.122  -7.297    0.00     3.82
-ATOM    264    O STP     8      15.979  10.444  -7.233    0.00     3.55
-ATOM    265    C STP     8      15.792  10.270  -7.031    0.00     3.50
-ATOM    266    O STP     9       3.602  29.013   1.016    0.00     3.55
-ATOM    267    C STP     9       5.556  23.790   2.238    0.00     3.66
-ATOM    268    C STP     9       4.374  24.558   2.469    0.00     3.55
-ATOM    269    C STP     9       6.248  22.839   2.662    0.00     3.65
-ATOM    270    C STP     9       6.687  23.325   2.417    0.00     3.80
-ATOM    271    O STP     9       3.605  28.995   0.988    0.00     3.53
-ATOM    272    C STP     9       6.666  23.871   2.160    0.00     3.91
-ATOM    273    C STP     9       6.778  23.571   2.298    0.00     3.87
-ATOM    274    C STP     9       6.777  25.942   2.510    0.00     3.88
-ATOM    275    O STP     9       3.851  24.675   2.332    0.00     3.51
-ATOM    276    C STP     9       3.757  24.628   2.235    0.00     3.46
-ATOM    277    O STP     9       3.932  27.786   1.618    0.00     3.45
-ATOM    278    O STP     9       4.637  26.459   2.777    0.00     3.76
-ATOM    279    C STP     9       4.889  27.180   2.881    0.00     4.07
-ATOM    280    O STP     9       3.599  29.091   1.545    0.00     3.89
-ATOM    281    C STP     9       7.492  23.806   0.509    0.00     3.43
-ATOM    282    C STP     9       7.257  23.839   1.162    0.00     3.57
-ATOM    283    C STP     9       7.637  23.976   0.562    0.00     3.48
-ATOM    284    C STP     9       6.839  23.523   2.245    0.00     3.83
-ATOM    285    C STP     9       6.757  23.101   2.378    0.00     3.69
-ATOM    286    C STP     9       6.868  27.794   3.414    0.00     4.36
-ATOM    287    C STP     9       6.830  26.126   2.605    0.00     3.89
-ATOM    288    O STP    10      -7.764  15.242   7.103    0.00     3.96
-ATOM    289    C STP    10      -5.783  13.019   6.568    0.00     4.49
-ATOM    290    O STP    10      -5.788  12.752   6.449    0.00     4.69
-ATOM    291    O STP    10      -7.309  14.474   6.726    0.00     4.12
-ATOM    292    O STP    10      -7.432  15.466   6.755    0.00     3.70
-ATOM    293    O STP    10      -7.395  15.658   6.560    0.00     3.50
-ATOM    294    C STP    10      -4.485  12.252   8.033    0.00     3.97
-ATOM    295    C STP    10      -4.567  13.020   7.587    0.00     3.99
-ATOM    296    C STP    10      -4.565  12.978   7.571    0.00     4.02
-ATOM    297    O STP    10      -4.654  11.597   3.673    0.00     3.94
-ATOM    298    O STP    10      -3.791  12.064   4.278    0.00     3.43
-ATOM    299    O STP    10      -4.242  12.235   5.610    0.00     3.94
-ATOM    300    O STP    10      -3.273  10.191   7.558    0.00     3.44
-ATOM    301    C STP    10      -4.073  12.143   8.369    0.00     3.67
-ATOM    302    C STP    10      -3.693  10.881   8.123    0.00     3.54
-ATOM    303    C STP    10      -3.402  10.565   8.181    0.00     3.46
-ATOM    304    O STP    11      16.399  30.997  -2.408    0.00     3.51
-ATOM    305    O STP    11      16.378  31.564  -2.092    0.00     3.53
-ATOM    306    O STP    11      16.438  31.064  -2.387    0.00     3.53
-ATOM    307    O STP    11      17.895  28.085  -5.613    0.00     3.60
-ATOM    308    O STP    11      18.864  28.710  -3.265    0.00     4.57
-ATOM    309    O STP    11      17.852  28.163  -5.642    0.00     3.57
-ATOM    310    O STP    11      17.748  28.256  -3.638    0.00     3.99
-ATOM    311    O STP    11      18.340  28.694  -3.618    0.00     4.44
-ATOM    312    O STP    11      17.987  28.173  -5.180    0.00     3.72
-ATOM    313    O STP    11      18.227  28.380  -4.224    0.00     4.14
-ATOM    314    O STP    11      18.119  28.193  -4.507    0.00     3.99
-ATOM    315    O STP    11      16.692  30.260  -3.367    0.00     3.43
-ATOM    316    O STP    11      17.772  29.567  -4.909    0.00     3.47
-ATOM    317    C STP    11      17.710  27.065  -6.133    0.00     3.50
-ATOM    318    O STP    11      17.725  26.987  -6.025    0.00     3.51
-ATOM    319    O STP    11      17.545  26.715  -6.183    0.00     3.43
-ATOM    320    C STP    12      -3.012  -8.100  -8.760    0.00     3.99
-ATOM    321    C STP    12      -3.458  -8.552  -8.865    0.00     4.13
-ATOM    322    C STP    12      -2.959  -8.581 -10.924    0.00     3.60
-ATOM    323    C STP    12      -3.348 -12.034  -7.768    0.00     3.58
-ATOM    324    C STP    12      -4.265 -11.238  -7.349    0.00     3.85
-ATOM    325    C STP    12      -3.688  -6.964  -9.269    0.00     3.51
-ATOM    326    C STP    12      -2.701  -7.221 -10.008    0.00     3.68
-ATOM    327    C STP    12      -5.618  -8.473  -9.251    0.00     4.02
-ATOM    328    C STP    12      -3.297  -7.983  -9.300    0.00     4.15
-ATOM    329    C STP    12      -3.480  -8.204  -9.300    0.00     4.19
-ATOM    330    C STP    12      -2.711  -7.550  -9.906    0.00     3.88
-ATOM    331    C STP    12      -3.130  -8.353 -10.547    0.00     3.78
-ATOM    332    C STP    12      -6.416  -7.590  -9.212    0.00     3.65
-ATOM    333    C STP    12      -6.562  -8.616  -9.387    0.00     4.21
-ATOM    334    C STP    12      -3.584  -8.558 -11.489    0.00     3.41
-ATOM    335    C STP    12      -2.190  -7.904  -8.566    0.00     3.57
-ATOM    336    C STP    12      -2.781  -7.847  -8.009    0.00     3.57
-ATOM    337    C STP    12      -4.480 -10.505  -7.436    0.00     3.94
-ATOM    338    C STP    12      -4.026  -9.106  -8.251    0.00     4.00
-ATOM    339    C STP    12      -4.477  -9.071  -8.355    0.00     3.93
-ATOM    340    C STP    12      -6.605  -8.625  -9.403    0.00     4.22
-ATOM    341    C STP    12      -7.298  -9.850 -11.196    0.00     3.43
-ATOM    342    C STP    12      -6.455  -7.572  -9.223    0.00     3.65
-ATOM    343    C STP    12      -6.421  -7.573  -9.212    0.00     3.65
-ATOM    344    O STP    12      -1.367  -6.997 -10.176    0.00     3.51
-ATOM    345    C STP    12      -1.239  -6.770 -10.255    0.00     3.42
-ATOM    346    C STP    12      -4.616 -11.435  -7.345    0.00     3.83
-ATOM    347    C STP    12      -4.811 -11.636  -7.371    0.00     3.80
-ATOM    348    C STP    12      -4.913 -11.381  -7.364    0.00     3.83
-ATOM    349    C STP    12      -6.933  -9.877  -8.296    0.00     4.23
-ATOM    350    C STP    12      -6.950  -9.879  -8.185    0.00     4.17
-ATOM    351    C STP    12      -6.960  -7.202  -9.484    0.00     3.47
-ATOM    352    C STP    12      -6.846  -7.861  -9.393    0.00     3.82
-ATOM    353    C STP    12      -7.673  -8.310  -9.533    0.00     4.10
-ATOM    354    C STP    12      -6.670  -8.554  -9.417    0.00     4.18
-ATOM    355    O STP    13      10.769   4.600  17.144    0.00     4.66
-ATOM    356    O STP    13       8.918   7.040  15.105    0.00     3.53
-ATOM    357    O STP    13       8.811   6.910  15.467    0.00     3.75
-ATOM    358    O STP    13       8.654   7.049  15.351    0.00     3.57
-ATOM    359    O STP    13       7.009   4.684  15.839    0.00     4.13
-ATOM    360    O STP    13      10.267   4.709  16.884    0.00     4.61
-ATOM    361    O STP    13       9.090   4.045  16.233    0.00     4.02
-ATOM    362    O STP    13       8.866   5.705  16.024    0.00     4.41
-ATOM    363    O STP    13       8.485   4.984  16.506    0.00     4.67
-ATOM    364    O STP    13       7.933   4.703  15.769    0.00     4.23
-ATOM    365    O STP    13       8.124   4.913  16.122    0.00     4.48
-ATOM    366    O STP    13       5.406   4.327  17.670    0.00     4.50
-ATOM    367    O STP    13       6.841   4.575  15.663    0.00     4.04
-ATOM    368    C STP    13       6.255   4.603  14.860    0.00     3.42
-ATOM    369    C STP    13       5.811   4.553  15.542    0.00     3.60
-ATOM    370    O STP    13       6.320   4.537  16.081    0.00     4.07
-ATOM    371    O STP    13       5.988   4.465  16.323    0.00     4.09
-ATOM    372    O STP    13       6.008   4.524  16.167    0.00     4.03
-ATOM    373    O STP    13       7.257   4.342  15.204    0.00     3.86
-ATOM    374    O STP    13       4.688   3.338  16.867    0.00     3.82
-ATOM    375    O STP    13       4.288   3.032  16.894    0.00     3.79
-ATOM    376    O STP    13       2.992   2.180  16.473    0.00     3.71
-ATOM    377    O STP    13       2.016   2.191  16.513    0.00     3.71
-ATOM    378    O STP    13       2.230   2.170  17.329    0.00     4.23
-ATOM    379    O STP    13       2.219   2.587  18.277    0.00     4.70
-ATOM    380    O STP    14       2.506 -11.531 -14.753    0.00     3.67
-ATOM    381    O STP    14       3.068 -10.223 -15.746    0.00     4.35
-ATOM    382    O STP    14       2.399  -9.985 -15.545    0.00     4.02
-ATOM    383    O STP    14       2.404  -9.971 -15.570    0.00     4.02
-ATOM    384    C STP    14       5.125 -10.220 -14.880    0.00     4.59
-ATOM    385    O STP    14       6.885 -10.576 -13.808    0.00     4.29
-ATOM    386    C STP    14       5.976 -10.559 -14.490    0.00     4.50
-ATOM    387    O STP    14       6.965 -10.686 -13.636    0.00     4.15
-ATOM    388    C STP    14       6.745 -10.296 -13.292    0.00     4.06
-ATOM    389    C STP    14       6.779 -10.238 -13.247    0.00     4.00
-ATOM    390    O STP    14       6.903 -10.566 -13.771    0.00     4.28
-ATOM    391    O STP    14       7.436 -10.329 -13.922    0.00     4.04
-ATOM    392    C STP    14       5.178  -9.990 -14.394    0.00     4.28
-ATOM    393    C STP    14       6.257  -9.980 -12.969    0.00     3.90
-ATOM    394    C STP    14       5.645 -10.172 -13.886    0.00     4.19
-ATOM    395    C STP    14       5.308 -10.126 -14.302    0.00     4.32
-ATOM    396    C STP    14       6.375  -9.340 -12.443    0.00     3.44
-ATOM    397    C STP    14       8.583  -7.677 -16.792    0.00     3.57
-ATOM    398    O STP    14       9.881  -9.702 -14.137    0.00     3.47
-ATOM    399    C STP    14       8.914  -9.764 -16.244    0.00     4.57
-ATOM    400    C STP    14       9.059  -9.645 -15.171    0.00     4.05
-ATOM    401    O STP    14      12.065 -10.289 -14.422    0.00     3.41
-ATOM    402    O STP    14       5.610  -9.461 -16.514    0.00     4.49
-ATOM    403    O STP    14       5.607  -9.484 -16.523    0.00     4.51
-ATOM    404    O STP    14       4.200  -8.861 -15.470    0.00     3.55
-ATOM    405    O STP    15      20.762 -15.016  15.628    0.00     4.47
-ATOM    406    O STP    15      20.093 -13.782  15.160    0.00     3.81
-ATOM    407    O STP    15      21.482 -16.110  15.016    0.00     4.50
-ATOM    408    O STP    15      21.091 -14.702  15.246    0.00     4.03
-ATOM    409    C STP    15      18.817 -14.364  15.540    0.00     4.62
-ATOM    410    C STP    15      15.023 -10.073  17.441    0.00     4.26
-ATOM    411    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM    412    O STP    15      20.585 -16.489  14.223    0.00     4.09
-ATOM    413    O STP    15      19.415 -15.607  15.364    0.00     4.66
-ATOM    414    C STP    15      15.015 -10.071  17.451    0.00     4.26
-ATOM    415    C STP    15      14.777 -10.089  16.406    0.00     3.47
-ATOM    416    C STP    15      14.855 -10.051  17.251    0.00     4.06
-ATOM    417    O STP    15      13.277  -9.665  17.514    0.00     3.56
-ATOM    418    C STP    15      14.805 -10.108  17.922    0.00     4.49
-ATOM    419    O STP    15      18.495 -14.244  14.923    0.00     4.22
-ATOM    420    O STP    15      18.480 -14.689  14.307    0.00     3.84
-ATOM    421    C STP    15      18.270 -13.858  15.512    0.00     4.47
-ATOM    422    C STP    15      15.741 -10.998  17.957    0.00     4.63
-ATOM    423    C STP    15      15.742 -10.997  17.953    0.00     4.62
-ATOM    424    C STP    15      15.760 -10.982  17.951    0.00     4.60
-ATOM    425    C STP    15      16.138 -10.636  17.830    0.00     4.10
-ATOM    426    C STP    15      16.014 -10.748  17.869    0.00     4.26
-ATOM    427    O STP    15      17.979 -13.868  13.441    0.00     3.43
-ATOM    428    O STP    15      18.105 -13.657  15.491    0.00     4.41
-ATOM    429    O STP    15      17.165 -13.262  16.453    0.00     4.67
-ATOM    430    O STP    15      15.637 -10.294  15.930    0.00     3.65
-ATOM    431    C STP    15      16.936 -12.523  16.560    0.00     4.44
-ATOM    432    C STP    15      17.083 -12.356  16.365    0.00     4.23
-ATOM    433    C STP    15      16.850 -12.331  16.545    0.00     4.35
-ATOM    434    O STP    16      21.605   9.274   6.445    0.00     3.95
-ATOM    435    O STP    16      23.052   4.027   8.218    0.00     3.68
-ATOM    436    O STP    16      20.037  10.202   7.733    0.00     4.60
-ATOM    437    O STP    16      22.942   3.882   8.664    0.00     3.49
-ATOM    438    O STP    16      22.985   4.910   9.082    0.00     3.75
-ATOM    439    O STP    16      22.778   4.706   8.980    0.00     3.57
-ATOM    440    O STP    16      22.932   4.338   8.689    0.00     3.66
-ATOM    441    O STP    16      22.819   4.391   8.749    0.00     3.58
-ATOM    442    O STP    16      22.943   3.580   7.482    0.00     3.63
-ATOM    443    O STP    16      22.800   7.841   5.222    0.00     3.89
-ATOM    444    C STP    16      23.308   3.741   7.149    0.00     3.81
-ATOM    445    O STP    16      23.140   5.515   5.119    0.00     3.59
-ATOM    446    O STP    16      22.972   4.082   6.110    0.00     3.44
-ATOM    447    O STP    16      23.254   3.825   6.901    0.00     3.72
-ATOM    448    O STP    16      23.595   4.080   7.336    0.00     3.93
-ATOM    449    O STP    16      24.143   3.706   7.296    0.00     3.56
-ATOM    450    O STP    16      23.426   3.868   7.200    0.00     3.86
-ATOM    451    C STP    17      20.079 -17.759  -0.802    0.00     3.67
-ATOM    452    O STP    17      21.058 -19.186  -2.154    0.00     3.88
-ATOM    453    O STP    17      22.470 -19.926  -1.235    0.00     4.53
-ATOM    454    O STP    17      22.448 -20.166  -0.692    0.00     4.42
-ATOM    455    C STP    17      21.929 -20.012  -0.119    0.00     4.06
-ATOM    456    O STP    17      21.994 -20.327   0.005    0.00     4.04
-ATOM    457    C STP    17      22.152 -19.454  -1.681    0.00     4.50
-ATOM    458    O STP    17      22.110 -19.403  -1.774    0.00     4.50
-ATOM    459    C STP    17      20.135 -17.782  -0.862    0.00     3.68
-ATOM    460    C STP    17      20.333 -17.868  -1.159    0.00     3.71
-ATOM    461    O STP    17      22.730 -19.052  -1.278    0.00     3.92
-ATOM    462    C STP    17      21.017 -18.682  -1.343    0.00     4.01
-ATOM    463    C STP    17      21.042 -18.693  -1.380    0.00     4.03
-ATOM    464    C STP    17      20.540 -18.564  -0.766    0.00     3.77
-ATOM    465    C STP    17      21.084 -19.267  -0.227    0.00     3.70
-ATOM    466    C STP    17      20.059 -17.765  -0.768    0.00     3.67
-ATOM    467    C STP    17      20.019 -17.679  -0.714    0.00     3.63
-ATOM    468    O STP    18      23.290   7.625 -10.006    0.00     3.65
-ATOM    469    O STP    18      21.998   7.158  -8.997    0.00     3.42
-ATOM    470    O STP    18      21.767   7.080  -9.018    0.00     3.44
-ATOM    471    O STP    18      24.354   9.432 -11.111    0.00     3.89
-ATOM    472    O STP    18      24.924  10.086 -10.852    0.00     3.50
-ATOM    473    O STP    18      24.124   8.241 -11.073    0.00     4.17
-ATOM    474    O STP    18      23.599   7.744 -10.504    0.00     3.89
-ATOM    475    O STP    18      25.034   7.815 -11.334    0.00     4.30
-ATOM    476    O STP    18      24.595   7.493 -10.910    0.00     4.00
-ATOM    477    O STP    18      24.583   8.688 -11.745    0.00     4.51
-ATOM    478    O STP    18      24.433   8.715 -11.668    0.00     4.47
-ATOM    479    O STP    18      24.019   8.832 -11.950    0.00     4.30
-ATOM    480    O STP    18      22.801   8.729 -12.139    0.00     3.77
-ATOM    481    O STP    18      22.207   7.260 -10.194    0.00     3.50
-ATOM    482    C STP    18      24.752   8.793 -13.468    0.00     4.56
-ATOM    483    O STP    18      26.139   6.551 -11.712    0.00     4.46
-ATOM    484    O STP    18      26.177   6.535 -11.779    0.00     4.47
-ATOM    485    O STP    18      26.104   6.506 -11.714    0.00     4.41
-ATOM    486    O STP    19      23.996 -17.991  11.091    0.00     4.35
-ATOM    487    C STP    19      24.960 -14.038   8.738    0.00     3.95
-ATOM    488    O STP    19      22.931 -16.813  10.494    0.00     3.98
-ATOM    489    O STP    19      23.730 -14.416   9.050    0.00     3.79
-ATOM    490    O STP    19      23.534 -14.640   9.195    0.00     3.74
-ATOM    491    O STP    19      23.541 -14.438   9.194    0.00     3.71
-ATOM    492    O STP    19      23.319 -13.996   9.166    0.00     3.47
-ATOM    493    O STP    19      23.506 -14.658   9.215    0.00     3.73
-ATOM    494    O STP    19      22.772 -16.806  10.680    0.00     3.95
-ATOM    495    O STP    19      23.478 -14.756   9.266    0.00     3.71
-ATOM    496    O STP    19      22.867 -16.689  10.427    0.00     3.96
-ATOM    497    O STP    19      22.668 -16.487  10.105    0.00     3.79
-ATOM    498    O STP    19      22.623 -16.471  10.089    0.00     3.76
-ATOM    499    O STP    19      22.761 -16.808  10.687    0.00     3.94
-ATOM    500    O STP    19      24.040 -13.911   7.306    0.00     3.54
-ATOM    501    C STP    19      24.558 -13.610   8.244    0.00     4.08
-ATOM    502    O STP    19      24.402 -13.618   8.240    0.00     4.06
-ATOM    503    O STP    19      23.982 -13.022   8.288    0.00     3.77
-ATOM    504    C STP    19      24.023 -12.020   8.383    0.00     3.50
-ATOM    505    O STP    19      22.709 -16.865  10.854    0.00     3.94
-ATOM    506    O STP    19      22.701 -16.860  10.841    0.00     3.93
+ATOM    107    C STP     2       5.666  -2.347   9.650    0.00     3.64
+ATOM    108    C STP     2       5.663  -2.342   9.659    0.00     3.64
+ATOM    109    C STP     2       4.857  -3.237  11.687    0.00     3.51
+ATOM    110    C STP     2       4.909  -3.421  12.179    0.00     3.52
+ATOM    111    C STP     2       4.463  -1.923  10.602    0.00     3.52
+ATOM    112    C STP     2       4.751  -3.640  11.929    0.00     3.49
+ATOM    113    C STP     2       4.816  -3.657  12.202    0.00     3.51
+ATOM    114    C STP     2       5.643  -2.334   9.598    0.00     3.62
+ATOM    115    C STP     2       5.573  -2.273   9.693    0.00     3.63
+ATOM    116    C STP     2       5.625  -2.300   9.658    0.00     3.64
+ATOM    117    C STP     2       5.618  -2.250   9.664    0.00     3.62
+ATOM    118    C STP     2       4.669  -1.977  10.488    0.00     3.53
+ATOM    119    C STP     2       4.819  -1.860  10.403    0.00     3.43
+ATOM    120    C STP     2       4.472  -1.924  10.605    0.00     3.53
+ATOM    121    C STP     2       4.423  -1.750  10.637    0.00     3.43
+ATOM    122    C STP     2       4.474  -1.928  10.609    0.00     3.53
+ATOM    123    C STP     2       4.552  -2.069  10.740    0.00     3.51
+ATOM    124    C STP     2       4.780  -3.687  12.261    0.00     3.48
+ATOM    125    O STP     3      10.707   8.465   9.562    0.00     3.56
+ATOM    126    O STP     3      11.897   7.600  10.387    0.00     3.53
+ATOM    127    O STP     3      11.713   7.651  10.429    0.00     3.61
+ATOM    128    O STP     3      11.722   7.673  10.440    0.00     3.59
+ATOM    129    O STP     3      11.706   7.635  10.442    0.00     3.60
+ATOM    130    O STP     3      13.057   5.577  11.209    0.00     3.45
+ATOM    131    C STP     3      13.599   4.782  12.622    0.00     3.56
+ATOM    132    O STP     3      12.926   5.521  11.298    0.00     3.49
+ATOM    133    O STP     3      11.593   6.620  11.138    0.00     3.56
+ATOM    134    O STP     3      11.150   6.837  11.229    0.00     3.58
+ATOM    135    O STP     3      11.203   6.847  11.061    0.00     3.66
+ATOM    136    O STP     3      10.100   6.854  10.639    0.00     3.72
+ATOM    137    O STP     3      10.043   6.829  10.609    0.00     3.72
+ATOM    138    O STP     3      10.008   6.832  11.002    0.00     3.55
+ATOM    139    O STP     3       9.996   6.814  10.721    0.00     3.65
+ATOM    140    O STP     3      14.136   3.921  15.176    0.00     4.64
+ATOM    141    O STP     3      13.450   4.065  15.198    0.00     4.27
+ATOM    142    O STP     3      14.349   4.009  14.805    0.00     4.61
+ATOM    143    O STP     3      13.844   4.358  14.153    0.00     4.07
+ATOM    144    C STP     3      14.400   4.002  14.664    0.00     4.57
+ATOM    145    C STP     3      13.873   4.433  13.491    0.00     3.88
+ATOM    146    C STP     3      13.578   4.355  12.749    0.00     3.43
+ATOM    147    O STP     3       9.524   6.563  10.325    0.00     3.47
+ATOM    148    C STP     3       9.327   7.050  10.077    0.00     3.46
+ATOM    149    O STP     3      10.903   8.245   9.723    0.00     3.55
+ATOM    150    O STP     3      11.424   7.798  10.169    0.00     3.58
+ATOM    151    O STP     3      10.102   6.908  10.584    0.00     3.71
+ATOM    152    O STP     3      10.425   8.337   9.557    0.00     3.58
+ATOM    153    O STP     3      10.324   8.322   9.469    0.00     3.54
+ATOM    154    O STP     3      10.351   8.314   9.560    0.00     3.59
+ATOM    155    C STP     3      10.082   7.855   9.856    0.00     3.56
+ATOM    156    C STP     3       9.763   7.428   9.952    0.00     3.52
+ATOM    157    C STP     3       9.808   6.869  10.405    0.00     3.64
+ATOM    158    O STP     3      10.016   6.824  10.586    0.00     3.71
+ATOM    159    O STP     3       9.960   6.815  10.553    0.00     3.70
+ATOM    160    O STP     3       9.895   6.462  10.350    0.00     3.45
+ATOM    161    O STP     3       9.826   6.743  10.451    0.00     3.64
+ATOM    162    O STP     4      17.904  16.846   2.034    0.00     4.00
+ATOM    163    C STP     4      13.212  24.010  -0.223    0.00     3.56
+ATOM    164    O STP     4      13.590  24.333  -0.124    0.00     3.66
+ATOM    165    O STP     4      16.890  22.935   1.418    0.00     4.64
+ATOM    166    C STP     4      16.767  18.684   1.078    0.00     4.22
+ATOM    167    C STP     4      16.715  18.704   1.057    0.00     4.20
+ATOM    168    O STP     4      17.342  17.855   1.830    0.00     4.24
+ATOM    169    O STP     4      17.041  17.846   1.980    0.00     4.08
+ATOM    170    O STP     4      16.580  19.060   0.747    0.00     4.27
+ATOM    171    O STP     4      17.635  17.024   1.403    0.00     3.80
+ATOM    172    O STP     4      17.395  17.419   1.401    0.00     3.89
+ATOM    173    C STP     4      16.900  18.376   1.091    0.00     4.07
+ATOM    174    O STP     4      17.782  16.444   1.256    0.00     3.57
+ATOM    175    O STP     4      14.632  22.244  -1.461    0.00     3.60
+ATOM    176    O STP     4      14.379  23.675  -0.187    0.00     4.18
+ATOM    177    C STP     4      16.642  20.313   0.285    0.00     4.56
+ATOM    178    O STP     4      15.401  22.803   0.789    0.00     4.49
+ATOM    179    O STP     4      14.950  20.959  -0.498    0.00     4.03
+ATOM    180    O STP     4      16.062  19.544  -0.072    0.00     4.25
+ATOM    181    O STP     4      16.188  19.842  -0.177    0.00     4.42
+ATOM    182    C STP     4      16.044  18.633   0.739    0.00     3.73
+ATOM    183    O STP     4      15.502  19.054  -0.011    0.00     3.68
+ATOM    184    O STP     5      -3.903   9.091  -8.804    0.00     4.57
+ATOM    185    O STP     5      -3.754   8.992  -8.593    0.00     4.51
+ATOM    186    O STP     5      -2.044   6.009  -7.092    0.00     3.61
+ATOM    187    O STP     5      -2.612   5.104  -6.282    0.00     3.41
+ATOM    188    O STP     5      -2.076   5.517  -6.742    0.00     3.61
+ATOM    189    O STP     5      -1.785   5.216  -7.035    0.00     3.65
+ATOM    190    O STP     5      -3.701   8.983  -8.573    0.00     4.49
+ATOM    191    O STP     5      -3.246   8.932  -8.467    0.00     4.30
+ATOM    192    O STP     5      -1.423   9.628  -8.928    0.00     3.47
+ATOM    193    O STP     5      -2.819   9.025  -8.670    0.00     4.13
+ATOM    194    O STP     5      -1.924   8.885  -8.753    0.00     3.78
+ATOM    195    O STP     5      -1.997   4.980  -6.859    0.00     3.52
+ATOM    196    O STP     5      -1.773   5.141  -7.052    0.00     3.64
+ATOM    197    O STP     5      -1.816   5.091  -7.152    0.00     3.55
+ATOM    198    O STP     5      -1.491   5.021  -7.121    0.00     3.59
+ATOM    199    O STP     5      -1.417   4.986  -7.145    0.00     3.57
+ATOM    200    O STP     5      -1.425   4.982  -7.131    0.00     3.57
+ATOM    201    O STP     5      -2.908   8.645  -8.261    0.00     4.08
+ATOM    202    O STP     5      -1.967   6.532  -7.237    0.00     3.55
+ATOM    203    C STP     5      -2.911   8.402  -8.137    0.00     3.98
+ATOM    204    O STP     5      -1.038   7.720  -7.892    0.00     3.49
+ATOM    205    O STP     5      -1.266   8.004  -8.024    0.00     3.55
+ATOM    206    C STP     6      17.284  -3.003  -7.392    0.00     3.79
+ATOM    207    C STP     6      17.140  -3.037  -7.495    0.00     3.70
+ATOM    208    C STP     6      17.287  -2.942  -7.558    0.00     3.71
+ATOM    209    O STP     6      15.862  -3.114  -6.582    0.00     3.49
+ATOM    210    O STP     6      18.410  -1.869  -6.831    0.00     3.46
+ATOM    211    O STP     6      18.093  -1.568  -4.665    0.00     3.47
+ATOM    212    O STP     6      18.176  -2.391  -6.545    0.00     3.68
+ATOM    213    O STP     6      18.178  -1.260  -4.556    0.00     3.40
+ATOM    214    O STP     6      18.146  -1.324  -4.503    0.00     3.45
+ATOM    215    O STP     6      17.446  -3.009  -6.936    0.00     3.90
+ATOM    216    O STP     6      17.338  -2.967  -7.164    0.00     3.86
+ATOM    217    O STP     6      16.971  -3.071  -6.456    0.00     3.78
+ATOM    218    O STP     6      16.372  -3.033  -6.540    0.00     3.63
+ATOM    219    O STP     6      16.616  -2.342  -4.591    0.00     3.50
+ATOM    220    O STP     6      16.735  -2.388  -4.679    0.00     3.51
+ATOM    221    C STP     6      16.003  -2.925  -6.361    0.00     3.50
+ATOM    222    C STP     6      15.537  -2.940  -6.326    0.00     3.41
+ATOM    223    O STP     7      15.640  11.395  -7.384    0.00     3.87
+ATOM    224    O STP     7      14.547  11.507  -5.506    0.00     3.47
+ATOM    225    C STP     7      15.133  11.716  -6.441    0.00     3.54
+ATOM    226    O STP     7      14.464  10.763  -5.571    0.00     3.51
+ATOM    227    O STP     7      14.467  10.370  -5.296    0.00     3.44
+ATOM    228    O STP     7      14.848  13.223  -6.639    0.00     3.50
+ATOM    229    O STP     7      15.418  12.203  -7.050    0.00     3.68
+ATOM    230    O STP     7      15.660  11.576  -7.445    0.00     3.87
+ATOM    231    O STP     7      16.047  11.948  -7.515    0.00     3.67
+ATOM    232    O STP     7      15.521  11.388  -7.841    0.00     3.75
+ATOM    233    O STP     7      15.570  11.317  -8.748    0.00     3.41
+ATOM    234    O STP     7      15.604  11.206  -7.376    0.00     3.86
+ATOM    235    O STP     7      15.544  11.122  -7.297    0.00     3.82
+ATOM    236    O STP     7      15.979  10.444  -7.233    0.00     3.55
+ATOM    237    C STP     7      15.792  10.270  -7.031    0.00     3.50
+ATOM    238    O STP     8       3.602  29.013   1.016    0.00     3.55
+ATOM    239    C STP     8       5.556  23.790   2.238    0.00     3.66
+ATOM    240    C STP     8       4.374  24.558   2.469    0.00     3.55
+ATOM    241    C STP     8       6.248  22.839   2.662    0.00     3.65
+ATOM    242    C STP     8       6.687  23.325   2.417    0.00     3.80
+ATOM    243    O STP     8       3.605  28.995   0.988    0.00     3.53
+ATOM    244    C STP     8       6.666  23.871   2.160    0.00     3.91
+ATOM    245    C STP     8       6.778  23.571   2.298    0.00     3.87
+ATOM    246    C STP     8       6.777  25.942   2.510    0.00     3.88
+ATOM    247    O STP     8       3.851  24.675   2.332    0.00     3.51
+ATOM    248    C STP     8       3.757  24.628   2.235    0.00     3.46
+ATOM    249    O STP     8       3.932  27.786   1.618    0.00     3.45
+ATOM    250    O STP     8       4.637  26.459   2.777    0.00     3.76
+ATOM    251    C STP     8       4.889  27.180   2.881    0.00     4.07
+ATOM    252    O STP     8       3.599  29.091   1.545    0.00     3.89
+ATOM    253    C STP     8       7.492  23.806   0.509    0.00     3.43
+ATOM    254    C STP     8       7.257  23.839   1.162    0.00     3.57
+ATOM    255    C STP     8       7.637  23.976   0.562    0.00     3.48
+ATOM    256    C STP     8       6.839  23.523   2.245    0.00     3.83
+ATOM    257    C STP     8       6.757  23.101   2.378    0.00     3.69
+ATOM    258    C STP     8       6.868  27.794   3.414    0.00     4.36
+ATOM    259    C STP     8       6.830  26.126   2.605    0.00     3.89
+ATOM    260    O STP     9      -7.764  15.242   7.103    0.00     3.96
+ATOM    261    C STP     9      -5.783  13.019   6.568    0.00     4.49
+ATOM    262    O STP     9      -5.788  12.752   6.449    0.00     4.69
+ATOM    263    O STP     9      -7.309  14.474   6.726    0.00     4.12
+ATOM    264    O STP     9      -7.432  15.466   6.755    0.00     3.70
+ATOM    265    O STP     9      -7.395  15.658   6.560    0.00     3.50
+ATOM    266    C STP     9      -4.485  12.252   8.033    0.00     3.97
+ATOM    267    C STP     9      -4.567  13.020   7.587    0.00     3.99
+ATOM    268    C STP     9      -4.565  12.978   7.571    0.00     4.02
+ATOM    269    O STP     9      -4.654  11.597   3.673    0.00     3.94
+ATOM    270    O STP     9      -3.791  12.064   4.278    0.00     3.43
+ATOM    271    O STP     9      -4.242  12.235   5.610    0.00     3.94
+ATOM    272    O STP     9      -3.273  10.191   7.558    0.00     3.44
+ATOM    273    C STP     9      -4.073  12.143   8.369    0.00     3.67
+ATOM    274    C STP     9      -3.693  10.881   8.123    0.00     3.54
+ATOM    275    C STP     9      -3.402  10.565   8.181    0.00     3.46
+ATOM    276    O STP    10      16.399  30.997  -2.408    0.00     3.51
+ATOM    277    O STP    10      16.378  31.564  -2.092    0.00     3.53
+ATOM    278    O STP    10      16.438  31.064  -2.387    0.00     3.53
+ATOM    279    O STP    10      17.895  28.085  -5.613    0.00     3.60
+ATOM    280    O STP    10      18.864  28.710  -3.265    0.00     4.57
+ATOM    281    O STP    10      17.852  28.163  -5.642    0.00     3.57
+ATOM    282    O STP    10      17.748  28.256  -3.638    0.00     3.99
+ATOM    283    O STP    10      18.340  28.694  -3.618    0.00     4.44
+ATOM    284    O STP    10      17.987  28.173  -5.180    0.00     3.72
+ATOM    285    O STP    10      18.227  28.380  -4.224    0.00     4.14
+ATOM    286    O STP    10      18.119  28.193  -4.507    0.00     3.99
+ATOM    287    O STP    10      16.692  30.260  -3.367    0.00     3.43
+ATOM    288    O STP    10      17.772  29.567  -4.909    0.00     3.47
+ATOM    289    C STP    10      17.710  27.065  -6.133    0.00     3.50
+ATOM    290    O STP    10      17.725  26.987  -6.025    0.00     3.51
+ATOM    291    O STP    10      17.545  26.715  -6.183    0.00     3.43
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+ATOM    293    O STP    11      -2.806 -16.644   5.884    0.00     3.82
+ATOM    294    O STP    11      -1.682 -16.022   4.590    0.00     3.66
+ATOM    295    O STP    11      -1.648 -15.823   4.692    0.00     3.85
+ATOM    296    C STP    11      -5.623 -13.895   2.816    0.00     3.42
+ATOM    297    C STP    11      -7.247 -14.004   3.331    0.00     3.65
+ATOM    298    C STP    11      -8.747 -13.072   4.181    0.00     3.82
+ATOM    299    C STP    11      -3.506 -14.247   3.643    0.00     3.79
+ATOM    300    O STP    11      -3.650 -14.469   3.805    0.00     3.84
+ATOM    301    O STP    11      -5.817 -14.938   3.693    0.00     3.87
+ATOM    302    C STP    11      -2.262 -14.253   4.649    0.00     4.35
+ATOM    303    O STP    11     -10.162 -12.809   7.673    0.00     4.49
+ATOM    304    O STP    11      -8.823 -12.829   5.969    0.00     3.78
+ATOM    305    C STP    11      -8.681 -12.900   4.221    0.00     3.68
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+ATOM    307    O STP    11      -1.417 -15.715   4.699    0.00     3.91
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+ATOM    310    C STP    11      -1.567 -13.472   5.345    0.00     4.45
+ATOM    311    O STP    11      -1.180 -15.075   6.105    0.00     4.34
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+ATOM    321    C STP    11      -1.682 -14.732   5.030    0.00     4.49
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+ATOM    337    O STP    12       6.841   4.575  15.663    0.00     4.04
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+ATOM    339    C STP    12       5.811   4.553  15.542    0.00     3.60
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+ATOM    341    O STP    12       5.988   4.465  16.323    0.00     4.09
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+ATOM    350    O STP    13       2.506 -11.531 -14.753    0.00     3.67
+ATOM    351    O STP    13       3.068 -10.223 -15.746    0.00     4.35
+ATOM    352    O STP    13       2.399  -9.985 -15.545    0.00     4.02
+ATOM    353    O STP    13       2.404  -9.971 -15.570    0.00     4.02
+ATOM    354    C STP    13       5.125 -10.220 -14.880    0.00     4.59
+ATOM    355    O STP    13       6.885 -10.576 -13.808    0.00     4.29
+ATOM    356    C STP    13       5.976 -10.559 -14.490    0.00     4.50
+ATOM    357    O STP    13       6.965 -10.686 -13.636    0.00     4.15
+ATOM    358    C STP    13       6.745 -10.296 -13.292    0.00     4.06
+ATOM    359    C STP    13       6.779 -10.238 -13.247    0.00     4.00
+ATOM    360    O STP    13       6.903 -10.566 -13.771    0.00     4.28
+ATOM    361    O STP    13       7.436 -10.329 -13.922    0.00     4.04
+ATOM    362    C STP    13       5.178  -9.990 -14.394    0.00     4.28
+ATOM    363    C STP    13       6.257  -9.980 -12.969    0.00     3.90
+ATOM    364    C STP    13       5.645 -10.172 -13.886    0.00     4.19
+ATOM    365    C STP    13       5.308 -10.126 -14.302    0.00     4.32
+ATOM    366    C STP    13       6.375  -9.340 -12.443    0.00     3.44
+ATOM    367    C STP    13       8.583  -7.677 -16.792    0.00     3.57
+ATOM    368    O STP    13       9.881  -9.702 -14.137    0.00     3.47
+ATOM    369    C STP    13       8.914  -9.764 -16.244    0.00     4.57
+ATOM    370    C STP    13       9.059  -9.645 -15.171    0.00     4.05
+ATOM    371    O STP    13      12.065 -10.289 -14.422    0.00     3.41
+ATOM    372    O STP    13       5.610  -9.461 -16.514    0.00     4.49
+ATOM    373    O STP    13       5.607  -9.484 -16.523    0.00     4.51
+ATOM    374    O STP    13       4.200  -8.861 -15.470    0.00     3.55
+ATOM    375    O STP    14      20.762 -15.016  15.628    0.00     4.47
+ATOM    376    O STP    14      20.093 -13.782  15.160    0.00     3.81
+ATOM    377    O STP    14      21.482 -16.110  15.016    0.00     4.50
+ATOM    378    O STP    14      21.091 -14.702  15.246    0.00     4.03
+ATOM    379    C STP    14      18.817 -14.364  15.540    0.00     4.62
+ATOM    380    C STP    14      15.023 -10.073  17.441    0.00     4.26
+ATOM    381    C STP    14      15.741 -10.998  17.957    0.00     4.63
+ATOM    382    O STP    14      20.585 -16.489  14.223    0.00     4.09
+ATOM    383    O STP    14      19.415 -15.607  15.364    0.00     4.66
+ATOM    384    C STP    14      15.015 -10.071  17.451    0.00     4.26
+ATOM    385    C STP    14      14.777 -10.089  16.406    0.00     3.47
+ATOM    386    C STP    14      14.855 -10.051  17.251    0.00     4.06
+ATOM    387    O STP    14      13.277  -9.665  17.514    0.00     3.56
+ATOM    388    C STP    14      14.805 -10.108  17.922    0.00     4.49
+ATOM    389    O STP    14      18.495 -14.244  14.923    0.00     4.22
+ATOM    390    O STP    14      18.480 -14.689  14.307    0.00     3.84
+ATOM    391    C STP    14      18.270 -13.858  15.512    0.00     4.47
+ATOM    392    C STP    14      15.741 -10.998  17.957    0.00     4.63
+ATOM    393    C STP    14      15.742 -10.997  17.953    0.00     4.62
+ATOM    394    C STP    14      15.760 -10.982  17.951    0.00     4.60
+ATOM    395    C STP    14      16.138 -10.636  17.830    0.00     4.10
+ATOM    396    C STP    14      16.014 -10.748  17.869    0.00     4.26
+ATOM    397    O STP    14      17.979 -13.868  13.441    0.00     3.43
+ATOM    398    O STP    14      18.105 -13.657  15.491    0.00     4.41
+ATOM    399    O STP    14      17.165 -13.262  16.453    0.00     4.67
+ATOM    400    O STP    14      15.637 -10.294  15.930    0.00     3.65
+ATOM    401    C STP    14      16.936 -12.523  16.560    0.00     4.44
+ATOM    402    C STP    14      17.083 -12.356  16.365    0.00     4.23
+ATOM    403    C STP    14      16.850 -12.331  16.545    0.00     4.35
+ATOM    404    C STP    15      -3.012  -8.100  -8.760    0.00     3.99
+ATOM    405    C STP    15      -3.458  -8.552  -8.865    0.00     4.13
+ATOM    406    C STP    15      -2.959  -8.581 -10.924    0.00     3.60
+ATOM    407    C STP    15      -3.348 -12.034  -7.768    0.00     3.58
+ATOM    408    C STP    15      -4.265 -11.238  -7.349    0.00     3.85
+ATOM    409    C STP    15      -3.688  -6.964  -9.269    0.00     3.51
+ATOM    410    C STP    15      -2.701  -7.221 -10.008    0.00     3.68
+ATOM    411    C STP    15      -5.618  -8.473  -9.251    0.00     4.02
+ATOM    412    C STP    15      -3.297  -7.983  -9.300    0.00     4.15
+ATOM    413    C STP    15      -3.480  -8.204  -9.300    0.00     4.19
+ATOM    414    C STP    15      -2.711  -7.550  -9.906    0.00     3.88
+ATOM    415    C STP    15      -3.130  -8.353 -10.547    0.00     3.78
+ATOM    416    C STP    15      -6.416  -7.590  -9.212    0.00     3.65
+ATOM    417    C STP    15      -6.562  -8.616  -9.387    0.00     4.21
+ATOM    418    C STP    15      -3.584  -8.558 -11.489    0.00     3.41
+ATOM    419    C STP    15      -2.190  -7.904  -8.566    0.00     3.57
+ATOM    420    C STP    15      -2.781  -7.847  -8.009    0.00     3.57
+ATOM    421    C STP    15      -4.480 -10.505  -7.436    0.00     3.94
+ATOM    422    C STP    15      -4.026  -9.106  -8.251    0.00     4.00
+ATOM    423    C STP    15      -4.477  -9.071  -8.355    0.00     3.93
+ATOM    424    C STP    15      -6.605  -8.625  -9.403    0.00     4.22
+ATOM    425    C STP    15      -7.298  -9.850 -11.196    0.00     3.43
+ATOM    426    C STP    15      -6.455  -7.572  -9.223    0.00     3.65
+ATOM    427    C STP    15      -6.421  -7.573  -9.212    0.00     3.65
+ATOM    428    C STP    15      -6.417  -7.568  -9.212    0.00     3.64
+ATOM    429    O STP    15      -1.367  -6.997 -10.176    0.00     3.51
+ATOM    430    C STP    15      -1.239  -6.770 -10.255    0.00     3.42
+ATOM    431    C STP    15      -4.616 -11.435  -7.345    0.00     3.83
+ATOM    432    C STP    15      -4.811 -11.636  -7.371    0.00     3.80
+ATOM    433    C STP    15      -4.913 -11.381  -7.364    0.00     3.83
+ATOM    434    C STP    15      -6.933  -9.877  -8.296    0.00     4.23
+ATOM    435    C STP    15      -6.950  -9.879  -8.185    0.00     4.17
+ATOM    436    C STP    15      -7.173  -9.977  -7.342    0.00     3.67
+ATOM    437    C STP    15      -9.158  -7.838  -9.913    0.00     4.26
+ATOM    438    C STP    15      -6.960  -7.202  -9.484    0.00     3.47
+ATOM    439    C STP    15      -6.846  -7.861  -9.393    0.00     3.82
+ATOM    440    C STP    15      -7.673  -8.310  -9.533    0.00     4.10
+ATOM    441    C STP    15      -6.670  -8.554  -9.417    0.00     4.18
+ATOM    442    O STP    16      21.605   9.274   6.445    0.00     3.95
+ATOM    443    O STP    16      23.052   4.027   8.218    0.00     3.68
+ATOM    444    O STP    16      20.037  10.202   7.733    0.00     4.60
+ATOM    445    O STP    16      22.942   3.882   8.664    0.00     3.49
+ATOM    446    O STP    16      22.985   4.910   9.082    0.00     3.75
+ATOM    447    O STP    16      22.778   4.706   8.980    0.00     3.57
+ATOM    448    O STP    16      22.932   4.338   8.689    0.00     3.66
+ATOM    449    O STP    16      22.819   4.391   8.749    0.00     3.58
+ATOM    450    O STP    16      22.943   3.580   7.482    0.00     3.63
+ATOM    451    O STP    16      22.800   7.841   5.222    0.00     3.89
+ATOM    452    C STP    16      23.308   3.741   7.149    0.00     3.81
+ATOM    453    O STP    16      23.140   5.515   5.119    0.00     3.59
+ATOM    454    O STP    16      22.972   4.082   6.110    0.00     3.44
+ATOM    455    O STP    16      23.254   3.825   6.901    0.00     3.72
+ATOM    456    O STP    16      23.595   4.080   7.336    0.00     3.93
+ATOM    457    O STP    16      24.143   3.706   7.296    0.00     3.56
+ATOM    458    O STP    16      23.426   3.868   7.200    0.00     3.86
+ATOM    459    C STP    17      20.079 -17.759  -0.802    0.00     3.67
+ATOM    460    O STP    17      21.058 -19.186  -2.154    0.00     3.88
+ATOM    461    O STP    17      22.470 -19.926  -1.235    0.00     4.53
+ATOM    462    O STP    17      22.448 -20.166  -0.692    0.00     4.42
+ATOM    463    C STP    17      21.929 -20.012  -0.119    0.00     4.06
+ATOM    464    O STP    17      21.994 -20.327   0.005    0.00     4.04
+ATOM    465    C STP    17      22.152 -19.454  -1.681    0.00     4.50
+ATOM    466    O STP    17      22.110 -19.403  -1.774    0.00     4.50
+ATOM    467    C STP    17      20.135 -17.782  -0.862    0.00     3.68
+ATOM    468    C STP    17      20.333 -17.868  -1.159    0.00     3.71
+ATOM    469    O STP    17      22.730 -19.052  -1.278    0.00     3.92
+ATOM    470    C STP    17      21.017 -18.682  -1.343    0.00     4.01
+ATOM    471    C STP    17      21.042 -18.693  -1.380    0.00     4.03
+ATOM    472    C STP    17      20.540 -18.564  -0.766    0.00     3.77
+ATOM    473    C STP    17      21.084 -19.267  -0.227    0.00     3.70
+ATOM    474    C STP    17      20.059 -17.765  -0.768    0.00     3.67
+ATOM    475    C STP    17      20.019 -17.679  -0.714    0.00     3.63
+ATOM    476    C STP    18      19.731  -9.845 -19.131    0.00     4.43
+ATOM    477    O STP    18      19.569  -9.317 -17.533    0.00     3.79
+ATOM    478    C STP    18      19.614  -8.814 -18.207    0.00     3.99
+ATOM    479    C STP    18      20.232  -9.555 -18.715    0.00     4.37
+ATOM    480    O STP    18      19.894  -9.360 -18.454    0.00     4.30
+ATOM    481    O STP    18      19.659  -8.864 -18.207    0.00     4.03
+ATOM    482    C STP    18      22.012 -10.240 -17.683    0.00     3.97
+ATOM    483    O STP    18      19.763  -9.200 -17.763    0.00     4.01
+ATOM    484    O STP    18      19.665  -8.895 -18.122    0.00     4.01
+ATOM    485    O STP    18      19.761  -9.178 -17.610    0.00     3.96
+ATOM    486    O STP    18      19.722  -9.037 -17.573    0.00     3.88
+ATOM    487    O STP    18      20.063  -9.001 -15.994    0.00     3.53
+ATOM    488    C STP    18      21.170  -9.679 -16.504    0.00     3.47
+ATOM    489    O STP    18      20.051  -9.115 -16.218    0.00     3.59
+ATOM    490    O STP    18      20.074  -9.041 -16.005    0.00     3.55
+ATOM    491    C STP    18      19.181  -8.215 -18.208    0.00     3.57
+ATOM    492    O STP    19      23.996 -17.991  11.091    0.00     4.35
+ATOM    493    C STP    19      24.960 -14.038   8.738    0.00     3.95
+ATOM    494    O STP    19      22.931 -16.813  10.494    0.00     3.98
+ATOM    495    O STP    19      23.730 -14.416   9.050    0.00     3.79
+ATOM    496    O STP    19      23.534 -14.640   9.195    0.00     3.74
+ATOM    497    O STP    19      23.541 -14.438   9.194    0.00     3.71
+ATOM    498    O STP    19      23.319 -13.996   9.166    0.00     3.47
+ATOM    499    O STP    19      23.506 -14.658   9.215    0.00     3.73
+ATOM    500    O STP    19      22.772 -16.806  10.680    0.00     3.95
+ATOM    501    O STP    19      23.478 -14.756   9.266    0.00     3.71
+ATOM    502    O STP    19      22.867 -16.689  10.427    0.00     3.96
+ATOM    503    O STP    19      22.668 -16.487  10.105    0.00     3.79
+ATOM    504    O STP    19      22.623 -16.471  10.089    0.00     3.76
+ATOM    505    O STP    19      22.761 -16.808  10.687    0.00     3.94
+ATOM    506    O STP    19      24.040 -13.911   7.306    0.00     3.54
+ATOM    507    C STP    19      24.558 -13.610   8.244    0.00     4.08
+ATOM    508    O STP    19      24.402 -13.618   8.240    0.00     4.06
+ATOM    509    O STP    19      23.982 -13.022   8.288    0.00     3.77
+ATOM    510    C STP    19      24.023 -12.020   8.383    0.00     3.50
+ATOM    511    O STP    19      22.709 -16.865  10.854    0.00     3.94
+ATOM    512    O STP    19      22.701 -16.860  10.841    0.00     3.93
+ATOM    513    O STP    20      25.040   9.651 -11.168    0.00     3.75
+ATOM    514    O STP    20      25.268   9.534 -10.955    0.00     3.50
+ATOM    515    O STP    20      23.290   7.625 -10.006    0.00     3.65
+ATOM    516    O STP    20      21.998   7.158  -8.997    0.00     3.42
+ATOM    517    O STP    20      21.767   7.080  -9.018    0.00     3.44
+ATOM    518    O STP    20      24.354   9.432 -11.111    0.00     3.89
+ATOM    519    O STP    20      24.924  10.086 -10.852    0.00     3.50
+ATOM    520    O STP    20      25.153   7.836 -11.282    0.00     4.23
+ATOM    521    O STP    20      24.124   8.241 -11.073    0.00     4.17
+ATOM    522    O STP    20      23.599   7.744 -10.504    0.00     3.89
+ATOM    523    O STP    20      25.034   7.815 -11.334    0.00     4.30
+ATOM    524    O STP    20      24.595   7.493 -10.910    0.00     4.00
+ATOM    525    O STP    20      24.583   8.688 -11.745    0.00     4.51
+ATOM    526    O STP    20      24.433   8.715 -11.668    0.00     4.47
+ATOM    527    O STP    20      24.019   8.832 -11.950    0.00     4.30
+ATOM    528    O STP    20      22.801   8.729 -12.139    0.00     3.77
+ATOM    529    O STP    20      22.207   7.260 -10.194    0.00     3.50
+ATOM    530    C STP    20      24.752   8.793 -13.468    0.00     4.56
+ATOM    531    O STP    20      26.139   6.551 -11.712    0.00     4.46
+ATOM    532    O STP    20      26.177   6.535 -11.779    0.00     4.47
+ATOM    533    O STP    20      26.104   6.506 -11.714    0.00     4.41
 TER
 END

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

tests/reference_output/1QNH_out/1QNH_info.txt

@@ -1,21 +1,21 @@
 Pocket 1 :
-	Score : 	5.845
+	Score : 	6.128
 	Druggability Score : 	1.000
-	Number of Alpha Spheres : 	217
-	Total SASA : 	319.981
-	Polar SASA : 	172.651
-	Apolar SASA : 	147.331
-	Volume : 	5091.737
-	Mean local hydrophobic density : 	13.444
-	Mean alpha sphere radius :	4.302
-	Mean alp. sph. solvent access : 	0.583
-	Apolar alpha sphere proportion : 	0.249
-	Hydrophobicity score:	16.815
-	Volume score: 	 3.889
-	Polarity score:	 16
+	Number of Alpha Spheres : 	225
+	Total SASA : 	353.188
+	Polar SASA : 	186.535
+	Apolar SASA : 	166.653
+	Volume : 	5738.319
+	Mean local hydrophobic density : 	13.345
+	Mean alpha sphere radius :	4.321
+	Mean alp. sph. solvent access : 	0.581
+	Apolar alpha sphere proportion : 	0.244
+	Hydrophobicity score:	18.464
+	Volume score: 	 4.000
+	Polarity score:	 17
 	Charge score :	 6
-	Proportion of polar atoms: 	43.262
-	Alpha sphere density : 	29.044
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	29.333
 	Cent. of mass - Alpha Sphere max dist: 	66.371
 	Flexibility : 	0.000
 

tests/reference_output/1QNH_out/1QNH_out.cif

@@ -481,7 +481,7 @@ ATOM      461    C   CZ .  PHE   A .   59 ?   16.521  46.943  23.448  0.00  0
 ATOM      462    N    N .  HIS   A .   60 ?   21.685  41.894  24.095  0.00  0   A
 ATOM      463    C   CA .  HIS   A .   60 ?   22.877  41.116  24.412  0.00  0   A
 ATOM      464    C    C .  HIS   A .   60 ?   24.158  41.904  24.638  0.00  0   A
-ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078  0.00  0   A
+ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078 -1.62  0   A
 ATOM      466    C   CB .  HIS   A .   60 ?   23.129  40.084  23.309  0.00  0   A
 ATOM      467    C   CG .  HIS   A .   60 ?   23.547  40.688  22.003  0.00  0   A
 ATOM      468    N  ND1 .  HIS   A .   60 ?   22.643  41.187  21.089  0.00  0   A
@@ -629,7 +629,7 @@ ATOM      609    O   OG .  SER   A .   79 ?   25.802  34.452  16.172  0.00  0
 ATOM      610    N    N .  GLY   A .   80 ?   23.617  36.549  14.815  0.00  0   A
 ATOM      611    C   CA .  GLY   A .   80 ?   22.490  36.294  13.936  0.00  0   A
 ATOM      612    C    C .  GLY   A .   80 ?   21.685  37.488  13.466  0.00  0   A
-ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380 -1.07  0   A
+ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380  0.00  0   A
 ATOM      614    N    N .  GLY   A .   81 ?   20.416  37.230  13.161  0.00  0   A
 ATOM      615    C   CA .  GLY   A .   81 ?   19.529  38.276  12.689  0.00  0   A
 ATOM      616    C    C .  GLY   A .   81 ?   18.939  37.935  11.332  0.00  0   A
@@ -682,8 +682,8 @@ ATOM      662    C   CG .  ARG   A .   87 ?   21.394  36.553   6.201  0.00  0
 ATOM      663    C   CD .  ARG   A .   87 ?   20.856  36.029   7.533  0.00  0   A
 ATOM      664    N   NE .  ARG   A .   87 ?   21.879  35.978   8.574  0.00  0   A
 ATOM      665    C   CZ .  ARG   A .   87 ?   22.430  37.047   9.144  0.00  0   A
-ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -2.61  0   A
-ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -4.12  0   A
+ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -4.12  0   A
+ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -1.93  0   A
 ATOM      668    N    N .  SER   A .   88 ?   19.796  39.808   4.725  0.00  0   A
 ATOM      669    C   CA .  SER   A .   88 ?   20.319  41.168   4.848  0.00  0   A
 ATOM      670    C    C .  SER   A .   88 ?   19.779  42.086   3.763  0.00  0   A
@@ -877,7 +877,7 @@ ATOM      857    N  ND2 .  ASN   A .  112 ?   25.973  47.831  -0.009  0.00  0
 ATOM      858    N    N .  THR   A .  113 ?   24.686  45.203   5.123  0.00  0   A
 ATOM      859    C   CA .  THR   A .  113 ?   24.527  43.954   5.854  0.00  0   A
 ATOM      860    C    C .  THR   A .  113 ?   23.498  44.091   6.974  0.00  0   A
-ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -4.69  0   A
+ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -5.36  0   A
 ATOM      862    C   CB .  THR   A .  113 ?   25.860  43.490   6.456  0.00  0   A
 ATOM      863    O  OG1 .  THR   A .  113 ?   26.407  44.539   7.260  0.00  0   A
 ATOM      864    C  CG2 .  THR   A .  113 ?   26.850  43.117   5.347  0.00  0   A
@@ -1807,7 +1807,7 @@ ATOM     1787    C   CD .  ARG   B .   61 ?   15.961  88.260  38.521  0.00  0
 ATOM     1788    N   NE .  ARG   B .   61 ?   14.906  89.269  38.594  0.00  0   B
 ATOM     1789    C   CZ .  ARG   B .   61 ?   13.831  89.292  37.808  0.00  0   B
 ATOM     1790    N  NH1 .  ARG   B .   61 ?   13.659  88.360  36.879  0.00  0   B
-ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -4.37  0   B
+ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -1.09  0   B
 ATOM     1792    N    N .  ILE   B .   62 ?   15.192  84.329  41.806  0.00  0   B
 ATOM     1793    C   CA .  ILE   B .   62 ?   13.926  83.743  42.225  0.00  0   B
 ATOM     1794    C    C .  ILE   B .   62 ?   13.156  84.764  43.053  0.00  0   B
@@ -2498,12 +2498,12 @@ ATOM     2478    C   CB .  ALA   B .  153 ?   15.056  87.549  48.607  0.00  0
 ATOM     2479    N    N .  LYS   B .  154 ?   12.406  88.974  47.844  0.00  0   B
 ATOM     2480    C   CA .  LYS   B .  154 ?   11.675  90.001  47.104  0.00  0   B
 ATOM     2481    C    C .  LYS   B .  154 ?   12.565  90.692  46.075  0.00  0   B
-ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036  0.00  0   B
+ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036 -0.54  0   B
 ATOM     2483    C   CB .  LYS   B .  154 ?   11.096  91.033  48.071  0.00  0   B
 ATOM     2484    N    N .  SER   B .  155 ?   13.858  90.777  46.370  0.00  0   B
 ATOM     2485    C   CA .  SER   B .  155 ?   14.806  91.415  45.464  0.00  0   B
 ATOM     2486    C    C .  SER   B .  155 ?   15.208  90.467  44.338  0.00  0   B
-ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -1.62  0   B
+ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -3.35  0   B
 ATOM     2488    C   CB .  SER   B .  155 ?   16.059  91.844  46.226  0.00  0   B
 ATOM     2489    O   OG .  SER   B .  155 ?   16.736  90.715  46.751  0.00  0   B
 ATOM     2490    N    N .  GLY   B .  156 ?   14.919  89.180  44.521  0.00  0   B
@@ -2689,154 +2689,162 @@ HETATM     64    V APOL .  STP   C .    1 ?   10.093  87.611  33.467  0.00  0
 HETATM     65    V APOL .  STP   C .    1 ?   10.538  87.926  33.379  0.00  0   C
 HETATM     66    V APOL .  STP   C .    1 ?   33.888  49.647  16.687  0.00  0   C
 HETATM     67    V APOL .  STP   C .    1 ?   17.468  87.092  29.886  0.00  0   C
-HETATM     68    V APOL .  STP   C .    1 ?   33.220  49.873  17.122  0.00  0   C
-HETATM     69    V APOL .  STP   C .    1 ?    9.423  86.425  34.239  0.00  0   C
-HETATM     70    V APOL .  STP   C .    1 ?    9.363  86.402  34.268  0.00  0   C
-HETATM     71    V APOL .  STP   C .    1 ?   17.156  90.553  34.548  0.00  0   C
-HETATM     72    V APOL .  STP   C .    1 ?   18.977  88.996  36.323  0.00  0   C
-HETATM     73    V APOL .  STP   C .    1 ?   18.801  90.804  35.327  0.00  0   C
-HETATM     74    V APOL .  STP   C .    1 ?   18.268  89.945  34.975  0.00  0   C
-HETATM     75    V APOL .  STP   C .    1 ?   18.868  89.208  35.945  0.00  0   C
-HETATM     76    V APOL .  STP   C .    1 ?   18.065  88.657  35.595  0.00  0   C
-HETATM     77    V APOL .  STP   C .    1 ?   18.379  89.193  35.362  0.00  0   C
-HETATM     78    V APOL .  STP   C .    1 ?   18.882  87.605  27.239  0.00  0   C
-HETATM     79    V APOL .  STP   C .    1 ?   13.300  94.652  30.063  0.00  0   C
-HETATM     80    V APOL .  STP   C .    1 ?   13.169  88.280  31.543  0.00  0   C
-HETATM     81    V APOL .  STP   C .    1 ?   12.965  87.866  31.201  0.00  0   C
-HETATM     82    V APOL .  STP   C .    1 ?   17.206  86.955  29.975  0.00  0   C
-HETATM     83    V APOL .  STP   C .    1 ?   17.313  86.932  29.848  0.00  0   C
-HETATM     84    V APOL .  STP   C .    1 ?   17.260  86.826  29.857  0.00  0   C
-HETATM     85    V APOL .  STP   C .    1 ?   17.647  86.903  29.170  0.00  0   C
-HETATM     86    V APOL .  STP   C .    1 ?   17.446  86.914  29.625  0.00  0   C
-HETATM     87    V APOL .  STP   C .    1 ?   17.540  86.349  29.071  0.00  0   C
-HETATM     88    V APOL .  STP   C .    1 ?   17.825  86.147  28.464  0.00  0   C
-HETATM     89    V APOL .  STP   C .    1 ?   17.638  86.291  28.817  0.00  0   C
-HETATM     90    V APOL .  STP   C .    1 ?   17.589  86.200  28.737  0.00  0   C
-HETATM     91    V APOL .  STP   C .    1 ?   17.310  86.348  29.432  0.00  0   C
-HETATM     92    V APOL .  STP   C .    1 ?   24.622  40.674  10.795  0.00  0   C
-HETATM     93    V APOL .  STP   C .    1 ?   27.005  49.985  17.993  0.00  0   C
-HETATM     94    V APOL .  STP   C .    1 ?   26.839  50.582  18.014  0.00  0   C
-HETATM     95    V APOL .  STP   C .    1 ?   27.676  50.218  16.945  0.00  0   C
-HETATM     96    V APOL .  STP   C .    1 ?   26.991  50.900  17.679  0.00  0   C
-HETATM     97    V APOL .  STP   C .    1 ?   30.592  49.040  16.768  0.00  0   C
-HETATM     98    V APOL .  STP   C .    1 ?   31.112  44.097  16.205  0.00  0   C
-HETATM     99    V APOL .  STP   C .    1 ?   26.685  48.719  17.768  0.00  0   C
-HETATM    100    V APOL .  STP   C .    1 ?   27.314  49.434  17.751  0.00  0   C
-HETATM    101    V APOL .  STP   C .    1 ?   30.711  48.752  16.393  0.00  0   C
-HETATM    102    V APOL .  STP   C .    1 ?   31.020  47.339  15.614  0.00  0   C
-HETATM    103    V APOL .  STP   C .    1 ?   29.111  49.193  16.737  0.00  0   C
-HETATM    104    V APOL .  STP   C .    1 ?   27.150  48.349  16.835  0.00  0   C
-HETATM    105    V APOL .  STP   C .    1 ?   28.085  46.923  16.028  0.00  0   C
-HETATM    106    V APOL .  STP   C .    1 ?   29.429  38.000  16.814  0.00  0   C
-HETATM    107    V APOL .  STP   C .    1 ?   25.337  41.857  10.796  0.00  0   C
-HETATM    108    V APOL .  STP   C .    1 ?   10.851  87.154  34.207  0.00  0   C
-HETATM    109    V APOL .  STP   C .    1 ?   10.692  87.013  34.265  0.00  0   C
-HETATM    110    V APOL .  STP   C .    1 ?   11.818  86.568  34.068  0.00  0   C
-HETATM    111    V APOL .  STP   C .    1 ?   12.318  85.510  34.106  0.00  0   C
-HETATM    112    V APOL .  STP   C .    1 ?    5.545  90.375  43.119  0.00  0   C
-HETATM    113    V APOL .  STP   C .    1 ?    4.561  89.333  40.639  0.00  0   C
-HETATM    114    V APOL .  STP   C .    1 ?    4.611  89.401  40.637  0.00  0   C
-HETATM    115    V APOL .  STP   C .    1 ?    6.032  91.564  41.830  0.00  0   C
-HETATM    116    V APOL .  STP   C .    1 ?    6.186  90.504  39.052  0.00  0   C
-HETATM    117    V APOL .  STP   C .    1 ?    6.160  90.509  39.113  0.00  0   C
-HETATM    118    V APOL .  STP   C .    1 ?   17.990  86.008  28.210  0.00  0   C
-HETATM    119    V APOL .  STP   C .    1 ?   18.006  86.098  28.176  0.00  0   C
-HETATM    120    V APOL .  STP   C .    1 ?   19.521  87.572  27.205  0.00  0   C
-HETATM    121    V APOL .  STP   C .    1 ?   19.240  87.483  27.521  0.00  0   C
-HETATM    122    V APOL .  STP   C .    1 ?   18.718  87.116  27.484  0.00  0   C
-HETATM    123    V APOL .  STP   C .    1 ?   18.711  87.054  27.742  0.00  0   C
-HETATM    124    V APOL .  STP   C .    1 ?   19.118  87.451  27.484  0.00  0   C
-HETATM    125    V APOL .  STP   C .    1 ?   19.138  87.454  27.544  0.00  0   C
-HETATM    126    V APOL .  STP   C .    1 ?   17.547  86.179  28.768  0.00  0   C
-HETATM    127    V APOL .  STP   C .    1 ?   24.404  40.531  10.860  0.00  0   C
-HETATM    128    V APOL .  STP   C .    1 ?   24.678  40.696  10.870  0.00  0   C
-HETATM    129    V APOL .  STP   C .    1 ?   25.061  40.721  10.992  0.00  0   C
-HETATM    130    V APOL .  STP   C .    1 ?   34.434  54.099  24.046  0.00  0   C
-HETATM    131    V APOL .  STP   C .    1 ?   34.785  54.066  24.214  0.00  0   C
-HETATM    132    V APOL .  STP   C .    1 ?   30.243  49.144  18.082  0.00  0   C
-HETATM    133    V APOL .  STP   C .    1 ?   33.629  50.117  17.900  0.00  0   C
-HETATM    134    V APOL .  STP   C .    1 ?   32.643  53.327  21.021  0.00  0   C
-HETATM    135    V APOL .  STP   C .    1 ?   33.259  50.367  13.555  0.00  0   C
-HETATM    136    V APOL .  STP   C .    1 ?   32.796  52.509  13.407  0.00  0   C
-HETATM    137    V APOL .  STP   C .    1 ?   31.179  49.730  10.161  0.00  0   C
-HETATM    138    V APOL .  STP   C .    1 ?   25.397  48.219  17.846  0.00  0   C
-HETATM    139    V APOL .  STP   C .    1 ?   25.657  48.105  17.477  0.00  0   C
-HETATM    140    V APOL .  STP   C .    1 ?   32.744  47.500  12.564  0.00  0   C
-HETATM    141    V APOL .  STP   C .    1 ?   32.680  48.711  11.135  0.00  0   C
-HETATM    142    V APOL .  STP   C .    1 ?   30.293  34.983  19.208  0.00  0   C
-HETATM    143    V APOL .  STP   C .    1 ?   30.515  37.558  12.012  0.00  0   C
-HETATM    144    V APOL .  STP   C .    1 ?   28.816  38.796  12.429  0.00  0   C
-HETATM    145    V APOL .  STP   C .    1 ?   25.694  40.137  11.519  0.00  0   C
-HETATM    146    V APOL .  STP   C .    1 ?   25.745  40.188  11.663  0.00  0   C
-HETATM    147    V APOL .  STP   C .    1 ?   30.778  40.864  18.244  0.00  0   C
-HETATM    148    V APOL .  STP   C .    1 ?   29.300  41.260  18.522  0.00  0   C
-HETATM    149    V APOL .  STP   C .    1 ?   29.435  42.951  17.876  0.00  0   C
-HETATM    150    V APOL .  STP   C .    1 ?   17.364  91.328  34.163  0.00  0   C
-HETATM    151    V APOL .  STP   C .    1 ?   17.378  91.256  34.191  0.00  0   C
-HETATM    152    V APOL .  STP   C .    1 ?   17.444  91.177  34.269  0.00  0   C
-HETATM    153    V APOL .  STP   C .    1 ?   17.348  91.074  34.310  0.00  0   C
-HETATM    154    V APOL .  STP   C .    1 ?   30.062  47.686  12.765  0.00  0   C
-HETATM    155    V APOL .  STP   C .    1 ?   26.323  48.692  15.710  0.00  0   C
-HETATM    156    V APOL .  STP   C .    1 ?   30.408  47.380  15.676  0.00  0   C
-HETATM    157    V APOL .  STP   C .    1 ?   28.125  47.095  15.991  0.00  0   C
-HETATM    158    V APOL .  STP   C .    1 ?   27.417  50.537  16.276  0.00  0   C
-HETATM    159    V APOL .  STP   C .    1 ?   27.373  50.707  16.089  0.00  0   C
-HETATM    160    V APOL .  STP   C .    1 ?   27.302  48.395  16.701  0.00  0   C
-HETATM    161    V APOL .  STP   C .    1 ?   27.841  49.832  16.849  0.00  0   C
-HETATM    162    V APOL .  STP   C .    1 ?   28.558  49.429  16.774  0.00  0   C
-HETATM    163    V APOL .  STP   C .    1 ?   27.865  49.337  16.994  0.00  0   C
-HETATM    164    V APOL .  STP   C .    1 ?   28.735  49.235  16.785  0.00  0   C
-HETATM    165    V APOL .  STP   C .    1 ?   31.288  55.409  23.269  0.00  0   C
-HETATM    166    V APOL .  STP   C .    1 ?   32.312  48.943  10.498  0.00  0   C
-HETATM    167    V APOL .  STP   C .    1 ?   34.237  48.223  11.050  0.00  0   C
-HETATM    168    V APOL .  STP   C .    1 ?   24.685  41.731  11.638  0.00  0   C
-HETATM    169    V APOL .  STP   C .    1 ?   23.857  42.701  11.472  0.00  0   C
-HETATM    170    V APOL .  STP   C .    1 ?   28.622  41.347  18.970  0.00  0   C
-HETATM    171    V APOL .  STP   C .    1 ?   28.182  41.101  20.281  0.00  0   C
-HETATM    172    V APOL .  STP   C .    1 ?   24.517  43.394  13.603  0.00  0   C
-HETATM    173    V APOL .  STP   C .    1 ?   24.414  43.155  13.231  0.00  0   C
-HETATM    174    V APOL .  STP   C .    1 ?   27.454  47.131  15.066  0.00  0   C
-HETATM    175    V APOL .  STP   C .    1 ?   25.046  43.340  13.819  0.00  0   C
-HETATM    176    V APOL .  STP   C .    1 ?   24.700  43.363  13.625  0.00  0   C
-HETATM    177    V APOL .  STP   C .    1 ?   28.073  46.895  16.026  0.00  0   C
-HETATM    178    V APOL .  STP   C .    1 ?   28.133  46.815  16.042  0.00  0   C
-HETATM    179    V APOL .  STP   C .    1 ?   30.376  42.824  16.523  0.00  0   C
-HETATM    180    V APOL .  STP   C .    1 ?   30.365  42.854  16.522  0.00  0   C
-HETATM    181    V APOL .  STP   C .    1 ?   30.061  42.491  17.173  0.00  0   C
-HETATM    182    V APOL .  STP   C .    1 ?   29.539  42.849  17.699  0.00  0   C
-HETATM    183    V APOL .  STP   C .    1 ?   29.681  42.794  17.547  0.00  0   C
-HETATM    184    V APOL .  STP   C .    1 ?   28.734  41.753  18.363  0.00  0   C
-HETATM    185    V APOL .  STP   C .    1 ?   27.985  42.238  18.956  0.00  0   C
-HETATM    186    V APOL .  STP   C .    1 ?   28.539  41.757  18.517  0.00  0   C
-HETATM    187    V APOL .  STP   C .    1 ?   29.507  42.806  17.744  0.00  0   C
-HETATM    188    V APOL .  STP   C .    1 ?   29.791  42.296  17.519  0.00  0   C
-HETATM    189    V APOL .  STP   C .    1 ?   25.552  40.651  11.800  0.00  0   C
-HETATM    190    V APOL .  STP   C .    1 ?   25.702  41.429  12.209  0.00  0   C
-HETATM    191    V APOL .  STP   C .    1 ?   25.788  41.400  12.282  0.00  0   C
-HETATM    192    V APOL .  STP   C .    1 ?   25.003  41.310  11.497  0.00  0   C
-HETATM    193    V APOL .  STP   C .    1 ?   25.002  41.301  11.494  0.00  0   C
-HETATM    194    V APOL .  STP   C .    1 ?   24.966  42.497  12.680  0.00  0   C
-HETATM    195    V APOL .  STP   C .    1 ?   24.684  41.731  11.659  0.00  0   C
-HETATM    196    V APOL .  STP   C .    1 ?   24.715  41.678  11.631  0.00  0   C
-HETATM    197    V APOL .  STP   C .    1 ?   24.813  41.386  11.520  0.00  0   C
-HETATM    198    V APOL .  STP   C .    1 ?   24.837  43.023  13.213  0.00  0   C
-HETATM    199    V APOL .  STP   C .    1 ?   24.938  43.175  13.547  0.00  0   C
-HETATM    200    V APOL .  STP   C .    1 ?   24.059  42.452  12.156  0.00  0   C
-HETATM    201    V APOL .  STP   C .    1 ?   24.523  43.068  13.102  0.00  0   C
-HETATM    202    V APOL .  STP   C .    1 ?   23.664  42.606  12.414  0.00  0   C
-HETATM    203    V APOL .  STP   C .    1 ?   24.396  43.128  13.200  0.00  0   C
-HETATM    204    V APOL .  STP   C .    1 ?   24.435  43.138  13.214  0.00  0   C
-HETATM    205    V APOL .  STP   C .    1 ?   24.518  43.086  13.129  0.00  0   C
-HETATM    206    V APOL .  STP   C .    1 ?   24.575  43.157  13.291  0.00  0   C
-HETATM    207    V APOL .  STP   C .    1 ?   31.063  55.664  23.330  0.00  0   C
-HETATM    208    V APOL .  STP   C .    1 ?   33.721  54.466  25.554  0.00  0   C
-HETATM    209    V APOL .  STP   C .    1 ?   25.197  43.355  14.014  0.00  0   C
-HETATM    210    V APOL .  STP   C .    1 ?   25.635  43.546  14.505  0.00  0   C
-HETATM    211    V APOL .  STP   C .    1 ?   25.403  43.098  14.044  0.00  0   C
-HETATM    212    V APOL .  STP   C .    1 ?   26.324  42.901  14.728  0.00  0   C
-HETATM    213    V APOL .  STP   C .    1 ?   26.006  42.758  14.370  0.00  0   C
-HETATM    214    V APOL .  STP   C .    1 ?   28.626  39.926  18.156  0.00  0   C
-HETATM    215    V APOL .  STP   C .    1 ?   30.514  38.191  17.400  0.00  0   C
-HETATM    216    V APOL .  STP   C .    1 ?   29.885  37.934  17.493  0.00  0   C
-HETATM    217    V APOL .  STP   C .    1 ?   29.459  38.005  16.840  0.00  0   C
+HETATM     68    V APOL .  STP   C .    1 ?   26.368  39.013   7.356  0.00  0   C
+HETATM     69    V APOL .  STP   C .    1 ?   33.220  49.873  17.122  0.00  0   C
+HETATM     70    V APOL .  STP   C .    1 ?   30.363  38.669  24.413  0.00  0   C
+HETATM     71    V APOL .  STP   C .    1 ?    9.423  86.425  34.239  0.00  0   C
+HETATM     72    V APOL .  STP   C .    1 ?    9.363  86.402  34.268  0.00  0   C
+HETATM     73    V APOL .  STP   C .    1 ?   17.156  90.553  34.548  0.00  0   C
+HETATM     74    V APOL .  STP   C .    1 ?   18.977  88.996  36.323  0.00  0   C
+HETATM     75    V APOL .  STP   C .    1 ?   18.801  90.804  35.327  0.00  0   C
+HETATM     76    V APOL .  STP   C .    1 ?   18.268  89.945  34.975  0.00  0   C
+HETATM     77    V APOL .  STP   C .    1 ?   18.868  89.208  35.945  0.00  0   C
+HETATM     78    V APOL .  STP   C .    1 ?   18.065  88.657  35.595  0.00  0   C
+HETATM     79    V APOL .  STP   C .    1 ?   18.379  89.193  35.362  0.00  0   C
+HETATM     80    V APOL .  STP   C .    1 ?   18.882  87.605  27.239  0.00  0   C
+HETATM     81    V APOL .  STP   C .    1 ?   13.300  94.652  30.063  0.00  0   C
+HETATM     82    V APOL .  STP   C .    1 ?   13.169  88.280  31.543  0.00  0   C
+HETATM     83    V APOL .  STP   C .    1 ?   12.965  87.866  31.201  0.00  0   C
+HETATM     84    V APOL .  STP   C .    1 ?   17.206  86.955  29.975  0.00  0   C
+HETATM     85    V APOL .  STP   C .    1 ?   17.313  86.932  29.848  0.00  0   C
+HETATM     86    V APOL .  STP   C .    1 ?   17.260  86.826  29.857  0.00  0   C
+HETATM     87    V APOL .  STP   C .    1 ?   17.647  86.903  29.170  0.00  0   C
+HETATM     88    V APOL .  STP   C .    1 ?   17.446  86.914  29.625  0.00  0   C
+HETATM     89    V APOL .  STP   C .    1 ?   17.540  86.349  29.071  0.00  0   C
+HETATM     90    V APOL .  STP   C .    1 ?   17.825  86.147  28.464  0.00  0   C
+HETATM     91    V APOL .  STP   C .    1 ?   17.638  86.291  28.817  0.00  0   C
+HETATM     92    V APOL .  STP   C .    1 ?   17.589  86.200  28.737  0.00  0   C
+HETATM     93    V APOL .  STP   C .    1 ?   17.310  86.348  29.432  0.00  0   C
+HETATM     94    V APOL .  STP   C .    1 ?   24.622  40.674  10.795  0.00  0   C
+HETATM     95    V APOL .  STP   C .    1 ?   27.005  49.985  17.993  0.00  0   C
+HETATM     96    V APOL .  STP   C .    1 ?   26.839  50.582  18.014  0.00  0   C
+HETATM     97    V APOL .  STP   C .    1 ?   27.676  50.218  16.945  0.00  0   C
+HETATM     98    V APOL .  STP   C .    1 ?   26.991  50.900  17.679  0.00  0   C
+HETATM     99    V APOL .  STP   C .    1 ?   30.592  49.040  16.768  0.00  0   C
+HETATM    100    V APOL .  STP   C .    1 ?   31.112  44.097  16.205  0.00  0   C
+HETATM    101    V APOL .  STP   C .    1 ?   26.685  48.719  17.768  0.00  0   C
+HETATM    102    V APOL .  STP   C .    1 ?   27.314  49.434  17.751  0.00  0   C
+HETATM    103    V APOL .  STP   C .    1 ?   30.711  48.752  16.393  0.00  0   C
+HETATM    104    V APOL .  STP   C .    1 ?   31.020  47.339  15.614  0.00  0   C
+HETATM    105    V APOL .  STP   C .    1 ?   29.111  49.193  16.737  0.00  0   C
+HETATM    106    V APOL .  STP   C .    1 ?   27.150  48.349  16.835  0.00  0   C
+HETATM    107    V APOL .  STP   C .    1 ?   28.085  46.923  16.028  0.00  0   C
+HETATM    108    V APOL .  STP   C .    1 ?   29.429  38.000  16.814  0.00  0   C
+HETATM    109    V APOL .  STP   C .    1 ?   25.337  41.857  10.796  0.00  0   C
+HETATM    110    V APOL .  STP   C .    1 ?   26.549  39.030   7.512  0.00  0   C
+HETATM    111    V APOL .  STP   C .    1 ?   25.458  40.233   9.519  0.00  0   C
+HETATM    112    V APOL .  STP   C .    1 ?   26.179  39.423   7.970  0.00  0   C
+HETATM    113    V APOL .  STP   C .    1 ?   25.736  40.004   8.551  0.00  0   C
+HETATM    114    V APOL .  STP   C .    1 ?   10.851  87.154  34.207  0.00  0   C
+HETATM    115    V APOL .  STP   C .    1 ?   10.692  87.013  34.265  0.00  0   C
+HETATM    116    V APOL .  STP   C .    1 ?   11.818  86.568  34.068  0.00  0   C
+HETATM    117    V APOL .  STP   C .    1 ?   12.318  85.510  34.106  0.00  0   C
+HETATM    118    V APOL .  STP   C .    1 ?    5.545  90.375  43.119  0.00  0   C
+HETATM    119    V APOL .  STP   C .    1 ?    4.561  89.333  40.639  0.00  0   C
+HETATM    120    V APOL .  STP   C .    1 ?    4.611  89.401  40.637  0.00  0   C
+HETATM    121    V APOL .  STP   C .    1 ?    6.032  91.564  41.830  0.00  0   C
+HETATM    122    V APOL .  STP   C .    1 ?    6.186  90.504  39.052  0.00  0   C
+HETATM    123    V APOL .  STP   C .    1 ?    6.160  90.509  39.113  0.00  0   C
+HETATM    124    V APOL .  STP   C .    1 ?   17.990  86.008  28.210  0.00  0   C
+HETATM    125    V APOL .  STP   C .    1 ?   18.006  86.098  28.176  0.00  0   C
+HETATM    126    V APOL .  STP   C .    1 ?   19.521  87.572  27.205  0.00  0   C
+HETATM    127    V APOL .  STP   C .    1 ?   19.240  87.483  27.521  0.00  0   C
+HETATM    128    V APOL .  STP   C .    1 ?   18.718  87.116  27.484  0.00  0   C
+HETATM    129    V APOL .  STP   C .    1 ?   18.711  87.054  27.742  0.00  0   C
+HETATM    130    V APOL .  STP   C .    1 ?   19.118  87.451  27.484  0.00  0   C
+HETATM    131    V APOL .  STP   C .    1 ?   19.138  87.454  27.544  0.00  0   C
+HETATM    132    V APOL .  STP   C .    1 ?   17.547  86.179  28.768  0.00  0   C
+HETATM    133    V APOL .  STP   C .    1 ?   24.404  40.531  10.860  0.00  0   C
+HETATM    134    V APOL .  STP   C .    1 ?   24.678  40.696  10.870  0.00  0   C
+HETATM    135    V APOL .  STP   C .    1 ?   25.061  40.721  10.992  0.00  0   C
+HETATM    136    V APOL .  STP   C .    1 ?   34.434  54.099  24.046  0.00  0   C
+HETATM    137    V APOL .  STP   C .    1 ?   34.785  54.066  24.214  0.00  0   C
+HETATM    138    V APOL .  STP   C .    1 ?   30.243  49.144  18.082  0.00  0   C
+HETATM    139    V APOL .  STP   C .    1 ?   33.629  50.117  17.900  0.00  0   C
+HETATM    140    V APOL .  STP   C .    1 ?   32.643  53.327  21.021  0.00  0   C
+HETATM    141    V APOL .  STP   C .    1 ?   33.259  50.367  13.555  0.00  0   C
+HETATM    142    V APOL .  STP   C .    1 ?   32.796  52.509  13.407  0.00  0   C
+HETATM    143    V APOL .  STP   C .    1 ?   31.179  49.730  10.161  0.00  0   C
+HETATM    144    V APOL .  STP   C .    1 ?   25.397  48.219  17.846  0.00  0   C
+HETATM    145    V APOL .  STP   C .    1 ?   25.657  48.105  17.477  0.00  0   C
+HETATM    146    V APOL .  STP   C .    1 ?   32.744  47.500  12.564  0.00  0   C
+HETATM    147    V APOL .  STP   C .    1 ?   32.680  48.711  11.135  0.00  0   C
+HETATM    148    V APOL .  STP   C .    1 ?   30.293  34.983  19.208  0.00  0   C
+HETATM    149    V APOL .  STP   C .    1 ?   30.515  37.558  12.012  0.00  0   C
+HETATM    150    V APOL .  STP   C .    1 ?   28.816  38.796  12.429  0.00  0   C
+HETATM    151    V APOL .  STP   C .    1 ?   25.694  40.137  11.519  0.00  0   C
+HETATM    152    V APOL .  STP   C .    1 ?   25.745  40.188  11.663  0.00  0   C
+HETATM    153    V APOL .  STP   C .    1 ?   30.778  40.864  18.244  0.00  0   C
+HETATM    154    V APOL .  STP   C .    1 ?   29.300  41.260  18.522  0.00  0   C
+HETATM    155    V APOL .  STP   C .    1 ?   30.155  39.400  23.865  0.00  0   C
+HETATM    156    V APOL .  STP   C .    1 ?   29.435  42.951  17.876  0.00  0   C
+HETATM    157    V APOL .  STP   C .    1 ?   17.364  91.328  34.163  0.00  0   C
+HETATM    158    V APOL .  STP   C .    1 ?   17.378  91.256  34.191  0.00  0   C
+HETATM    159    V APOL .  STP   C .    1 ?   17.444  91.177  34.269  0.00  0   C
+HETATM    160    V APOL .  STP   C .    1 ?   17.348  91.074  34.310  0.00  0   C
+HETATM    161    V APOL .  STP   C .    1 ?   30.062  47.686  12.765  0.00  0   C
+HETATM    162    V APOL .  STP   C .    1 ?   26.323  48.692  15.710  0.00  0   C
+HETATM    163    V APOL .  STP   C .    1 ?   30.408  47.380  15.676  0.00  0   C
+HETATM    164    V APOL .  STP   C .    1 ?   28.125  47.095  15.991  0.00  0   C
+HETATM    165    V APOL .  STP   C .    1 ?   27.417  50.537  16.276  0.00  0   C
+HETATM    166    V APOL .  STP   C .    1 ?   27.373  50.707  16.089  0.00  0   C
+HETATM    167    V APOL .  STP   C .    1 ?   27.302  48.395  16.701  0.00  0   C
+HETATM    168    V APOL .  STP   C .    1 ?   27.841  49.832  16.849  0.00  0   C
+HETATM    169    V APOL .  STP   C .    1 ?   28.558  49.429  16.774  0.00  0   C
+HETATM    170    V APOL .  STP   C .    1 ?   27.865  49.337  16.994  0.00  0   C
+HETATM    171    V APOL .  STP   C .    1 ?   28.735  49.235  16.785  0.00  0   C
+HETATM    172    V APOL .  STP   C .    1 ?   30.286  38.810  24.532  0.00  0   C
+HETATM    173    V APOL .  STP   C .    1 ?   31.288  55.409  23.269  0.00  0   C
+HETATM    174    V APOL .  STP   C .    1 ?   32.312  48.943  10.498  0.00  0   C
+HETATM    175    V APOL .  STP   C .    1 ?   34.237  48.223  11.050  0.00  0   C
+HETATM    176    V APOL .  STP   C .    1 ?   24.685  41.731  11.638  0.00  0   C
+HETATM    177    V APOL .  STP   C .    1 ?   23.857  42.701  11.472  0.00  0   C
+HETATM    178    V APOL .  STP   C .    1 ?   28.622  41.347  18.970  0.00  0   C
+HETATM    179    V APOL .  STP   C .    1 ?   28.182  41.101  20.281  0.00  0   C
+HETATM    180    V APOL .  STP   C .    1 ?   24.517  43.394  13.603  0.00  0   C
+HETATM    181    V APOL .  STP   C .    1 ?   24.414  43.155  13.231  0.00  0   C
+HETATM    182    V APOL .  STP   C .    1 ?   27.454  47.131  15.066  0.00  0   C
+HETATM    183    V APOL .  STP   C .    1 ?   25.046  43.340  13.819  0.00  0   C
+HETATM    184    V APOL .  STP   C .    1 ?   24.700  43.363  13.625  0.00  0   C
+HETATM    185    V APOL .  STP   C .    1 ?   28.073  46.895  16.026  0.00  0   C
+HETATM    186    V APOL .  STP   C .    1 ?   28.133  46.815  16.042  0.00  0   C
+HETATM    187    V APOL .  STP   C .    1 ?   30.376  42.824  16.523  0.00  0   C
+HETATM    188    V APOL .  STP   C .    1 ?   30.365  42.854  16.522  0.00  0   C
+HETATM    189    V APOL .  STP   C .    1 ?   30.061  42.491  17.173  0.00  0   C
+HETATM    190    V APOL .  STP   C .    1 ?   29.539  42.849  17.699  0.00  0   C
+HETATM    191    V APOL .  STP   C .    1 ?   29.681  42.794  17.547  0.00  0   C
+HETATM    192    V APOL .  STP   C .    1 ?   28.734  41.753  18.363  0.00  0   C
+HETATM    193    V APOL .  STP   C .    1 ?   27.985  42.238  18.956  0.00  0   C
+HETATM    194    V APOL .  STP   C .    1 ?   28.539  41.757  18.517  0.00  0   C
+HETATM    195    V APOL .  STP   C .    1 ?   29.507  42.806  17.744  0.00  0   C
+HETATM    196    V APOL .  STP   C .    1 ?   29.791  42.296  17.519  0.00  0   C
+HETATM    197    V APOL .  STP   C .    1 ?   25.552  40.651  11.800  0.00  0   C
+HETATM    198    V APOL .  STP   C .    1 ?   25.702  41.429  12.209  0.00  0   C
+HETATM    199    V APOL .  STP   C .    1 ?   25.788  41.400  12.282  0.00  0   C
+HETATM    200    V APOL .  STP   C .    1 ?   25.003  41.310  11.497  0.00  0   C
+HETATM    201    V APOL .  STP   C .    1 ?   25.002  41.301  11.494  0.00  0   C
+HETATM    202    V APOL .  STP   C .    1 ?   24.966  42.497  12.680  0.00  0   C
+HETATM    203    V APOL .  STP   C .    1 ?   24.684  41.731  11.659  0.00  0   C
+HETATM    204    V APOL .  STP   C .    1 ?   24.715  41.678  11.631  0.00  0   C
+HETATM    205    V APOL .  STP   C .    1 ?   24.813  41.386  11.520  0.00  0   C
+HETATM    206    V APOL .  STP   C .    1 ?   24.837  43.023  13.213  0.00  0   C
+HETATM    207    V APOL .  STP   C .    1 ?   24.938  43.175  13.547  0.00  0   C
+HETATM    208    V APOL .  STP   C .    1 ?   24.059  42.452  12.156  0.00  0   C
+HETATM    209    V APOL .  STP   C .    1 ?   24.523  43.068  13.102  0.00  0   C
+HETATM    210    V APOL .  STP   C .    1 ?   23.664  42.606  12.414  0.00  0   C
+HETATM    211    V APOL .  STP   C .    1 ?   24.396  43.128  13.200  0.00  0   C
+HETATM    212    V APOL .  STP   C .    1 ?   24.435  43.138  13.214  0.00  0   C
+HETATM    213    V APOL .  STP   C .    1 ?   24.518  43.086  13.129  0.00  0   C
+HETATM    214    V APOL .  STP   C .    1 ?   24.575  43.157  13.291  0.00  0   C
+HETATM    215    V APOL .  STP   C .    1 ?   31.063  55.664  23.330  0.00  0   C
+HETATM    216    V APOL .  STP   C .    1 ?   33.721  54.466  25.554  0.00  0   C
+HETATM    217    V APOL .  STP   C .    1 ?   25.197  43.355  14.014  0.00  0   C
+HETATM    218    V APOL .  STP   C .    1 ?   25.635  43.546  14.505  0.00  0   C
+HETATM    219    V APOL .  STP   C .    1 ?   25.403  43.098  14.044  0.00  0   C
+HETATM    220    V APOL .  STP   C .    1 ?   26.324  42.901  14.728  0.00  0   C
+HETATM    221    V APOL .  STP   C .    1 ?   26.006  42.758  14.370  0.00  0   C
+HETATM    222    V APOL .  STP   C .    1 ?   28.626  39.926  18.156  0.00  0   C
+HETATM    223    V APOL .  STP   C .    1 ?   30.514  38.191  17.400  0.00  0   C
+HETATM    224    V APOL .  STP   C .    1 ?   29.885  37.934  17.493  0.00  0   C
+HETATM    225    V APOL .  STP   C .    1 ?   29.459  38.005  16.840  0.00  0   C
 # 

tests/reference_output/1QNH_out/1QNH_pockets.pqr

@@ -68,155 +68,163 @@ ATOM     64    C STP     1      10.093  87.611  33.467    0.00     4.07
 ATOM     65    C STP     1      10.538  87.926  33.379    0.00     4.35
 ATOM     66    O STP     1      33.888  49.647  16.687    0.00     6.03
 ATOM     67    O STP     1      17.468  87.092  29.886    0.00     3.61
-ATOM     68    O STP     1      33.220  49.873  17.122    0.00     5.53
-ATOM     69    C STP     1       9.423  86.425  34.239    0.00     3.53
-ATOM     70    C STP     1       9.363  86.402  34.268    0.00     3.50
-ATOM     71    O STP     1      17.156  90.553  34.548    0.00     4.74
-ATOM     72    O STP     1      18.977  88.996  36.323    0.00     3.80
-ATOM     73    O STP     1      18.801  90.804  35.327    0.00     4.97
-ATOM     74    O STP     1      18.268  89.945  34.975    0.00     4.55
-ATOM     75    O STP     1      18.868  89.208  35.945    0.00     4.00
-ATOM     76    O STP     1      18.065  88.657  35.595    0.00     3.63
-ATOM     77    O STP     1      18.379  89.193  35.362    0.00     4.09
-ATOM     78    O STP     1      18.882  87.605  27.239    0.00     3.92
-ATOM     79    O STP     1      13.300  94.652  30.063    0.00     5.74
-ATOM     80    O STP     1      13.169  88.280  31.543    0.00     3.79
-ATOM     81    C STP     1      12.965  87.866  31.201    0.00     3.42
-ATOM     82    O STP     1      17.206  86.955  29.975    0.00     3.57
-ATOM     83    O STP     1      17.313  86.932  29.848    0.00     3.60
-ATOM     84    O STP     1      17.260  86.826  29.857    0.00     3.56
-ATOM     85    O STP     1      17.647  86.903  29.170    0.00     3.65
-ATOM     86    O STP     1      17.446  86.914  29.625    0.00     3.62
-ATOM     87    O STP     1      17.540  86.349  29.071    0.00     3.57
-ATOM     88    O STP     1      17.825  86.147  28.464    0.00     3.66
-ATOM     89    O STP     1      17.638  86.291  28.817    0.00     3.62
-ATOM     90    O STP     1      17.589  86.200  28.737    0.00     3.57
-ATOM     91    C STP     1      17.310  86.348  29.432    0.00     3.47
-ATOM     92    O STP     1      24.622  40.674  10.795    0.00     4.05
-ATOM     93    C STP     1      27.005  49.985  17.993    0.00     3.82
-ATOM     94    C STP     1      26.839  50.582  18.014    0.00     3.60
-ATOM     95    C STP     1      27.676  50.218  16.945    0.00     4.09
-ATOM     96    C STP     1      26.991  50.900  17.679    0.00     3.59
-ATOM     97    O STP     1      30.592  49.040  16.768    0.00     4.84
-ATOM     98    O STP     1      31.112  44.097  16.205    0.00     5.49
-ATOM     99    O STP     1      26.685  48.719  17.768    0.00     3.95
-ATOM    100    C STP     1      27.314  49.434  17.751    0.00     4.15
-ATOM    101    O STP     1      30.711  48.752  16.393    0.00     5.04
-ATOM    102    O STP     1      31.020  47.339  15.614    0.00     5.44
-ATOM    103    O STP     1      29.111  49.193  16.737    0.00     4.56
-ATOM    104    O STP     1      27.150  48.349  16.835    0.00     4.29
-ATOM    105    O STP     1      28.085  46.923  16.028    0.00     4.46
-ATOM    106    O STP     1      29.429  38.000  16.814    0.00     3.95
-ATOM    107    O STP     1      25.337  41.857  10.796    0.00     3.65
-ATOM    108    C STP     1      10.851  87.154  34.207    0.00     4.06
-ATOM    109    C STP     1      10.692  87.013  34.265    0.00     3.95
-ATOM    110    O STP     1      11.818  86.568  34.068    0.00     3.81
-ATOM    111    C STP     1      12.318  85.510  34.106    0.00     3.44
-ATOM    112    O STP     1       5.545  90.375  43.119    0.00     4.74
-ATOM    113    C STP     1       4.561  89.333  40.639    0.00     3.85
-ATOM    114    C STP     1       4.611  89.401  40.637    0.00     3.86
-ATOM    115    C STP     1       6.032  91.564  41.830    0.00     5.21
-ATOM    116    C STP     1       6.186  90.504  39.052    0.00     3.61
-ATOM    117    C STP     1       6.160  90.509  39.113    0.00     3.63
-ATOM    118    O STP     1      17.990  86.008  28.210    0.00     3.70
-ATOM    119    O STP     1      18.006  86.098  28.176    0.00     3.73
-ATOM    120    O STP     1      19.521  87.572  27.205    0.00     4.19
-ATOM    121    O STP     1      19.240  87.483  27.521    0.00     4.22
-ATOM    122    O STP     1      18.718  87.116  27.484    0.00     3.98
-ATOM    123    O STP     1      18.711  87.054  27.742    0.00     4.02
-ATOM    124    O STP     1      19.118  87.451  27.484    0.00     4.20
-ATOM    125    O STP     1      19.138  87.454  27.544    0.00     4.22
-ATOM    126    O STP     1      17.547  86.179  28.768    0.00     3.54
-ATOM    127    O STP     1      24.404  40.531  10.860    0.00     3.87
-ATOM    128    O STP     1      24.678  40.696  10.870    0.00     4.10
-ATOM    129    O STP     1      25.061  40.721  10.992    0.00     4.29
-ATOM    130    C STP     1      34.434  54.099  24.046    0.00     5.83
-ATOM    131    C STP     1      34.785  54.066  24.214    0.00     6.17
-ATOM    132    O STP     1      30.243  49.144  18.082    0.00     3.84
-ATOM    133    O STP     1      33.629  50.117  17.900    0.00     5.37
-ATOM    134    C STP     1      32.643  53.327  21.021    0.00     3.69
-ATOM    135    O STP     1      33.259  50.367  13.555    0.00     5.25
-ATOM    136    O STP     1      32.796  52.509  13.407    0.00     3.99
-ATOM    137    O STP     1      31.179  49.730  10.161    0.00     4.05
-ATOM    138    C STP     1      25.397  48.219  17.846    0.00     3.48
-ATOM    139    C STP     1      25.657  48.105  17.477    0.00     3.55
-ATOM    140    O STP     1      32.744  47.500  12.564    0.00     5.68
-ATOM    141    O STP     1      32.680  48.711  11.135    0.00     5.22
-ATOM    142    O STP     1      30.293  34.983  19.208    0.00     5.09
-ATOM    143    C STP     1      30.515  37.558  12.012    0.00     5.68
-ATOM    144    O STP     1      28.816  38.796  12.429    0.00     4.55
-ATOM    145    O STP     1      25.694  40.137  11.519    0.00     4.25
-ATOM    146    O STP     1      25.745  40.188  11.663    0.00     4.25
-ATOM    147    O STP     1      30.778  40.864  18.244    0.00     5.65
-ATOM    148    O STP     1      29.300  41.260  18.522    0.00     4.72
-ATOM    149    O STP     1      29.435  42.951  17.876    0.00     4.50
-ATOM    150    O STP     1      17.364  91.328  34.163    0.00     5.47
-ATOM    151    O STP     1      17.378  91.256  34.191    0.00     5.43
-ATOM    152    O STP     1      17.444  91.177  34.269    0.00     5.37
-ATOM    153    O STP     1      17.348  91.074  34.310    0.00     5.25
-ATOM    154    O STP     1      30.062  47.686  12.765    0.00     3.67
-ATOM    155    C STP     1      26.323  48.692  15.710    0.00     3.43
-ATOM    156    O STP     1      30.408  47.380  15.676    0.00     5.15
-ATOM    157    O STP     1      28.125  47.095  15.991    0.00     4.51
-ATOM    158    C STP     1      27.417  50.537  16.276    0.00     3.74
-ATOM    159    C STP     1      27.373  50.707  16.089    0.00     3.59
-ATOM    160    C STP     1      27.302  48.395  16.701    0.00     4.37
-ATOM    161    C STP     1      27.841  49.832  16.849    0.00     4.30
-ATOM    162    C STP     1      28.558  49.429  16.774    0.00     4.43
-ATOM    163    C STP     1      27.865  49.337  16.994    0.00     4.49
-ATOM    164    O STP     1      28.735  49.235  16.785    0.00     4.53
-ATOM    165    C STP     1      31.288  55.409  23.269    0.00     3.49
-ATOM    166    O STP     1      32.312  48.943  10.498    0.00     4.81
-ATOM    167    O STP     1      34.237  48.223  11.050    0.00     6.07
-ATOM    168    O STP     1      24.685  41.731  11.638    0.00     4.16
-ATOM    169    O STP     1      23.857  42.701  11.472    0.00     3.56
-ATOM    170    O STP     1      28.622  41.347  18.970    0.00     4.24
-ATOM    171    O STP     1      28.182  41.101  20.281    0.00     3.62
-ATOM    172    C STP     1      24.517  43.394  13.603    0.00     3.46
-ATOM    173    C STP     1      24.414  43.155  13.231    0.00     3.58
-ATOM    174    O STP     1      27.454  47.131  15.066    0.00     3.72
-ATOM    175    O STP     1      25.046  43.340  13.819    0.00     3.59
-ATOM    176    C STP     1      24.700  43.363  13.625    0.00     3.53
-ATOM    177    O STP     1      28.073  46.895  16.026    0.00     4.44
-ATOM    178    O STP     1      28.133  46.815  16.042    0.00     4.43
-ATOM    179    O STP     1      30.376  42.824  16.523    0.00     5.68
-ATOM    180    O STP     1      30.365  42.854  16.522    0.00     5.67
-ATOM    181    O STP     1      30.061  42.491  17.173    0.00     5.36
-ATOM    182    O STP     1      29.539  42.849  17.699    0.00     4.70
-ATOM    183    O STP     1      29.681  42.794  17.547    0.00     4.87
-ATOM    184    O STP     1      28.734  41.753  18.363    0.00     4.47
-ATOM    185    O STP     1      27.985  42.238  18.956    0.00     3.70
-ATOM    186    O STP     1      28.539  41.757  18.517    0.00     4.33
-ATOM    187    O STP     1      29.507  42.806  17.744    0.00     4.69
-ATOM    188    O STP     1      29.791  42.296  17.519    0.00     5.14
-ATOM    189    O STP     1      25.552  40.651  11.800    0.00     4.24
-ATOM    190    O STP     1      25.702  41.429  12.209    0.00     4.09
-ATOM    191    O STP     1      25.788  41.400  12.282    0.00     4.07
-ATOM    192    O STP     1      25.003  41.310  11.497    0.00     4.32
-ATOM    193    O STP     1      25.002  41.301  11.494    0.00     4.32
-ATOM    194    O STP     1      24.966  42.497  12.680    0.00     3.75
-ATOM    195    O STP     1      24.684  41.731  11.659    0.00     4.16
-ATOM    196    O STP     1      24.715  41.678  11.631    0.00     4.18
-ATOM    197    O STP     1      24.813  41.386  11.520    0.00     4.25
-ATOM    198    O STP     1      24.837  43.023  13.213    0.00     3.66
-ATOM    199    O STP     1      24.938  43.175  13.547    0.00     3.62
-ATOM    200    O STP     1      24.059  42.452  12.156    0.00     3.85
-ATOM    201    O STP     1      24.523  43.068  13.102    0.00     3.64
-ATOM    202    O STP     1      23.664  42.606  12.414    0.00     3.66
-ATOM    203    O STP     1      24.396  43.128  13.200    0.00     3.58
-ATOM    204    O STP     1      24.435  43.138  13.214    0.00     3.59
-ATOM    205    O STP     1      24.518  43.086  13.129    0.00     3.63
-ATOM    206    O STP     1      24.575  43.157  13.291    0.00     3.61
-ATOM    207    C STP     1      31.063  55.664  23.330    0.00     3.47
-ATOM    208    O STP     1      33.721  54.466  25.554    0.00     5.34
-ATOM    209    O STP     1      25.197  43.355  14.014    0.00     3.58
-ATOM    210    O STP     1      25.635  43.546  14.505    0.00     3.53
-ATOM    211    O STP     1      25.403  43.098  14.044    0.00     3.59
-ATOM    212    O STP     1      26.324  42.901  14.728    0.00     3.68
-ATOM    213    O STP     1      26.006  42.758  14.370    0.00     3.65
-ATOM    214    O STP     1      28.626  39.926  18.156    0.00     3.63
-ATOM    215    O STP     1      30.514  38.191  17.400    0.00     5.05
-ATOM    216    O STP     1      29.885  37.934  17.493    0.00     4.48
-ATOM    217    O STP     1      29.459  38.005  16.840    0.00     3.98
+ATOM     68    O STP     1      26.368  39.013   7.356    0.00     4.59
+ATOM     69    O STP     1      33.220  49.873  17.122    0.00     5.53
+ATOM     70    O STP     1      30.363  38.669  24.413    0.00     5.89
+ATOM     71    C STP     1       9.423  86.425  34.239    0.00     3.53
+ATOM     72    C STP     1       9.363  86.402  34.268    0.00     3.50
+ATOM     73    O STP     1      17.156  90.553  34.548    0.00     4.74
+ATOM     74    O STP     1      18.977  88.996  36.323    0.00     3.80
+ATOM     75    O STP     1      18.801  90.804  35.327    0.00     4.97
+ATOM     76    O STP     1      18.268  89.945  34.975    0.00     4.55
+ATOM     77    O STP     1      18.868  89.208  35.945    0.00     4.00
+ATOM     78    O STP     1      18.065  88.657  35.595    0.00     3.63
+ATOM     79    O STP     1      18.379  89.193  35.362    0.00     4.09
+ATOM     80    O STP     1      18.882  87.605  27.239    0.00     3.92
+ATOM     81    O STP     1      13.300  94.652  30.063    0.00     5.74
+ATOM     82    O STP     1      13.169  88.280  31.543    0.00     3.79
+ATOM     83    C STP     1      12.965  87.866  31.201    0.00     3.42
+ATOM     84    O STP     1      17.206  86.955  29.975    0.00     3.57
+ATOM     85    O STP     1      17.313  86.932  29.848    0.00     3.60
+ATOM     86    O STP     1      17.260  86.826  29.857    0.00     3.56
+ATOM     87    O STP     1      17.647  86.903  29.170    0.00     3.65
+ATOM     88    O STP     1      17.446  86.914  29.625    0.00     3.62
+ATOM     89    O STP     1      17.540  86.349  29.071    0.00     3.57
+ATOM     90    O STP     1      17.825  86.147  28.464    0.00     3.66
+ATOM     91    O STP     1      17.638  86.291  28.817    0.00     3.62
+ATOM     92    O STP     1      17.589  86.200  28.737    0.00     3.57
+ATOM     93    C STP     1      17.310  86.348  29.432    0.00     3.47
+ATOM     94    O STP     1      24.622  40.674  10.795    0.00     4.05
+ATOM     95    C STP     1      27.005  49.985  17.993    0.00     3.82
+ATOM     96    C STP     1      26.839  50.582  18.014    0.00     3.60
+ATOM     97    C STP     1      27.676  50.218  16.945    0.00     4.09
+ATOM     98    C STP     1      26.991  50.900  17.679    0.00     3.59
+ATOM     99    O STP     1      30.592  49.040  16.768    0.00     4.84
+ATOM    100    O STP     1      31.112  44.097  16.205    0.00     5.49
+ATOM    101    O STP     1      26.685  48.719  17.768    0.00     3.95
+ATOM    102    C STP     1      27.314  49.434  17.751    0.00     4.15
+ATOM    103    O STP     1      30.711  48.752  16.393    0.00     5.04
+ATOM    104    O STP     1      31.020  47.339  15.614    0.00     5.44
+ATOM    105    O STP     1      29.111  49.193  16.737    0.00     4.56
+ATOM    106    O STP     1      27.150  48.349  16.835    0.00     4.29
+ATOM    107    O STP     1      28.085  46.923  16.028    0.00     4.46
+ATOM    108    O STP     1      29.429  38.000  16.814    0.00     3.95
+ATOM    109    O STP     1      25.337  41.857  10.796    0.00     3.65
+ATOM    110    C STP     1      26.549  39.030   7.512    0.00     4.64
+ATOM    111    O STP     1      25.458  40.233   9.519    0.00     3.99
+ATOM    112    O STP     1      26.179  39.423   7.970    0.00     4.35
+ATOM    113    O STP     1      25.736  40.004   8.551    0.00     4.07
+ATOM    114    C STP     1      10.851  87.154  34.207    0.00     4.06
+ATOM    115    C STP     1      10.692  87.013  34.265    0.00     3.95
+ATOM    116    O STP     1      11.818  86.568  34.068    0.00     3.81
+ATOM    117    C STP     1      12.318  85.510  34.106    0.00     3.44
+ATOM    118    O STP     1       5.545  90.375  43.119    0.00     4.74
+ATOM    119    C STP     1       4.561  89.333  40.639    0.00     3.85
+ATOM    120    C STP     1       4.611  89.401  40.637    0.00     3.86
+ATOM    121    C STP     1       6.032  91.564  41.830    0.00     5.21
+ATOM    122    C STP     1       6.186  90.504  39.052    0.00     3.61
+ATOM    123    C STP     1       6.160  90.509  39.113    0.00     3.63
+ATOM    124    O STP     1      17.990  86.008  28.210    0.00     3.70
+ATOM    125    O STP     1      18.006  86.098  28.176    0.00     3.73
+ATOM    126    O STP     1      19.521  87.572  27.205    0.00     4.19
+ATOM    127    O STP     1      19.240  87.483  27.521    0.00     4.22
+ATOM    128    O STP     1      18.718  87.116  27.484    0.00     3.98
+ATOM    129    O STP     1      18.711  87.054  27.742    0.00     4.02
+ATOM    130    O STP     1      19.118  87.451  27.484    0.00     4.20
+ATOM    131    O STP     1      19.138  87.454  27.544    0.00     4.22
+ATOM    132    O STP     1      17.547  86.179  28.768    0.00     3.54
+ATOM    133    O STP     1      24.404  40.531  10.860    0.00     3.87
+ATOM    134    O STP     1      24.678  40.696  10.870    0.00     4.10
+ATOM    135    O STP     1      25.061  40.721  10.992    0.00     4.29
+ATOM    136    C STP     1      34.434  54.099  24.046    0.00     5.83
+ATOM    137    C STP     1      34.785  54.066  24.214    0.00     6.17
+ATOM    138    O STP     1      30.243  49.144  18.082    0.00     3.84
+ATOM    139    O STP     1      33.629  50.117  17.900    0.00     5.37
+ATOM    140    C STP     1      32.643  53.327  21.021    0.00     3.69
+ATOM    141    O STP     1      33.259  50.367  13.555    0.00     5.25
+ATOM    142    O STP     1      32.796  52.509  13.407    0.00     3.99
+ATOM    143    O STP     1      31.179  49.730  10.161    0.00     4.05
+ATOM    144    C STP     1      25.397  48.219  17.846    0.00     3.48
+ATOM    145    C STP     1      25.657  48.105  17.477    0.00     3.55
+ATOM    146    O STP     1      32.744  47.500  12.564    0.00     5.68
+ATOM    147    O STP     1      32.680  48.711  11.135    0.00     5.22
+ATOM    148    O STP     1      30.293  34.983  19.208    0.00     5.09
+ATOM    149    C STP     1      30.515  37.558  12.012    0.00     5.68
+ATOM    150    O STP     1      28.816  38.796  12.429    0.00     4.55
+ATOM    151    O STP     1      25.694  40.137  11.519    0.00     4.25
+ATOM    152    O STP     1      25.745  40.188  11.663    0.00     4.25
+ATOM    153    O STP     1      30.778  40.864  18.244    0.00     5.65
+ATOM    154    O STP     1      29.300  41.260  18.522    0.00     4.72
+ATOM    155    O STP     1      30.155  39.400  23.865    0.00     5.50
+ATOM    156    O STP     1      29.435  42.951  17.876    0.00     4.50
+ATOM    157    O STP     1      17.364  91.328  34.163    0.00     5.47
+ATOM    158    O STP     1      17.378  91.256  34.191    0.00     5.43
+ATOM    159    O STP     1      17.444  91.177  34.269    0.00     5.37
+ATOM    160    O STP     1      17.348  91.074  34.310    0.00     5.25
+ATOM    161    O STP     1      30.062  47.686  12.765    0.00     3.67
+ATOM    162    C STP     1      26.323  48.692  15.710    0.00     3.43
+ATOM    163    O STP     1      30.408  47.380  15.676    0.00     5.15
+ATOM    164    O STP     1      28.125  47.095  15.991    0.00     4.51
+ATOM    165    C STP     1      27.417  50.537  16.276    0.00     3.74
+ATOM    166    C STP     1      27.373  50.707  16.089    0.00     3.59
+ATOM    167    C STP     1      27.302  48.395  16.701    0.00     4.37
+ATOM    168    C STP     1      27.841  49.832  16.849    0.00     4.30
+ATOM    169    C STP     1      28.558  49.429  16.774    0.00     4.43
+ATOM    170    C STP     1      27.865  49.337  16.994    0.00     4.49
+ATOM    171    O STP     1      28.735  49.235  16.785    0.00     4.53
+ATOM    172    O STP     1      30.286  38.810  24.532    0.00     5.75
+ATOM    173    C STP     1      31.288  55.409  23.269    0.00     3.49
+ATOM    174    O STP     1      32.312  48.943  10.498    0.00     4.81
+ATOM    175    O STP     1      34.237  48.223  11.050    0.00     6.07
+ATOM    176    O STP     1      24.685  41.731  11.638    0.00     4.16
+ATOM    177    O STP     1      23.857  42.701  11.472    0.00     3.56
+ATOM    178    O STP     1      28.622  41.347  18.970    0.00     4.24
+ATOM    179    O STP     1      28.182  41.101  20.281    0.00     3.62
+ATOM    180    C STP     1      24.517  43.394  13.603    0.00     3.46
+ATOM    181    C STP     1      24.414  43.155  13.231    0.00     3.58
+ATOM    182    O STP     1      27.454  47.131  15.066    0.00     3.72
+ATOM    183    O STP     1      25.046  43.340  13.819    0.00     3.59
+ATOM    184    C STP     1      24.700  43.363  13.625    0.00     3.53
+ATOM    185    O STP     1      28.073  46.895  16.026    0.00     4.44
+ATOM    186    O STP     1      28.133  46.815  16.042    0.00     4.43
+ATOM    187    O STP     1      30.376  42.824  16.523    0.00     5.68
+ATOM    188    O STP     1      30.365  42.854  16.522    0.00     5.67
+ATOM    189    O STP     1      30.061  42.491  17.173    0.00     5.36
+ATOM    190    O STP     1      29.539  42.849  17.699    0.00     4.70
+ATOM    191    O STP     1      29.681  42.794  17.547    0.00     4.87
+ATOM    192    O STP     1      28.734  41.753  18.363    0.00     4.47
+ATOM    193    O STP     1      27.985  42.238  18.956    0.00     3.70
+ATOM    194    O STP     1      28.539  41.757  18.517    0.00     4.33
+ATOM    195    O STP     1      29.507  42.806  17.744    0.00     4.69
+ATOM    196    O STP     1      29.791  42.296  17.519    0.00     5.14
+ATOM    197    O STP     1      25.552  40.651  11.800    0.00     4.24
+ATOM    198    O STP     1      25.702  41.429  12.209    0.00     4.09
+ATOM    199    O STP     1      25.788  41.400  12.282    0.00     4.07
+ATOM    200    O STP     1      25.003  41.310  11.497    0.00     4.32
+ATOM    201    O STP     1      25.002  41.301  11.494    0.00     4.32
+ATOM    202    O STP     1      24.966  42.497  12.680    0.00     3.75
+ATOM    203    O STP     1      24.684  41.731  11.659    0.00     4.16
+ATOM    204    O STP     1      24.715  41.678  11.631    0.00     4.18
+ATOM    205    O STP     1      24.813  41.386  11.520    0.00     4.25
+ATOM    206    O STP     1      24.837  43.023  13.213    0.00     3.66
+ATOM    207    O STP     1      24.938  43.175  13.547    0.00     3.62
+ATOM    208    O STP     1      24.059  42.452  12.156    0.00     3.85
+ATOM    209    O STP     1      24.523  43.068  13.102    0.00     3.64
+ATOM    210    O STP     1      23.664  42.606  12.414    0.00     3.66
+ATOM    211    O STP     1      24.396  43.128  13.200    0.00     3.58
+ATOM    212    O STP     1      24.435  43.138  13.214    0.00     3.59
+ATOM    213    O STP     1      24.518  43.086  13.129    0.00     3.63
+ATOM    214    O STP     1      24.575  43.157  13.291    0.00     3.61
+ATOM    215    C STP     1      31.063  55.664  23.330    0.00     3.47
+ATOM    216    O STP     1      33.721  54.466  25.554    0.00     5.34
+ATOM    217    O STP     1      25.197  43.355  14.014    0.00     3.58
+ATOM    218    O STP     1      25.635  43.546  14.505    0.00     3.53
+ATOM    219    O STP     1      25.403  43.098  14.044    0.00     3.59
+ATOM    220    O STP     1      26.324  42.901  14.728    0.00     3.68
+ATOM    221    O STP     1      26.006  42.758  14.370    0.00     3.65
+ATOM    222    O STP     1      28.626  39.926  18.156    0.00     3.63
+ATOM    223    O STP     1      30.514  38.191  17.400    0.00     5.05
+ATOM    224    O STP     1      29.885  37.934  17.493    0.00     4.48
+ATOM    225    O STP     1      29.459  38.005  16.840    0.00     3.98
 TER
 END

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

@@ -6,21 +6,21 @@ 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                      : 5.8454
+0  - Pocket Score                      : 6.1285
 1  - Drug Score                        : 1.0000
-2  - Number of alpha spheres           :   217
-3  - Mean alpha-sphere radius          : 4.3019
-4  - Mean alpha-sphere Solvent Acc.    : 0.5830
+2  - Number of alpha spheres           :   225
+3  - Mean alpha-sphere radius          : 4.3213
+4  - Mean alpha-sphere Solvent Acc.    : 0.5807
 5  - Mean B-factor of pocket residues  : 0.0000
-6  - Hydrophobicity Score              : 16.8148
-7  - Polarity Score                    :    16
-8  - Amino Acid based volume Score     : 3.8889
-9  - Pocket volume (Monte Carlo)       : 5091.7368
-10  -Pocket volume (convex hull)       : 10904.4561
+6  - Hydrophobicity Score              : 18.4643
+7  - Polarity Score                    :    17
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 5738.3193
+10  -Pocket volume (convex hull)       : 11845.1973
 11 - Charge Score                      :     6
-12 - Local hydrophobic density Score   : 13.4444
-13 - Number of apolar alpha sphere     :    54
-14 - Proportion of apolar alpha sphere : 0.2488
+12 - Local hydrophobic density Score   : 13.3455
+13 - Number of apolar alpha sphere     :    55
+14 - Proportion of apolar alpha sphere : 0.2444
 # 
 loop_
 _atom_site.group_PDB
@@ -50,7 +50,7 @@ ATOM     2286    C  CD1 .  LEU   B .  128 ?    6.202  86.633  32.781  0.00  0
 ATOM     2318    N  NE2 .  HIS   B .  132 ?    9.242  88.831  29.145 -5.47  0   B
 ATOM     2317    C  CE1 .  HIS   B .  132 ?   10.323  88.078  29.041  0.00  0   B
 ATOM     2135    O  OD1 .  ASN   B .  108 ?   12.641  89.570  26.461 -2.14  0   B
-ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -4.37  0   B
+ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -1.09  0   B
 ATOM     1855    C   CD .  GLN   B .   69 ?   15.725  85.545  34.857  0.00  0   B
 ATOM     1833    C  CE2 .  PHE   B .   66 ?    8.952  88.462  37.965  0.00  0   B
 ATOM     2274    N  NE1 .  TRP   B .  127 ?    4.665  90.424  35.013  0.00  0   B
@@ -66,9 +66,9 @@ ATOM     2277    C  CZ2 .  TRP   B .  127 ?    3.617  89.154  36.912  0.00  0
 ATOM     1830    C  CD1 .  PHE   B .   66 ?    6.646  86.985  38.413  0.00  0   B
 ATOM     1818    O    O .  GLN   B .   65 ?    4.153  85.911  42.353  0.00  0   B
 ATOM     2279    C  CH2 .  TRP   B .  127 ?    2.401  88.785  37.428  0.00  0   B
-ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036  0.00  0   B
+ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036 -0.54  0   B
 ATOM     1807    C  CD1 .  ILE   B .   63 ?   11.752  89.132  41.153  0.00  0   B
-ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -1.62  0   B
+ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -3.35  0   B
 ATOM     1789    C   CZ .  ARG   B .   61 ?   13.831  89.292  37.808  0.00  0   B
 ATOM     1911    C    C .  GLY   B .   78 ?   21.795  87.544  32.811  0.00  0   B
 ATOM     1904    O    O .  ASN   B .   77 ?   22.544  87.676  36.296  0.00  0   B
@@ -104,7 +104,15 @@ ATOM     2272    C  CD1 .  TRP   B .  127 ?    4.169  91.116  33.936  0.00  0
 ATOM      971    N  NE1 .  TRP   A .  127 ?   31.690  55.125  17.941  0.00  0   A
 ATOM      482    N  NH2 .  ARG   A .   61 ?   30.854  46.734  21.014 -1.09  0   A
 ATOM     2194    C   CD .  GLN   B .  117 ?   19.437  84.530  31.487  0.00  0   B
+ATOM      862    C   CB .  THR   A .  113 ?   25.860  43.490   6.456  0.00  0   A
+ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -4.12  0   A
+ATOM      864    C  CG2 .  THR   A .  113 ?   26.850  43.117   5.347  0.00  0   A
+ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -1.93  0   A
 ATOM      525    C   CZ .  PHE   A .   66 ?   29.230  52.224  20.147  0.00  0   A
+ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078 -1.62  0   A
+ATOM      595    O    O .  ASN   A .   77 ?   26.312  38.006  20.189  0.00  0   A
+ATOM     1184    O    O .  SER   A .  155 ?   31.853  44.086  26.183  0.00  0   A
+ATOM     1197    C  CD1 .  TYR   A .  157 ?   28.532  39.033  29.999  0.00  0   A
 ATOM     1840    C   CG .  MET   B .   67 ?    9.633  84.822  37.381  0.00  0   B
 ATOM     1787    C   CD .  ARG   B .   61 ?   15.961  88.260  38.521  0.00  0   B
 ATOM     1778    C  CD2 .  HIS   B .   60 ?   19.860  85.375  37.081  0.00  0   B
@@ -116,9 +124,7 @@ ATOM     2129    N    N .  ASN   B .  108 ?   14.150  86.948  28.128  0.00  0
 ATOM     2192    C   CB .  GLN   B .  117 ?   17.733  83.041  30.399  0.00  0   B
 ATOM     2127    O    O .  ALA   B .  107 ?   14.577  84.908  27.317  0.00  0   B
 ATOM      878    O   OG .  SER   A .  115 ?   20.631  41.367  10.780 -3.21  0   A
-ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -2.61  0   A
-ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -4.69  0   A
-ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -4.12  0   A
+ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -5.36  0   A
 ATOM      531    C   CG .  MET   A .   67 ?   25.856  51.243  21.414  0.00  0   A
 ATOM      911    C  CD1 .  LEU   A .  119 ?   23.851  52.591  18.054  0.00  0   A
 ATOM      983    C  CD1 .  LEU   A .  128 ?   27.372  54.269  16.512  0.00  0   A
@@ -142,7 +148,7 @@ ATOM     1829    C   CG .  PHE   B .   66 ?    7.541  87.175  39.460  0.00  0
 ATOM     1831    C  CD2 .  PHE   B .   66 ?    8.694  87.919  39.225  0.00  0   B
 ATOM     2181    O   OG .  SER   B .  115 ?   19.809  83.527  26.162 -4.29  0   B
 ATOM     2126    C    C .  ALA   B .  107 ?   14.097  85.624  28.193  0.00  0   B
-ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380 -1.07  0   A
+ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380  0.00  0   A
 ATOM      520    C   CG .  PHE   A .   66 ?   28.847  52.956  22.827  0.00  0   A
 ATOM      974    C  CZ2 .  TRP   A .  127 ?   31.017  56.465  19.955  0.00  0   A
 ATOM      519    C   CB .  PHE   A .   66 ?   28.655  53.352  24.272  0.00  0   A
@@ -156,7 +162,6 @@ ATOM      546    C   CD .  GLN   A .   69 ?   25.009  44.971  19.024  0.00  0
 ATOM      839    N    N .  GLY   A .  110 ?   29.407  45.801   8.294  0.00  0   A
 ATOM      597    C   CG .  ASN   A .   77 ?   25.222  34.668  19.575  0.00  0   A
 ATOM      598    O  OD1 .  ASN   A .   77 ?   25.256  35.283  18.510 -1.07  0   A
-ATOM      595    O    O .  ASN   A .   77 ?   26.312  38.006  20.189  0.00  0   A
 ATOM      607    O    O .  SER   A .   79 ?   25.110  36.261  13.164  0.00  0   A
 ATOM      479    N   NE .  ARG   A .   61 ?   29.569  45.021  21.872 -2.19  0   A
 ATOM      478    C   CD .  ARG   A .   61 ?   28.334  44.256  22.042  0.00  0   A
@@ -164,6 +169,7 @@ ATOM      601    C   CA .  GLY   A .   78 ?   25.067  39.217  18.072  0.00  0
 ATOM     1788    N   NE .  ARG   B .   61 ?   14.906  89.269  38.594  0.00  0   B
 ATOM     1014    C  CE1 .  HIS   A .  132 ?   27.139  49.898  12.602  0.00  0   A
 ATOM      822    C   CA .  ALA   A .  107 ?   23.846  47.439  13.692  0.00  0   A
+ATOM     1192    C   CA .  TYR   A .  157 ?   28.602  42.056  28.964  0.00  0   A
 ATOM      521    C  CD1 .  PHE   A .   66 ?   28.541  53.842  21.796  0.00  0   A
 ATOM      840    C   CA .  GLY   A .  110 ?   29.978  46.428   7.122  0.00  0   A
 ATOM      827    C   CA .  ASN   A .  108 ?   25.685  45.693  10.863  0.00  0   A

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

@@ -4,20 +4,20 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     1:
-HEADER 0  - Pocket Score                      : 5.8454
+HEADER 0  - Pocket Score                      : 6.1285
 HEADER 1  - Drug Score                        : 1.0000
-HEADER 2  - Number of V. Vertices             :   217
-HEADER 3  - Mean alpha-sphere radius          : 4.3019
-HEADER 4  - Mean alpha-sphere SA              : 0.5830
+HEADER 2  - Number of V. Vertices             :   225
+HEADER 3  - Mean alpha-sphere radius          : 4.3213
+HEADER 4  - Mean alpha-sphere SA              : 0.5807
 HEADER 5  - Mean B-factor                     : 0.0000
-HEADER 6  - Hydrophobicity Score              : 16.8148
-HEADER 7  - Polarity Score                    :    16
-HEADER 8  - Volume Score                      : 3.8889
-HEADER 9  - Real volume (approximation)       : 5091.7368
+HEADER 6  - Hydrophobicity Score              : 18.4643
+HEADER 7  - Polarity Score                    :    17
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 5738.3193
 HEADER 10 - Charge Score                      :     6
-HEADER 11 - Local hydrophobic density Score   : 13.4444
-HEADER 12 - Number of apolar alpha sphere     :    54
-HEADER 13 - Proportion of apolar alpha sphere : 0.2488
+HEADER 11 - Local hydrophobic density Score   : 13.3455
+HEADER 12 - Number of apolar alpha sphere     :    55
+HEADER 13 - Proportion of apolar alpha sphere : 0.2444
 ATOM      1    O STP     1      13.304  88.665  32.454    0.00     4.42
 ATOM      2    C STP     1       9.417  86.428  34.234    0.00     3.53
 ATOM      3    O STP     1      12.036  91.586  29.846    0.00     3.99
@@ -85,155 +85,163 @@ ATOM     64    C STP     1      10.093  87.611  33.467    0.00     4.07
 ATOM     65    C STP     1      10.538  87.926  33.379    0.00     4.35
 ATOM     66    O STP     1      33.888  49.647  16.687    0.00     6.03
 ATOM     67    O STP     1      17.468  87.092  29.886    0.00     3.61
-ATOM     68    O STP     1      33.220  49.873  17.122    0.00     5.53
-ATOM     69    C STP     1       9.423  86.425  34.239    0.00     3.53
-ATOM     70    C STP     1       9.363  86.402  34.268    0.00     3.50
-ATOM     71    O STP     1      17.156  90.553  34.548    0.00     4.74
-ATOM     72    O STP     1      18.977  88.996  36.323    0.00     3.80
-ATOM     73    O STP     1      18.801  90.804  35.327    0.00     4.97
-ATOM     74    O STP     1      18.268  89.945  34.975    0.00     4.55
-ATOM     75    O STP     1      18.868  89.208  35.945    0.00     4.00
-ATOM     76    O STP     1      18.065  88.657  35.595    0.00     3.63
-ATOM     77    O STP     1      18.379  89.193  35.362    0.00     4.09
-ATOM     78    O STP     1      18.882  87.605  27.239    0.00     3.92
-ATOM     79    O STP     1      13.300  94.652  30.063    0.00     5.74
-ATOM     80    O STP     1      13.169  88.280  31.543    0.00     3.79
-ATOM     81    C STP     1      12.965  87.866  31.201    0.00     3.42
-ATOM     82    O STP     1      17.206  86.955  29.975    0.00     3.57
-ATOM     83    O STP     1      17.313  86.932  29.848    0.00     3.60
-ATOM     84    O STP     1      17.260  86.826  29.857    0.00     3.56
-ATOM     85    O STP     1      17.647  86.903  29.170    0.00     3.65
-ATOM     86    O STP     1      17.446  86.914  29.625    0.00     3.62
-ATOM     87    O STP     1      17.540  86.349  29.071    0.00     3.57
-ATOM     88    O STP     1      17.825  86.147  28.464    0.00     3.66
-ATOM     89    O STP     1      17.638  86.291  28.817    0.00     3.62
-ATOM     90    O STP     1      17.589  86.200  28.737    0.00     3.57
-ATOM     91    C STP     1      17.310  86.348  29.432    0.00     3.47
-ATOM     92    O STP     1      24.622  40.674  10.795    0.00     4.05
-ATOM     93    C STP     1      27.005  49.985  17.993    0.00     3.82
-ATOM     94    C STP     1      26.839  50.582  18.014    0.00     3.60
-ATOM     95    C STP     1      27.676  50.218  16.945    0.00     4.09
-ATOM     96    C STP     1      26.991  50.900  17.679    0.00     3.59
-ATOM     97    O STP     1      30.592  49.040  16.768    0.00     4.84
-ATOM     98    O STP     1      31.112  44.097  16.205    0.00     5.49
-ATOM     99    O STP     1      26.685  48.719  17.768    0.00     3.95
-ATOM    100    C STP     1      27.314  49.434  17.751    0.00     4.15
-ATOM    101    O STP     1      30.711  48.752  16.393    0.00     5.04
-ATOM    102    O STP     1      31.020  47.339  15.614    0.00     5.44
-ATOM    103    O STP     1      29.111  49.193  16.737    0.00     4.56
-ATOM    104    O STP     1      27.150  48.349  16.835    0.00     4.29
-ATOM    105    O STP     1      28.085  46.923  16.028    0.00     4.46
-ATOM    106    O STP     1      29.429  38.000  16.814    0.00     3.95
-ATOM    107    O STP     1      25.337  41.857  10.796    0.00     3.65
-ATOM    108    C STP     1      10.851  87.154  34.207    0.00     4.06
-ATOM    109    C STP     1      10.692  87.013  34.265    0.00     3.95
-ATOM    110    O STP     1      11.818  86.568  34.068    0.00     3.81
-ATOM    111    C STP     1      12.318  85.510  34.106    0.00     3.44
-ATOM    112    O STP     1       5.545  90.375  43.119    0.00     4.74
-ATOM    113    C STP     1       4.561  89.333  40.639    0.00     3.85
-ATOM    114    C STP     1       4.611  89.401  40.637    0.00     3.86
-ATOM    115    C STP     1       6.032  91.564  41.830    0.00     5.21
-ATOM    116    C STP     1       6.186  90.504  39.052    0.00     3.61
-ATOM    117    C STP     1       6.160  90.509  39.113    0.00     3.63
-ATOM    118    O STP     1      17.990  86.008  28.210    0.00     3.70
-ATOM    119    O STP     1      18.006  86.098  28.176    0.00     3.73
-ATOM    120    O STP     1      19.521  87.572  27.205    0.00     4.19
-ATOM    121    O STP     1      19.240  87.483  27.521    0.00     4.22
-ATOM    122    O STP     1      18.718  87.116  27.484    0.00     3.98
-ATOM    123    O STP     1      18.711  87.054  27.742    0.00     4.02
-ATOM    124    O STP     1      19.118  87.451  27.484    0.00     4.20
-ATOM    125    O STP     1      19.138  87.454  27.544    0.00     4.22
-ATOM    126    O STP     1      17.547  86.179  28.768    0.00     3.54
-ATOM    127    O STP     1      24.404  40.531  10.860    0.00     3.87
-ATOM    128    O STP     1      24.678  40.696  10.870    0.00     4.10
-ATOM    129    O STP     1      25.061  40.721  10.992    0.00     4.29
-ATOM    130    C STP     1      34.434  54.099  24.046    0.00     5.83
-ATOM    131    C STP     1      34.785  54.066  24.214    0.00     6.17
-ATOM    132    O STP     1      30.243  49.144  18.082    0.00     3.84
-ATOM    133    O STP     1      33.629  50.117  17.900    0.00     5.37
-ATOM    134    C STP     1      32.643  53.327  21.021    0.00     3.69
-ATOM    135    O STP     1      33.259  50.367  13.555    0.00     5.25
-ATOM    136    O STP     1      32.796  52.509  13.407    0.00     3.99
-ATOM    137    O STP     1      31.179  49.730  10.161    0.00     4.05
-ATOM    138    C STP     1      25.397  48.219  17.846    0.00     3.48
-ATOM    139    C STP     1      25.657  48.105  17.477    0.00     3.55
-ATOM    140    O STP     1      32.744  47.500  12.564    0.00     5.68
-ATOM    141    O STP     1      32.680  48.711  11.135    0.00     5.22
-ATOM    142    O STP     1      30.293  34.983  19.208    0.00     5.09
-ATOM    143    C STP     1      30.515  37.558  12.012    0.00     5.68
-ATOM    144    O STP     1      28.816  38.796  12.429    0.00     4.55
-ATOM    145    O STP     1      25.694  40.137  11.519    0.00     4.25
-ATOM    146    O STP     1      25.745  40.188  11.663    0.00     4.25
-ATOM    147    O STP     1      30.778  40.864  18.244    0.00     5.65
-ATOM    148    O STP     1      29.300  41.260  18.522    0.00     4.72
-ATOM    149    O STP     1      29.435  42.951  17.876    0.00     4.50
-ATOM    150    O STP     1      17.364  91.328  34.163    0.00     5.47
-ATOM    151    O STP     1      17.378  91.256  34.191    0.00     5.43
-ATOM    152    O STP     1      17.444  91.177  34.269    0.00     5.37
-ATOM    153    O STP     1      17.348  91.074  34.310    0.00     5.25
-ATOM    154    O STP     1      30.062  47.686  12.765    0.00     3.67
-ATOM    155    C STP     1      26.323  48.692  15.710    0.00     3.43
-ATOM    156    O STP     1      30.408  47.380  15.676    0.00     5.15
-ATOM    157    O STP     1      28.125  47.095  15.991    0.00     4.51
-ATOM    158    C STP     1      27.417  50.537  16.276    0.00     3.74
-ATOM    159    C STP     1      27.373  50.707  16.089    0.00     3.59
-ATOM    160    C STP     1      27.302  48.395  16.701    0.00     4.37
-ATOM    161    C STP     1      27.841  49.832  16.849    0.00     4.30
-ATOM    162    C STP     1      28.558  49.429  16.774    0.00     4.43
-ATOM    163    C STP     1      27.865  49.337  16.994    0.00     4.49
-ATOM    164    O STP     1      28.735  49.235  16.785    0.00     4.53
-ATOM    165    C STP     1      31.288  55.409  23.269    0.00     3.49
-ATOM    166    O STP     1      32.312  48.943  10.498    0.00     4.81
-ATOM    167    O STP     1      34.237  48.223  11.050    0.00     6.07
-ATOM    168    O STP     1      24.685  41.731  11.638    0.00     4.16
-ATOM    169    O STP     1      23.857  42.701  11.472    0.00     3.56
-ATOM    170    O STP     1      28.622  41.347  18.970    0.00     4.24
-ATOM    171    O STP     1      28.182  41.101  20.281    0.00     3.62
-ATOM    172    C STP     1      24.517  43.394  13.603    0.00     3.46
-ATOM    173    C STP     1      24.414  43.155  13.231    0.00     3.58
-ATOM    174    O STP     1      27.454  47.131  15.066    0.00     3.72
-ATOM    175    O STP     1      25.046  43.340  13.819    0.00     3.59
-ATOM    176    C STP     1      24.700  43.363  13.625    0.00     3.53
-ATOM    177    O STP     1      28.073  46.895  16.026    0.00     4.44
-ATOM    178    O STP     1      28.133  46.815  16.042    0.00     4.43
-ATOM    179    O STP     1      30.376  42.824  16.523    0.00     5.68
-ATOM    180    O STP     1      30.365  42.854  16.522    0.00     5.67
-ATOM    181    O STP     1      30.061  42.491  17.173    0.00     5.36
-ATOM    182    O STP     1      29.539  42.849  17.699    0.00     4.70
-ATOM    183    O STP     1      29.681  42.794  17.547    0.00     4.87
-ATOM    184    O STP     1      28.734  41.753  18.363    0.00     4.47
-ATOM    185    O STP     1      27.985  42.238  18.956    0.00     3.70
-ATOM    186    O STP     1      28.539  41.757  18.517    0.00     4.33
-ATOM    187    O STP     1      29.507  42.806  17.744    0.00     4.69
-ATOM    188    O STP     1      29.791  42.296  17.519    0.00     5.14
-ATOM    189    O STP     1      25.552  40.651  11.800    0.00     4.24
-ATOM    190    O STP     1      25.702  41.429  12.209    0.00     4.09
-ATOM    191    O STP     1      25.788  41.400  12.282    0.00     4.07
-ATOM    192    O STP     1      25.003  41.310  11.497    0.00     4.32
-ATOM    193    O STP     1      25.002  41.301  11.494    0.00     4.32
-ATOM    194    O STP     1      24.966  42.497  12.680    0.00     3.75
-ATOM    195    O STP     1      24.684  41.731  11.659    0.00     4.16
-ATOM    196    O STP     1      24.715  41.678  11.631    0.00     4.18
-ATOM    197    O STP     1      24.813  41.386  11.520    0.00     4.25
-ATOM    198    O STP     1      24.837  43.023  13.213    0.00     3.66
-ATOM    199    O STP     1      24.938  43.175  13.547    0.00     3.62
-ATOM    200    O STP     1      24.059  42.452  12.156    0.00     3.85
-ATOM    201    O STP     1      24.523  43.068  13.102    0.00     3.64
-ATOM    202    O STP     1      23.664  42.606  12.414    0.00     3.66
-ATOM    203    O STP     1      24.396  43.128  13.200    0.00     3.58
-ATOM    204    O STP     1      24.435  43.138  13.214    0.00     3.59
-ATOM    205    O STP     1      24.518  43.086  13.129    0.00     3.63
-ATOM    206    O STP     1      24.575  43.157  13.291    0.00     3.61
-ATOM    207    C STP     1      31.063  55.664  23.330    0.00     3.47
-ATOM    208    O STP     1      33.721  54.466  25.554    0.00     5.34
-ATOM    209    O STP     1      25.197  43.355  14.014    0.00     3.58
-ATOM    210    O STP     1      25.635  43.546  14.505    0.00     3.53
-ATOM    211    O STP     1      25.403  43.098  14.044    0.00     3.59
-ATOM    212    O STP     1      26.324  42.901  14.728    0.00     3.68
-ATOM    213    O STP     1      26.006  42.758  14.370    0.00     3.65
-ATOM    214    O STP     1      28.626  39.926  18.156    0.00     3.63
-ATOM    215    O STP     1      30.514  38.191  17.400    0.00     5.05
-ATOM    216    O STP     1      29.885  37.934  17.493    0.00     4.48
-ATOM    217    O STP     1      29.459  38.005  16.840    0.00     3.98
+ATOM     68    O STP     1      26.368  39.013   7.356    0.00     4.59
+ATOM     69    O STP     1      33.220  49.873  17.122    0.00     5.53
+ATOM     70    O STP     1      30.363  38.669  24.413    0.00     5.89
+ATOM     71    C STP     1       9.423  86.425  34.239    0.00     3.53
+ATOM     72    C STP     1       9.363  86.402  34.268    0.00     3.50
+ATOM     73    O STP     1      17.156  90.553  34.548    0.00     4.74
+ATOM     74    O STP     1      18.977  88.996  36.323    0.00     3.80
+ATOM     75    O STP     1      18.801  90.804  35.327    0.00     4.97
+ATOM     76    O STP     1      18.268  89.945  34.975    0.00     4.55
+ATOM     77    O STP     1      18.868  89.208  35.945    0.00     4.00
+ATOM     78    O STP     1      18.065  88.657  35.595    0.00     3.63
+ATOM     79    O STP     1      18.379  89.193  35.362    0.00     4.09
+ATOM     80    O STP     1      18.882  87.605  27.239    0.00     3.92
+ATOM     81    O STP     1      13.300  94.652  30.063    0.00     5.74
+ATOM     82    O STP     1      13.169  88.280  31.543    0.00     3.79
+ATOM     83    C STP     1      12.965  87.866  31.201    0.00     3.42
+ATOM     84    O STP     1      17.206  86.955  29.975    0.00     3.57
+ATOM     85    O STP     1      17.313  86.932  29.848    0.00     3.60
+ATOM     86    O STP     1      17.260  86.826  29.857    0.00     3.56
+ATOM     87    O STP     1      17.647  86.903  29.170    0.00     3.65
+ATOM     88    O STP     1      17.446  86.914  29.625    0.00     3.62
+ATOM     89    O STP     1      17.540  86.349  29.071    0.00     3.57
+ATOM     90    O STP     1      17.825  86.147  28.464    0.00     3.66
+ATOM     91    O STP     1      17.638  86.291  28.817    0.00     3.62
+ATOM     92    O STP     1      17.589  86.200  28.737    0.00     3.57
+ATOM     93    C STP     1      17.310  86.348  29.432    0.00     3.47
+ATOM     94    O STP     1      24.622  40.674  10.795    0.00     4.05
+ATOM     95    C STP     1      27.005  49.985  17.993    0.00     3.82
+ATOM     96    C STP     1      26.839  50.582  18.014    0.00     3.60
+ATOM     97    C STP     1      27.676  50.218  16.945    0.00     4.09
+ATOM     98    C STP     1      26.991  50.900  17.679    0.00     3.59
+ATOM     99    O STP     1      30.592  49.040  16.768    0.00     4.84
+ATOM    100    O STP     1      31.112  44.097  16.205    0.00     5.49
+ATOM    101    O STP     1      26.685  48.719  17.768    0.00     3.95
+ATOM    102    C STP     1      27.314  49.434  17.751    0.00     4.15
+ATOM    103    O STP     1      30.711  48.752  16.393    0.00     5.04
+ATOM    104    O STP     1      31.020  47.339  15.614    0.00     5.44
+ATOM    105    O STP     1      29.111  49.193  16.737    0.00     4.56
+ATOM    106    O STP     1      27.150  48.349  16.835    0.00     4.29
+ATOM    107    O STP     1      28.085  46.923  16.028    0.00     4.46
+ATOM    108    O STP     1      29.429  38.000  16.814    0.00     3.95
+ATOM    109    O STP     1      25.337  41.857  10.796    0.00     3.65
+ATOM    110    C STP     1      26.549  39.030   7.512    0.00     4.64
+ATOM    111    O STP     1      25.458  40.233   9.519    0.00     3.99
+ATOM    112    O STP     1      26.179  39.423   7.970    0.00     4.35
+ATOM    113    O STP     1      25.736  40.004   8.551    0.00     4.07
+ATOM    114    C STP     1      10.851  87.154  34.207    0.00     4.06
+ATOM    115    C STP     1      10.692  87.013  34.265    0.00     3.95
+ATOM    116    O STP     1      11.818  86.568  34.068    0.00     3.81
+ATOM    117    C STP     1      12.318  85.510  34.106    0.00     3.44
+ATOM    118    O STP     1       5.545  90.375  43.119    0.00     4.74
+ATOM    119    C STP     1       4.561  89.333  40.639    0.00     3.85
+ATOM    120    C STP     1       4.611  89.401  40.637    0.00     3.86
+ATOM    121    C STP     1       6.032  91.564  41.830    0.00     5.21
+ATOM    122    C STP     1       6.186  90.504  39.052    0.00     3.61
+ATOM    123    C STP     1       6.160  90.509  39.113    0.00     3.63
+ATOM    124    O STP     1      17.990  86.008  28.210    0.00     3.70
+ATOM    125    O STP     1      18.006  86.098  28.176    0.00     3.73
+ATOM    126    O STP     1      19.521  87.572  27.205    0.00     4.19
+ATOM    127    O STP     1      19.240  87.483  27.521    0.00     4.22
+ATOM    128    O STP     1      18.718  87.116  27.484    0.00     3.98
+ATOM    129    O STP     1      18.711  87.054  27.742    0.00     4.02
+ATOM    130    O STP     1      19.118  87.451  27.484    0.00     4.20
+ATOM    131    O STP     1      19.138  87.454  27.544    0.00     4.22
+ATOM    132    O STP     1      17.547  86.179  28.768    0.00     3.54
+ATOM    133    O STP     1      24.404  40.531  10.860    0.00     3.87
+ATOM    134    O STP     1      24.678  40.696  10.870    0.00     4.10
+ATOM    135    O STP     1      25.061  40.721  10.992    0.00     4.29
+ATOM    136    C STP     1      34.434  54.099  24.046    0.00     5.83
+ATOM    137    C STP     1      34.785  54.066  24.214    0.00     6.17
+ATOM    138    O STP     1      30.243  49.144  18.082    0.00     3.84
+ATOM    139    O STP     1      33.629  50.117  17.900    0.00     5.37
+ATOM    140    C STP     1      32.643  53.327  21.021    0.00     3.69
+ATOM    141    O STP     1      33.259  50.367  13.555    0.00     5.25
+ATOM    142    O STP     1      32.796  52.509  13.407    0.00     3.99
+ATOM    143    O STP     1      31.179  49.730  10.161    0.00     4.05
+ATOM    144    C STP     1      25.397  48.219  17.846    0.00     3.48
+ATOM    145    C STP     1      25.657  48.105  17.477    0.00     3.55
+ATOM    146    O STP     1      32.744  47.500  12.564    0.00     5.68
+ATOM    147    O STP     1      32.680  48.711  11.135    0.00     5.22
+ATOM    148    O STP     1      30.293  34.983  19.208    0.00     5.09
+ATOM    149    C STP     1      30.515  37.558  12.012    0.00     5.68
+ATOM    150    O STP     1      28.816  38.796  12.429    0.00     4.55
+ATOM    151    O STP     1      25.694  40.137  11.519    0.00     4.25
+ATOM    152    O STP     1      25.745  40.188  11.663    0.00     4.25
+ATOM    153    O STP     1      30.778  40.864  18.244    0.00     5.65
+ATOM    154    O STP     1      29.300  41.260  18.522    0.00     4.72
+ATOM    155    O STP     1      30.155  39.400  23.865    0.00     5.50
+ATOM    156    O STP     1      29.435  42.951  17.876    0.00     4.50
+ATOM    157    O STP     1      17.364  91.328  34.163    0.00     5.47
+ATOM    158    O STP     1      17.378  91.256  34.191    0.00     5.43
+ATOM    159    O STP     1      17.444  91.177  34.269    0.00     5.37
+ATOM    160    O STP     1      17.348  91.074  34.310    0.00     5.25
+ATOM    161    O STP     1      30.062  47.686  12.765    0.00     3.67
+ATOM    162    C STP     1      26.323  48.692  15.710    0.00     3.43
+ATOM    163    O STP     1      30.408  47.380  15.676    0.00     5.15
+ATOM    164    O STP     1      28.125  47.095  15.991    0.00     4.51
+ATOM    165    C STP     1      27.417  50.537  16.276    0.00     3.74
+ATOM    166    C STP     1      27.373  50.707  16.089    0.00     3.59
+ATOM    167    C STP     1      27.302  48.395  16.701    0.00     4.37
+ATOM    168    C STP     1      27.841  49.832  16.849    0.00     4.30
+ATOM    169    C STP     1      28.558  49.429  16.774    0.00     4.43
+ATOM    170    C STP     1      27.865  49.337  16.994    0.00     4.49
+ATOM    171    O STP     1      28.735  49.235  16.785    0.00     4.53
+ATOM    172    O STP     1      30.286  38.810  24.532    0.00     5.75
+ATOM    173    C STP     1      31.288  55.409  23.269    0.00     3.49
+ATOM    174    O STP     1      32.312  48.943  10.498    0.00     4.81
+ATOM    175    O STP     1      34.237  48.223  11.050    0.00     6.07
+ATOM    176    O STP     1      24.685  41.731  11.638    0.00     4.16
+ATOM    177    O STP     1      23.857  42.701  11.472    0.00     3.56
+ATOM    178    O STP     1      28.622  41.347  18.970    0.00     4.24
+ATOM    179    O STP     1      28.182  41.101  20.281    0.00     3.62
+ATOM    180    C STP     1      24.517  43.394  13.603    0.00     3.46
+ATOM    181    C STP     1      24.414  43.155  13.231    0.00     3.58
+ATOM    182    O STP     1      27.454  47.131  15.066    0.00     3.72
+ATOM    183    O STP     1      25.046  43.340  13.819    0.00     3.59
+ATOM    184    C STP     1      24.700  43.363  13.625    0.00     3.53
+ATOM    185    O STP     1      28.073  46.895  16.026    0.00     4.44
+ATOM    186    O STP     1      28.133  46.815  16.042    0.00     4.43
+ATOM    187    O STP     1      30.376  42.824  16.523    0.00     5.68
+ATOM    188    O STP     1      30.365  42.854  16.522    0.00     5.67
+ATOM    189    O STP     1      30.061  42.491  17.173    0.00     5.36
+ATOM    190    O STP     1      29.539  42.849  17.699    0.00     4.70
+ATOM    191    O STP     1      29.681  42.794  17.547    0.00     4.87
+ATOM    192    O STP     1      28.734  41.753  18.363    0.00     4.47
+ATOM    193    O STP     1      27.985  42.238  18.956    0.00     3.70
+ATOM    194    O STP     1      28.539  41.757  18.517    0.00     4.33
+ATOM    195    O STP     1      29.507  42.806  17.744    0.00     4.69
+ATOM    196    O STP     1      29.791  42.296  17.519    0.00     5.14
+ATOM    197    O STP     1      25.552  40.651  11.800    0.00     4.24
+ATOM    198    O STP     1      25.702  41.429  12.209    0.00     4.09
+ATOM    199    O STP     1      25.788  41.400  12.282    0.00     4.07
+ATOM    200    O STP     1      25.003  41.310  11.497    0.00     4.32
+ATOM    201    O STP     1      25.002  41.301  11.494    0.00     4.32
+ATOM    202    O STP     1      24.966  42.497  12.680    0.00     3.75
+ATOM    203    O STP     1      24.684  41.731  11.659    0.00     4.16
+ATOM    204    O STP     1      24.715  41.678  11.631    0.00     4.18
+ATOM    205    O STP     1      24.813  41.386  11.520    0.00     4.25
+ATOM    206    O STP     1      24.837  43.023  13.213    0.00     3.66
+ATOM    207    O STP     1      24.938  43.175  13.547    0.00     3.62
+ATOM    208    O STP     1      24.059  42.452  12.156    0.00     3.85
+ATOM    209    O STP     1      24.523  43.068  13.102    0.00     3.64
+ATOM    210    O STP     1      23.664  42.606  12.414    0.00     3.66
+ATOM    211    O STP     1      24.396  43.128  13.200    0.00     3.58
+ATOM    212    O STP     1      24.435  43.138  13.214    0.00     3.59
+ATOM    213    O STP     1      24.518  43.086  13.129    0.00     3.63
+ATOM    214    O STP     1      24.575  43.157  13.291    0.00     3.61
+ATOM    215    C STP     1      31.063  55.664  23.330    0.00     3.47
+ATOM    216    O STP     1      33.721  54.466  25.554    0.00     5.34
+ATOM    217    O STP     1      25.197  43.355  14.014    0.00     3.58
+ATOM    218    O STP     1      25.635  43.546  14.505    0.00     3.53
+ATOM    219    O STP     1      25.403  43.098  14.044    0.00     3.59
+ATOM    220    O STP     1      26.324  42.901  14.728    0.00     3.68
+ATOM    221    O STP     1      26.006  42.758  14.370    0.00     3.65
+ATOM    222    O STP     1      28.626  39.926  18.156    0.00     3.63
+ATOM    223    O STP     1      30.514  38.191  17.400    0.00     5.05
+ATOM    224    O STP     1      29.885  37.934  17.493    0.00     4.48
+ATOM    225    O STP     1      29.459  38.005  16.840    0.00     3.98
 TER
 END

tests/reference_output/1UYD_out/1UYD_info.txt

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

tests/reference_output/1UYD_out/1UYD_out.pdb

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

tests/reference_output/1UYD_out/1UYD_pockets.pqr

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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