fixing mmcif writing for db mode

Fixmmcifwriting

.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'
@@ -184,8 +186,8 @@ typedef struct s_fparams
 	char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
 	char custom_pocket_arg[M_MAX_CUSTOM_POCKET_LEN];
 	char **pdb_lst;
-	char xlig_chain_code[3];
-	char xlig_resname[3];
+	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

@@ -142,10 +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/writepocket.h

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

makefile

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

src/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;
 }
 
@@ -122,7 +124,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     char *apt;
     char *residue_string[M_MAX_CUSTOM_POCKET_LEN];
     short custom_ligand_i = 0;
-
+    const char *separators = ",:";
     static struct option fplong_options[] = {/*long options args located in fparams.h*/
                                              {"file", required_argument, 0, M_PAR_PDB_FILE},
                                              {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
@@ -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)
                     {
@@ -971,10 +975,10 @@ 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);

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])
@@ -317,7 +313,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -342,7 +338,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ligfound = 1;
                         }
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -354,9 +350,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
-                            // 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);
+
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_id = at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
-                        // printf("ins:%s",at_in[i].insertion);
 
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
@@ -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])
@@ -473,7 +465,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        strncpy(atom->chain, at_in[i].chain, 2);
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_id = at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
                         atom->x = ts_in.coords[(3 * i)];
@@ -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)
@@ -510,7 +502,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -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;
@@ -548,7 +540,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -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++)
@@ -586,7 +578,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                     strcpy(atom->name, at_in[i].type);
                                     atom->pdb_aloc = at_in[i].altloc[0];
                                     strcpy(atom->res_name, at_in[i].resname);
-                                    strncpy(atom->chain, at_in[i].chain, 2);
+                                    strcpy(atom->chain, at_in[i].chain_auth);
                                     atom->res_id = at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
@@ -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++;
                 }
             }

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),
@@ -1469,11 +1436,6 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     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))
     {
@@ -1580,50 +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/write_visu.c

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

src/writepocket.c

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

tests/environment.yml

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

tests/reference_output/123abc_out/pocket10_atm.cif

@@ -0,0 +1,76 @@
+data_pocket10_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    10:
+0  - Pocket Score                      : 0.0405
+1  - Drug Score                        : 0.0230
+2  - Number of alpha spheres           :    57
+3  - Mean alpha-sphere radius          : 3.8604
+4  - Mean alpha-sphere Solvent Acc.    : 0.4592
+5  - Mean B-factor of pocket residues  : 0.2769
+6  - Hydrophobicity Score              : 40.0769
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 433.6981
+10  -Pocket volume (convex hull)       : 76.0139
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 32.4571
+13 - Number of apolar alpha sphere     :    35
+14 - Proportion of apolar alpha sphere : 0.6140
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3335    C  CG2 .  THR   B .  167 ?   23.611  41.302  32.855  0.00  0   B
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     3399    C  CD1 .  ILE   B .  176 ?   22.413  39.457  35.570  0.00  0   B
+ATOM     3397    C  CG1 .  ILE   B .  176 ?   21.483  40.079  36.568  0.00  0   B
+ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
+ATOM     3378    C   CB .  PHE   B .  174 ?   18.390  43.943  35.478  0.00  0   B
+ATOM     3332    O    O .  THR   B .  167 ?   21.633  44.211  32.694 -1.07  0   B
+ATOM     3735    C   CA .  SER   B .  219 ?   24.536  33.701  35.059  0.00  0   B
+ATOM     3729    O    O .  LEU   B .  218 ?   23.720  35.415  36.830  0.00  0   B
+ATOM     1239    C   CB .  ALA   A .  168 ?   21.952  31.542  32.252  0.00  0   A
+ATOM     3454    O    O .  SER   B .  183 ?   12.618  40.049  35.823 -1.07  0   B
+ATOM     3488    O  OD1 .  ASN   B .  187 ?   12.383  40.631  32.241 -1.07  0   B
+ATOM     3380    C  CD1 .  PHE   B .  174 ?   16.492  43.534  33.887  0.00  0   B
+ATOM     3460    O    O .  LEU   B .  184 ?   14.089  37.175  34.255 -3.21  0   B
+ATOM     3458    C   CA .  LEU   B .  184 ?   14.473  38.083  36.400  0.00  0   B
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
+ATOM     3760    C   CB .  TYR   B .  222 ?   18.259  32.959  38.062  0.00  0   B
+ATOM     3756    N    N .  TYR   B .  222 ?   20.251  33.164  39.466 -1.09  0   B
+ATOM     3398    C  CG2 .  ILE   B .  176 ?   21.928  38.594  38.565  0.00  0   B
+ATOM     3463    C  CD1 .  LEU   B .  184 ?   17.369  37.208  38.932  0.00  0   B
+ATOM     3737    O    O .  SER   B .  219 ?   23.395  31.686  35.276 -1.07  0   B
+ATOM     3728    C    C .  LEU   B .  218 ?   24.912  35.395  36.613  0.00  0   B
+ATOM     3730    C   CB .  LEU   B .  218 ?   25.994  37.693  36.437  0.00  0   B
+ATOM     3738    C   CB .  SER   B .  219 ?   25.152  33.376  33.704  0.00  0   B
+ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
+ATOM     3464    C  CD2 .  LEU   B .  184 ?   17.512  38.953  37.066  0.00  0   B
+ATOM     3734    N    N .  SER   B .  219 ?   25.438  34.466  35.848 -1.09  0   B
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     3461    C   CB .  LEU   B .  184 ?   15.552  37.271  37.155  0.00  0   B
+ATOM     1250    N    N .  ALA   A .  170 ?   17.224  33.325  33.516 -4.79  0   A
+ATOM     1255    N    N .  GLY   A .  171 ?   17.151  30.558  34.884 -1.09  0   A
+ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket10_env_atm.cif

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

tests/reference_output/123abc_out/pocket10_vert.pqr

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

tests/reference_output/123abc_out/pocket11_atm.cif

@@ -0,0 +1,63 @@
+data_pocket11_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    11:
+0  - Pocket Score                      : 0.0388
+1  - Drug Score                        : 0.0007
+2  - Number of alpha spheres           :    30
+3  - Mean alpha-sphere radius          : 3.6177
+4  - Mean alpha-sphere Solvent Acc.    : 0.4151
+5  - Mean B-factor of pocket residues  : 0.1046
+6  - Hydrophobicity Score              : 17.4167
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.8333
+9  - Pocket volume (Monte Carlo)       : 155.2499
+10  -Pocket volume (convex hull)       : 11.3291
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.2000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1405    C  CD2 .  PHE   A .  189 ?   10.703  31.452  22.157  0.00  0   A
+ATOM     1435    O    O .  SER   A .  193 ?   11.879  32.960  15.552 -3.21  0   A
+ATOM     1407    C  CE2 .  PHE   A .  189 ?   11.966  31.656  22.739  0.00  0   A
+ATOM      996    O    O .  ARG   A .  135 ?   13.454  28.096  20.320 -4.69  0   A
+ATOM     1436    C   CB .  SER   A .  193 ?    9.997  34.149  17.982  0.00  0   A
+ATOM     1329    N    N .  ALA   A .  180 ?   14.229  35.929  18.757 -1.09  0   A
+ATOM     1327    O  OG1 .  THR   A .  179 ?   17.108  33.330  21.134 -2.14  0   A
+ATOM     1290    C   CD .  PRO   A .  175 ?   18.295  29.738  22.438  0.00  0   A
+ATOM     1323    C   CA .  THR   A .  179 ?   16.193  34.623  19.411  0.00  0   A
+ATOM     1437    O   OG .  SER   A .  193 ?    9.317  33.077  18.605  0.00  0   A
+ATOM     1289    C   CG .  PRO   A .  175 ?   18.737  29.443  21.033  0.00  0   A
+ATOM     1312    C   CB .  TRP   A .  178 ?   18.807  31.481  17.128  0.00  0   A
+ATOM     1005    C   CA .  ASP   A .  136 ?   14.988  26.627  18.681  0.00  0   A
+ATOM     1311    O    O .  TRP   A .  178 ?   16.495  33.261  16.896 -2.14  0   A
+ATOM     1471    C   CB .  ALA   A .  197 ?   14.926  31.065  14.885  0.00  0   A
+ATOM     1355    O   OG .  SER   A .  183 ?   10.954  35.267  20.964  0.00  0   A
+ATOM     1012    N    N .  LEU   A .  137 ?   14.970  26.942  16.300  0.00  0   A
+ATOM     1444    O  OD1 .  ASP   A .  194 ?   10.115  28.834  16.531  0.00  0   A
+ATOM      995    C    C .  ARG   A .  135 ?   12.856  27.406  19.519  0.00  0   A
+ATOM      994    C   CA .  ARG   A .  135 ?   11.309  27.407  19.509  0.00  0   A
+ATOM     1328    C  CG2 .  THR   A .  179 ?   15.235  34.657  21.794  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket11_env_atm.cif

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

tests/reference_output/123abc_out/pocket11_vert.pqr

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

tests/reference_output/123abc_out/pocket12_atm.cif

@@ -0,0 +1,61 @@
+data_pocket12_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    12:
+0  - Pocket Score                      : 0.0380
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    22
+3  - Mean alpha-sphere radius          : 4.0091
+4  - Mean alpha-sphere Solvent Acc.    : 0.5656
+5  - Mean B-factor of pocket residues  : 0.1891
+6  - Hydrophobicity Score              : 14.1667
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.4167
+9  - Pocket volume (Monte Carlo)       : 292.3979
+10  -Pocket volume (convex hull)       : 19.5893
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.0909
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     3271    O   OG .  SER   B .  158 ?   19.353  51.914  34.201 -4.02  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     3383    C  CE2 .  PHE   B .  174 ?   15.221  45.900  34.664  0.00  0   B
+ATOM     3094    O    O .  ARG   B .  135 ?   14.784  48.309  40.445 -7.50  0   B
+ATOM     3097    C   CD .  ARG   B .  135 ?   10.822  49.558  37.921  0.00  0   B
+ATOM     3504    C  CE2 .  PHE   B .  189 ?   12.691  45.021  38.263  0.00  0   B
+ATOM     3368    O    O .  LYS   B .  173 ?   18.932  47.542  34.352 -3.62  0   B
+ATOM     3109    O  OD2 .  ASP   B .  136 ?   19.063  51.084  39.753 -0.40  0   B
+ATOM     3258    N    N .  LEU   B .  157 ?   20.869  54.873  37.697  0.00  0   B
+ATOM     3095    C   CB .  ARG   B .  135 ?   12.276  49.729  39.764  0.00  0   B
+ATOM     3084    O    O .  HIS   B .  134 ?   12.372  52.048  41.332 -1.07  0   B
+ATOM     3381    C  CD2 .  PHE   B .  174 ?   16.430  45.506  35.243  0.00  0   B
+ATOM     3270    C   CB .  SER   B .  158 ?   20.116  50.947  34.907  0.00  0   B
+ATOM     3326    C  CE2 .  TYR   B .  166 ?   21.152  49.314  38.053  0.00  0   B
+ATOM     3391    C   CD .  PRO   B .  175 ?   19.172  45.854  38.445  0.00  0   B
+ATOM     3106    C   CB .  ASP   B .  136 ?   17.005  50.806  40.933  0.00  0   B
+ATOM     3107    C   CG .  ASP   B .  136 ?   18.465  50.434  40.626  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket12_env_atm.cif

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

tests/reference_output/123abc_out/pocket12_vert.pqr

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

tests/reference_output/123abc_out/pocket13_atm.cif

@@ -0,0 +1,74 @@
+data_pocket13_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    13:
+0  - Pocket Score                      : 0.0342
+1  - Drug Score                        : 0.3180
+2  - Number of alpha spheres           :    51
+3  - Mean alpha-sphere radius          : 3.7908
+4  - Mean alpha-sphere Solvent Acc.    : 0.4415
+5  - Mean B-factor of pocket residues  : 0.1092
+6  - Hydrophobicity Score              : 59.0769
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 403.2792
+10  -Pocket volume (convex hull)       : 39.2787
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 37.1163
+13 - Number of apolar alpha sphere     :    43
+14 - Proportion of apolar alpha sphere : 0.8431
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     7064    N    N .  VAL   D .  111 ?   48.340  24.744  22.841  0.00  0   D
+ATOM     7069    C  CG1 .  VAL   D .  111 ?   50.065  24.177  20.697  0.00  0   D
+ATOM     7068    C   CB .  VAL   D .  111 ?   49.531  23.019  21.320  0.00  0   D
+ATOM     7063    C   CB .  ALA   D .  110 ?   45.905  26.806  22.761  0.00  0   D
+ATOM     8096    C  CG1 .  VAL   D .  241 ?   40.339  21.749  29.386  0.00  0   D
+ATOM     7780    O    O .  LEU   D .  202 ?   42.550  24.062  33.744  0.00  0   D
+ATOM     7784    C  CD2 .  LEU   D .  202 ?   42.820  19.922  32.429  0.00  0   D
+ATOM     7814    C  CG2 .  ILE   D .  205 ?   46.612  24.182  31.921  0.00  0   D
+ATOM     7081    O    O .  LEU   D .  113 ?   47.597  21.725  29.219 -1.07  0   D
+ATOM     7086    N    N .  LEU   D .  114 ?   47.359  21.989  26.988  0.00  0   D
+ATOM     7087    C   CA .  LEU   D .  114 ?   46.823  20.670  26.737  0.00  0   D
+ATOM     7080    C    C .  LEU   D .  113 ?   47.767  22.386  28.183  0.00  0   D
+ATOM     7062    O    O .  ALA   D .  110 ?   47.080  24.204  24.629 -3.21  0   D
+ATOM     7093    C  CD2 .  LEU   D .  114 ?   45.275  20.097  23.190  0.00  0   D
+ATOM     8079    C   CG .  PRO   D .  238 ?   40.497  24.257  24.472  0.00  0   D
+ATOM     7061    C    C .  ALA   D .  110 ?   47.472  25.051  23.811  0.00  0   D
+ATOM     8080    C   CD .  PRO   D .  238 ?   40.408  25.135  25.676  0.00  0   D
+ATOM     8067    O    O .  GLY   D .  236 ?   40.728  28.470  25.473 -1.21  0   D
+ATOM     7060    C   CA .  ALA   D .  110 ?   46.959  26.484  23.905  0.00  0   D
+ATOM     7084    C  CD1 .  LEU   D .  113 ?   46.418  27.158  28.740  0.00  0   D
+ATOM     7817    C   CA .  ALA   D .  206 ?   43.249  27.236  31.702  0.00  0   D
+ATOM     7819    O    O .  ALA   D .  206 ?   43.166  29.530  31.087 -4.69  0   D
+ATOM     8069    C   CA .  CYS   D .  237 ?   39.173  27.291  27.413  0.00  0   D
+ATOM     7118    C   CB .  ALA   D .  117 ?   45.712  18.926  30.827  0.00  0   D
+ATOM     7820    C   CB .  ALA   D .  206 ?   41.725  26.810  31.590  0.00  0   D
+ATOM     8073    S   SG .  CYS   D .  237 ?   38.662  25.215  29.286  0.00  0   D
+ATOM     7816    N    N .  ALA   D .  206 ?   43.950  26.440  32.723  0.00  0   D
+ATOM     7065    C   CA .  VAL   D .  111 ?   48.863  23.360  22.717  0.00  0   D
+ATOM     7082    C   CB .  LEU   D .  113 ?   47.325  24.825  28.299  0.00  0   D
+ATOM     8097    C  CG2 .  VAL   D .  241 ?   40.590  21.066  26.854  0.00  0   D
+ATOM     7092    C  CD1 .  LEU   D .  114 ?   44.050  19.857  25.449  0.00  0   D
+ATOM     8308    C  CE1 .  PHE   D .  266 ?   42.431  17.800  28.875  0.00  0   D
+# 

tests/reference_output/123abc_out/pocket13_env_atm.cif

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

tests/reference_output/123abc_out/pocket13_vert.pqr

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

tests/reference_output/123abc_out/pocket14_atm.cif

@@ -0,0 +1,55 @@
+data_pocket14_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    14:
+0  - Pocket Score                      : 0.0287
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    20
+3  - Mean alpha-sphere radius          : 3.7199
+4  - Mean alpha-sphere Solvent Acc.    : 0.5390
+5  - Mean B-factor of pocket residues  : 0.2120
+6  - Hydrophobicity Score              : -27.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.5000
+9  - Pocket volume (Monte Carlo)       : 155.2399
+10  -Pocket volume (convex hull)       : 1.4197
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     0
+14 - Proportion of apolar alpha sphere : 0.0000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3238    O    O .  ASP   B .  154 ?   17.212  58.730  41.018 -2.14  0   B
+ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
+ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
+ATOM     2491    O  OE1 .  GLU   B .   59 ?   14.831  61.607  36.581  0.00  0   B
+ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
+ATOM     2492    O  OE2 .  GLU   B .   59 ?   15.137  61.777  38.754 -1.07  0   B
+ATOM     2389    N   NZ .  LYS   B .   44 ?   17.801  61.554  36.438 -1.51  0   B
+ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
+ATOM     2489    C   CG .  GLU   B .   59 ?   12.912  61.584  38.000  0.00  0   B
+ATOM     2490    C   CD .  GLU   B .   59 ?   14.404  61.663  37.759  0.00  0   B
+ATOM     3239    C   CB .  ASP   B .  154 ?   15.520  56.620  41.941  0.00  0   B
+ATOM     2488    C   CB .  GLU   B .   59 ?   12.087  61.638  36.697  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket14_env_atm.cif

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

tests/reference_output/123abc_out/pocket14_vert.pqr

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

tests/reference_output/123abc_out/pocket15_atm.cif

@@ -0,0 +1,67 @@
+data_pocket15_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    15:
+0  - Pocket Score                      : 0.0219
+1  - Drug Score                        : 0.0431
+2  - Number of alpha spheres           :    39
+3  - Mean alpha-sphere radius          : 3.7453
+4  - Mean alpha-sphere Solvent Acc.    : 0.4087
+5  - Mean B-factor of pocket residues  : 0.1166
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 221.5000
+10  -Pocket volume (convex hull)       : 14.5929
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 33.0000
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8718
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3639    C   CA .  ALA   B .  206 ?   25.485  44.511  57.685  0.00  0   B
+ATOM     2914    C  CD1 .  LEU   B .  113 ?   26.128  47.415  60.882  0.00  0   B
+ATOM     3642    C   CB .  ALA   B .  206 ?   24.633  43.235  57.872  0.00  0   B
+ATOM     3641    O    O .  ALA   B .  206 ?   27.664  43.745  58.449 -4.29  0   B
+ATOM     2922    C  CD1 .  LEU   B .  114 ?   18.369  46.670  63.743  0.00  0   B
+ATOM     3902    C   CD .  PRO   B .  238 ?   22.462  42.067  63.671  0.00  0   B
+ATOM     2892    O    O .  ALA   B .  110 ?   23.079  48.277  64.744 -3.21  0   B
+ATOM     3901    C   CG .  PRO   B .  238 ?   21.818  42.336  65.023  0.00  0   B
+ATOM     3919    C  CG2 .  VAL   B .  241 ?   18.754  43.171  62.407  0.00  0   B
+ATOM     2890    C   CA .  ALA   B .  110 ?   25.351  47.954  65.540  0.00  0   B
+ATOM     3918    C  CG1 .  VAL   B .  241 ?   19.352  42.826  59.944  0.00  0   B
+ATOM     3895    S   SG .  CYS   B .  237 ?   22.468  40.332  60.148  0.00  0   B
+ATOM     2893    C   CB .  ALA   B .  110 ?   25.301  47.008  66.740  0.00  0   B
+ATOM     2916    N    N .  LEU   B .  114 ?   21.229  49.545  62.399 -2.19  0   B
+ATOM     3889    O    O .  GLY   B .  236 ?   25.751  41.531  64.057  0.00  0   B
+ATOM     2912    C   CB .  LEU   B .  113 ?   24.074  48.764  61.348  0.00  0   B
+ATOM     2917    C   CA .  LEU   B .  114 ?   19.825  49.298  62.629  0.00  0   B
+ATOM     4130    C  CE1 .  PHE   B .  266 ?   16.326  46.124  60.459  0.00  0   B
+ATOM     2948    C   CB .  ALA   B .  117 ?   17.953  48.663  58.385  0.00  0   B
+ATOM     2910    C    C .  LEU   B .  113 ?   21.785  49.807  61.241  0.00  0   B
+ATOM     3891    C   CA .  CYS   B .  237 ?   24.487  40.444  62.093  0.00  0   B
+ATOM     2911    O    O .  LEU   B .  113 ?   21.152  49.905  60.239  0.00  0   B
+ATOM     3636    C  CG2 .  ILE   B .  205 ?   23.388  48.453  57.534  0.00  0   B
+ATOM     3602    O    O .  LEU   B .  202 ?   22.353  44.476  55.620 -1.07  0   B
+ATOM     3606    C  CD2 .  LEU   B .  202 ?   18.004  45.680  56.609  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket15_env_atm.cif

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

tests/reference_output/123abc_out/pocket15_vert.pqr

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

tests/reference_output/123abc_out/pocket16_atm.cif

@@ -0,0 +1,63 @@
+data_pocket16_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    16:
+0  - Pocket Score                      : 0.0116
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    28
+3  - Mean alpha-sphere radius          : 3.7712
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.1225
+6  - Hydrophobicity Score              : 11.6923
+7  - Polarity Score                    :     9
+8  - Amino Acid based volume Score     : 4.5385
+9  - Pocket volume (Monte Carlo)       : 380.3267
+10  -Pocket volume (convex hull)       : 34.1542
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 6.5000
+13 - Number of apolar alpha sphere     :     8
+14 - Proportion of apolar alpha sphere : 0.2857
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     7853    C   CA .  SER   D .  211 ?   42.974  31.063  42.423  0.00  0   D
+ATOM     7600    C  CH2 .  TRP   D .  178 ?   43.960  26.363  45.206  0.00  0   D
+ATOM     7847    O    O .  MET   D .  210 ?   44.036  29.741  40.141 -1.07  0   D
+ATOM     7857    O   OG .  SER   D .  211 ?   44.316  32.109  43.942  0.00  0   D
+ATOM     7598    C  CZ2 .  TRP   D .  178 ?   44.202  25.607  44.069  0.00  0   D
+ATOM     7864    C   CD .  PRO   D .  212 ?   41.974  28.366  43.102  0.00  0   D
+ATOM     7302    C   CB .  ARG   D .  140 ?   50.864  24.591  44.728  0.00  0   D
+ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
+ATOM     6936    N  ND2 .  ASN   D .   95 ?   54.321  26.577  41.672  0.00  0   D
+ATOM     6952    C  CD2 .  LEU   D .   97 ?   49.815  28.277  43.031  0.00  0   D
+ATOM     7493    O  OG1 .  THR   D .  165 ?   46.860  28.337  49.111 -0.95  0   D
+ATOM     7307    N  NH1 .  ARG   D .  140 ?   46.275  24.168  46.062  0.00  0   D
+ATOM     7304    C   CD .  ARG   D .  140 ?   49.165  24.333  46.741  0.00  0   D
+ATOM     7468    C   CE .  MET   D .  161 ?   51.743  26.507  49.224  0.00  0   D
+ATOM     6959    O  OD1 .  ASP   D .   98 ?   54.141  30.867  42.252 -4.02  0   D
+ATOM     7806    O  OE1 .  GLU   D .  204 ?   46.278  25.826  41.102 -2.14  0   D
+ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
+ATOM     6991    N  NH2 .  ARG   D .  101 ?   47.806  31.880  42.344 -2.61  0   D
+ATOM     6951    C  CD1 .  LEU   D .   97 ?   48.963  28.362  40.622  0.00  0   D
+ATOM     6990    N  NH1 .  ARG   D .  101 ?   49.983  32.573  42.931 -3.70  0   D
+ATOM     7467    S   SD .  MET   D .  161 ?   50.163  27.152  49.858  0.00  0   D
+# 

tests/reference_output/123abc_out/pocket16_env_atm.cif

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

tests/reference_output/123abc_out/pocket16_vert.pqr

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

tests/reference_output/123abc_out/pocket17_atm.cif

@@ -0,0 +1,57 @@
+data_pocket17_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    17:
+0  - Pocket Score                      : 0.0075
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    19
+3  - Mean alpha-sphere radius          : 3.5999
+4  - Mean alpha-sphere Solvent Acc.    : 0.4164
+5  - Mean B-factor of pocket residues  : 0.1872
+6  - Hydrophobicity Score              : 12.0000
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 154.0510
+10  -Pocket volume (convex hull)       : 5.2942
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     1
+14 - Proportion of apolar alpha sphere : 0.0526
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3171    O    O .  GLY   B .  145 ?   24.279  62.076  57.870  0.00  0   B
+ATOM     2751    C  CE1 .  TYR   B .   93 ?   27.916  64.065  57.675  0.00  0   B
+ATOM     3181    N    N .  ASN   B .  147 ?   24.353  63.017  61.460 -3.03  0   B
+ATOM     3189    N    N .  HIS   B .  148 ?   23.808  60.293  60.791  0.00  0   B
+ATOM     2872    O  OE1 .  GLU   B .  107 ?   31.484  58.761  62.681 -0.95  0   B
+ATOM     2752    C  CE2 .  TYR   B .   93 ?   30.166  63.254  57.309  0.00  0   B
+ATOM     2873    O  OE2 .  GLU   B .  107 ?   29.348  59.201  62.656 -7.90  0   B
+ATOM     2754    O   OH .  TYR   B .   93 ?   29.703  64.823  59.044  0.00  0   B
+ATOM     2753    C   CZ .  TYR   B .   93 ?   29.259  64.044  58.017  0.00  0   B
+ATOM     2837    N    N .  ASN   B .  104 ?   33.994  55.404  60.098 -1.09  0   B
+ATOM     2835    C   CB .  CYS   B .  103 ?   31.652  54.686  58.227  0.00  0   B
+ATOM     2832    C   CA .  CYS   B .  103 ?   33.088  55.081  57.860  0.00  0   B
+ATOM     3198    N  NE2 .  HIS   B .  148 ?   27.061  57.958  62.310  0.00  0   B
+ATOM     2802    O   OH .  TYR   B .   99 ?   28.273  57.952  59.075 -7.50  0   B
+ATOM     2799    C  CE1 .  TYR   B .   99 ?   29.022  58.408  56.848  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket17_env_atm.cif

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

tests/reference_output/123abc_out/pocket17_vert.pqr

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

tests/reference_output/123abc_out/pocket18_atm.cif

@@ -0,0 +1,65 @@
+data_pocket18_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    18:
+0  - Pocket Score                      : 0.0041
+1  - Drug Score                        : 0.0027
+2  - Number of alpha spheres           :    33
+3  - Mean alpha-sphere radius          : 3.9082
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.2780
+6  - Hydrophobicity Score              : 53.6000
+7  - Polarity Score                    :     4
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 282.0984
+10  -Pocket volume (convex hull)       : 22.1820
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 17.8947
+13 - Number of apolar alpha sphere     :    19
+14 - Proportion of apolar alpha sphere : 0.5758
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1359    O    O .  LEU   A .  184 ?   14.349  39.319  26.613 -1.07  0   A
+ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
+ATOM     1363    C  CD2 .  LEU   A .  184 ?   17.375  37.076  23.709  0.00  0   A
+ATOM     3351    N    N .  ALA   B .  170 ?   17.691  42.856  27.354 -6.98  0   B
+ATOM     3340    C   CB .  ALA   B .  168 ?   22.786  43.694  28.595  0.00  0   B
+ATOM     1640    O    O .  SER   A .  219 ?   23.891  43.579  25.385 -1.07  0   A
+ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
+ATOM     1632    O    O .  LEU   A .  218 ?   23.990  39.840  23.886  0.00  0   A
+ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
+ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
+ATOM     1298    C  CD1 .  ILE   A .  176 ?   20.379  35.378  24.896  0.00  0   A
+ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
+ATOM     1279    C  CD1 .  PHE   A .  174 ?   15.732  32.610  26.953  0.00  0   A
+ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
+ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
+ATOM     1297    C  CG2 .  ILE   A .  176 ?   21.592  37.080  22.335  0.00  0   A
+ATOM     1663    C   CB .  TYR   A .  222 ?   18.792  43.075  23.036  0.00  0   A
+ATOM     1659    N    N .  TYR   A .  222 ?   20.759  42.581  21.578 -1.09  0   A
+ATOM     1362    C  CD1 .  LEU   A .  184 ?   17.407  38.949  21.882  0.00  0   A
+ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
+ATOM     1357    C   CA .  LEU   A .  184 ?   14.567  38.323  24.463  0.00  0   A
+ATOM     1353    O    O .  SER   A .  183 ?   12.402  36.556  25.117  0.00  0   A
+ATOM     1360    C   CB .  LEU   A .  184 ?   15.704  39.018  23.710  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket18_env_atm.cif

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

tests/reference_output/123abc_out/pocket18_vert.pqr

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

tests/reference_output/123abc_out/pocket19_atm.cif

@@ -0,0 +1,74 @@
+data_pocket19_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    19:
+0  - Pocket Score                      : 0.0000
+1  - Drug Score                        : 0.0491
+2  - Number of alpha spheres           :    40
+3  - Mean alpha-sphere radius          : 3.9057
+4  - Mean alpha-sphere Solvent Acc.    : 0.5724
+5  - Mean B-factor of pocket residues  : 0.2564
+6  - Hydrophobicity Score              : 62.1111
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 4.3333
+9  - Pocket volume (Monte Carlo)       : 430.3055
+10  -Pocket volume (convex hull)       : 67.6357
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 28.1176
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8500
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     7944    C   CZ .  TYR   D .  222 ?   28.663  18.750  51.374  0.00  0   D
+ATOM     7943    C  CE2 .  TYR   D .  222 ?   27.884  19.861  51.731  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
+ATOM     7647    C   CB .  ALA   D .  185 ?   30.355  15.757  53.617  0.00  0   D
+ATOM     7644    C   CA .  ALA   D .  185 ?   31.641  16.003  54.405  0.00  0   D
+ATOM     7942    C  CE1 .  TYR   D .  222 ?   29.998  18.906  51.064  0.00  0   D
+ATOM     7940    C  CD1 .  TYR   D .  222 ?   30.563  20.141  51.099  0.00  0   D
+ATOM     7941    C  CD2 .  TYR   D .  222 ?   28.465  21.119  51.770  0.00  0   D
+ATOM     7577    C  CD1 .  ILE   D .  176 ?   37.672  25.382  53.690  0.00  0   D
+ATOM     7576    C  CG2 .  ILE   D .  176 ?   36.592  24.562  50.949  0.00  0   D
+ATOM     7575    C  CG1 .  ILE   D .  176 ?   38.212  24.231  52.898  0.00  0   D
+ATOM     7642    C  CD2 .  LEU   D .  184 ?   36.369  20.233  52.078  0.00  0   D
+ATOM     7641    C  CD1 .  LEU   D .  184 ?   34.448  20.808  50.650  0.00  0   D
+ATOM     7938    C   CB .  TYR   D .  222 ?   30.486  22.638  51.402  0.00  0   D
+ATOM     7934    N    N .  TYR   D .  222 ?   31.202  24.455  49.938 -1.09  0   D
+ATOM     7907    O    O .  LEU   D .  218 ?   34.008  27.525  52.271 -0.40  0   D
+ATOM     7639    C   CB .  LEU   D .  184 ?   34.244  18.838  52.215  0.00  0   D
+ATOM     7939    C   CG .  TYR   D .  222 ?   29.832  21.273  51.448  0.00  0   D
+ATOM     7560    C  CE1 .  PHE   D .  174 ?   39.595  17.433  56.140  0.00  0   D
+ATOM     7638    O    O .  LEU   D .  184 ?   33.870  17.251  55.188  0.00  0   D
+ATOM     7525    N  ND1 .  HIS   D .  169 ?   36.365  20.155  60.429 -1.93  0   D
+ATOM     7558    C  CD1 .  PHE   D .  174 ?   39.696  18.611  55.390  0.00  0   D
+ATOM     7524    C   CG .  HIS   D .  169 ?   36.743  21.442  60.097  0.00  0   D
+ATOM     7527    C  CE1 .  HIS   D .  169 ?   35.170  20.180  60.996  0.00  0   D
+ATOM     7528    N  NE2 .  HIS   D .  169 ?   34.778  21.438  61.089  0.00  0   D
+ATOM     7526    C  CD2 .  HIS   D .  169 ?   35.750  22.249  60.547  0.00  0   D
+ATOM     7637    C    C .  LEU   D .  184 ?   33.727  17.072  53.991  0.00  0   D
+ATOM     7523    C   CB .  HIS   D .  169 ?   38.074  21.770  59.468  0.00  0   D
+ATOM     7556    C   CB .  PHE   D .  174 ?   40.965  20.182  53.857  0.00  0   D
+ATOM     7513    C  CG2 .  THR   D .  167 ?   39.795  26.405  56.782  0.00  0   D
+ATOM     7510    O    O .  THR   D .  167 ?   41.927  23.289  56.784  0.00  0   D
+ATOM     7517    O    O .  ALA   D .  168 ?   40.187  24.764  60.121 -3.35  0   D
+# 

tests/reference_output/123abc_out/pocket19_env_atm.cif

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

tests/reference_output/123abc_out/pocket19_vert.pqr

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

tests/reference_output/123abc_out/pocket1_atm.cif

@@ -0,0 +1,158 @@
+data_pocket1_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket     1:
+0  - Pocket Score                      : 1.0099
+1  - Drug Score                        : 0.9898
+2  - Number of alpha spheres           :   213
+3  - Mean alpha-sphere radius          : 4.0060
+4  - Mean alpha-sphere Solvent Acc.    : 0.5026
+5  - Mean B-factor of pocket residues  : 0.1858
+6  - Hydrophobicity Score              : 39.5476
+7  - Polarity Score                    :    18
+8  - Amino Acid based volume Score     : 4.2857
+9  - Pocket volume (Monte Carlo)       : 1739.6467
+10  -Pocket volume (convex hull)       : 1610.3746
+11 - Charge Score                      :    -4
+12 - Local hydrophobic density Score   : 53.0308
+13 - Number of apolar alpha sphere     :   130
+14 - Proportion of apolar alpha sphere : 0.6103
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     5124    C  CD1 .  LEU   C .  127 ?   52.412  62.880  19.111  0.00  0   C
+ATOM     5175    O    O .  ILE   C .  133 ?   50.155  63.679  13.849 -1.07  0   C
+ATOM     4642    C  CD1 .  ILE   C .   66 ?   57.564  64.926  16.918  0.00  0   C
+ATOM     5181    C   CA .  HIS   C .  134 ?   49.968  61.358  15.298  0.00  0   C
+ATOM     5168    C  CD2 .  PHE   C .  132 ?   53.775  68.288  14.726  0.00  0   C
+ATOM     5165    C   CB .  PHE   C .  132 ?   52.152  67.148  16.265  0.00  0   C
+ATOM     4607    C  CG1 .  VAL   C .   62 ?   56.843  66.361  13.193  0.00  0   C
+ATOM     5349    C  CD2 .  PHE   C .  155 ?   58.617  52.809  14.766  0.00  0   C
+ATOM     4806    C  CG2 .  THR   C .   88 ?   64.918  58.267  15.934  0.00  0   C
+ATOM     5351    C  CE2 .  PHE   C .  155 ?   58.958  52.743  16.096  0.00  0   C
+ATOM     4805    O  OG1 .  THR   C .   88 ?   65.292  56.165  17.041  0.00  0   C
+ATOM     5166    C   CG .  PHE   C .  132 ?   53.337  68.020  16.020  0.00  0   C
+ATOM     5187    C  CD2 .  HIS   C .  134 ?   52.038  58.986  17.107  0.00  0   C
+ATOM     5125    C  CD2 .  LEU   C .  127 ?   53.933  64.923  19.034  0.00  0   C
+ATOM     4367    C  CG1 .  VAL   C .   29 ?   65.278  51.087  12.687  0.00  0   C
+ATOM     4342    C   CG .  TYR   C .   26 ?   60.508  48.226  13.248  0.00  0   C
+ATOM     4680    C  CD2 .  LEU   C .   71 ?   55.947  61.004  20.573  0.00  0   C
+ATOM     5338    C   CB .  ASP   C .  154 ?   55.209  57.618  13.892  0.00  0   C
+ATOM     4684    O    O .  VAL   C .   72 ?   61.863  60.416  19.355 -5.36  0   C
+ATOM     4640    C  CG1 .  ILE   C .   66 ?   58.912  65.273  17.720  0.00  0   C
+ATOM     4677    C   CB .  LEU   C .   71 ?   58.112  61.528  21.791  0.00  0   C
+ATOM     5341    O  OD2 .  ASP   C .  154 ?   53.714  58.561  12.241 -0.14  0   C
+ATOM     5183    O    O .  HIS   C .  134 ?   50.262  60.307  13.190  0.00  0   C
+ATOM     4608    C  CG2 .  VAL   C .   62 ?   57.086  66.805  10.673  0.00  0   C
+ATOM     4606    C   CB .  VAL   C .   62 ?   57.804  66.325  11.964  0.00  0   C
+ATOM     4849    C  CD2 .  TYR   C .   93 ?   62.771  44.062  27.626  0.00  0   C
+ATOM     4898    C  CE1 .  TYR   C .   99 ?   58.734  44.320  28.340  0.00  0   C
+ATOM     4896    C  CD1 .  TYR   C .   99 ?   58.352  44.217  27.023  0.00  0   C
+ATOM     4924    O    O .  GLU   C .  102 ?   56.618  37.405  27.670 -1.21  0   C
+ATOM     4533    C   CB .  GLU   C .   52 ?   60.007  57.267   0.138  0.00  0   C
+ATOM     4493    N   NZ .  LYS   C .   44 ?   59.948  55.800   8.159  0.00  0   C
+ATOM     4492    C   CE .  LYS   C .   44 ?   61.398  55.419   7.935  0.00  0   C
+ATOM     4565    C  CD1 .  PHE   C .   56 ?   63.711  58.360   4.956  0.00  0   C
+ATOM     4491    C   CD .  LYS   C .   44 ?   62.464  55.863   8.961  0.00  0   C
+ATOM     4591    O  OE2 .  GLU   C .   59 ?   60.141  58.852  10.727 -1.07  0   C
+ATOM     4489    C   CB .  LYS   C .   44 ?   64.904  55.444   9.602  0.00  0   C
+ATOM     4344    C  CD2 .  TYR   C .   26 ?   59.377  48.648  13.987  0.00  0   C
+ATOM     4477    C   CB .  ALA   C .   42 ?   66.815  52.711  16.102  0.00  0   C
+ATOM     4928    O  OE1 .  GLU   C .  102 ?   58.396  38.729  22.754 -0.95  0   C
+ATOM     4845    O    O .  TYR   C .   93 ?   60.677  45.046  23.639 -4.02  0   C
+ATOM     4507    C  CD1 .  LEU   C .   46 ?   63.457  56.650   1.429  0.00  0   C
+ATOM     4614    C   CG .  MET   C .   63 ?   60.952  62.629  14.053  0.00  0   C
+ATOM     4615    S   SD .  MET   C .   63 ?   61.859  61.128  13.673  0.00  0   C
+ATOM     5334    N    N .  ASP   C .  154 ?   56.468  56.249  15.507  0.00  0   C
+ATOM     4854    N    N .  GLY   C .   94 ?   61.926  46.515  22.505 -1.09  0   C
+ATOM     4855    C   CA .  GLY   C .   94 ?   61.148  46.414  21.286  0.00  0   C
+ATOM     4826    C   CZ .  PHE   C .   90 ?   68.029  47.527  20.408  0.00  0   C
+ATOM     4838    O    O .  THR   C .   92 ?   65.169  45.657  23.913  0.00  0   C
+ATOM     4858    N    N .  ASN   C .   95 ?   58.837  46.563  20.532 -2.19  0   C
+ATOM     4864    O  OD1 .  ASN   C .   95 ?   57.197  45.110  18.091 -1.07  0   C
+ATOM     4889    O  OD2 .  ASP   C .   98 ?   56.786  42.248  18.314 -0.81  0   C
+ATOM     4931    C   CA .  CYS   C .  103 ?   55.713  39.474  29.139  0.00  0   C
+ATOM     4923    C    C .  GLU   C .  102 ?   55.803  38.136  27.151  0.00  0   C
+ATOM     5337    O    O .  ASP   C .  154 ?   57.341  56.209  12.768 -1.07  0   C
+ATOM     4891    C   CA .  TYR   C .   99 ?   56.204  43.137  24.766  0.00  0   C
+ATOM     4890    N    N .  TYR   C .   99 ?   55.885  43.129  23.365 -2.19  0   C
+ATOM     4925    C   CB .  GLU   C .  102 ?   56.670  38.222  24.775  0.00  0   C
+ATOM     4341    C   CB .  TYR   C .   26 ?   60.784  48.778  11.861  0.00  0   C
+ATOM     4686    C  CG1 .  VAL   C .   72 ?   60.468  57.953  18.334  0.00  0   C
+ATOM     5333    C   CB .  ALA   C .  153 ?   57.973  55.244  17.737  0.00  0   C
+ATOM     4687    C  CG2 .  VAL   C .   72 ?   62.471  56.742  19.102  0.00  0   C
+ATOM     4314    C  CD1 .  LEU   C .   21 ?   66.372  48.924  15.249  0.00  0   C
+ATOM     4822    C  CD1 .  PHE   C .   90 ?   68.357  49.652  19.357  0.00  0   C
+ATOM     4827    N    N .  MET   C .   91 ?   65.600  51.395  21.975  0.00  0   C
+ATOM     4587    C   CB .  GLU   C .   59 ?   59.660  61.810   8.754  0.00  0   C
+ATOM     4584    C   CA .  GLU   C .   59 ?   59.760  63.312   8.983  0.00  0   C
+ATOM     4348    O   OH .  TYR   C .   26 ?   59.736  46.661  17.066 -2.14  0   C
+ATOM     4335    O  OE1 .  GLN   C .   25 ?   58.998  43.247  14.898 -4.69  0   C
+ATOM     4886    C   CB .  ASP   C .   98 ?   56.203  41.956  20.500  0.00  0   C
+ATOM     4929    O  OE2 .  GLU   C .  102 ?   57.083  38.222  21.105 -0.54  0   C
+ATOM     4316    N    N .  GLY   C .   22 ?   64.012  43.884  14.345 -6.98  0   C
+ATOM     4315    C  CD2 .  LEU   C .   21 ?   67.339  46.763  16.058  0.00  0   C
+ATOM     4312    C   CB .  LEU   C .   21 ?   65.502  46.661  14.421  0.00  0   C
+ATOM     4893    O    O .  TYR   C .   99 ?   55.173  41.873  26.595  0.00  0   C
+ATOM     5331    C    C .  ALA   C .  153 ?   55.953  56.313  16.712  0.00  0   C
+ATOM     5332    O    O .  ALA   C .  153 ?   54.761  56.347  16.907  0.00  0   C
+ATOM     4485    N    N .  LYS   C .   44 ?   66.985  54.643  10.662  0.00  0   C
+ATOM     4317    C   CA .  GLY   C .   22 ?   62.747  43.150  14.231  0.00  0   C
+ATOM     4343    C  CD1 .  TYR   C .   26 ?   61.357  47.296  13.808  0.00  0   C
+ATOM     4830    O    O .  MET   C .   91 ?   64.488  48.834  22.426  0.00  0   C
+ATOM     4824    C  CE1 .  PHE   C .   90 ?   68.165  48.287  19.279  0.00  0   C
+ATOM     5258    C  CD1 .  LEU   C .  143 ?   60.801  52.853  19.522  0.00  0   C
+ATOM     4810    O    O .  GLU   C .   89 ?   66.226  54.641  19.567  0.00  0   C
+ATOM     4590    O  OE1 .  GLU   C .   59 ?   60.143  59.180   8.562  0.00  0   C
+ATOM     4560    C   CA .  PHE   C .   56 ?   61.727  61.139   4.612  0.00  0   C
+ATOM     4552    C    C .  GLU   C .   55 ?   59.443  61.938   4.041  0.00  0   C
+ATOM     4553    O    O .  GLU   C .   55 ?   59.074  62.152   5.210 -0.40  0   C
+ATOM     4559    N    N .  PHE   C .   56 ?   60.677  61.556   3.690  0.00  0   C
+ATOM     5354    C   CA .  GLY   C .  156 ?   55.185  54.289   9.070  0.00  0   C
+ATOM     5340    O  OD1 .  ASP   C .  154 ?   54.160  56.484  12.072 -0.40  0   C
+ATOM     4588    C   CG .  GLU   C .   59 ?   59.879  61.018  10.009  0.00  0   C
+ATOM     4586    O    O .  GLU   C .   59 ?   60.890  64.044  10.965  0.00  0   C
+ATOM     4554    C   CB .  GLU   C .   55 ?   57.705  60.840   2.562  0.00  0   C
+ATOM     5356    O    O .  GLY   C .  156 ?   55.311  52.499   7.563 -3.62  0   C
+ATOM     5376    C   CG .  ARG   C .  159 ?   54.486  53.056   3.655  0.00  0   C
+ATOM     5259    C  CD2 .  LEU   C .  143 ?   60.391  50.436  19.544  0.00  0   C
+ATOM     4346    C  CE2 .  TYR   C .   26 ?   59.090  48.126  15.277  0.00  0   C
+ATOM     4347    C   CZ .  TYR   C .   26 ?   59.971  47.200  15.806  0.00  0   C
+ATOM     4345    C  CE1 .  TYR   C .   26 ?   61.109  46.769  15.049  0.00  0   C
+ATOM     4790    C  CG2 .  ILE   C .   86 ?   65.267  59.719  11.684  0.00  0   C
+ATOM     5343    C   CA .  PHE   C .  155 ?   57.162  53.520  12.244  0.00  0   C
+ATOM     5345    O    O .  PHE   C .  155 ?   57.545  52.974   9.992 -1.07  0   C
+ATOM     4476    O    O .  ALA   C .   42 ?   68.283  54.987  14.590  0.00  0   C
+ATOM     4497    O    O .  THR   C .   45 ?   65.625  53.907   4.664 -2.55  0   C
+ATOM     4368    C  CG2 .  VAL   C .   29 ?   63.667  51.380  10.691  0.00  0   C
+ATOM     5346    C   CB .  PHE   C .  155 ?   57.304  52.068  12.736  0.00  0   C
+ATOM     5353    N    N .  GLY   C .  156 ?   55.685  54.235  10.437  0.00  0   C
+ATOM     5330    C   CA .  ALA   C .  153 ?   56.928  56.348  17.874  0.00  0   C
+ATOM     5325    O    O .  VAL   C .  152 ?   57.290  57.718  20.233  0.00  0   C
+ATOM     4589    C   CD .  GLU   C .   59 ?   60.082  59.588   9.746  0.00  0   C
+ATOM     5339    C   CG .  ASP   C .  154 ?   54.313  57.558  12.649  0.00  0   C
+ATOM     4787    O    O .  ILE   C .   86 ?   67.579  57.024  11.540  0.00  0   C
+ATOM     4532    O    O .  GLU   C .   52 ?   60.629  60.058   1.220 -1.07  0   C
+ATOM     4563    C   CB .  PHE   C .   56 ?   62.803  60.407   3.827  0.00  0   C
+ATOM     4555    C   CG .  GLU   C .   55 ?   56.341  60.714   3.218  0.00  0   C
+ATOM     4557    O  OE1 .  GLU   C .   55 ?   54.968  62.335   4.361  0.00  0   C
+# 

tests/reference_output/123abc_out/pocket1_env_atm.cif

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

tests/reference_output/123abc_out/pocket1_vert.pqr

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

tests/reference_output/123abc_out/pocket20_atm.cif

@@ -0,0 +1,66 @@
+data_pocket20_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    20:
+0  - Pocket Score                      : -0.0058
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    37
+3  - Mean alpha-sphere radius          : 3.7789
+4  - Mean alpha-sphere Solvent Acc.    : 0.4544
+5  - Mean B-factor of pocket residues  : 0.2229
+6  - Hydrophobicity Score              : 11.7857
+7  - Polarity Score                    :    10
+8  - Amino Acid based volume Score     : 4.4286
+9  - Pocket volume (Monte Carlo)       : 418.3302
+10  -Pocket volume (convex hull)       : 54.0760
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 7.4000
+13 - Number of apolar alpha sphere     :    10
+14 - Proportion of apolar alpha sphere : 0.2703
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1578    C   CA .  SER   A .  211 ?   28.519  31.580  13.536  0.00  0   A
+ATOM      729    N  NH2 .  ARG   A .  101 ?   29.744  27.079  13.417 -2.19  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1531    O  OE1 .  GLU   A .  204 ?   23.660  27.646  12.432 -1.07  0   A
+ATOM     1572    O    O .  MET   A .  210 ?   27.392  30.484  11.286 -2.14  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1192    C   CE .  MET   A .  161 ?   25.473  22.258  20.061  0.00  0   A
+ATOM     1193    N    N .  THR   A .  162 ?   27.717  23.001  24.543 -3.28  0   A
+ATOM     1196    O    O .  THR   A .  162 ?   30.318  24.681  23.653 -0.54  0   A
+ATOM     1190    C   CG .  MET   A .  161 ?   25.693  23.794  22.437  0.00  0   A
+ATOM     1191    S   SD .  MET   A .  161 ?   25.108  23.914  20.726  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1197    C   CB .  THR   A .  162 ?   30.043  22.165  24.907  0.00  0   A
+ATOM      728    N  NH1 .  ARG   A .  101 ?   30.641  25.059  14.054  0.00  0   A
+ATOM     1319    C  CZ2 .  TRP   A .  178 ?   23.312  29.778  15.389  0.00  0   A
+ATOM      690    C  CD2 .  LEU   A .   97 ?   26.615  24.712  14.130  0.00  0   A
+ATOM     1039    N  NH1 .  ARG   A .  140 ?   22.161  27.219  17.402 -2.19  0   A
+ATOM     1036    C   CD .  ARG   A .  140 ?   22.384  24.464  18.025  0.00  0   A
+ATOM      697    O  OD1 .  ASP   A .   98 ?   29.383  20.437  13.443  0.00  0   A
+ATOM      136    N  NE2 .  GLN   A .   25 ?   26.655  17.754  17.106 -1.51  0   A
+ATOM     1034    C   CB .  ARG   A .  140 ?   22.854  23.046  15.953  0.00  0   A
+ATOM      674    N  ND2 .  ASN   A .   95 ?   25.138  19.957  12.965 -2.19  0   A
+ATOM     1198    O  OG1 .  THR   A .  162 ?   29.373  20.894  24.874 -2.55  0   A
+# 

tests/reference_output/123abc_out/pocket20_env_atm.cif

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

tests/reference_output/123abc_out/pocket20_vert.pqr

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

tests/reference_output/123abc_out/pocket21_atm.cif

@@ -0,0 +1,74 @@
+data_pocket21_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    21:
+0  - Pocket Score                      : -0.0129
+1  - Drug Score                        : 0.0844
+2  - Number of alpha spheres           :    48
+3  - Mean alpha-sphere radius          : 3.7739
+4  - Mean alpha-sphere Solvent Acc.    : 0.4618
+5  - Mean B-factor of pocket residues  : 0.0755
+6  - Hydrophobicity Score              : 51.7143
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 3.8571
+9  - Pocket volume (Monte Carlo)       : 338.1321
+10  -Pocket volume (convex hull)       : 33.9441
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 32.5294
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.7083
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     5013    C  CD1 .  LEU   C .  113 ?   47.637  45.537  32.420  0.00  0   C
+ATOM     5969    O    O .  GLY   C .  236 ?   41.436  44.926  35.683 -1.88  0   C
+ATOM     5742    C  CE2 .  TYR   C .  208 ?   47.578  41.887  31.506  0.00  0   C
+ATOM     5744    O   OH .  TYR   C .  208 ?   49.149  42.483  33.247  0.00  0   C
+ATOM     5967    C   CA .  GLY   C .  236 ?   40.408  42.885  35.092  0.00  0   C
+ATOM     5960    O    O .  GLU   C .  235 ?   40.959  41.746  32.508 -6.17  0   C
+ATOM     5724    O    O .  ALA   C .  206 ?   44.035  43.617  29.804 -4.29  0   C
+ATOM     4992    C   CB .  ALA   C .  110 ?   46.896  45.998  37.907  0.00  0   C
+ATOM     4989    C   CA .  ALA   C .  110 ?   48.023  46.286  36.893  0.00  0   C
+ATOM     4988    N    N .  ALA   C .  110 ?   49.019  45.250  37.006 -1.09  0   C
+ATOM     5722    C   CA .  ALA   C .  206 ?   44.400  45.936  29.263  0.00  0   C
+ATOM     5011    C   CB .  LEU   C .  113 ?   48.507  47.814  32.706  0.00  0   C
+ATOM     5725    C   CB .  ALA   C .  206 ?   43.007  46.611  29.412  0.00  0   C
+ATOM     5971    C   CA .  CYS   C .  237 ?   40.269  46.381  33.554  0.00  0   C
+ATOM     5968    C    C .  GLY   C .  236 ?   40.655  44.362  34.916  0.00  0   C
+ATOM     5009    C    C .  LEU   C .  113 ?   49.262  50.208  32.866  0.00  0   C
+ATOM     6002    C  CG1 .  VAL   C .  241 ?   41.927  51.680  31.567  0.00  0   C
+ATOM     5010    O    O .  LEU   C .  113 ?   49.304  50.941  31.905  0.00  0   C
+ATOM     5982    C   CD .  PRO   C .  238 ?   41.741  48.427  35.286  0.00  0   C
+ATOM     5975    S   SG .  CYS   C .  237 ?   39.866  48.440  31.675  0.00  0   C
+ATOM     4991    O    O .  ALA   C .  110 ?   48.119  48.581  36.365 -4.29  0   C
+ATOM     5021    C  CD1 .  LEU   C .  114 ?   45.548  52.723  35.306  0.00  0   C
+ATOM     6003    C  CG2 .  VAL   C .  241 ?   42.161  52.318  34.092  0.00  0   C
+ATOM     5981    C   CG .  PRO   C .  238 ?   41.902  49.346  36.487  0.00  0   C
+ATOM     5015    N    N .  LEU   C .  114 ?   48.853  50.629  34.038 -1.09  0   C
+ATOM     5016    C   CA .  LEU   C .  114 ?   48.437  52.025  34.290  0.00  0   C
+ATOM     5047    C   CB .  ALA   C .  117 ?   47.619  53.976  30.267  0.00  0   C
+ATOM     5689    C  CD2 .  LEU   C .  202 ?   44.675  53.384  28.357  0.00  0   C
+ATOM     6210    C  CE1 .  PHE   C .  266 ?   44.724  55.322  32.190  0.00  0   C
+ATOM     5719    C  CG2 .  ILE   C .  205 ?   48.010  48.643  29.034  0.00  0   C
+ATOM     5685    O    O .  LEU   C .  202 ?   43.911  49.067  27.179 -2.14  0   C
+ATOM     5721    N    N .  ALA   C .  206 ?   45.181  46.650  28.250  0.00  0   C
+# 

tests/reference_output/123abc_out/pocket21_env_atm.cif

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

tests/reference_output/123abc_out/pocket21_vert.pqr

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

tests/reference_output/123abc_out/pocket22_atm.cif

@@ -0,0 +1,77 @@
+data_pocket22_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    22:
+0  - Pocket Score                      : -0.0139
+1  - Drug Score                        : 0.0034
+2  - Number of alpha spheres           :    36
+3  - Mean alpha-sphere radius          : 3.9913
+4  - Mean alpha-sphere Solvent Acc.    : 0.6555
+5  - Mean B-factor of pocket residues  : 0.2200
+6  - Hydrophobicity Score              : 9.7857
+7  - Polarity Score                    :     8
+8  - Amino Acid based volume Score     : 4.0714
+9  - Pocket volume (Monte Carlo)       : 668.7173
+10  -Pocket volume (convex hull)       : 117.8604
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 17.8095
+13 - Number of apolar alpha sphere     :    21
+14 - Proportion of apolar alpha sphere : 0.5833
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     4048    O    O .  ARG   B .  256 ?    5.584  39.776  52.007 -0.40  0   B
+ATOM     4034    O    O .  SER   B .  254 ?    3.034  36.722  50.663 -3.35  0   B
+ATOM     4092    O  OE1 .  GLU   B .  261 ?    4.400  40.941  57.227  0.00  0   B
+ATOM     4093    O  OE2 .  GLU   B .  261 ?    2.933  42.122  56.184  0.00  0   B
+ATOM     4040    O    O .  ASP   B .  255 ?    6.559  36.007  52.815  0.00  0   B
+ATOM     4057    C   CA .  PRO   B .  257 ?    6.624  40.819  54.353  0.00  0   B
+ATOM     4143    C   CB .  THR   B .  268 ?   10.227  46.401  67.772  0.00  0   B
+ATOM     4118    C   CA .  ALA   B .  265 ?    9.929  45.031  63.065  0.00  0   B
+ATOM     4145    C  CG2 .  THR   B .  268 ?   10.384  45.639  69.065  0.00  0   B
+ATOM     4144    O  OG1 .  THR   B .  268 ?    8.840  46.564  67.429  0.00  0   B
+ATOM     4120    O    O .  ALA   B .  265 ?   11.641  45.676  64.603 -1.48  0   B
+ATOM     4089    C   CB .  GLU   B .  261 ?    5.421  43.577  58.123  0.00  0   B
+ATOM     4060    C   CB .  PRO   B .  257 ?    7.583  41.016  55.523  0.00  0   B
+ATOM     3947    C  CD1 .  LEU   B .  244 ?   11.916  41.124  59.300  0.00  0   B
+ATOM     4047    C    C .  ARG   B .  256 ?    6.658  39.348  52.433  0.00  0   B
+ATOM     3972    C   CB .  ALA   B .  247 ?   11.015  37.196  55.846  0.00  0   B
+ATOM     3937    C   CG .  GLU   B .  243 ?   13.561  35.641  61.217  0.00  0   B
+ATOM     3940    O  OE2 .  GLU   B .  243 ?   11.836  34.934  62.719  0.00  0   B
+ATOM     3935    O    O .  GLU   B .  243 ?   13.956  36.736  57.962 -1.48  0   B
+ATOM     4062    C   CD .  PRO   B .  257 ?    8.652  39.555  53.954  0.00  0   B
+ATOM     3938    C   CD .  GLU   B .  243 ?   12.975  35.501  62.669  0.00  0   B
+ATOM     3911    O    O .  LYS   B .  240 ?   15.567  39.731  61.909 -3.21  0   B
+ATOM     3939    O  OE1 .  GLU   B .  243 ?   13.626  35.936  63.713  0.00  0   B
+ATOM     4152    S   SD .  MET   B .  269 ?   15.508  43.520  64.899  0.00  0   B
+ATOM     4153    C   CE .  MET   B .  269 ?   14.440  43.776  63.513  0.00  0   B
+ATOM     3912    C   CB .  LYS   B .  240 ?   15.915  39.653  65.197  0.00  0   B
+ATOM     4151    C   CG .  MET   B .  269 ?   14.602  44.443  66.216  0.00  0   B
+ATOM     4121    C   CB .  ALA   B .  265 ?   10.310  43.906  62.117  0.00  0   B
+ATOM     4088    O    O .  GLU   B .  261 ?    7.481  45.179  60.241 -3.62  0   B
+ATOM     3528    N   NZ .  LYS   B .  192 ?    4.513  41.805  50.925  0.00  0   B
+ATOM     4056    N    N .  PRO   B .  257 ?    7.275  39.856  53.515 -1.09  0   B
+ATOM     4061    C   CG .  PRO   B .  257 ?    8.908  40.517  55.032  0.00  0   B
+ATOM     3948    C  CD2 .  LEU   B .  244 ?   13.574  42.584  60.502  0.00  0   B
+ATOM     4087    C    C .  GLU   B .  261 ?    7.103  45.132  59.045  0.00  0   B
+ATOM     4094    N    N .  ILE   B .  262 ?    7.932  45.257  57.985  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket22_env_atm.cif

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

tests/reference_output/123abc_out/pocket22_vert.pqr

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

tests/reference_output/123abc_out/pocket23_atm.cif

@@ -0,0 +1,59 @@
+data_pocket23_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    23:
+0  - Pocket Score                      : -0.0164
+1  - Drug Score                        : 0.0005
+2  - Number of alpha spheres           :    21
+3  - Mean alpha-sphere radius          : 3.6900
+4  - Mean alpha-sphere Solvent Acc.    : 0.4917
+5  - Mean B-factor of pocket residues  : 0.2299
+6  - Hydrophobicity Score              : 10.2857
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 245.5694
+10  -Pocket volume (convex hull)       : 9.4367
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 6.0000
+13 - Number of apolar alpha sphere     :     7
+14 - Proportion of apolar alpha sphere : 0.3333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     8199    C   CG .  ASN   D .  252 ?   27.586   9.214  42.829  0.00  0   D
+ATOM     8186    C  CD1 .  TRP   D .  251 ?   26.276  14.665  45.063  0.00  0   D
+ATOM     8201    N  ND2 .  ASN   D .  252 ?   28.367   8.903  43.871  0.00  0   D
+ATOM     8198    C   CB .  ASN   D .  252 ?   27.436  10.710  42.437  0.00  0   D
+ATOM     8195    C   CA .  ASN   D .  252 ?   28.576  11.606  42.953  0.00  0   D
+ATOM     8188    N  NE1 .  TRP   D .  251 ?   26.256  14.921  46.406 -0.17  0   D
+ATOM     8183    O    O .  TRP   D .  251 ?   29.606  13.897  44.157 -1.07  0   D
+ATOM     8208    C   CD .  PRO   D .  253 ?   30.672  10.672  44.713  0.00  0   D
+ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
+ATOM     8191    C  CZ2 .  TRP   D .  251 ?   27.038  16.816  47.830  0.00  0   D
+ATOM     7656    C  CE1 .  TYR   D .  186 ?   28.922  12.123  52.576  0.00  0   D
+ATOM     7659    O   OH .  TYR   D .  186 ?   26.735  12.867  53.246  0.00  0   D
+ATOM     7620    N    N .  GLU   D .  182 ?   32.487  14.873  49.114  0.00  0   D
+ATOM     8189    C  CE2 .  TRP   D .  251 ?   26.844  16.141  46.643  0.00  0   D
+ATOM     7617    C   CB .  PRO   D .  181 ?   30.988  17.092  47.631  0.00  0   D
+ATOM     7624    C   CB .  GLU   D .  182 ?   32.311  12.417  49.315  0.00  0   D
+ATOM     7621    C   CA .  GLU   D .  182 ?   32.543  13.747  50.045  0.00  0   D
+# 

tests/reference_output/123abc_out/pocket23_env_atm.cif

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

tests/reference_output/123abc_out/pocket23_vert.pqr

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

tests/reference_output/123abc_out/pocket24_atm.cif

@@ -0,0 +1,73 @@
+data_pocket24_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    24:
+0  - Pocket Score                      : -0.0278
+1  - Drug Score                        : 0.0029
+2  - Number of alpha spheres           :    41
+3  - Mean alpha-sphere radius          : 3.9593
+4  - Mean alpha-sphere Solvent Acc.    : 0.5927
+5  - Mean B-factor of pocket residues  : 0.1915
+6  - Hydrophobicity Score              : 10.6364
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.7273
+9  - Pocket volume (Monte Carlo)       : 470.3947
+10  -Pocket volume (convex hull)       : 89.6285
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 10.0000
+13 - Number of apolar alpha sphere     :    14
+14 - Proportion of apolar alpha sphere : 0.3415
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1634    C   CG .  LEU   A .  218 ?   26.546  36.235  23.630  0.00  0   A
+ATOM     1635    C  CD1 .  LEU   A .  218 ?   26.663  34.961  24.461  0.00  0   A
+ATOM     1625    C   CB .  ASP   A .  217 ?   29.707  40.718  23.735  0.00  0   A
+ATOM     1633    C   CB .  LEU   A .  218 ?   25.982  37.405  24.438  0.00  0   A
+ATOM     1616    O    O .  ILE   A .  216 ?   28.714  38.833  20.120 -0.40  0   A
+ATOM     1208    C   CB .  ASP   A .  164 ?   29.178  31.688  24.167  0.00  0   A
+ATOM     1307    N   NZ .  LYS   A .  177 ?   28.045  36.395  18.402 -5.21  0   A
+ATOM     1636    C  CD2 .  LEU   A .  218 ?   25.660  35.987  22.435  0.00  0   A
+ATOM     1207    O    O .  ASP   A .  164 ?   26.463  31.466  23.365 -2.55  0   A
+ATOM     1306    C   CE .  LYS   A .  177 ?   26.638  36.392  18.974  0.00  0   A
+ATOM     1305    C   CD .  LYS   A .  177 ?   25.713  35.218  18.453  0.00  0   A
+ATOM     1212    O    O .  THR   A .  165 ?   23.541  30.232  22.305 -2.14  0   A
+ATOM     1299    N    N .  LYS   A .  177 ?   21.604  34.670  19.815  0.00  0   A
+ATOM     1586    O    O .  PRO   A .  212 ?   27.163  35.309  15.349 -2.14  0   A
+ATOM     1581    C   CB .  SER   A .  211 ?   29.357  31.629  14.802  0.00  0   A
+ATOM     1320    C  CZ3 .  TRP   A .  178 ?   23.462  30.785  17.625  0.00  0   A
+ATOM     1637    N    N .  SER   A .  219 ?   25.769  40.519  25.023  0.00  0   A
+ATOM     1642    O   OG .  SER   A .  219 ?   26.959  42.469  26.857  0.00  0   A
+ATOM     1641    C   CB .  SER   A .  219 ?   25.796  41.724  27.105  0.00  0   A
+ATOM     1629    N    N .  LEU   A .  218 ?   27.266  38.964  23.188  0.00  0   A
+ATOM     1622    C   CA .  ASP   A .  217 ?   29.148  40.081  22.440  0.00  0   A
+ATOM     1582    O   OG .  SER   A .  211 ?   29.670  30.318  15.225  0.00  0   A
+ATOM     1321    C  CH2 .  TRP   A .  178 ?   24.064  30.155  16.482  0.00  0   A
+ATOM     1214    O  OG1 .  THR   A .  165 ?   26.599  27.686  20.315  0.00  0   A
+ATOM     1206    C    C .  ASP   A .  164 ?   27.100  30.422  23.545  0.00  0   A
+ATOM     1589    C   CD .  PRO   A .  212 ?   25.953  32.242  14.398  0.00  0   A
+ATOM     1204    N    N .  ASP   A .  164 ?   29.062  29.235  24.428 -0.84  0   A
+ATOM     1209    N    N .  THR   A .  165 ?   26.804  29.250  22.931  0.00  0   A
+ATOM     1210    C   CA .  THR   A .  165 ?   25.644  29.125  21.999  0.00  0   A
+ATOM     1611    C    C .  GLY   A .  215 ?   31.790  39.345  18.361  0.00  0   A
+ATOM     1610    C   CA .  GLY   A .  215 ?   32.619  38.349  17.567  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket24_env_atm.cif

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

tests/reference_output/123abc_out/pocket24_vert.pqr

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

tests/reference_output/123abc_out/pocket25_atm.cif

@@ -0,0 +1,56 @@
+data_pocket25_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    25:
+0  - Pocket Score                      : -0.0372
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 4.0910
+4  - Mean alpha-sphere Solvent Acc.    : 0.5844
+5  - Mean B-factor of pocket residues  : 0.6654
+6  - Hydrophobicity Score              : 5.1667
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 276.7805
+10  -Pocket volume (convex hull)       : 4.5972
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.1333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     6291    O    O .  GLU   D .    9 ?   72.604   3.890  48.729  0.00  0   D
+ATOM     6300    O    O .  MET   D .   10 ?   74.107   7.374  51.316 -2.14  0   D
+ATOM     6293    C   CG .  GLU   D .    9 ?   71.423   4.039  52.375  0.00  0   D
+ATOM     6312    O  OE1 .  GLU   D .   11 ?   77.808   6.551  52.358  0.00  0   D
+ATOM     6299    C    C .  MET   D .   10 ?   74.371   7.293  50.096  0.00  0   D
+ATOM     6305    N    N .  GLU   D .   11 ?   75.439   7.869  49.548 -2.19  0   D
+ATOM     6309    C   CB .  GLU   D .   11 ?   77.861   8.128  49.916  0.00  0   D
+ATOM     6510    C   CE .  LYS   D .   36 ?   78.782   6.894  42.671  0.00  0   D
+ATOM     6511    N   NZ .  LYS   D .   36 ?   78.219   5.612  42.198  0.00  0   D
+ATOM     6301    C   CB .  MET   D .   10 ?   73.225   7.186  47.771  0.00  0   D
+ATOM     6335    O  OD2 .  ASP   D .   14 ?   78.726   9.496  45.541 -2.55  0   D
+ATOM     6298    C   CA .  MET   D .   10 ?   73.486   6.472  49.131  0.00  0   D
+ATOM     6491    C  CZ2 .  TRP   D .   34 ?   73.535   8.757  43.118  0.00  0   D
+ATOM     6488    N  NE1 .  TRP   D .   34 ?   75.151  10.418  44.105 -1.09  0   D
+# 

tests/reference_output/123abc_out/pocket25_env_atm.cif

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

tests/reference_output/123abc_out/pocket25_vert.pqr

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

tests/reference_output/123abc_out/pocket26_atm.cif

@@ -0,0 +1,69 @@
+data_pocket26_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    26:
+0  - Pocket Score                      : -0.0384
+1  - Drug Score                        : 0.0846
+2  - Number of alpha spheres           :    45
+3  - Mean alpha-sphere radius          : 3.7304
+4  - Mean alpha-sphere Solvent Acc.    : 0.4267
+5  - Mean B-factor of pocket residues  : 0.1353
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 227.3031
+10  -Pocket volume (convex hull)       : 15.0678
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 38.0000
+13 - Number of apolar alpha sphere     :    39
+14 - Proportion of apolar alpha sphere : 0.8667
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1821    C  CG1 .  VAL   A .  241 ?   18.722  33.273   0.801  0.00  0   A
+ATOM      824    N    N .  LEU   A .  114 ?   19.877  26.311  -1.669  0.00  0   A
+ATOM      818    C    C .  LEU   A .  113 ?   20.351  26.072  -0.464  0.00  0   A
+ATOM      825    C   CA .  LEU   A .  114 ?   18.529  26.785  -1.887  0.00  0   A
+ATOM      798    C   CA .  ALA   A .  110 ?   24.131  27.516  -4.659  0.00  0   A
+ATOM     1805    C   CD .  PRO   A .  238 ?   21.822  33.590  -2.836  0.00  0   A
+ATOM     1792    O    O .  GLY   A .  236 ?   25.501  33.661  -3.290 -6.17  0   A
+ATOM      801    C   CB .  ALA   A .  110 ?   24.277  28.499  -5.862  0.00  0   A
+ATOM      819    O    O .  LEU   A .  113 ?   19.663  26.116   0.542 -1.07  0   A
+ATOM      856    C   CB .  ALA   A .  117 ?   16.641  27.654   2.208  0.00  0   A
+ATOM     1539    C  CG2 .  ILE   A .  205 ?   21.953  27.141   3.249  0.00  0   A
+ATOM     1509    C  CD2 .  LEU   A .  202 ?   16.995  30.754   4.286  0.00  0   A
+ATOM     1505    O    O .  LEU   A .  202 ?   21.436  31.217   5.146 -3.21  0   A
+ATOM      820    C   CB .  LEU   A .  113 ?   22.728  26.946  -0.496  0.00  0   A
+ATOM      830    C  CD1 .  LEU   A .  114 ?   17.000  29.244  -2.786  0.00  0   A
+ATOM     2030    C  CE1 .  PHE   A .  266 ?   15.255  30.669   0.284  0.00  0   A
+ATOM      828    C   CB .  LEU   A .  114 ?   18.476  27.301  -3.305  0.00  0   A
+ATOM     1804    C   CG .  PRO   A .  238 ?   21.078  33.317  -4.111  0.00  0   A
+ATOM     1822    C  CG2 .  VAL   A .  241 ?   17.795  32.913  -1.514  0.00  0   A
+ATOM      800    O    O .  ALA   A .  110 ?   21.862  27.166  -3.931 -1.07  0   A
+ATOM     1545    C   CB .  ALA   A .  206 ?   24.087  32.253   2.900  0.00  0   A
+ATOM     1541    N    N .  ALA   A .  206 ?   24.014  29.985   3.998  0.00  0   A
+ATOM     1798    S   SG .  CYS   A .  237 ?   22.030  35.316   0.634  0.00  0   A
+ATOM     1794    C   CA .  CYS   A .  237 ?   24.026  34.922  -1.329  0.00  0   A
+ATOM     1544    O    O .  ALA   A .  206 ?   26.983  31.382   2.492 -3.21  0   A
+ATOM     1542    C   CA .  ALA   A .  206 ?   24.748  30.821   3.023  0.00  0   A
+ATOM      822    C  CD1 .  LEU   A .  113 ?   25.012  27.872  -0.209  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket26_env_atm.cif

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

tests/reference_output/123abc_out/pocket26_vert.pqr

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

tests/reference_output/123abc_out/pocket27_atm.cif

@@ -0,0 +1,58 @@
+data_pocket27_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    27:
+0  - Pocket Score                      : -0.0425
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    17
+3  - Mean alpha-sphere radius          : 3.8983
+4  - Mean alpha-sphere Solvent Acc.    : 0.5210
+5  - Mean B-factor of pocket residues  : 0.3129
+6  - Hydrophobicity Score              : -21.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.7500
+9  - Pocket volume (Monte Carlo)       : 244.3582
+10  -Pocket volume (convex hull)       : 8.0231
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 8.0000
+13 - Number of apolar alpha sphere     :     9
+14 - Proportion of apolar alpha sphere : 0.5294
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     1256    C   CA .  GLY   A .  171 ?   17.074  29.084  34.902  0.00  0   A
+ATOM     3772    C   CB .  GLU   B .  223 ?   20.899  28.443  38.451  0.00  0   B
+ATOM     3769    C   CA .  GLU   B .  223 ?   19.756  29.026  39.321  0.00  0   B
+ATOM     3800    O  OE1 .  GLU   B .  226 ?   14.870  27.408  38.360 -0.81  0   B
+ATOM     1258    O    O .  GLY   A .  171 ?   17.211  27.237  33.384  0.00  0   A
+ATOM     3810    N   NZ .  LYS   B .  227 ?   18.871  22.046  40.724  0.00  0   B
+ATOM     3799    C   CD .  GLU   B .  226 ?   13.993  27.306  39.282  0.00  0   B
+ATOM     3798    C   CG .  GLU   B .  226 ?   14.425  27.213  40.755  0.00  0   B
+ATOM     3809    C   CE .  LYS   B .  227 ?   19.628  23.270  41.089  0.00  0   B
+ATOM     3774    C   CD .  GLU   B .  223 ?   21.775  28.184  36.070  0.00  0   B
+ATOM     3775    O  OE1 .  GLU   B .  223 ?   22.737  27.521  36.550  0.00  0   B
+ATOM     3771    O    O .  GLU   B .  223 ?   19.336  27.833  41.335  0.00  0   B
+ATOM     3797    C   CB .  GLU   B .  226 ?   15.576  28.210  41.069  0.00  0   B
+ATOM     3773    C   CG .  GLU   B .  223 ?   20.865  28.953  37.013  0.00  0   B
+ATOM     3808    C   CD .  LYS   B .  227 ?   19.254  23.527  42.569  0.00  0   B
+ATOM     3796    O    O .  GLU   B .  226 ?   15.035  26.681  43.850  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket27_env_atm.cif

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

tests/reference_output/123abc_out/pocket27_vert.pqr

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

tests/reference_output/123abc_out/pocket28_atm.cif

@@ -0,0 +1,54 @@
+data_pocket28_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    28:
+0  - Pocket Score                      : -0.0435
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 3.8178
+4  - Mean alpha-sphere Solvent Acc.    : 0.5111
+5  - Mean B-factor of pocket residues  : 0.2583
+6  - Hydrophobicity Score              : 47.8000
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 4.6000
+9  - Pocket volume (Monte Carlo)       : 153.5727
+10  -Pocket volume (convex hull)       : 1.1933
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.4000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     5155    C    C .  ASN   C .  131 ?   49.791  69.967  16.216  0.00  0   C
+ATOM     5164    O    O .  PHE   C .  132 ?   48.967  66.829  17.018  0.00  0   C
+ATOM     5154    C   CA .  ASN   C .  131 ?   49.335  70.969  17.293  0.00  0   C
+ATOM     5156    O    O .  ASN   C .  131 ?   49.458  70.110  15.000 -2.55  0   C
+ATOM     5177    C  CG1 .  ILE   C .  133 ?   46.547  66.252  14.171  0.00  0   C
+ATOM     5179    C  CD1 .  ILE   C .  133 ?   45.747  66.718  12.918  0.00  0   C
+ATOM     5159    O  OD1 .  ASN   C .  131 ?   46.848  72.862  17.330  0.00  0   C
+ATOM     5600    C  CG1 .  ILE   C .  191 ?   45.611  66.019  19.250  0.00  0   C
+ATOM     5129    O    O .  GLU   C .  128 ?   48.054  70.332  20.849 -1.48  0   C
+ATOM     5595    N    N .  ILE   C .  191 ?   43.539  65.578  16.244  0.00  0   C
+ATOM     5599    C   CB .  ILE   C .  191 ?   44.408  66.418  18.397  0.00  0   C
+ATOM     5601    C  CG2 .  ILE   C .  191 ?   43.280  67.132  19.172  0.00  0   C
+# 

tests/reference_output/123abc_out/pocket28_env_atm.cif

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

tests/reference_output/123abc_out/pocket28_vert.pqr

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

tests/reference_output/123abc_out/pocket29_atm.cif

@@ -0,0 +1,60 @@
+data_pocket29_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    29:
+0  - Pocket Score                      : -0.0486
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    18
+3  - Mean alpha-sphere radius          : 4.0946
+4  - Mean alpha-sphere Solvent Acc.    : 0.6067
+5  - Mean B-factor of pocket residues  : 0.3394
+6  - Hydrophobicity Score              : 23.8333
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.0833
+9  - Pocket volume (Monte Carlo)       : 280.7122
+10  -Pocket volume (convex hull)       : 12.3014
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 4.0000
+13 - Number of apolar alpha sphere     :     5
+14 - Proportion of apolar alpha sphere : 0.2778
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM      633    C  CE1 .  PHE   A .   90 ?   23.219   7.620  12.523  0.00  0   A
+ATOM      115    C  CD2 .  LEU   A .   21 ?   23.833   8.296  15.998  0.00  0   A
+ATOM      116    N    N .  GLY   A .   22 ?   26.977  10.989  17.772  0.00  0   A
+ATOM      664    C   CA .  GLY   A .   94 ?   24.159  13.940  10.732  0.00  0   A
+ATOM      148    O   OH .  TYR   A .   26 ?   24.138  15.654  15.314  0.00  0   A
+ATOM      667    N    N .  ASN   A .   95 ?   23.996  16.143  11.694  0.00  0   A
+ATOM      673    O  OD1 .  ASN   A .   95 ?   25.880  18.114  13.960 -2.14  0   A
+ATOM      135    O  OE1 .  GLN   A .   25 ?   27.558  15.740  17.545 -2.14  0   A
+ATOM      117    C   CA .  GLY   A .   22 ?   27.711  12.259  17.704  0.00  0   A
+ATOM      635    C   CZ .  PHE   A .   90 ?   23.754   7.359  11.279  0.00  0   A
+ATOM      639    O    O .  MET   A .   91 ?   22.317  10.826   9.705  0.00  0   A
+ATOM      647    O    O .  THR   A .   92 ?   25.377  10.176   8.230  0.00  0   A
+ATOM      698    O  OD2 .  ASP   A .   98 ?   28.581  18.421  13.874  0.00  0   A
+ATOM      695    C   CB .  ASP   A .   98 ?   28.818  18.983  11.564  0.00  0   A
+ATOM      654    O    O .  TYR   A .   93 ?   25.886  14.436   8.543 -2.95  0   A
+ATOM      737    O  OE1 .  GLU   A .  102 ?   31.683  16.733   9.180  0.00  0   A
+ATOM      738    O  OE2 .  GLU   A .  102 ?   32.646  17.951  10.762 -1.88  0   A
+ATOM      145    C  CE1 .  TYR   A .   26 ?   24.215  14.118  17.108  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket29_env_atm.cif

@@ -0,0 +1,55 @@
+data_pocket29_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM      109    C   CA .  LEU   A .   21 ?   25.411   9.365  18.618  0.00  0   A
+ATOM      110    C    C .  LEU   A .   21 ?   26.217  10.637  18.809  0.00  0   A
+ATOM      112    C   CB .  LEU   A .   21 ?   24.055   9.763  18.043  0.00  0   A
+ATOM      113    C   CG .  LEU   A .   21 ?   23.240   8.692  17.348  0.00  0   A
+ATOM      115    C  CD2 .  LEU   A .   21 ?   23.833   8.296  15.998  0.00  0   A
+ATOM      116    N    N .  GLY   A .   22 ?   26.977  10.989  17.772  0.00  0   A
+ATOM      117    C   CA .  GLY   A .   22 ?   27.711  12.259  17.704  0.00  0   A
+ATOM      134    C   CD .  GLN   A .   25 ?   26.983  16.776  17.929  0.00  0   A
+ATOM      135    O  OE1 .  GLN   A .   25 ?   27.558  15.740  17.545 -2.14  0   A
+ATOM      136    N  NE2 .  GLN   A .   25 ?   26.655  17.754  17.106 -1.51  0   A
+ATOM      143    C  CD1 .  TYR   A .   26 ?   23.817  13.724  18.368  0.00  0   A
+ATOM      145    C  CE1 .  TYR   A .   26 ?   24.215  14.118  17.108  0.00  0   A
+ATOM      147    C   CZ .  TYR   A .   26 ?   23.727  15.310  16.576  0.00  0   A
+ATOM      148    O   OH .  TYR   A .   26 ?   24.138  15.654  15.314  0.00  0   A
+ATOM      633    C  CE1 .  PHE   A .   90 ?   23.219   7.620  12.523  0.00  0   A
+ATOM      635    C   CZ .  PHE   A .   90 ?   23.754   7.359  11.279  0.00  0   A
+ATOM      639    O    O .  MET   A .   91 ?   22.317  10.826   9.705  0.00  0   A
+ATOM      646    C    C .  THR   A .   92 ?   24.325  10.445   7.647  0.00  0   A
+ATOM      647    O    O .  THR   A .   92 ?   25.377  10.176   8.230  0.00  0   A
+ATOM      653    C    C .  TYR   A .   93 ?   25.046  13.581   8.441  0.00  0   A
+ATOM      654    O    O .  TYR   A .   93 ?   25.886  14.436   8.543 -2.95  0   A
+ATOM      663    N    N .  GLY   A .   94 ?   24.175  13.288   9.414  0.00  0   A
+ATOM      664    C   CA .  GLY   A .   94 ?   24.159  13.940  10.732  0.00  0   A
+ATOM      665    C    C .  GLY   A .   94 ?   23.592  15.331  10.711  0.00  0   A
+ATOM      667    N    N .  ASN   A .   95 ?   23.996  16.143  11.694  0.00  0   A
+ATOM      668    C   CA .  ASN   A .   95 ?   23.482  17.523  11.792  0.00  0   A
+ATOM      670    O    O .  ASN   A .   95 ?   25.129  18.291  10.166  0.00  0   A
+ATOM      672    C   CG .  ASN   A .   95 ?   24.977  18.738  13.399  0.00  0   A
+ATOM      673    O  OD1 .  ASN   A .   95 ?   25.880  18.114  13.960 -2.14  0   A
+ATOM      695    C   CB .  ASP   A .   98 ?   28.818  18.983  11.564  0.00  0   A
+ATOM      696    C   CG .  ASP   A .   98 ?   28.941  19.302  13.063  0.00  0   A
+ATOM      698    O  OD2 .  ASP   A .   98 ?   28.581  18.421  13.874  0.00  0   A
+ATOM      736    C   CD .  GLU   A .  102 ?   32.361  17.729   9.573  0.00  0   A
+ATOM      737    O  OE1 .  GLU   A .  102 ?   31.683  16.733   9.180  0.00  0   A
+ATOM      738    O  OE2 .  GLU   A .  102 ?   32.646  17.951  10.762 -1.88  0   A
+#

tests/reference_output/123abc_out/pocket29_vert.pqr

@@ -0,0 +1,20 @@
+ATOM      1    C STP    29      26.501  10.802  13.181    0.00     4.62
+ATOM      2    O STP    29      27.345  14.426  13.176    0.00     4.05
+ATOM      3    O STP    29      27.867  13.817  13.407    0.00     4.57
+ATOM      4    C STP    29      25.186  10.654  11.968    0.00     3.66
+ATOM      5    O STP    29      25.270  10.640  11.859    0.00     3.66
+ATOM      6    O STP    29      28.039  13.821  13.320    0.00     4.67
+ATOM      7    O STP    29      27.893  13.935  13.363    0.00     4.57
+ATOM      8    O STP    29      27.667  14.237  13.248    0.00     4.33
+ATOM      9    O STP    29      27.652  14.502  13.710    0.00     4.03
+ATOM     10    O STP    29      27.610  14.613  12.794    0.00     4.08
+ATOM     11    O STP    29      27.445  15.813  11.887    0.00     3.47
+ATOM     12    O STP    29      27.806  14.969  12.010    0.00     4.00
+ATOM     13    O STP    29      27.744  15.301  11.793    0.00     3.84
+ATOM     14    O STP    29      30.269  15.937  12.207    0.00     3.43
+ATOM     15    O STP    29      28.849  14.622  11.742    0.00     4.36
+ATOM     16    C STP    29      25.360  11.610  13.977    0.00     4.17
+ATOM     17    C STP    29      26.019  12.187  13.955    0.00     4.11
+ATOM     18    C STP    29      26.102  12.342  13.950    0.00     4.08
+TER
+END

tests/reference_output/123abc_out/pocket2_atm.cif

@@ -0,0 +1,142 @@
+data_pocket2_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket     2:
+0  - Pocket Score                      : 0.9163
+1  - Drug Score                        : 0.9867
+2  - Number of alpha spheres           :   194
+3  - Mean alpha-sphere radius          : 3.9774
+4  - Mean alpha-sphere Solvent Acc.    : 0.4989
+5  - Mean B-factor of pocket residues  : 0.2573
+6  - Hydrophobicity Score              : 37.0000
+7  - Polarity Score                    :    16
+8  - Amino Acid based volume Score     : 4.1892
+9  - Pocket volume (Monte Carlo)       : 1476.5808
+10  -Pocket volume (convex hull)       : 979.8676
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 59.3440
+13 - Number of apolar alpha sphere     :   125
+14 - Proportion of apolar alpha sphere : 0.6443
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     6631    O  OE1 .  GLU   D .   55 ?   52.035  10.097  57.244  0.00  0   D
+ATOM     6656    C   CB .  LYS   D .   58 ?   55.399   5.853  55.510  0.00  0   D
+ATOM     6682    C  CG2 .  VAL   D .   62 ?   54.426   5.381  50.458  0.00  0   D
+ATOM     6657    N    N .  GLU   D .   59 ?   57.037   7.697  53.496  0.00  0   D
+ATOM     6663    C   CD .  GLU   D .   59 ?   57.497  12.310  51.368  0.00  0   D
+ATOM     7425    C   CA .  GLY   D .  156 ?   53.352  17.790  52.036  0.00  0   D
+ATOM     7412    O  OD2 .  ASP   D .  154 ?   51.451  13.986  48.870 -1.62  0   D
+ATOM     6664    O  OE1 .  GLU   D .   59 ?   57.674  12.906  52.458 -2.28  0   D
+ATOM     6658    C   CA .  GLU   D .   59 ?   57.186   8.499  52.273  0.00  0   D
+ATOM     7239    C  CD2 .  PHE   D .  132 ?   50.695   4.565  46.284  0.00  0   D
+ATOM     6713    C  CD1 .  ILE   D .   66 ?   54.653   7.398  44.141  0.00  0   D
+ATOM     7196    C  CD2 .  LEU   D .  127 ?   50.885   7.312  42.017  0.00  0   D
+ATOM     7236    C   CB .  PHE   D .  132 ?   48.964   5.452  44.735  0.00  0   D
+ATOM     6926    C   CA .  GLY   D .   94 ?   60.034  24.932  39.574  0.00  0   D
+ATOM     6395    N    N .  GLY   D .   22 ?   63.445  27.361  46.787 -2.19  0   D
+ATOM     6396    C   CA .  GLY   D .   22 ?   62.352  28.355  46.720  0.00  0   D
+ATOM     6424    C  CE1 .  TYR   D .   26 ?   59.877  24.854  46.075  0.00  0   D
+ATOM     6897    C   CZ .  PHE   D .   90 ?   66.475  23.808  40.403  0.00  0   D
+ATOM     6909    O    O .  THR   D .   92 ?   63.997  25.572  36.851  0.00  0   D
+ATOM     6925    N    N .  GLY   D .   94 ?   60.701  24.762  38.280  0.00  0   D
+ATOM     7409    C   CB .  ASP   D .  154 ?   52.864  14.692  47.175  0.00  0   D
+ATOM     6751    C  CD2 .  LEU   D .   71 ?   53.389  10.979  40.449  0.00  0   D
+ATOM     7258    C  CD2 .  HIS   D .  134 ?   49.543  13.548  43.730  0.00  0   D
+ATOM     6654    C    C .  LYS   D .   58 ?   56.799   6.379  53.467  0.00  0   D
+ATOM     7424    N    N .  GLY   D .  156 ?   53.836  17.822  50.662  0.00  0   D
+ATOM     7408    O    O .  ASP   D .  154 ?   55.352  15.791  48.188  0.00  0   D
+ATOM     6572    N   NZ .  LYS   D .   44 ?   57.996  15.644  52.375 -3.28  0   D
+ATOM     6662    C   CG .  GLU   D .   59 ?   57.119  10.830  51.310  0.00  0   D
+ATOM     6661    C   CB .  GLU   D .   59 ?   57.413   9.994  52.562  0.00  0   D
+ATOM     6629    C   CG .  GLU   D .   55 ?   54.143  11.051  57.889  0.00  0   D
+ATOM     6665    O  OE2 .  GLU   D .   59 ?   57.595  12.886  50.275  0.00  0   D
+ATOM     6570    C   CD .  LYS   D .   44 ?   60.499  15.433  51.975  0.00  0   D
+ATOM     6689    S   SD .  MET   D .   63 ?   59.342  10.341  47.098  0.00  0   D
+ATOM     6447    C  CG2 .  VAL   D .   29 ?   61.867  19.746  50.754  0.00  0   D
+ATOM     7414    C   CA .  PHE   D .  155 ?   55.356  18.410  48.844  0.00  0   D
+ATOM     7416    O    O .  PHE   D .  155 ?   55.635  19.113  51.089 -1.07  0   D
+ATOM     6571    C   CE .  LYS   D .   44 ?   59.381  16.004  52.877  0.00  0   D
+ATOM     6681    C  CG1 .  VAL   D .   62 ?   53.788   5.636  48.109  0.00  0   D
+ATOM     7329    C  CD1 .  LEU   D .  143 ?   59.244  18.841  41.193  0.00  0   D
+ATOM     6758    C  CG2 .  VAL   D .   72 ?   60.178  15.150  41.326  0.00  0   D
+ATOM     6876    O  OG1 .  THR   D .   88 ?   63.295  15.440  44.108  0.00  0   D
+ATOM     7422    C  CE2 .  PHE   D .  155 ?   57.327  18.902  44.964  0.00  0   D
+ATOM     7402    C    C .  ALA   D .  153 ?   53.826  15.699  44.308  0.00  0   D
+ATOM     7401    C   CA .  ALA   D .  153 ?   54.851  15.556  43.189  0.00  0   D
+ATOM     6757    C  CG1 .  VAL   D .   72 ?   58.423  13.974  42.618  0.00  0   D
+ATOM     7195    C  CD1 .  LEU   D .  127 ?   49.551   9.478  41.993  0.00  0   D
+ATOM     6755    O    O .  VAL   D .   72 ?   59.541  11.227  41.576 -7.50  0   D
+ATOM     6748    C   CB .  LEU   D .   71 ?   55.487  10.215  39.179  0.00  0   D
+ATOM     6711    C  CG1 .  ILE   D .   66 ?   55.748   6.675  43.366  0.00  0   D
+ATOM     6752    N    N .  VAL   D .   72 ?   57.585  12.696  39.928 -1.09  0   D
+ATOM     6627    O    O .  GLU   D .   55 ?   56.504   9.379  56.126 -3.21  0   D
+ATOM     6427    O   OH .  TYR   D .   26 ?   58.288  24.914  44.228 -2.14  0   D
+ATOM     6414    O  OE1 .  GLN   D .   25 ?   58.455  28.443  46.071 -5.09  0   D
+ATOM     6929    N    N .  ASN   D .   95 ?   57.778  24.953  40.502 -2.19  0   D
+ATOM     6935    O  OD1 .  ASN   D .   95 ?   56.159  26.889  42.866 -2.14  0   D
+ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
+ATOM     6957    C   CB .  ASP   D .   98 ?   55.535  30.185  40.403  0.00  0   D
+ATOM     6916    O    O .  TYR   D .   93 ?   59.826  26.639  37.454  0.00  0   D
+ATOM     7420    C  CD2 .  PHE   D .  155 ?   56.995  18.870  46.332  0.00  0   D
+ATOM     6446    C  CG1 .  VAL   D .   29 ?   63.424  19.965  48.777  0.00  0   D
+ATOM     6420    C   CB .  TYR   D .   26 ?   59.704  22.984  49.387  0.00  0   D
+ATOM     7404    C   CB .  ALA   D .  153 ?   55.891  16.596  43.353  0.00  0   D
+ATOM     6555    O    O .  ALA   D .   42 ?   66.250  15.967  46.440  0.00  0   D
+ATOM     6564    N    N .  LYS   D .   44 ?   65.071  16.285  50.374  0.00  0   D
+ATOM     6688    C   CG .  MET   D .   63 ?   58.233   8.978  46.901  0.00  0   D
+ATOM     6680    C   CB .  VAL   D .   62 ?   54.934   5.664  49.113  0.00  0   D
+ATOM     6660    O    O .  GLU   D .   59 ?   57.982   7.657  50.173  0.00  0   D
+ATOM     6556    C   CB .  ALA   D .   42 ?   64.982  18.340  44.987  0.00  0   D
+ATOM     6881    O    O .  GLU   D .   89 ?   64.168  16.713  41.645  0.00  0   D
+ATOM     6898    N    N .  MET   D .   91 ?   63.736  19.963  39.260  0.00  0   D
+ATOM     6393    C  CD1 .  LEU   D .   21 ?   64.675  22.066  45.945  0.00  0   D
+ATOM     6888    C   CA .  PHE   D .   90 ?   65.499  18.836  40.501  0.00  0   D
+ATOM     6394    C  CD2 .  LEU   D .   21 ?   66.139  23.878  45.329  0.00  0   D
+ATOM     6376    C  CE1 .  HIS   D .   19 ?   68.713  27.227  46.138  0.00  0   D
+ATOM     6893    C  CD1 .  PHE   D .   90 ?   66.360  21.823  41.727  0.00  0   D
+ATOM     6901    O    O .  MET   D .   91 ?   63.034  22.679  38.496  0.00  0   D
+ATOM     6877    C  CG2 .  THR   D .   88 ?   62.489  13.239  44.727  0.00  0   D
+ATOM     6861    C  CG2 .  ILE   D .   86 ?   62.965  11.227  49.042  0.00  0   D
+ATOM     7405    N    N .  ASP   D .  154 ?   54.325  15.719  45.523  0.00  0   D
+ATOM     6426    C   CZ .  TYR   D .   26 ?   58.649  24.458  45.487  0.00  0   D
+ATOM     7330    C  CD2 .  LEU   D .  143 ?   58.782  21.410  41.356  0.00  0   D
+ATOM     6421    C   CG .  TYR   D .   26 ?   59.341  23.509  48.032  0.00  0   D
+ATOM     6423    C  CD2 .  TYR   D .   26 ?   58.135  23.117  47.412  0.00  0   D
+ATOM     6422    C  CD1 .  TYR   D .   26 ?   60.183  24.385  47.362  0.00  0   D
+ATOM     6425    C  CE2 .  TYR   D .   26 ?   57.795  23.589  46.140  0.00  0   D
+ATOM     7423    C   CZ .  PHE   D .  155 ?   56.783  19.883  44.153  0.00  0   D
+ATOM     7417    C   CB .  PHE   D .  155 ?   55.748  19.792  48.329  0.00  0   D
+ATOM     7396    O    O .  VAL   D .  152 ?   55.001  14.074  40.818  0.00  0   D
+ATOM     6690    C   CE .  MET   D .   63 ?   59.360  10.409  48.847  0.00  0   D
+ATOM     6915    C    C .  TYR   D .   93 ?   60.588  25.697  37.338  0.00  0   D
+ATOM     6391    C   CB .  LEU   D .   21 ?   64.362  24.273  46.981  0.00  0   D
+ATOM     6895    C  CE1 .  PHE   D .   90 ?   66.251  23.209  41.616  0.00  0   D
+ATOM     6467    O  OE1 .  GLU   D .   31 ?   70.105  25.647  44.001  0.00  0   D
+ATOM     7246    O    O .  ILE   D .  133 ?   47.623   9.183  47.095  0.00  0   D
+ATOM     6858    O    O .  ILE   D .   86 ?   65.641  13.840  49.353  0.00  0   D
+ATOM     7252    C   CA .  HIS   D .  134 ?   47.370  11.498  45.668  0.00  0   D
+ATOM     7254    O    O .  HIS   D .  134 ?   47.812  12.555  47.804  0.00  0   D
+ATOM     7403    O    O .  ALA   D .  153 ?   52.619  15.769  44.076  0.00  0   D
+ATOM     6568    C   CB .  LYS   D .   44 ?   62.898  15.688  51.283  0.00  0   D
+ATOM     7260    N  NE2 .  HIS   D .  134 ?   50.218  14.635  44.230  0.00  0   D
+# 

tests/reference_output/123abc_out/pocket2_env_atm.cif

@@ -0,0 +1,197 @@
+data_pocket2_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     6374    N  ND1 .  HIS   D .   19 ?   68.624  27.394  47.446  0.00  0   D
+ATOM     6376    C  CE1 .  HIS   D .   19 ?   68.713  27.227  46.138  0.00  0   D
+ATOM     6377    N  NE2 .  HIS   D .   19 ?   69.990  27.294  45.797  0.00  0   D
+ATOM     6388    C   CA .  LEU   D .   21 ?   64.781  25.564  47.694  0.00  0   D
+ATOM     6389    C    C .  LEU   D .   21 ?   63.581  26.477  47.783  0.00  0   D
+ATOM     6391    C   CB .  LEU   D .   21 ?   64.362  24.273  46.981  0.00  0   D
+ATOM     6392    C   CG .  LEU   D .   21 ?   65.376  23.265  46.446  0.00  0   D
+ATOM     6393    C  CD1 .  LEU   D .   21 ?   64.675  22.066  45.945  0.00  0   D
+ATOM     6394    C  CD2 .  LEU   D .   21 ?   66.139  23.878  45.329  0.00  0   D
+ATOM     6395    N    N .  GLY   D .   22 ?   63.445  27.361  46.787 -2.19  0   D
+ATOM     6396    C   CA .  GLY   D .   22 ?   62.352  28.355  46.720  0.00  0   D
+ATOM     6413    C   CD .  GLN   D .   25 ?   57.407  27.989  46.515  0.00  0   D
+ATOM     6414    O  OE1 .  GLN   D .   25 ?   58.455  28.443  46.071 -5.09  0   D
+ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
+ATOM     6419    O    O .  TYR   D .   26 ?   59.073  21.717  51.991 -1.07  0   D
+ATOM     6420    C   CB .  TYR   D .   26 ?   59.704  22.984  49.387  0.00  0   D
+ATOM     6421    C   CG .  TYR   D .   26 ?   59.341  23.509  48.032  0.00  0   D
+ATOM     6422    C  CD1 .  TYR   D .   26 ?   60.183  24.385  47.362  0.00  0   D
+ATOM     6423    C  CD2 .  TYR   D .   26 ?   58.135  23.117  47.412  0.00  0   D
+ATOM     6424    C  CE1 .  TYR   D .   26 ?   59.877  24.854  46.075  0.00  0   D
+ATOM     6425    C  CE2 .  TYR   D .   26 ?   57.795  23.589  46.140  0.00  0   D
+ATOM     6426    C   CZ .  TYR   D .   26 ?   58.649  24.458  45.487  0.00  0   D
+ATOM     6427    O   OH .  TYR   D .   26 ?   58.288  24.914  44.228 -2.14  0   D
+ATOM     6445    C   CB .  VAL   D .   29 ?   62.944  20.625  50.067  0.00  0   D
+ATOM     6446    C  CG1 .  VAL   D .   29 ?   63.424  19.965  48.777  0.00  0   D
+ATOM     6447    C  CG2 .  VAL   D .   29 ?   61.867  19.746  50.754  0.00  0   D
+ATOM     6466    C   CD .  GLU   D .   31 ?   70.736  24.607  43.729  0.00  0   D
+ATOM     6467    O  OE1 .  GLU   D .   31 ?   70.105  25.647  44.001  0.00  0   D
+ATOM     6553    C   CA .  ALA   D .   42 ?   66.460  18.078  45.473  0.00  0   D
+ATOM     6554    C    C .  ALA   D .   42 ?   66.467  17.150  46.611  0.00  0   D
+ATOM     6555    O    O .  ALA   D .   42 ?   66.250  15.967  46.440  0.00  0   D
+ATOM     6556    C   CB .  ALA   D .   42 ?   64.982  18.340  44.987  0.00  0   D
+ATOM     6557    N    N .  VAL   D .   43 ?   66.710  17.707  47.791  0.00  0   D
+ATOM     6558    C   CA .  VAL   D .   43 ?   66.934  16.896  48.965  0.00  0   D
+ATOM     6559    C    C .  VAL   D .   43 ?   65.965  17.202  50.086  0.00  0   D
+ATOM     6564    N    N .  LYS   D .   44 ?   65.071  16.285  50.374  0.00  0   D
+ATOM     6565    C   CA .  LYS   D .   44 ?   64.214  16.433  51.505  0.00  0   D
+ATOM     6568    C   CB .  LYS   D .   44 ?   62.898  15.688  51.283  0.00  0   D
+ATOM     6569    C   CG .  LYS   D .   44 ?   61.806  16.127  52.262  0.00  0   D
+ATOM     6570    C   CD .  LYS   D .   44 ?   60.499  15.433  51.975  0.00  0   D
+ATOM     6571    C   CE .  LYS   D .   44 ?   59.381  16.004  52.877  0.00  0   D
+ATOM     6572    N   NZ .  LYS   D .   44 ?   57.996  15.644  52.375 -3.28  0   D
+ATOM     6626    C    C .  GLU   D .   55 ?   56.900   9.604  57.277  0.00  0   D
+ATOM     6627    O    O .  GLU   D .   55 ?   56.504   9.379  56.126 -3.21  0   D
+ATOM     6629    C   CG .  GLU   D .   55 ?   54.143  11.051  57.889  0.00  0   D
+ATOM     6630    C   CD .  GLU   D .   55 ?   52.863  10.284  58.185  0.00  0   D
+ATOM     6631    O  OE1 .  GLU   D .   55 ?   52.035  10.097  57.244  0.00  0   D
+ATOM     6653    C   CA .  LYS   D .   58 ?   56.760   5.661  54.816  0.00  0   D
+ATOM     6654    C    C .  LYS   D .   58 ?   56.799   6.379  53.467  0.00  0   D
+ATOM     6655    O    O .  LYS   D .   58 ?   56.637   5.732  52.412  0.00  0   D
+ATOM     6656    C   CB .  LYS   D .   58 ?   55.399   5.853  55.510  0.00  0   D
+ATOM     6657    N    N .  GLU   D .   59 ?   57.037   7.697  53.496  0.00  0   D
+ATOM     6658    C   CA .  GLU   D .   59 ?   57.186   8.499  52.273  0.00  0   D
+ATOM     6659    C    C .  GLU   D .   59 ?   58.269   7.947  51.334  0.00  0   D
+ATOM     6660    O    O .  GLU   D .   59 ?   57.982   7.657  50.173  0.00  0   D
+ATOM     6661    C   CB .  GLU   D .   59 ?   57.413   9.994  52.562  0.00  0   D
+ATOM     6662    C   CG .  GLU   D .   59 ?   57.119  10.830  51.310  0.00  0   D
+ATOM     6663    C   CD .  GLU   D .   59 ?   57.497  12.310  51.368  0.00  0   D
+ATOM     6664    O  OE1 .  GLU   D .   59 ?   57.674  12.906  52.458 -2.28  0   D
+ATOM     6665    O  OE2 .  GLU   D .   59 ?   57.595  12.886  50.275  0.00  0   D
+ATOM     6680    C   CB .  VAL   D .   62 ?   54.934   5.664  49.113  0.00  0   D
+ATOM     6681    C  CG1 .  VAL   D .   62 ?   53.788   5.636  48.109  0.00  0   D
+ATOM     6682    C  CG2 .  VAL   D .   62 ?   54.426   5.381  50.458  0.00  0   D
+ATOM     6683    N    N .  MET   D .   63 ?   57.661   5.982  47.544  0.00  0   D
+ATOM     6684    C   CA .  MET   D .   63 ?   58.332   6.530  46.387  0.00  0   D
+ATOM     6687    C   CB .  MET   D .   63 ?   59.097   7.770  46.788  0.00  0   D
+ATOM     6688    C   CG .  MET   D .   63 ?   58.233   8.978  46.901  0.00  0   D
+ATOM     6689    S   SD .  MET   D .   63 ?   59.342  10.341  47.098  0.00  0   D
+ATOM     6690    C   CE .  MET   D .   63 ?   59.360  10.409  48.847  0.00  0   D
+ATOM     6711    C  CG1 .  ILE   D .   66 ?   55.748   6.675  43.366  0.00  0   D
+ATOM     6713    C  CD1 .  ILE   D .   66 ?   54.653   7.398  44.141  0.00  0   D
+ATOM     6745    C   CA .  LEU   D .   71 ?   56.003  11.469  38.527  0.00  0   D
+ATOM     6746    C    C .  LEU   D .   71 ?   57.426  11.851  38.922  0.00  0   D
+ATOM     6748    C   CB .  LEU   D .   71 ?   55.487  10.215  39.179  0.00  0   D
+ATOM     6749    C   CG .  LEU   D .   71 ?   53.967  10.145  39.248  0.00  0   D
+ATOM     6750    C  CD1 .  LEU   D .   71 ?   53.599   8.721  39.390  0.00  0   D
+ATOM     6751    C  CD2 .  LEU   D .   71 ?   53.389  10.979  40.449  0.00  0   D
+ATOM     6752    N    N .  VAL   D .   72 ?   57.585  12.696  39.928 -1.09  0   D
+ATOM     6753    C   CA .  VAL   D .   72 ?   58.931  13.215  40.228  0.00  0   D
+ATOM     6754    C    C .  VAL   D .   72 ?   59.856  12.001  40.654  0.00  0   D
+ATOM     6755    O    O .  VAL   D .   72 ?   59.541  11.227  41.576 -7.50  0   D
+ATOM     6756    C   CB .  VAL   D .   72 ?   58.870  14.428  41.240  0.00  0   D
+ATOM     6757    C  CG1 .  VAL   D .   72 ?   58.423  13.974  42.618  0.00  0   D
+ATOM     6758    C  CG2 .  VAL   D .   72 ?   60.178  15.150  41.326  0.00  0   D
+ATOM     6856    C   CA .  ILE   D .   86 ?   65.111  11.772  50.324  0.00  0   D
+ATOM     6857    C    C .  ILE   D .   86 ?   65.591  12.642  49.200  0.00  0   D
+ATOM     6858    O    O .  ILE   D .   86 ?   65.641  13.840  49.353  0.00  0   D
+ATOM     6859    C   CB .  ILE   D .   86 ?   63.580  11.714  50.371  0.00  0   D
+ATOM     6861    C  CG2 .  ILE   D .   86 ?   62.965  11.227  49.042  0.00  0   D
+ATOM     6863    N    N .  ILE   D .   87 ?   66.006  12.036  48.105  0.00  0   D
+ATOM     6871    N    N .  THR   D .   88 ?   65.495  13.640  45.119  0.00  0   D
+ATOM     6875    C   CB .  THR   D .   88 ?   63.341  14.038  43.772  0.00  0   D
+ATOM     6876    O  OG1 .  THR   D .   88 ?   63.295  15.440  44.108  0.00  0   D
+ATOM     6877    C  CG2 .  THR   D .   88 ?   62.489  13.239  44.727  0.00  0   D
+ATOM     6880    C    C .  GLU   D .   89 ?   65.113  16.493  40.871  0.00  0   D
+ATOM     6881    O    O .  GLU   D .   89 ?   64.168  16.713  41.645  0.00  0   D
+ATOM     6887    N    N .  PHE   D .   90 ?   65.755  17.460  40.261 -1.09  0   D
+ATOM     6888    C   CA .  PHE   D .   90 ?   65.499  18.836  40.501  0.00  0   D
+ATOM     6889    C    C .  PHE   D .   90 ?   64.882  19.302  39.199  0.00  0   D
+ATOM     6891    C   CB .  PHE   D .   90 ?   66.817  19.555  40.732  0.00  0   D
+ATOM     6892    C   CG .  PHE   D .   90 ?   66.705  21.047  40.608  0.00  0   D
+ATOM     6893    C  CD1 .  PHE   D .   90 ?   66.360  21.823  41.727  0.00  0   D
+ATOM     6895    C  CE1 .  PHE   D .   90 ?   66.251  23.209  41.616  0.00  0   D
+ATOM     6896    C  CE2 .  PHE   D .   90 ?   66.827  23.019  39.259  0.00  0   D
+ATOM     6897    C   CZ .  PHE   D .   90 ?   66.475  23.808  40.403  0.00  0   D
+ATOM     6898    N    N .  MET   D .   91 ?   63.736  19.963  39.260  0.00  0   D
+ATOM     6899    C   CA .  MET   D .   91 ?   63.043  20.365  38.022  0.00  0   D
+ATOM     6900    C    C .  MET   D .   91 ?   63.336  21.794  37.710  0.00  0   D
+ATOM     6901    O    O .  MET   D .   91 ?   63.034  22.679  38.496  0.00  0   D
+ATOM     6902    C   CB .  MET   D .   91 ?   61.552  20.075  38.131  0.00  0   D
+ATOM     6908    C    C .  THR   D .   92 ?   63.568  24.501  36.393  0.00  0   D
+ATOM     6909    O    O .  THR   D .   92 ?   63.997  25.572  36.851  0.00  0   D
+ATOM     6914    C   CA .  TYR   D .   93 ?   61.441  25.543  36.069  0.00  0   D
+ATOM     6915    C    C .  TYR   D .   93 ?   60.588  25.697  37.338  0.00  0   D
+ATOM     6916    O    O .  TYR   D .   93 ?   59.826  26.639  37.454  0.00  0   D
+ATOM     6925    N    N .  GLY   D .   94 ?   60.701  24.762  38.280  0.00  0   D
+ATOM     6926    C   CA .  GLY   D .   94 ?   60.034  24.932  39.574  0.00  0   D
+ATOM     6927    C    C .  GLY   D .   94 ?   58.584  24.495  39.537  0.00  0   D
+ATOM     6929    N    N .  ASN   D .   95 ?   57.778  24.953  40.502 -2.19  0   D
+ATOM     6930    C   CA .  ASN   D .   95 ?   56.386  24.517  40.572  0.00  0   D
+ATOM     6932    O    O .  ASN   D .   95 ?   55.729  26.285  39.010  0.00  0   D
+ATOM     6934    C   CG .  ASN   D .   95 ?   55.423  26.157  42.216  0.00  0   D
+ATOM     6935    O  OD1 .  ASN   D .   95 ?   56.159  26.889  42.866 -2.14  0   D
+ATOM     6957    C   CB .  ASP   D .   98 ?   55.535  30.185  40.403  0.00  0   D
+ATOM     6958    C   CG .  ASP   D .   98 ?   55.143  30.209  41.861  0.00  0   D
+ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
+ATOM     7194    C   CG .  LEU   D .  127 ?   49.824   8.196  41.228  0.00  0   D
+ATOM     7195    C  CD1 .  LEU   D .  127 ?   49.551   9.478  41.993  0.00  0   D
+ATOM     7196    C  CD2 .  LEU   D .  127 ?   50.885   7.312  42.017  0.00  0   D
+ATOM     7236    C   CB .  PHE   D .  132 ?   48.964   5.452  44.735  0.00  0   D
+ATOM     7237    C   CG .  PHE   D .  132 ?   50.048   4.498  45.077  0.00  0   D
+ATOM     7239    C  CD2 .  PHE   D .  132 ?   50.695   4.565  46.284  0.00  0   D
+ATOM     7241    C  CE2 .  PHE   D .  132 ?   51.716   3.665  46.583  0.00  0   D
+ATOM     7243    N    N .  ILE   D .  133 ?   46.537   6.891  46.024 -1.93  0   D
+ATOM     7245    C    C .  ILE   D .  133 ?   46.737   9.259  46.259  0.00  0   D
+ATOM     7246    O    O .  ILE   D .  133 ?   47.623   9.183  47.095  0.00  0   D
+ATOM     7251    N    N .  HIS   D .  134 ?   46.595  10.297  45.460  0.00  0   D
+ATOM     7252    C   CA .  HIS   D .  134 ?   47.370  11.498  45.668  0.00  0   D
+ATOM     7253    C    C .  HIS   D .  134 ?   46.953  12.278  46.936  0.00  0   D
+ATOM     7254    O    O .  HIS   D .  134 ?   47.812  12.555  47.804  0.00  0   D
+ATOM     7255    C   CB .  HIS   D .  134 ?   47.334  12.399  44.428  0.00  0   D
+ATOM     7256    C   CG .  HIS   D .  134 ?   48.415  13.421  44.453  0.00  0   D
+ATOM     7257    N  ND1 .  HIS   D .  134 ?   48.485  14.377  45.431  0.00  0   D
+ATOM     7258    C  CD2 .  HIS   D .  134 ?   49.543  13.548  43.730  0.00  0   D
+ATOM     7259    C  CE1 .  HIS   D .  134 ?   49.558  15.116  45.253  0.00  0   D
+ATOM     7260    N  NE2 .  HIS   D .  134 ?   50.218  14.635  44.230  0.00  0   D
+ATOM     7328    C   CG .  LEU   D .  143 ?   58.274  20.017  40.820  0.00  0   D
+ATOM     7329    C  CD1 .  LEU   D .  143 ?   59.244  18.841  41.193  0.00  0   D
+ATOM     7330    C  CD2 .  LEU   D .  143 ?   58.782  21.410  41.356  0.00  0   D
+ATOM     7395    C    C .  VAL   D .  152 ?   54.278  15.041  40.879  0.00  0   D
+ATOM     7396    O    O .  VAL   D .  152 ?   55.001  14.074  40.818  0.00  0   D
+ATOM     7398    C  CG1 .  VAL   D .  152 ?   51.341  14.429  40.809  0.00  0   D
+ATOM     7400    N    N .  ALA   D .  153 ?   54.162  15.769  41.970  0.00  0   D
+ATOM     7401    C   CA .  ALA   D .  153 ?   54.851  15.556  43.189  0.00  0   D
+ATOM     7402    C    C .  ALA   D .  153 ?   53.826  15.699  44.308  0.00  0   D
+ATOM     7403    O    O .  ALA   D .  153 ?   52.619  15.769  44.076  0.00  0   D
+ATOM     7404    C   CB .  ALA   D .  153 ?   55.891  16.596  43.353  0.00  0   D
+ATOM     7405    N    N .  ASP   D .  154 ?   54.325  15.719  45.523  0.00  0   D
+ATOM     7406    C   CA .  ASP   D .  154 ?   53.526  15.970  46.675  0.00  0   D
+ATOM     7407    C    C .  ASP   D .  154 ?   54.490  16.514  47.699  0.00  0   D
+ATOM     7408    O    O .  ASP   D .  154 ?   55.352  15.791  48.188  0.00  0   D
+ATOM     7409    C   CB .  ASP   D .  154 ?   52.864  14.692  47.175  0.00  0   D
+ATOM     7410    C   CG .  ASP   D .  154 ?   51.982  14.931  48.357  0.00  0   D
+ATOM     7411    O  OD1 .  ASP   D .  154 ?   51.809  16.053  48.830 -4.29  0   D
+ATOM     7412    O  OD2 .  ASP   D .  154 ?   51.451  13.986  48.870 -1.62  0   D
+ATOM     7413    N    N .  PHE   D .  155 ?   54.377  17.799  47.998  0.00  0   D
+ATOM     7414    C   CA .  PHE   D .  155 ?   55.356  18.410  48.844  0.00  0   D
+ATOM     7415    C    C .  PHE   D .  155 ?   54.936  18.484  50.300  0.00  0   D
+ATOM     7416    O    O .  PHE   D .  155 ?   55.635  19.113  51.089 -1.07  0   D
+ATOM     7417    C   CB .  PHE   D .  155 ?   55.748  19.792  48.329  0.00  0   D
+ATOM     7418    C   CG .  PHE   D .  155 ?   56.120  19.814  46.868  0.00  0   D
+ATOM     7420    C  CD2 .  PHE   D .  155 ?   56.995  18.870  46.332  0.00  0   D
+ATOM     7421    C  CE1 .  PHE   D .  155 ?   55.921  20.831  44.680  0.00  0   D
+ATOM     7422    C  CE2 .  PHE   D .  155 ?   57.327  18.902  44.964  0.00  0   D
+ATOM     7423    C   CZ .  PHE   D .  155 ?   56.783  19.883  44.153  0.00  0   D
+ATOM     7424    N    N .  GLY   D .  156 ?   53.836  17.822  50.662  0.00  0   D
+ATOM     7425    C   CA .  GLY   D .  156 ?   53.352  17.790  52.036  0.00  0   D
+#

tests/reference_output/123abc_out/pocket2_vert.pqr

@@ -0,0 +1,196 @@
+ATOM      1    O STP     2      52.663   8.457  53.152    0.00     4.45
+ATOM      2    O STP     2      54.050  14.008  51.721    0.00     3.86
+ATOM      3    O STP     2      52.640   8.878  52.851    0.00     4.60
+ATOM      4    C STP     2      51.364   8.061  45.543    0.00     3.64
+ATOM      5    C STP     2      62.008  26.618  42.895    0.00     4.22
+ATOM      6    O STP     2      63.439  25.725  40.395    0.00     3.59
+ATOM      7    C STP     2      53.001  11.272  44.665    0.00     4.24
+ATOM      8    C STP     2      53.449   7.673  53.074    0.00     3.61
+ATOM      9    O STP     2      54.236  14.162  51.376    0.00     3.75
+ATOM     10    O STP     2      54.190  14.144  51.474    0.00     3.78
+ATOM     11    O STP     2      54.354  14.261  51.534    0.00     3.70
+ATOM     12    O STP     2      54.742  14.616  51.679    0.00     3.48
+ATOM     13    C STP     2      52.757   9.892  52.647    0.00     4.66
+ATOM     14    O STP     2      53.265  12.551  52.646    0.00     4.43
+ATOM     15    C STP     2      53.739  11.834  53.714    0.00     4.27
+ATOM     16    O STP     2      53.693  11.858  53.692    0.00     4.30
+ATOM     17    C STP     2      53.713  11.808  53.703    0.00     4.28
+ATOM     18    O STP     2      58.767  15.919  48.967    0.00     3.50
+ATOM     19    O STP     2      55.833  12.120  46.832    0.00     3.94
+ATOM     20    O STP     2      54.244  14.125  51.330    0.00     3.73
+ATOM     21    O STP     2      54.146  12.414  50.419    0.00     3.48
+ATOM     22    O STP     2      54.377  11.487  48.685    0.00     3.85
+ATOM     23    O STP     2      54.826  14.600  51.453    0.00     3.46
+ATOM     24    O STP     2      54.886  14.651  51.373    0.00     3.41
+ATOM     25    O STP     2      54.490  14.343  51.467    0.00     3.63
+ATOM     26    O STP     2      54.308  14.210  51.381    0.00     3.71
+ATOM     27    C STP     2      58.994  17.737  49.432    0.00     3.75
+ATOM     28    O STP     2      58.832  18.028  49.782    0.00     3.62
+ATOM     29    C STP     2      59.100  17.870  50.023    0.00     3.42
+ATOM     30    C STP     2      52.777   9.708  50.101    0.00     4.64
+ATOM     31    C STP     2      53.802  10.216  47.676    0.00     4.60
+ATOM     32    C STP     2      60.296  17.247  44.127    0.00     3.50
+ATOM     33    C STP     2      53.093  11.708  44.432    0.00     4.06
+ATOM     34    C STP     2      53.824  11.499  44.604    0.00     4.21
+ATOM     35    C STP     2      54.523  11.572  44.436    0.00     4.19
+ATOM     36    O STP     2      58.972  14.445  46.695    0.00     4.14
+ATOM     37    C STP     2      59.937  16.508  44.607    0.00     3.56
+ATOM     38    C STP     2      52.515  10.852  44.424    0.00     4.07
+ATOM     39    C STP     2      56.372  10.058  42.589    0.00     3.53
+ATOM     40    O STP     2      56.191  10.838  42.565    0.00     3.51
+ATOM     41    C STP     2      56.170  10.437  42.771    0.00     3.66
+ATOM     42    O STP     2      56.116  11.126  42.911    0.00     3.68
+ATOM     43    C STP     2      56.051  10.949  43.307    0.00     3.91
+ATOM     44    O STP     2      53.439   8.717  54.021    0.00     3.78
+ATOM     45    O STP     2      53.834  11.441  53.850    0.00     4.07
+ATOM     46    O STP     2      53.473   9.629  53.445    0.00     4.05
+ATOM     47    O STP     2      53.440   9.627  53.440    0.00     4.08
+ATOM     48    O STP     2      53.441   9.635  53.438    0.00     4.08
+ATOM     49    O STP     2      54.208  11.802  54.008    0.00     3.95
+ATOM     50    C STP     2      61.781  26.779  42.891    0.00     4.18
+ATOM     51    O STP     2      60.822  27.302  43.733    0.00     3.52
+ATOM     52    O STP     2      61.022  27.879  42.611    0.00     4.35
+ATOM     53    O STP     2      59.801  27.719  42.152    0.00     3.80
+ATOM     54    O STP     2      60.090  28.105  42.262    0.00     4.16
+ATOM     55    O STP     2      60.122  28.665  41.967    0.00     4.44
+ATOM     56    O STP     2      58.384  28.314  40.694    0.00     3.42
+ATOM     57    O STP     2      59.442  28.507  41.260    0.00     4.00
+ATOM     58    O STP     2      59.046  28.598  40.692    0.00     3.86
+ATOM     59    O STP     2      59.278  28.620  40.860    0.00     3.98
+ATOM     60    C STP     2      59.049  17.678  49.287    0.00     3.79
+ATOM     61    C STP     2      60.060  19.894  47.734    0.00     3.52
+ATOM     62    O STP     2      58.790  16.977  48.989    0.00     3.72
+ATOM     63    O STP     2      58.849  16.922  48.950    0.00     3.75
+ATOM     64    C STP     2      58.900  17.234  49.108    0.00     3.74
+ATOM     65    C STP     2      60.895  17.686  46.526    0.00     4.08
+ATOM     66    O STP     2      59.689  15.717  47.695    0.00     4.37
+ATOM     67    C STP     2      58.259  15.550  45.836    0.00     3.59
+ATOM     68    C STP     2      58.189  15.455  45.934    0.00     3.64
+ATOM     69    O STP     2      62.838  16.603  47.522    0.00     3.64
+ATOM     70    C STP     2      54.077  10.407  47.985    0.00     4.53
+ATOM     71    C STP     2      53.877  10.231  47.745    0.00     4.61
+ATOM     72    C STP     2      53.958  10.227  48.030    0.00     4.60
+ATOM     73    C STP     2      53.868  10.225  47.695    0.00     4.61
+ATOM     74    C STP     2      55.818  12.098  46.841    0.00     3.95
+ATOM     75    C STP     2      54.714  11.010  47.893    0.00     4.18
+ATOM     76    C STP     2      55.527  11.586  44.764    0.00     4.32
+ATOM     77    C STP     2      57.451  11.134  44.321    0.00     3.45
+ATOM     78    C STP     2      56.461  10.866  43.965    0.00     3.91
+ATOM     79    C STP     2      57.074   9.916  43.714    0.00     3.52
+ATOM     80    C STP     2      53.031   9.596  50.020    0.00     4.46
+ATOM     81    C STP     2      54.191   8.974  50.327    0.00     3.60
+ATOM     82    C STP     2      55.061   9.298  48.699    0.00     3.66
+ATOM     83    C STP     2      54.461   9.686  48.385    0.00     4.11
+ATOM     84    O STP     2      61.848  18.545  43.485    0.00     3.48
+ATOM     85    O STP     2      62.463  19.805  42.721    0.00     3.69
+ATOM     86    C STP     2      61.156  18.627  44.542    0.00     3.86
+ATOM     87    C STP     2      61.267  20.139  44.574    0.00     4.15
+ATOM     88    O STP     2      62.944  19.789  42.612    0.00     3.45
+ATOM     89    C STP     2      61.120  18.198  46.024    0.00     4.00
+ATOM     90    C STP     2      61.251  19.943  45.329    0.00     4.08
+ATOM     91    O STP     2      62.919  16.738  47.389    0.00     3.55
+ATOM     92    C STP     2      65.633  27.648  42.766    0.00     4.59
+ATOM     93    C STP     2      63.278  20.434  42.722    0.00     3.52
+ATOM     94    C STP     2      62.936  20.713  42.876    0.00     3.78
+ATOM     95    O STP     2      63.430  25.679  40.396    0.00     3.57
+ATOM     96    O STP     2      63.439  25.687  40.376    0.00     3.57
+ATOM     97    C STP     2      59.040  14.477  46.707    0.00     4.17
+ATOM     98    C STP     2      60.636  14.362  48.108    0.00     4.02
+ATOM     99    O STP     2      59.043  14.513  46.712    0.00     4.18
+ATOM    100    C STP     2      60.391  16.124  47.507    0.00     4.52
+ATOM    101    C STP     2      59.877  15.620  47.519    0.00     4.50
+ATOM    102    O STP     2      59.717  15.506  47.370    0.00     4.45
+ATOM    103    C STP     2      59.251  15.277  46.578    0.00     4.25
+ATOM    104    C STP     2      59.751  15.886  45.827    0.00     3.96
+ATOM    105    C STP     2      59.854  15.963  46.233    0.00     4.08
+ATOM    106    C STP     2      59.546  15.686  46.152    0.00     4.08
+ATOM    107    O STP     2      57.649  14.973  45.793    0.00     3.42
+ATOM    108    O STP     2      57.078  13.186  46.062    0.00     3.78
+ATOM    109    O STP     2      55.903  12.229  46.541    0.00     3.96
+ATOM    110    C STP     2      56.109  12.076  45.361    0.00     4.06
+ATOM    111    C STP     2      55.575  11.663  44.856    0.00     4.30
+ATOM    112    C STP     2      55.841  12.139  46.430    0.00     3.99
+ATOM    113    C STP     2      54.444  11.557  44.832    0.00     4.22
+ATOM    114    C STP     2      55.099  11.493  45.372    0.00     4.30
+ATOM    115    C STP     2      54.799  11.595  44.686    0.00     4.23
+ATOM    116    C STP     2      55.467  11.596  44.836    0.00     4.33
+ATOM    117    C STP     2      60.835  21.029  44.941    0.00     4.10
+ATOM    118    C STP     2      61.198  20.312  44.536    0.00     4.14
+ATOM    119    C STP     2      60.840  21.033  44.893    0.00     4.11
+ATOM    120    C STP     2      60.858  21.073  44.864    0.00     4.09
+ATOM    121    C STP     2      62.159  23.405  42.860    0.00     4.20
+ATOM    122    C STP     2      61.707  23.561  42.851    0.00     3.93
+ATOM    123    C STP     2      62.260  20.592  43.131    0.00     3.99
+ATOM    124    C STP     2      62.368  20.621  42.973    0.00     4.01
+ATOM    125    C STP     2      62.375  20.641  42.977    0.00     4.02
+ATOM    126    C STP     2      62.518  21.592  42.658    0.00     3.96
+ATOM    127    O STP     2      62.509  22.061  42.314    0.00     3.90
+ATOM    128    C STP     2      60.911  20.622  45.683    0.00     4.04
+ATOM    129    C STP     2      60.470  20.281  46.484    0.00     3.75
+ATOM    130    C STP     2      60.351  20.351  46.457    0.00     3.67
+ATOM    131    C STP     2      60.178  20.121  47.323    0.00     3.56
+ATOM    132    C STP     2      60.818  20.990  45.191    0.00     4.07
+ATOM    133    C STP     2      60.835  21.017  45.214    0.00     4.05
+ATOM    134    C STP     2      60.790  21.002  45.192    0.00     4.06
+ATOM    135    C STP     2      60.094  21.204  44.711    0.00     3.61
+ATOM    136    C STP     2      60.347  21.160  44.783    0.00     3.78
+ATOM    137    C STP     2      60.750  21.024  45.167    0.00     4.03
+ATOM    138    C STP     2      60.742  21.034  45.131    0.00     4.03
+ATOM    139    C STP     2      58.886  18.428  49.318    0.00     3.56
+ATOM    140    C STP     2      58.768  18.573  49.619    0.00     3.50
+ATOM    141    O STP     2      56.036  11.303  42.851    0.00     3.59
+ATOM    142    C STP     2      55.349  11.513  44.094    0.00     4.17
+ATOM    143    C STP     2      55.387  11.512  44.097    0.00     4.18
+ATOM    144    C STP     2      55.413  11.485  44.046    0.00     4.16
+ATOM    145    C STP     2      60.559  13.746  47.829    0.00     3.69
+ATOM    146    C STP     2      60.340  13.977  47.822    0.00     3.84
+ATOM    147    C STP     2      60.492  14.007  47.958    0.00     3.88
+ATOM    148    O STP     2      62.748  27.496  39.806    0.00     3.74
+ATOM    149    O STP     2      62.787  27.939  39.967    0.00     4.10
+ATOM    150    C STP     2      62.865  25.283  43.300    0.00     4.10
+ATOM    151    C STP     2      62.731  24.365  43.375    0.00     3.96
+ATOM    152    C STP     2      66.556  27.021  42.779    0.00     4.00
+ATOM    153    C STP     2      66.171  27.224  42.809    0.00     4.19
+ATOM    154    C STP     2      66.571  26.899  42.879    0.00     3.91
+ATOM    155    C STP     2      63.418  26.891  42.136    0.00     4.67
+ATOM    156    C STP     2      65.325  27.418  42.748    0.00     4.46
+ATOM    157    C STP     2      63.215  25.020  41.175    0.00     3.56
+ATOM    158    C STP     2      62.785  25.511  42.900    0.00     4.35
+ATOM    159    C STP     2      62.849  25.380  43.041    0.00     4.28
+ATOM    160    C STP     2      62.262  23.582  42.864    0.00     4.20
+ATOM    161    C STP     2      62.708  24.333  43.225    0.00     4.05
+ATOM    162    C STP     2      62.222  23.346  42.787    0.00     4.20
+ATOM    163    C STP     2      62.278  23.159  42.457    0.00     4.06
+ATOM    164    C STP     2      62.482  22.290  42.604    0.00     4.00
+ATOM    165    C STP     2      62.494  22.273  42.385    0.00     3.95
+ATOM    166    C STP     2      51.526   8.496  46.417    0.00     4.02
+ATOM    167    C STP     2      51.272   8.426  45.855    0.00     3.93
+ATOM    168    O STP     2      52.161   9.806  47.136    0.00     4.58
+ATOM    169    C STP     2      51.709  10.273  45.778    0.00     4.43
+ATOM    170    C STP     2      51.241   8.484  45.745    0.00     3.92
+ATOM    171    C STP     2      50.390   8.536  45.180    0.00     3.43
+ATOM    172    C STP     2      51.326   9.117  45.567    0.00     4.01
+ATOM    173    O STP     2      51.777  10.493  46.104    0.00     4.47
+ATOM    174    O STP     2      51.894  10.381  46.155    0.00     4.53
+ATOM    175    C STP     2      51.859  10.416  46.050    0.00     4.53
+ATOM    176    O STP     2      62.947  15.425  47.650    0.00     3.56
+ATOM    177    C STP     2      51.391  10.322  45.661    0.00     4.19
+ATOM    178    O STP     2      50.939  11.438  46.334    0.00     3.63
+ATOM    179    O STP     2      51.537  10.657  46.179    0.00     4.28
+ATOM    180    O STP     2      51.091  10.861  46.588    0.00     3.89
+ATOM    181    C STP     2      53.011  11.947  44.149    0.00     3.84
+ATOM    182    O STP     2      62.505  16.501  47.630    0.00     3.76
+ATOM    183    C STP     2      60.482  16.825  47.877    0.00     4.33
+ATOM    184    C STP     2      60.561  16.833  47.789    0.00     4.36
+ATOM    185    C STP     2      60.446  16.212  47.526    0.00     4.52
+ATOM    186    C STP     2      60.690  16.662  47.524    0.00     4.47
+ATOM    187    C STP     2      60.458  16.106  47.531    0.00     4.50
+ATOM    188    C STP     2      60.807  14.447  48.129    0.00     3.98
+ATOM    189    C STP     2      62.481  14.543  47.989    0.00     3.51
+ATOM    190    O STP     2      62.836  15.384  47.687    0.00     3.61
+ATOM    191    O STP     2      62.780  15.300  47.687    0.00     3.62
+ATOM    192    C STP     2      52.967  11.948  44.474    0.00     3.85
+ATOM    193    O STP     2      52.960  11.975  44.424    0.00     3.83
+ATOM    194    O STP     2      52.949  12.006  44.489    0.00     3.80
+TER
+END

tests/reference_output/123abc_out/pocket30_atm.cif

@@ -0,0 +1,70 @@
+data_pocket30_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    30:
+0  - Pocket Score                      : -0.0514
+1  - Drug Score                        : 0.0008
+2  - Number of alpha spheres           :    35
+3  - Mean alpha-sphere radius          : 3.8712
+4  - Mean alpha-sphere Solvent Acc.    : 0.5258
+5  - Mean B-factor of pocket residues  : 0.1606
+6  - Hydrophobicity Score              : 13.1000
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 3.9000
+9  - Pocket volume (Monte Carlo)       : 361.6746
+10  -Pocket volume (convex hull)       : 39.9031
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 13.0000
+13 - Number of apolar alpha sphere     :    14
+14 - Proportion of apolar alpha sphere : 0.4000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3308    O    O .  ASP   B .  164 ?   27.151  43.554  37.600 -1.21  0   B
+ATOM     3313    O    O .  THR   B .  165 ?   24.462  45.035  38.384 -2.14  0   B
+ATOM     3405    C   CG .  LYS   B .  177 ?   24.464  39.615  42.306  0.00  0   B
+ATOM     3406    C   CD .  LYS   B .  177 ?   25.964  39.772  42.543  0.00  0   B
+ATOM     3422    C  CH2 .  TRP   B .  178 ?   24.948  45.190  44.295  0.00  0   B
+ATOM     3678    C   CB .  SER   B .  211 ?   30.018  43.102  45.878  0.00  0   B
+ATOM     3686    C   CD .  PRO   B .  212 ?   26.363  42.775  46.525  0.00  0   B
+ATOM     3683    O    O .  PRO   B .  212 ?   27.502  39.687  45.538 -1.07  0   B
+ATOM     3408    N   NZ .  LYS   B .  177 ?   28.079  38.314  42.470  0.00  0   B
+ATOM     3315    O  OG1 .  THR   B .  165 ?   27.785  47.295  40.411 -2.69  0   B
+ATOM     3679    O   OG .  SER   B .  211 ?   30.571  44.344  45.570  0.00  0   B
+ATOM     3421    C  CZ3 .  TRP   B .  178 ?   24.294  44.617  43.200  0.00  0   B
+ATOM     3733    C  CD2 .  LEU   B .  218 ?   25.994  39.197  38.463  0.00  0   B
+ATOM     3407    C   CE .  LYS   B .  177 ?   26.663  38.511  41.999  0.00  0   B
+ATOM     3309    C   CB .  ASP   B .  164 ?   29.556  43.103  36.104  0.00  0   B
+ATOM     3731    C   CG .  LEU   B .  218 ?   26.746  38.765  37.215  0.00  0   B
+ATOM     3732    C  CD1 .  LEU   B .  218 ?   26.904  39.928  36.336  0.00  0   B
+ATOM     3400    N    N .  LYS   B .  177 ?   22.059  41.042  41.095  0.00  0   B
+ATOM     3404    C   CB .  LYS   B .  177 ?   23.625  40.732  42.913  0.00  0   B
+ATOM     3311    C   CA .  THR   B .  165 ?   26.568  46.000  38.856  0.00  0   B
+ATOM     3310    N    N .  THR   B .  165 ?   27.717  45.708  37.984 -1.09  0   B
+ATOM     3307    C    C .  ASP   B .  164 ?   27.840  44.547  37.321  0.00  0   B
+ATOM     3713    O    O .  ILE   B .  216 ?   28.851  36.052  40.595 -4.02  0   B
+ATOM     3707    C   CA .  GLY   B .  215 ?   32.598  35.981  43.265  0.00  0   B
+ATOM     3709    O    O .  GLY   B .  215 ?   32.021  34.395  41.605  0.00  0   B
+ATOM     3708    C    C .  GLY   B .  215 ?   31.630  35.052  42.556  0.00  0   B
+ATOM     3706    N    N .  GLY   B .  215 ?   31.992  36.921  44.159  0.00  0   B
+ATOM     3700    C   CA .  PRO   B .  214 ?   30.804  37.638  46.187  0.00  0   B
+# 

tests/reference_output/123abc_out/pocket30_env_atm.cif

@@ -0,0 +1,70 @@
+data_pocket30_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM     3305    N    N .  ASP   B .  164 ?   29.908  45.575  36.198  0.00  0   B
+ATOM     3306    C   CA .  ASP   B .  164 ?   28.891  44.496  36.165  0.00  0   B
+ATOM     3307    C    C .  ASP   B .  164 ?   27.840  44.547  37.321  0.00  0   B
+ATOM     3308    O    O .  ASP   B .  164 ?   27.151  43.554  37.600 -1.21  0   B
+ATOM     3309    C   CB .  ASP   B .  164 ?   29.556  43.103  36.104  0.00  0   B
+ATOM     3310    N    N .  THR   B .  165 ?   27.717  45.708  37.984 -1.09  0   B
+ATOM     3311    C   CA .  THR   B .  165 ?   26.568  46.000  38.856  0.00  0   B
+ATOM     3312    C    C .  THR   B .  165 ?   25.293  45.859  38.052  0.00  0   B
+ATOM     3313    O    O .  THR   B .  165 ?   24.462  45.035  38.384 -2.14  0   B
+ATOM     3314    C   CB .  THR   B .  165 ?   26.698  47.367  39.497  0.00  0   B
+ATOM     3315    O  OG1 .  THR   B .  165 ?   27.785  47.295  40.411 -2.69  0   B
+ATOM     3392    N    N .  ILE   B .  176 ?   21.472  42.362  38.641  0.00  0   B
+ATOM     3393    C   CA .  ILE   B .  176 ?   21.108  40.929  38.881  0.00  0   B
+ATOM     3394    C    C .  ILE   B .  176 ?   21.071  40.558  40.347  0.00  0   B
+ATOM     3396    C   CB .  ILE   B .  176 ?   21.966  39.989  38.044  0.00  0   B
+ATOM     3400    N    N .  LYS   B .  177 ?   22.059  41.042  41.095  0.00  0   B
+ATOM     3401    C   CA .  LYS   B .  177 ?   22.185  40.603  42.480  0.00  0   B
+ATOM     3404    C   CB .  LYS   B .  177 ?   23.625  40.732  42.913  0.00  0   B
+ATOM     3405    C   CG .  LYS   B .  177 ?   24.464  39.615  42.306  0.00  0   B
+ATOM     3406    C   CD .  LYS   B .  177 ?   25.964  39.772  42.543  0.00  0   B
+ATOM     3407    C   CE .  LYS   B .  177 ?   26.663  38.511  41.999  0.00  0   B
+ATOM     3408    N   NZ .  LYS   B .  177 ?   28.079  38.314  42.470  0.00  0   B
+ATOM     3419    C  CE3 .  TRP   B .  178 ?   22.913  44.513  43.164  0.00  0   B
+ATOM     3421    C  CZ3 .  TRP   B .  178 ?   24.294  44.617  43.200  0.00  0   B
+ATOM     3422    C  CH2 .  TRP   B .  178 ?   24.948  45.190  44.295  0.00  0   B
+ATOM     3675    C   CA .  SER   B .  211 ?   29.156  43.225  47.157  0.00  0   B
+ATOM     3676    C    C .  SER   B .  211 ?   28.502  41.873  47.480  0.00  0   B
+ATOM     3677    O    O .  SER   B .  211 ?   29.157  40.946  47.931 -1.07  0   B
+ATOM     3678    C   CB .  SER   B .  211 ?   30.018  43.102  45.878  0.00  0   B
+ATOM     3679    O   OG .  SER   B .  211 ?   30.571  44.344  45.570  0.00  0   B
+ATOM     3680    N    N .  PRO   B .  212 ?   27.212  41.746  47.193  0.00  0   B
+ATOM     3683    O    O .  PRO   B .  212 ?   27.502  39.687  45.538 -1.07  0   B
+ATOM     3685    C   CG .  PRO   B .  212 ?   25.063  42.030  46.210  0.00  0   B
+ATOM     3686    C   CD .  PRO   B .  212 ?   26.363  42.775  46.525  0.00  0   B
+ATOM     3689    C    C .  TYR   B .  213 ?   28.452  37.120  45.720  0.00  0   B
+ATOM     3690    O    O .  TYR   B .  213 ?   28.681  37.094  44.519  0.00  0   B
+ATOM     3699    N    N .  PRO   B .  214 ?   29.411  37.369  46.621  0.00  0   B
+ATOM     3700    C   CA .  PRO   B .  214 ?   30.804  37.638  46.187  0.00  0   B
+ATOM     3701    C    C .  PRO   B .  214 ?   31.439  36.545  45.323  0.00  0   B
+ATOM     3703    C   CB .  PRO   B .  214 ?   31.573  37.783  47.505  0.00  0   B
+ATOM     3706    N    N .  GLY   B .  215 ?   31.992  36.921  44.159  0.00  0   B
+ATOM     3707    C   CA .  GLY   B .  215 ?   32.598  35.981  43.265  0.00  0   B
+ATOM     3708    C    C .  GLY   B .  215 ?   31.630  35.052  42.556  0.00  0   B
+ATOM     3709    O    O .  GLY   B .  215 ?   32.021  34.395  41.605  0.00  0   B
+ATOM     3710    N    N .  ILE   B .  216 ?   30.363  34.987  42.973  0.00  0   B
+ATOM     3712    C    C .  ILE   B .  216 ?   29.102  34.842  40.748  0.00  0   B
+ATOM     3713    O    O .  ILE   B .  216 ?   28.851  36.052  40.595 -4.02  0   B
+ATOM     3731    C   CG .  LEU   B .  218 ?   26.746  38.765  37.215  0.00  0   B
+ATOM     3732    C  CD1 .  LEU   B .  218 ?   26.904  39.928  36.336  0.00  0   B
+ATOM     3733    C  CD2 .  LEU   B .  218 ?   25.994  39.197  38.463  0.00  0   B
+#

tests/reference_output/123abc_out/pocket30_vert.pqr

@@ -0,0 +1,37 @@
+ATOM      1    O STP    30      25.303  42.215  40.193    0.00     3.45
+ATOM      2    C STP    30      27.634  42.997  43.087    0.00     3.67
+ATOM      3    O STP    30      28.816  41.620  43.024    0.00     3.43
+ATOM      4    O STP    30      28.197  43.828  42.381    0.00     4.01
+ATOM      5    O STP    30      29.389  42.532  41.417    0.00     4.54
+ATOM      6    O STP    30      28.595  43.188  41.728    0.00     4.39
+ATOM      7    O STP    30      29.082  43.230  41.561    0.00     4.42
+ATOM      8    C STP    30      27.772  43.115  42.802    0.00     3.81
+ATOM      9    C STP    30      28.201  43.368  42.027    0.00     4.27
+ATOM     10    C STP    30      28.166  43.672  42.274    0.00     4.09
+ATOM     11    O STP    30      25.700  42.692  40.653    0.00     3.49
+ATOM     12    C STP    30      27.305  42.901  43.192    0.00     3.47
+ATOM     13    C STP    30      28.401  41.155  40.285    0.00     3.60
+ATOM     14    O STP    30      28.504  41.305  40.265    0.00     3.74
+ATOM     15    O STP    30      29.603  40.881  39.599    0.00     4.14
+ATOM     16    C STP    30      29.848  40.536  39.396    0.00     4.18
+ATOM     17    C STP    30      29.258  40.864  39.048    0.00     3.71
+ATOM     18    C STP    30      29.420  40.729  39.072    0.00     3.80
+ATOM     19    C STP    30      25.323  42.122  40.126    0.00     3.43
+ATOM     20    O STP    30      25.150  42.118  40.058    0.00     3.43
+ATOM     21    O STP    30      25.230  42.139  40.088    0.00     3.45
+ATOM     22    C STP    30      25.268  42.324  40.343    0.00     3.44
+ATOM     23    C STP    30      25.427  42.601  40.635    0.00     3.45
+ATOM     24    O STP    30      25.135  42.267  40.264    0.00     3.41
+ATOM     25    O STP    30      28.111  43.296  41.694    0.00     4.21
+ATOM     26    C STP    30      28.001  43.337  41.745    0.00     4.18
+ATOM     27    C STP    30      27.720  43.263  41.575    0.00     4.03
+ATOM     28    O STP    30      28.540  43.776  40.958    0.00     3.64
+ATOM     29    O STP    30      29.930  43.371  41.184    0.00     4.54
+ATOM     30    O STP    30      29.990  43.359  41.159    0.00     4.56
+ATOM     31    O STP    30      30.681  39.929  39.133    0.00     4.53
+ATOM     32    O STP    30      32.056  37.717  40.107    0.00     3.64
+ATOM     33    O STP    30      31.781  39.145  40.531    0.00     4.26
+ATOM     34    O STP    30      30.799  40.297  43.755    0.00     3.60
+ATOM     35    O STP    30      30.525  40.269  43.951    0.00     3.46
+TER
+END

tests/reference_output/123abc_out/pocket31_atm.cif

@@ -0,0 +1,64 @@
+data_pocket31_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    31:
+0  - Pocket Score                      : -0.0515
+1  - Drug Score                        : 0.0073
+2  - Number of alpha spheres           :    29
+3  - Mean alpha-sphere radius          : 3.8569
+4  - Mean alpha-sphere Solvent Acc.    : 0.4383
+5  - Mean B-factor of pocket residues  : 0.7965
+6  - Hydrophobicity Score              : 14.5000
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 4.1250
+9  - Pocket volume (Monte Carlo)       : 311.7435
+10  -Pocket volume (convex hull)       : 18.5779
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 19.0000
+13 - Number of apolar alpha sphere     :    20
+14 - Proportion of apolar alpha sphere : 0.6897
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM      578    C  CE1 .  PHE   A .   84 ?    9.022   7.022  32.326  0.00  0   A
+ATOM      347    C   CB .  VAL   A .   53 ?    9.518  11.423  34.079  0.00  0   A
+ATOM      318    C   CB .  ASP   A .   49 ?   15.460   8.001  36.408  0.00  0   A
+ATOM      576    C  CD1 .  PHE   A .   84 ?   10.020   7.279  31.353  0.00  0   A
+ATOM      325    O    O .  THR   A .   50 ?   13.753  11.886  36.017 -0.54  0   A
+ATOM      321    O  OD2 .  ASP   A .   49 ?   14.516   5.990  37.244 -0.95  0   A
+ATOM      349    C  CG2 .  VAL   A .   53 ?    8.506  10.392  33.534  0.00  0   A
+ATOM      561    C   CG .  PRO   A .   82 ?   10.732   3.280  34.195  0.00  0   A
+ATOM      348    C  CG1 .  VAL   A .   53 ?    9.081  12.091  35.427  0.00  0   A
+ATOM      319    C   CG .  ASP   A .   49 ?   15.469   6.493  36.614  0.00  0   A
+ATOM      560    C   CB .  PRO   A .   82 ?   12.030   2.927  33.492  0.00  0   A
+ATOM      564    C   CA .  PRO   A .   83 ?   14.000   2.962  30.575  0.00  0   A
+ATOM      320    O  OD1 .  ASP   A .   49 ?   16.422   5.816  36.164 -0.95  0   A
+ATOM      568    C   CG .  PRO   A .   83 ?   15.808   1.347  30.237  0.00  0   A
+ATOM      563    N    N .  PRO   A .   83 ?   13.592   1.581  30.904  0.00  0   A
+ATOM      304    O    O .  LEU   A .   46 ?   16.573   7.011  31.379 -2.14  0   A
+ATOM      570    N    N .  PHE   A .   84 ?   12.779   4.833  29.577  0.00  0   A
+ATOM      567    C   CB .  PRO   A .   83 ?   15.457   2.812  30.082  0.00  0   A
+ATOM      312    O    O .  LYS   A .   47 ?   19.128   6.617  33.897  0.00  0   A
+ATOM      308    C  CD2 .  LEU   A .   46 ?   12.808  10.745  31.273  0.00  0   A
+ATOM      306    C   CG .  LEU   A .   46 ?   14.285  10.407  31.218  0.00  0   A
+ATOM      305    C   CB .  LEU   A .   46 ?   14.483   9.154  30.366  0.00  0   A
+# 

tests/reference_output/123abc_out/pocket31_env_atm.cif

@@ -0,0 +1,54 @@
+data_pocket31_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM      302    C   CA .  LEU   A .   46 ?   15.918   8.854  29.945  0.00  0   A
+ATOM      303    C    C .  LEU   A .   46 ?   16.720   8.211  31.087  0.00  0   A
+ATOM      304    O    O .  LEU   A .   46 ?   16.573   7.011  31.379 -2.14  0   A
+ATOM      305    C   CB .  LEU   A .   46 ?   14.483   9.154  30.366  0.00  0   A
+ATOM      306    C   CG .  LEU   A .   46 ?   14.285  10.407  31.218  0.00  0   A
+ATOM      308    C  CD2 .  LEU   A .   46 ?   12.808  10.745  31.273  0.00  0   A
+ATOM      311    C    C .  LYS   A .   47 ?   18.202   7.333  33.490  0.00  0   A
+ATOM      312    O    O .  LYS   A .   47 ?   19.128   6.617  33.897  0.00  0   A
+ATOM      318    C   CB .  ASP   A .   49 ?   15.460   8.001  36.408  0.00  0   A
+ATOM      319    C   CG .  ASP   A .   49 ?   15.469   6.493  36.614  0.00  0   A
+ATOM      320    O  OD1 .  ASP   A .   49 ?   16.422   5.816  36.164 -0.95  0   A
+ATOM      321    O  OD2 .  ASP   A .   49 ?   14.516   5.990  37.244 -0.95  0   A
+ATOM      325    O    O .  THR   A .   50 ?   13.753  11.886  36.017 -0.54  0   A
+ATOM      344    C   CA .  VAL   A .   53 ?    9.902  12.497  32.989  0.00  0   A
+ATOM      347    C   CB .  VAL   A .   53 ?    9.518  11.423  34.079  0.00  0   A
+ATOM      348    C  CG1 .  VAL   A .   53 ?    9.081  12.091  35.427  0.00  0   A
+ATOM      349    C  CG2 .  VAL   A .   53 ?    8.506  10.392  33.534  0.00  0   A
+ATOM      557    C   CA .  PRO   A .   82 ?   11.584   2.421  32.113  0.00  0   A
+ATOM      558    C    C .  PRO   A .   82 ?   12.478   1.262  31.610  0.00  0   A
+ATOM      560    C   CB .  PRO   A .   82 ?   12.030   2.927  33.492  0.00  0   A
+ATOM      561    C   CG .  PRO   A .   82 ?   10.732   3.280  34.195  0.00  0   A
+ATOM      563    N    N .  PRO   A .   83 ?   13.592   1.581  30.904  0.00  0   A
+ATOM      564    C   CA .  PRO   A .   83 ?   14.000   2.962  30.575  0.00  0   A
+ATOM      565    C    C .  PRO   A .   83 ?   13.073   3.538  29.477  0.00  0   A
+ATOM      567    C   CB .  PRO   A .   83 ?   15.457   2.812  30.082  0.00  0   A
+ATOM      568    C   CG .  PRO   A .   83 ?   15.808   1.347  30.237  0.00  0   A
+ATOM      569    C   CD .  PRO   A .   83 ?   14.509   0.587  30.313  0.00  0   A
+ATOM      570    N    N .  PHE   A .   84 ?   12.779   4.833  29.577  0.00  0   A
+ATOM      571    C   CA .  PHE   A .   84 ?   11.890   5.469  28.614  0.00  0   A
+ATOM      574    C   CB .  PHE   A .   84 ?   11.248   6.723  29.215  0.00  0   A
+ATOM      575    C   CG .  PHE   A .   84 ?   10.188   6.434  30.264  0.00  0   A
+ATOM      576    C  CD1 .  PHE   A .   84 ?   10.020   7.279  31.353  0.00  0   A
+ATOM      578    C  CE1 .  PHE   A .   84 ?    9.022   7.022  32.326  0.00  0   A
+ATOM      580    C   CZ .  PHE   A .   84 ?    8.195   5.904  32.211  0.00  0   A
+#