issue-151 fix of chain reading atoms in read_mmcif & descriptor output writing

Bug fixes for 4.2 release

Dockerfile

@@ -0,0 +1,22 @@
+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/*
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+
+RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]

README.md

@@ -81,10 +81,10 @@ docker build -t fpocket/fpocket .
 This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using: 
 
 ```bash
-docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
+docker run -v `pwd`:/workdir fpocket/fpocket fpocket -f /workdir/yourfile.pdb
 ```
 
-Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
+Here you mount your current directory with your input files into the preconfigured `/workdir` in the docker container and then run fpocket on a file in that mounted folder. Make sure that the folder is writeable to others if you run it through docker.
 
 ### Installing
 

headers/atom.h

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

headers/descriptors.h

@@ -81,8 +81,8 @@ typedef struct s_desc
                 characterChain2,                         /**< 0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket*/
                 numResChain1,                            /**<number of resdiues on chain 1*/
                 numResChain2;                           /**<number of res on chain 2*/
-        char nameChain1[2],        /**<name of the first chain in contact with the pocket*/
-                nameChain2[2];     /**<name of the second chain in contact with the pocket, if there is*/
+        char nameChain1[255],        /**<name of the first chain in contact with the pocket*/
+                nameChain2[255];     /**<name of the second chain in contact with the pocket, if there is*/
         char ligTag[8];           /**<het atom tag of ligands situated in the pocket*/
         
 } s_desc ;

headers/utils.h

@@ -33,7 +33,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 /* ------------------------------- PUBLIC MACROS ---------------------------- */
 
-#define M_MAX_PDB_NAME_LEN 200  /**< maximum pdb filename length*/
+#define M_MAX_PDB_NAME_LEN 2000  /**< maximum pdb filename length*/
 #define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
 #define M_SIGN 1
 #define M_NO_SIGN 0

headers/writepdb.h

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

headers/writepocket.h

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

makefile

@@ -1,7 +1,7 @@
 #------------------------------------------------------------
 # Makefile.
 #------------------------------------------------------------
-#ARCH	    = MACOSXX86_64
+# ARCH	    = MACOSXX86_64
 ARCH	    = LINUXAMD64
 export ARCH
 

src/descriptors.c

@@ -65,7 +65,6 @@ s_desc* allocate_s_desc(void)
 	s_desc *desc = (s_desc*)my_malloc(sizeof(s_desc)) ;
 	
 	reset_desc(desc) ;
-
 	return desc ;
 }
 
@@ -364,7 +363,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
 		nb_res_ids = 0 ;	/* Current number of residus */
 
 	int nb_polar_atm = 0 ;
-        char curChainName[2];
+        char *curChainName = (char*)my_malloc(255*sizeof(char));
         
         if(atoms && natoms>1){
             firstatom=atoms[0];
@@ -373,8 +372,8 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
             if(element_in_std_res(firstatom->res_name))             desc->characterChain1=0;
             else if(element_in_nucl_acid(firstatom->res_name))      desc->characterChain1=1;
             else if(element_in_kept_res(firstatom->res_name))       desc->characterChain1=2;
-            strncpy(desc->nameChain1,firstatom->chain,2);
-            strncpy(curChainName,firstatom->chain,2);
+            strcpy(desc->nameChain1,firstatom->chain);
+            strcpy(curChainName,firstatom->chain);
             desc->numResChain1 = countResidues(all_atoms,all_natoms,firstatom->chain);
 
             for(i = 0 ; i < natoms ; i++) {
@@ -384,7 +383,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
                             desc->interChain = 1;
                             if(!desc->numResChain2){
                                 desc->numResChain2 = countResidues(all_atoms,all_natoms,curatom->chain);
-                                strncpy(curChainName,curatom->chain,1);
+                                strcpy(curChainName,curatom->chain);
                             }
                         }
 

src/pertable.c

@@ -260,11 +260,13 @@ float pte_get_enegativity(const char *symbol)
 */
 char *pte_get_element_from_number(int atomicnumber)
 {
+	
 	char *tmp=malloc(sizeof(char)*3) ;
 	if(atomicnumber>0 && atomicnumber<112){
 	
 		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
 		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
+		tmp[2]='\0';
 		return tmp;
 	} else {
 		tmp[0]='-';

src/read_mmcif.c

@@ -63,7 +63,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     void *h_in;
     molfile_timestep_t ts_in;
     molfile_atom_t *at_in;
-    int optflags = 0x0040;
+    int optflags[] = {0x0001,0x0040};
     int rc;
     int rc2;
     int j;
@@ -75,7 +75,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     }
     at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
-    rc2 = api->read_structure(h_in, &optflags, at_in);
+    rc2 = api->read_structure(h_in, optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
     if (!model_number)
         model_number = 1;
@@ -124,9 +124,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             if (par->xlig_resnumber > -1)
             {
 
-                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])))
+                // if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+                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)==0 && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+
                 {
+
                     pdb->n_xlig_atoms++;
+
                 }
             }
         }
@@ -179,7 +183,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             }
             if (par->xlig_resnumber > -1)
             {   
-                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]))
+                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid_auth == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
                 {
                     pdb->n_xlig_atoms++;
                 }
@@ -313,8 +317,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -350,8 +356,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -395,8 +403,11 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
 
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
 
                         atom->x = ts_in.coords[(3 * i)];
@@ -429,7 +440,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
             {
                 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]))
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
                 {
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
@@ -465,9 +476,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
+
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
                         atom->z = ts_in.coords[(3 * i) + 2];
@@ -502,8 +516,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -540,9 +556,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
+
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
                             atom->z = ts_in.coords[(3 * i) + 2];
@@ -578,8 +597,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                     strcpy(atom->name, at_in[i].type);
                                     atom->pdb_aloc = at_in[i].altloc[0];
                                     strcpy(atom->res_name, at_in[i].resname);
-                                    strncpy(atom->chain, at_in[i].chain, 2);
-                                    atom->res_id = at_in[i].resid;
+                                    strcpy(atom->chain, at_in[i].chain_auth);
+                                    strcpy(atom->label_asym_id, at_in[i].chain);
+                                    atom->res_id = at_in[i].resid_auth;
+                                    atom->label_seq_id=at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
                                     atom->y = ts_in.coords[(3 * i) + 1];
@@ -607,15 +628,14 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
-
+                                                         
             if (pdb->n_xlig_atoms)
             {
 
                 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]))
-                {
-                                        
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth, params->xlig_chain_code)==0 && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && strcmp(at_in[i].chain_auth, 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];

src/rpdb.c

@@ -1161,6 +1161,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+
 
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
@@ -1189,7 +1192,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
 
@@ -1215,6 +1220,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             // printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain  : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
                             // atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
                             // printf("electroneg : %s\n",atom->symbol);
@@ -1284,7 +1292,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
-
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             atoms_p[iatoms] = atom;
                             atm_lig[iatm_lig] = atom;
 
@@ -1310,7 +1320,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 atm_lig[iatm_lig] = atom;
 
@@ -1338,7 +1350,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 pdb->lhetatm[ihetatm] = atom;
                                 ihetatm++;
@@ -1366,7 +1380,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                         atom->radius = pte_get_vdw_ray(atom->symbol);
                                         atom->electroneg = pte_get_enegativity(atom->symbol);
                                         atom->sort_x = -1;
-
+                                        atom->label_seq_id=atom->res_id;
+                                        strcpy(atom->label_asym_id, atom->chain);
+                                
                                         atoms_p[iatoms] = atom;
                                         pdb->lhetatm[ihetatm] = atom;
                                         ihetatm++;

src/voronoi.c

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

src/writepdb.c

@@ -206,7 +206,7 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
 
 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
 						   char alt_loc, const char res_name[], const char chain[],
-						   int res_id, const char insert, float x, float y, float z, float occ,
+						   int res_id, const char label_asym_id[],int label_seq_id, char insert, float x, float y, float z, float occ,
 						   float bfactor, int abpa, const char *symbol, int charge, float abpa_prob)
 {
 	int status = 0;
@@ -214,19 +214,13 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 		 res_id_buf[5] = "****",
 		 charge_buf[3] = "  \0";
 
-	if (id < 100000)
-		sprintf(id_buf, "%5d", id);
-	else
-		sprintf(id_buf, "%05x", id);
+	
+	sprintf(id_buf, "%d", id);
+	
+	sprintf(res_id_buf, "%d", res_id);
 
-	if (res_id < 10000)
-		sprintf(res_id_buf, "%4d", res_id);
-	else if (res_id < 65536)
-		sprintf(res_id_buf, "%04x", res_id);
-	else
-		sprintf(res_id_buf, "****");
-
-	alt_loc = (alt_loc == '\0') ? ' ' : alt_loc;
+	alt_loc = (alt_loc == '\0' || (alt_loc == ' '))  ? '?' : alt_loc;
+	insert = (insert == '\0' || insert==' ') ? '?' : insert;
 
 	if (charge == -1)
 		sprintf(charge_buf, " 0");
@@ -237,14 +231,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 	if (abpa)
 		finalabpa = abpa_prob;
 
-	//status = fprintf(f, "%-7s %6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %4s %4s %2s %4s\n",
-	//				 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, res_id_buf, res_name, chain, atom_name);
+	status = fprintf(f, "%-7s %-6s %3s %4s %c %4s %6s %d %c %8.3f %8.3f %8.3f %6.2f %2s %d %s\n",
+					 rec_name, id_buf, symbol, atom_name,alt_loc, res_name, label_asym_id, label_seq_id,insert, x, y, z, occ, charge_buf, res_id,chain);
 
-	status = fprintf(f, "%-7s %-6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s  %2s\n",
-					 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, chain);
+}
 
-	/*"ATOM %d %s %s . %s %s . %d ? %f %f %f %f %f %s\n",
-            i + 1, atoms[i].name, atoms[i].type, atoms[i].resname, atoms[i].chain,
-            atoms[i].resid, *x, *y, *z, atoms[i].occupancy,
-            atoms[i].charge, atoms[i].chain);*/
-}

src/writepocket.c

@@ -44,7 +44,6 @@ static const char atomSiteHeader[] =
     "_atom_site.label_alt_id\n"
     "_atom_site.label_comp_id\n"
     "_atom_site.label_asym_id\n"
-    "_atom_site.label_entity_id\n"
     "_atom_site.label_seq_id\n"
     "_atom_site.pdbx_PDB_ins_code\n"
     "_atom_site.Cartn_x\n"
@@ -52,6 +51,7 @@ static const char atomSiteHeader[] =
     "_atom_site.Cartn_z\n"
     "_atom_site.occupancy\n"
     "_atom_site.pdbx_formal_charge\n"
+    "_atom_site.auth_seq_id\n"
     "_atom_site.auth_asym_id\n";
 
     /*static const char atomSiteHeader[] =
@@ -83,7 +83,6 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
     out[0] = '\0';
 
     node_pocket *pcur;
-
     int i = 0;
     if (pockets) {
         pcur = pockets->first;
@@ -92,13 +91,26 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i + 1);
             write_pocket_pqr_DB(out, pcur->pocket);
 
-            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
-            write_pocket_pdb_DB(out, pcur->pocket, pdb);
-
-            
+            if(write_mode[0] == 'p' || write_mode[0] == 'b'){
+        
             sprintf(out, "%s/pocket%d_atm.pdb", out_path, i + 1);
             write_pocket_pdb(out, pcur->pocket);
 
+            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
+            write_pocket_pdb_DB(out, pcur->pocket, pdb);
+            // sprintf(out, "%s/pocket%d_atm.pdb", out_path, i+1);
+            // write_pocket_pdb_DB(out, pcur->pocket);
+            }
+
+            if(write_mode[0] == 'm' || write_mode[0] == 'b'){
+            sprintf(out, "%s/pocket%d_atm.cif", out_path, i + 1);
+            write_pocket_mmcif(out, pcur->pocket);
+
+            sprintf(out, "%s/pocket%d_env_atm.cif", out_path, i+1);
+            write_pocket_mmcif_DB(out, pcur->pocket,pdb);
+            }
+
+
             pcur = pcur->next;
             i++;
         }
@@ -144,14 +156,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
 
         node_vertice *nvcur = pocket->v_lst->first;
 
-       /* 
-                                fprintf(stdout, "A Pocket:\n") ;
-        */
         while (nvcur) {
-            /*
-                                            fprintf(stdout, "Vertice %d: %p %d %f\n", i, nvcur->vertice, nvcur->vertice->id, nvcur->vertice->ray) ;
-                                            fprintf(stdout, "Atom %s\n", nvcur->vertice->neigh[0]->name) ;
-             */
 
             tab_vert[nvert] = nvcur->vertice;
             nvcur = nvcur->next;
@@ -159,7 +164,6 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
         }
         sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
         for (i = 0; i < n_sa; i++) {
-            //atom = pocket->sou_atoms[i] ;
             atom = pdb->latoms_p[sa[i]];
             write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
                     atom->res_name, atom->chain, atom->res_id,
@@ -167,36 +171,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);
         }
-        /*
-                    vcur = pocket->v_lst->first ;
-
-                        while(vcur){
-                                for(i = 0 ; i < 4 ; i++) {
-                                        if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
-                                                if(cur_size >= cur_allocated-1) {
-                                                        cur_allocated *= 2 ;
-                                                        atms = (s_atm**) my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
-                                                }
-                                                atms[cur_size] = vcur->vertice->neigh[i] ;
-                                                cur_size ++ ;
-                                        }
-
-                                }
-                                vcur = vcur->next ;
-                        }
-         */
-        // Then write atoms...
-        /*
-                        for(i = 0 ; i < cur_size ; i++) {
-                                atom = atms[i] ;
-
-                                write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                                                                                atom->res_name, atom->chain, atom->res_id,
-                                                                                atom->pdb_insert, atom->x, atom->y, atom->z,
-                                                                                atom->occupancy, atom->bfactor, atom->symbol,
-                                                                                atom->charge);
-                        }
-         */
+        
         fprintf(f, "TER\nEND\n");
         fclose(f);
     } else {
@@ -207,6 +182,56 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
     my_free(atms);
 }
 
+
+
+void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
+    int i = 0, nvert = 0;
+    s_atm **atms = (s_atm **) my_malloc(sizeof (s_atm*)*10);
+    s_atm *atom = NULL;
+    int n_sa = 0;
+    int *sa = NULL; /*surrounding atoms container*/
+    s_vvertice **tab_vert = NULL;
+    char tmp[250];
+    strcpy(tmp,out);
+    remove_ext(tmp);
+    remove_path(tmp);
+    FILE *f = fopen(out, "w");
+    fprintf(f,"data_%s\n# \n",tmp);
+    fprintf(f,"%s",atomSiteHeader);/*print the header*/
+    if (f && pocket) {
+        // First get the list of atoms
+        tab_vert = (s_vvertice **) my_malloc(pocket->v_lst->n_vertices * sizeof (s_vvertice*));
+
+        node_vertice *nvcur = pocket->v_lst->first;
+
+        while (nvcur) {
+
+            tab_vert[nvert] = nvcur->vertice;
+            nvcur = nvcur->next;
+            nvert++;
+        }
+        sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
+        for (i = 0; i < n_sa; i++) {
+            atom = pdb->latoms_p[sa[i]];
+            write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
+                    atom->pdb_insert, atom->x, atom->y, atom->z,
+                    atom->dA, atom->a0, atom->abpa, atom->symbol,
+                    atom->charge, atom->abpa_sourrounding_prob);
+        }
+        
+        fprintf(f, "#\n");
+        fclose(f);
+    } else {
+        if (!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
+        else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
+    }
+
+    my_free(atms);
+}
+
+
+
 /**
    ## FUNCTION: 
         write_single_pdb
@@ -350,9 +375,9 @@ void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms) {
     for (i = 0; i < natoms; i++) {
         atom = atoms + i;
         //atom->chain[1]='\0';
-        //printf("%d:%s|symb:%s\t",i,atom->chain,atom->symbol);
+        // printf("%d:%s vs %s\n",i,atom->chain,atom->label_asym_id);
         write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                atom->res_name, atom->chain, atom->res_id,
+                atom->res_name, atom->chain,atom->res_id,atom->label_asym_id,atom->label_seq_id,
                 atom->pdb_insert, atom->x, atom->y, atom->z,
                 atom->dA, atom->a0, atom->abpa, atom->symbol,
                 atom->charge, atom->abpa_sourrounding_prob);
@@ -483,7 +508,7 @@ void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
     int i = 1;
     if (pockets) {
         pcur = pockets->first;
-        
+
         while (pcur) {
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i);
 
@@ -717,7 +742,7 @@ void write_pocket_mmcif(const char out[], s_pocket *pocket) {
             atom = atms[i];
 
             write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                    atom->res_name, atom->chain, atom->res_id,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
                     atom->pdb_insert, atom->x, atom->y, atom->z,
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);

tests/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)       : 433.1334
+10  -Pocket volume (convex hull)       : 76.0139
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 32.4571
+13 - Number of apolar alpha sphere     :    35
+14 - Proportion of apolar alpha sphere : 0.6140
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3335     C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    3399     C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM    3397     C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3378     C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM    3332     O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM    3735     C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM    3729     O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM    1239     C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM    3454     O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM    3488     O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM    3380     C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM    3460     O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM    3458     C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    3760     C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM    3756     N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM    3398     C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM    3463     C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM    3737     O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM    3728     C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM    3730     C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM    3738     C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3464     C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM    3734     N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    3461     C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM    1250     N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM    1255     N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+# 

tests/reference_output/123abc_out/pocket10_env_atm.cif

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

tests/reference_output/123abc_out/pocket10_vert.pqr

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

tests/reference_output/123abc_out/pocket11_atm.cif

@@ -0,0 +1,63 @@
+data_pocket11_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    11:
+0  - Pocket Score                      : 0.0388
+1  - Drug Score                        : 0.0007
+2  - Number of alpha spheres           :    30
+3  - Mean alpha-sphere radius          : 3.6177
+4  - Mean alpha-sphere Solvent Acc.    : 0.4151
+5  - Mean B-factor of pocket residues  : 0.1046
+6  - Hydrophobicity Score              : 17.4167
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.8333
+9  - Pocket volume (Monte Carlo)       : 157.8834
+10  -Pocket volume (convex hull)       : 11.3291
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.2000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1405     C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM    1435     O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM    1407     C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM    996      O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM    1436     C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM    1329     N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM    1327     O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM    1290     C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM    1323     C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM    1437     O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM    1289     C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM    1312     C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM    1005     C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM    1311     O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM    1471     C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+ATOM    1355     O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM    1012     N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM    1444     O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM    995      C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM    994      C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM    1328     C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+# 

tests/reference_output/123abc_out/pocket11_env_atm.cif

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

tests/reference_output/123abc_out/pocket11_vert.pqr

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

tests/reference_output/123abc_out/pocket12_atm.cif

@@ -0,0 +1,61 @@
+data_pocket12_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    12:
+0  - Pocket Score                      : 0.0380
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    22
+3  - Mean alpha-sphere radius          : 4.0091
+4  - Mean alpha-sphere Solvent Acc.    : 0.5656
+5  - Mean B-factor of pocket residues  : 0.1891
+6  - Hydrophobicity Score              : 14.1667
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.4167
+9  - Pocket volume (Monte Carlo)       : 288.4808
+10  -Pocket volume (convex hull)       : 19.5893
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.0909
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3271     O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3383     C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM    3094     O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM    3097     C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM    3504     C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM    3368     O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM    3109     O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM    3258     N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM    3095     C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM    3084     O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM    3381     C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM    3270     C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM    3326     C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM    3391     C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM    3106     C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM    3107     C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+# 

tests/reference_output/123abc_out/pocket12_env_atm.cif

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

tests/reference_output/123abc_out/pocket12_vert.pqr

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

tests/reference_output/123abc_out/pocket13_atm.cif

@@ -0,0 +1,74 @@
+data_pocket13_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    13:
+0  - Pocket Score                      : 0.0342
+1  - Drug Score                        : 0.3180
+2  - Number of alpha spheres           :    51
+3  - Mean alpha-sphere radius          : 3.7908
+4  - Mean alpha-sphere Solvent Acc.    : 0.4415
+5  - Mean B-factor of pocket residues  : 0.1092
+6  - Hydrophobicity Score              : 59.0769
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 411.4784
+10  -Pocket volume (convex hull)       : 39.2787
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 37.1163
+13 - Number of apolar alpha sphere     :    43
+14 - Proportion of apolar alpha sphere : 0.8431
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    7064     N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM    7069     C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM    7068     C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM    7063     C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM    8096     C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM    7780     O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM    7784     C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM    7814     C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM    7081     O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM    7086     N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM    7087     C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM    7080     C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM    7062     O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM    7093     C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM    8079     C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM    7061     C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM    8080     C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM    8067     O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM    7060     C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM    7084     C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM    7817     C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM    7819     O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM    8069     C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM    7118     C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM    7820     C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM    8073     S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM    7816     N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM    7065     C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM    7082     C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM    8097     C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM    7092     C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM    8308     C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+# 

tests/reference_output/123abc_out/pocket13_env_atm.cif

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

tests/reference_output/123abc_out/pocket13_vert.pqr

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

tests/reference_output/123abc_out/pocket14_atm.cif

@@ -0,0 +1,55 @@
+data_pocket14_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    14:
+0  - Pocket Score                      : 0.0287
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    20
+3  - Mean alpha-sphere radius          : 3.7199
+4  - Mean alpha-sphere Solvent Acc.    : 0.5390
+5  - Mean B-factor of pocket residues  : 0.2120
+6  - Hydrophobicity Score              : -27.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.5000
+9  - Pocket volume (Monte Carlo)       : 158.8699
+10  -Pocket volume (convex hull)       : 1.4197
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     0
+14 - Proportion of apolar alpha sphere : 0.0000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3238     O    O ?  ASP    Bxp 154 ?   17.212   58.730   41.018  -2.14  0 381 B
+ATOM    3240     C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    2491     O  OE1 ?  GLU    Bxp 59 ?   14.831   61.607   36.581   0.00  0 286 B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    2492     O  OE2 ?  GLU    Bxp 59 ?   15.137   61.777   38.754  -1.07  0 286 B
+ATOM    2389     N   NZ ?  LYS    Bxp 44 ?   17.801   61.554   36.438  -1.51  0 271 B
+ATOM    3254     N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM    2489     C   CG ?  GLU    Bxp 59 ?   12.912   61.584   38.000   0.00  0 286 B
+ATOM    2490     C   CD ?  GLU    Bxp 59 ?   14.404   61.663   37.759   0.00  0 286 B
+ATOM    3239     C   CB ?  ASP    Bxp 154 ?   15.520   56.620   41.941   0.00  0 381 B
+ATOM    2488     C   CB ?  GLU    Bxp 59 ?   12.087   61.638   36.697   0.00  0 286 B
+# 

tests/reference_output/123abc_out/pocket14_env_atm.cif

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

tests/reference_output/123abc_out/pocket14_vert.pqr

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

tests/reference_output/123abc_out/pocket15_atm.cif

@@ -0,0 +1,67 @@
+data_pocket15_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    15:
+0  - Pocket Score                      : 0.0219
+1  - Drug Score                        : 0.0431
+2  - Number of alpha spheres           :    39
+3  - Mean alpha-sphere radius          : 3.7453
+4  - Mean alpha-sphere Solvent Acc.    : 0.4087
+5  - Mean B-factor of pocket residues  : 0.1166
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 222.3455
+10  -Pocket volume (convex hull)       : 14.5929
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 33.0000
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8718
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3639     C   CA ?  ALA    Bxp 206 ?   25.485   44.511   57.685   0.00  0 433 B
+ATOM    2914     C  CD1 ?  LEU    Bxp 113 ?   26.128   47.415   60.882   0.00  0 340 B
+ATOM    3642     C   CB ?  ALA    Bxp 206 ?   24.633   43.235   57.872   0.00  0 433 B
+ATOM    3641     O    O ?  ALA    Bxp 206 ?   27.664   43.745   58.449  -4.29  0 433 B
+ATOM    2922     C  CD1 ?  LEU    Bxp 114 ?   18.369   46.670   63.743   0.00  0 341 B
+ATOM    3902     C   CD ?  PRO    Bxp 238 ?   22.462   42.067   63.671   0.00  0 465 B
+ATOM    2892     O    O ?  ALA    Bxp 110 ?   23.079   48.277   64.744  -3.21  0 337 B
+ATOM    3901     C   CG ?  PRO    Bxp 238 ?   21.818   42.336   65.023   0.00  0 465 B
+ATOM    3919     C  CG2 ?  VAL    Bxp 241 ?   18.754   43.171   62.407   0.00  0 468 B
+ATOM    2890     C   CA ?  ALA    Bxp 110 ?   25.351   47.954   65.540   0.00  0 337 B
+ATOM    3918     C  CG1 ?  VAL    Bxp 241 ?   19.352   42.826   59.944   0.00  0 468 B
+ATOM    3895     S   SG ?  CYS    Bxp 237 ?   22.468   40.332   60.148   0.00  0 464 B
+ATOM    2893     C   CB ?  ALA    Bxp 110 ?   25.301   47.008   66.740   0.00  0 337 B
+ATOM    2916     N    N ?  LEU    Bxp 114 ?   21.229   49.545   62.399  -2.19  0 341 B
+ATOM    3889     O    O ?  GLY    Bxp 236 ?   25.751   41.531   64.057   0.00  0 463 B
+ATOM    2912     C   CB ?  LEU    Bxp 113 ?   24.074   48.764   61.348   0.00  0 340 B
+ATOM    2917     C   CA ?  LEU    Bxp 114 ?   19.825   49.298   62.629   0.00  0 341 B
+ATOM    4130     C  CE1 ?  PHE    Bxp 266 ?   16.326   46.124   60.459   0.00  0 493 B
+ATOM    2948     C   CB ?  ALA    Bxp 117 ?   17.953   48.663   58.385   0.00  0 344 B
+ATOM    2910     C    C ?  LEU    Bxp 113 ?   21.785   49.807   61.241   0.00  0 340 B
+ATOM    3891     C   CA ?  CYS    Bxp 237 ?   24.487   40.444   62.093   0.00  0 464 B
+ATOM    2911     O    O ?  LEU    Bxp 113 ?   21.152   49.905   60.239   0.00  0 340 B
+ATOM    3636     C  CG2 ?  ILE    Bxp 205 ?   23.388   48.453   57.534   0.00  0 432 B
+ATOM    3602     O    O ?  LEU    Bxp 202 ?   22.353   44.476   55.620  -1.07  0 429 B
+ATOM    3606     C  CD2 ?  LEU    Bxp 202 ?   18.004   45.680   56.609   0.00  0 429 B
+# 

tests/reference_output/123abc_out/pocket15_env_atm.cif

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

tests/reference_output/123abc_out/pocket15_vert.pqr

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

tests/reference_output/123abc_out/pocket16_atm.cif

@@ -0,0 +1,63 @@
+data_pocket16_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    16:
+0  - Pocket Score                      : 0.0116
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    28
+3  - Mean alpha-sphere radius          : 3.7712
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.1225
+6  - Hydrophobicity Score              : 11.6923
+7  - Polarity Score                    :     9
+8  - Amino Acid based volume Score     : 4.5385
+9  - Pocket volume (Monte Carlo)       : 372.5160
+10  -Pocket volume (convex hull)       : 34.1542
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 6.5000
+13 - Number of apolar alpha sphere     :     8
+14 - Proportion of apolar alpha sphere : 0.2857
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    7853     C   CA ?  SER    Dxp 211 ?   42.974   31.063   42.423   0.00  0 438 D
+ATOM    7600     C  CH2 ?  TRP    Dxp 178 ?   43.960   26.363   45.206   0.00  0 405 D
+ATOM    7847     O    O ?  MET    Dxp 210 ?   44.036   29.741   40.141  -1.07  0 437 D
+ATOM    7857     O   OG ?  SER    Dxp 211 ?   44.316   32.109   43.942   0.00  0 438 D
+ATOM    7598     C  CZ2 ?  TRP    Dxp 178 ?   44.202   25.607   44.069   0.00  0 405 D
+ATOM    7864     C   CD ?  PRO    Dxp 212 ?   41.974   28.366   43.102   0.00  0 439 D
+ATOM    7302     C   CB ?  ARG    Dxp 140 ?   50.864   24.591   44.728   0.00  0 367 D
+ATOM    6415     N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM    6936     N  ND2 ?  ASN    Dxp 95 ?   54.321   26.577   41.672   0.00  0 322 D
+ATOM    6952     C  CD2 ?  LEU    Dxp 97 ?   49.815   28.277   43.031   0.00  0 324 D
+ATOM    7493     O  OG1 ?  THR    Dxp 165 ?   46.860   28.337   49.111  -0.95  0 392 D
+ATOM    7307     N  NH1 ?  ARG    Dxp 140 ?   46.275   24.168   46.062   0.00  0 367 D
+ATOM    7304     C   CD ?  ARG    Dxp 140 ?   49.165   24.333   46.741   0.00  0 367 D
+ATOM    7468     C   CE ?  MET    Dxp 161 ?   51.743   26.507   49.224   0.00  0 388 D
+ATOM    6959     O  OD1 ?  ASP    Dxp 98 ?   54.141   30.867   42.252  -4.02  0 325 D
+ATOM    7806     O  OE1 ?  GLU    Dxp 204 ?   46.278   25.826   41.102  -2.14  0 431 D
+ATOM    6960     O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM    6991     N  NH2 ?  ARG    Dxp 101 ?   47.806   31.880   42.344  -2.61  0 328 D
+ATOM    6951     C  CD1 ?  LEU    Dxp 97 ?   48.963   28.362   40.622   0.00  0 324 D
+ATOM    6990     N  NH1 ?  ARG    Dxp 101 ?   49.983   32.573   42.931  -3.70  0 328 D
+ATOM    7467     S   SD ?  MET    Dxp 161 ?   50.163   27.152   49.858   0.00  0 388 D
+# 

tests/reference_output/123abc_out/pocket16_env_atm.cif

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

tests/reference_output/123abc_out/pocket16_vert.pqr

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

tests/reference_output/123abc_out/pocket17_atm.cif

@@ -0,0 +1,57 @@
+data_pocket17_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    17:
+0  - Pocket Score                      : 0.0075
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    19
+3  - Mean alpha-sphere radius          : 3.5999
+4  - Mean alpha-sphere Solvent Acc.    : 0.4164
+5  - Mean B-factor of pocket residues  : 0.1872
+6  - Hydrophobicity Score              : 12.0000
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 155.6925
+10  -Pocket volume (convex hull)       : 5.2942
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 0.0000
+13 - Number of apolar alpha sphere     :     1
+14 - Proportion of apolar alpha sphere : 0.0526
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3171     O    O ?  GLY    Bxp 145 ?   24.279   62.076   57.870   0.00  0 372 B
+ATOM    2751     C  CE1 ?  TYR    Bxp 93 ?   27.916   64.065   57.675   0.00  0 320 B
+ATOM    3181     N    N ?  ASN    Bxp 147 ?   24.353   63.017   61.460  -3.03  0 374 B
+ATOM    3189     N    N ?  HIS    Bxp 148 ?   23.808   60.293   60.791   0.00  0 375 B
+ATOM    2872     O  OE1 ?  GLU    Bxp 107 ?   31.484   58.761   62.681  -0.95  0 334 B
+ATOM    2752     C  CE2 ?  TYR    Bxp 93 ?   30.166   63.254   57.309   0.00  0 320 B
+ATOM    2873     O  OE2 ?  GLU    Bxp 107 ?   29.348   59.201   62.656  -7.90  0 334 B
+ATOM    2754     O   OH ?  TYR    Bxp 93 ?   29.703   64.823   59.044   0.00  0 320 B
+ATOM    2753     C   CZ ?  TYR    Bxp 93 ?   29.259   64.044   58.017   0.00  0 320 B
+ATOM    2837     N    N ?  ASN    Bxp 104 ?   33.994   55.404   60.098  -1.09  0 331 B
+ATOM    2835     C   CB ?  CYS    Bxp 103 ?   31.652   54.686   58.227   0.00  0 330 B
+ATOM    2832     C   CA ?  CYS    Bxp 103 ?   33.088   55.081   57.860   0.00  0 330 B
+ATOM    3198     N  NE2 ?  HIS    Bxp 148 ?   27.061   57.958   62.310   0.00  0 375 B
+ATOM    2802     O   OH ?  TYR    Bxp 99 ?   28.273   57.952   59.075  -7.50  0 326 B
+ATOM    2799     C  CE1 ?  TYR    Bxp 99 ?   29.022   58.408   56.848   0.00  0 326 B
+# 

tests/reference_output/123abc_out/pocket17_env_atm.cif

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

tests/reference_output/123abc_out/pocket17_vert.pqr

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

tests/reference_output/123abc_out/pocket18_atm.cif

@@ -0,0 +1,65 @@
+data_pocket18_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    18:
+0  - Pocket Score                      : 0.0041
+1  - Drug Score                        : 0.0027
+2  - Number of alpha spheres           :    33
+3  - Mean alpha-sphere radius          : 3.9082
+4  - Mean alpha-sphere Solvent Acc.    : 0.4275
+5  - Mean B-factor of pocket residues  : 0.2780
+6  - Hydrophobicity Score              : 53.6000
+7  - Polarity Score                    :     4
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 286.0757
+10  -Pocket volume (convex hull)       : 22.1820
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 17.8947
+13 - Number of apolar alpha sphere     :    19
+14 - Proportion of apolar alpha sphere : 0.5758
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1359     O    O ?  LEU    Axp 184 ?   14.349   39.319   26.613  -1.07  0 411 A
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    1363     C  CD2 ?  LEU    Axp 184 ?   17.375   37.076   23.709   0.00  0 411 A
+ATOM    3351     N    N ?  ALA    Bxp 170 ?   17.691   42.856   27.354  -6.98  0 397 B
+ATOM    3340     C   CB ?  ALA    Bxp 168 ?   22.786   43.694   28.595   0.00  0 395 B
+ATOM    1640     O    O ?  SER    Axp 219 ?   23.891   43.579   25.385  -1.07  0 446 A
+ATOM    1638     C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM    1632     O    O ?  LEU    Axp 218 ?   23.990   39.840   23.886   0.00  0 445 A
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    3338     C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM    1298     C  CD1 ?  ILE    Axp 176 ?   20.379   35.378   24.896   0.00  0 403 A
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    1279     C  CD1 ?  PHE    Axp 174 ?   15.732   32.610   26.953   0.00  0 401 A
+ATOM    1244     C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM    3342     C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM    1297     C  CG2 ?  ILE    Axp 176 ?   21.592   37.080   22.335   0.00  0 403 A
+ATOM    1663     C   CB ?  TYR    Axp 222 ?   18.792   43.075   23.036   0.00  0 449 A
+ATOM    1659     N    N ?  TYR    Axp 222 ?   20.759   42.581   21.578  -1.09  0 449 A
+ATOM    1362     C  CD1 ?  LEU    Axp 184 ?   17.407   38.949   21.882   0.00  0 411 A
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    1357     C   CA ?  LEU    Axp 184 ?   14.567   38.323   24.463   0.00  0 411 A
+ATOM    1353     O    O ?  SER    Axp 183 ?   12.402   36.556   25.117   0.00  0 410 A
+ATOM    1360     C   CB ?  LEU    Axp 184 ?   15.704   39.018   23.710   0.00  0 411 A
+# 

tests/reference_output/123abc_out/pocket18_env_atm.cif

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

tests/reference_output/123abc_out/pocket18_vert.pqr

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

tests/reference_output/123abc_out/pocket19_atm.cif

@@ -0,0 +1,74 @@
+data_pocket19_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    19:
+0  - Pocket Score                      : 0.0000
+1  - Drug Score                        : 0.0491
+2  - Number of alpha spheres           :    40
+3  - Mean alpha-sphere radius          : 3.9057
+4  - Mean alpha-sphere Solvent Acc.    : 0.5724
+5  - Mean B-factor of pocket residues  : 0.2564
+6  - Hydrophobicity Score              : 62.1111
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 4.3333
+9  - Pocket volume (Monte Carlo)       : 433.0316
+10  -Pocket volume (convex hull)       : 67.6357
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 28.1176
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.8500
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    7944     C   CZ ?  TYR    Dxp 222 ?   28.663   18.750   51.374   0.00  0 449 D
+ATOM    7943     C  CE2 ?  TYR    Dxp 222 ?   27.884   19.861   51.731   0.00  0 449 D
+ATOM    7945     O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM    7647     C   CB ?  ALA    Dxp 185 ?   30.355   15.757   53.617   0.00  0 412 D
+ATOM    7644     C   CA ?  ALA    Dxp 185 ?   31.641   16.003   54.405   0.00  0 412 D
+ATOM    7942     C  CE1 ?  TYR    Dxp 222 ?   29.998   18.906   51.064   0.00  0 449 D
+ATOM    7940     C  CD1 ?  TYR    Dxp 222 ?   30.563   20.141   51.099   0.00  0 449 D
+ATOM    7941     C  CD2 ?  TYR    Dxp 222 ?   28.465   21.119   51.770   0.00  0 449 D
+ATOM    7577     C  CD1 ?  ILE    Dxp 176 ?   37.672   25.382   53.690   0.00  0 403 D
+ATOM    7576     C  CG2 ?  ILE    Dxp 176 ?   36.592   24.562   50.949   0.00  0 403 D
+ATOM    7575     C  CG1 ?  ILE    Dxp 176 ?   38.212   24.231   52.898   0.00  0 403 D
+ATOM    7642     C  CD2 ?  LEU    Dxp 184 ?   36.369   20.233   52.078   0.00  0 411 D
+ATOM    7641     C  CD1 ?  LEU    Dxp 184 ?   34.448   20.808   50.650   0.00  0 411 D
+ATOM    7938     C   CB ?  TYR    Dxp 222 ?   30.486   22.638   51.402   0.00  0 449 D
+ATOM    7934     N    N ?  TYR    Dxp 222 ?   31.202   24.455   49.938  -1.09  0 449 D
+ATOM    7907     O    O ?  LEU    Dxp 218 ?   34.008   27.525   52.271  -0.40  0 445 D
+ATOM    7639     C   CB ?  LEU    Dxp 184 ?   34.244   18.838   52.215   0.00  0 411 D
+ATOM    7939     C   CG ?  TYR    Dxp 222 ?   29.832   21.273   51.448   0.00  0 449 D
+ATOM    7560     C  CE1 ?  PHE    Dxp 174 ?   39.595   17.433   56.140   0.00  0 401 D
+ATOM    7638     O    O ?  LEU    Dxp 184 ?   33.870   17.251   55.188   0.00  0 411 D
+ATOM    7525     N  ND1 ?  HIS    Dxp 169 ?   36.365   20.155   60.429  -1.93  0 396 D
+ATOM    7558     C  CD1 ?  PHE    Dxp 174 ?   39.696   18.611   55.390   0.00  0 401 D
+ATOM    7524     C   CG ?  HIS    Dxp 169 ?   36.743   21.442   60.097   0.00  0 396 D
+ATOM    7527     C  CE1 ?  HIS    Dxp 169 ?   35.170   20.180   60.996   0.00  0 396 D
+ATOM    7528     N  NE2 ?  HIS    Dxp 169 ?   34.778   21.438   61.089   0.00  0 396 D
+ATOM    7526     C  CD2 ?  HIS    Dxp 169 ?   35.750   22.249   60.547   0.00  0 396 D
+ATOM    7637     C    C ?  LEU    Dxp 184 ?   33.727   17.072   53.991   0.00  0 411 D
+ATOM    7523     C   CB ?  HIS    Dxp 169 ?   38.074   21.770   59.468   0.00  0 396 D
+ATOM    7556     C   CB ?  PHE    Dxp 174 ?   40.965   20.182   53.857   0.00  0 401 D
+ATOM    7513     C  CG2 ?  THR    Dxp 167 ?   39.795   26.405   56.782   0.00  0 394 D
+ATOM    7510     O    O ?  THR    Dxp 167 ?   41.927   23.289   56.784   0.00  0 394 D
+ATOM    7517     O    O ?  ALA    Dxp 168 ?   40.187   24.764   60.121  -3.35  0 395 D
+# 

tests/reference_output/123abc_out/pocket19_env_atm.cif

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

tests/reference_output/123abc_out/pocket19_vert.pqr

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

tests/reference_output/123abc_out/pocket1_atm.cif

@@ -0,0 +1,158 @@
+data_pocket1_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket     1:
+0  - Pocket Score                      : 1.0099
+1  - Drug Score                        : 0.9898
+2  - Number of alpha spheres           :   213
+3  - Mean alpha-sphere radius          : 4.0060
+4  - Mean alpha-sphere Solvent Acc.    : 0.5026
+5  - Mean B-factor of pocket residues  : 0.1858
+6  - Hydrophobicity Score              : 39.5476
+7  - Polarity Score                    :    18
+8  - Amino Acid based volume Score     : 4.2857
+9  - Pocket volume (Monte Carlo)       : 1760.2584
+10  -Pocket volume (convex hull)       : 1610.3746
+11 - Charge Score                      :    -4
+12 - Local hydrophobic density Score   : 53.0308
+13 - Number of apolar alpha sphere     :   130
+14 - Proportion of apolar alpha sphere : 0.6103
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    5124     C  CD1 ?  LEU    Cxp 127 ?   52.412   62.880   19.111   0.00  0 354 C
+ATOM    5175     O    O ?  ILE    Cxp 133 ?   50.155   63.679   13.849  -1.07  0 360 C
+ATOM    4642     C  CD1 ?  ILE    Cxp 66 ?   57.564   64.926   16.918   0.00  0 293 C
+ATOM    5181     C   CA ?  HIS    Cxp 134 ?   49.968   61.358   15.298   0.00  0 361 C
+ATOM    5168     C  CD2 ?  PHE    Cxp 132 ?   53.775   68.288   14.726   0.00  0 359 C
+ATOM    5165     C   CB ?  PHE    Cxp 132 ?   52.152   67.148   16.265   0.00  0 359 C
+ATOM    4607     C  CG1 ?  VAL    Cxp 62 ?   56.843   66.361   13.193   0.00  0 289 C
+ATOM    5349     C  CD2 ?  PHE    Cxp 155 ?   58.617   52.809   14.766   0.00  0 382 C
+ATOM    4806     C  CG2 ?  THR    Cxp 88 ?   64.918   58.267   15.934   0.00  0 315 C
+ATOM    5351     C  CE2 ?  PHE    Cxp 155 ?   58.958   52.743   16.096   0.00  0 382 C
+ATOM    4805     O  OG1 ?  THR    Cxp 88 ?   65.292   56.165   17.041   0.00  0 315 C
+ATOM    5166     C   CG ?  PHE    Cxp 132 ?   53.337   68.020   16.020   0.00  0 359 C
+ATOM    5187     C  CD2 ?  HIS    Cxp 134 ?   52.038   58.986   17.107   0.00  0 361 C
+ATOM    5125     C  CD2 ?  LEU    Cxp 127 ?   53.933   64.923   19.034   0.00  0 354 C
+ATOM    4367     C  CG1 ?  VAL    Cxp 29 ?   65.278   51.087   12.687   0.00  0 256 C
+ATOM    4342     C   CG ?  TYR    Cxp 26 ?   60.508   48.226   13.248   0.00  0 253 C
+ATOM    4680     C  CD2 ?  LEU    Cxp 71 ?   55.947   61.004   20.573   0.00  0 298 C
+ATOM    5338     C   CB ?  ASP    Cxp 154 ?   55.209   57.618   13.892   0.00  0 381 C
+ATOM    4684     O    O ?  VAL    Cxp 72 ?   61.863   60.416   19.355  -5.36  0 299 C
+ATOM    4640     C  CG1 ?  ILE    Cxp 66 ?   58.912   65.273   17.720   0.00  0 293 C
+ATOM    4677     C   CB ?  LEU    Cxp 71 ?   58.112   61.528   21.791   0.00  0 298 C
+ATOM    5341     O  OD2 ?  ASP    Cxp 154 ?   53.714   58.561   12.241  -0.14  0 381 C
+ATOM    5183     O    O ?  HIS    Cxp 134 ?   50.262   60.307   13.190   0.00  0 361 C
+ATOM    4608     C  CG2 ?  VAL    Cxp 62 ?   57.086   66.805   10.673   0.00  0 289 C
+ATOM    4606     C   CB ?  VAL    Cxp 62 ?   57.804   66.325   11.964   0.00  0 289 C
+ATOM    4849     C  CD2 ?  TYR    Cxp 93 ?   62.771   44.062   27.626   0.00  0 320 C
+ATOM    4898     C  CE1 ?  TYR    Cxp 99 ?   58.734   44.320   28.340   0.00  0 326 C
+ATOM    4896     C  CD1 ?  TYR    Cxp 99 ?   58.352   44.217   27.023   0.00  0 326 C
+ATOM    4924     O    O ?  GLU    Cxp 102 ?   56.618   37.405   27.670  -1.21  0 329 C
+ATOM    4533     C   CB ?  GLU    Cxp 52 ?   60.007   57.267    0.138   0.00  0 279 C
+ATOM    4493     N   NZ ?  LYS    Cxp 44 ?   59.948   55.800    8.159   0.00  0 271 C
+ATOM    4492     C   CE ?  LYS    Cxp 44 ?   61.398   55.419    7.935   0.00  0 271 C
+ATOM    4565     C  CD1 ?  PHE    Cxp 56 ?   63.711   58.360    4.956   0.00  0 283 C
+ATOM    4491     C   CD ?  LYS    Cxp 44 ?   62.464   55.863    8.961   0.00  0 271 C
+ATOM    4591     O  OE2 ?  GLU    Cxp 59 ?   60.141   58.852   10.727  -1.07  0 286 C
+ATOM    4489     C   CB ?  LYS    Cxp 44 ?   64.904   55.444    9.602   0.00  0 271 C
+ATOM    4344     C  CD2 ?  TYR    Cxp 26 ?   59.377   48.648   13.987   0.00  0 253 C
+ATOM    4477     C   CB ?  ALA    Cxp 42 ?   66.815   52.711   16.102   0.00  0 269 C
+ATOM    4928     O  OE1 ?  GLU    Cxp 102 ?   58.396   38.729   22.754  -0.95  0 329 C
+ATOM    4845     O    O ?  TYR    Cxp 93 ?   60.677   45.046   23.639  -4.02  0 320 C
+ATOM    4507     C  CD1 ?  LEU    Cxp 46 ?   63.457   56.650    1.429   0.00  0 273 C
+ATOM    4614     C   CG ?  MET    Cxp 63 ?   60.952   62.629   14.053   0.00  0 290 C
+ATOM    4615     S   SD ?  MET    Cxp 63 ?   61.859   61.128   13.673   0.00  0 290 C
+ATOM    5334     N    N ?  ASP    Cxp 154 ?   56.468   56.249   15.507   0.00  0 381 C
+ATOM    4854     N    N ?  GLY    Cxp 94 ?   61.926   46.515   22.505  -1.09  0 321 C
+ATOM    4855     C   CA ?  GLY    Cxp 94 ?   61.148   46.414   21.286   0.00  0 321 C
+ATOM    4826     C   CZ ?  PHE    Cxp 90 ?   68.029   47.527   20.408   0.00  0 317 C
+ATOM    4838     O    O ?  THR    Cxp 92 ?   65.169   45.657   23.913   0.00  0 319 C
+ATOM    4858     N    N ?  ASN    Cxp 95 ?   58.837   46.563   20.532  -2.19  0 322 C
+ATOM    4864     O  OD1 ?  ASN    Cxp 95 ?   57.197   45.110   18.091  -1.07  0 322 C
+ATOM    4889     O  OD2 ?  ASP    Cxp 98 ?   56.786   42.248   18.314  -0.81  0 325 C
+ATOM    4931     C   CA ?  CYS    Cxp 103 ?   55.713   39.474   29.139   0.00  0 330 C
+ATOM    4923     C    C ?  GLU    Cxp 102 ?   55.803   38.136   27.151   0.00  0 329 C
+ATOM    5337     O    O ?  ASP    Cxp 154 ?   57.341   56.209   12.768  -1.07  0 381 C
+ATOM    4891     C   CA ?  TYR    Cxp 99 ?   56.204   43.137   24.766   0.00  0 326 C
+ATOM    4890     N    N ?  TYR    Cxp 99 ?   55.885   43.129   23.365  -2.19  0 326 C
+ATOM    4925     C   CB ?  GLU    Cxp 102 ?   56.670   38.222   24.775   0.00  0 329 C
+ATOM    4341     C   CB ?  TYR    Cxp 26 ?   60.784   48.778   11.861   0.00  0 253 C
+ATOM    4686     C  CG1 ?  VAL    Cxp 72 ?   60.468   57.953   18.334   0.00  0 299 C
+ATOM    5333     C   CB ?  ALA    Cxp 153 ?   57.973   55.244   17.737   0.00  0 380 C
+ATOM    4687     C  CG2 ?  VAL    Cxp 72 ?   62.471   56.742   19.102   0.00  0 299 C
+ATOM    4314     C  CD1 ?  LEU    Cxp 21 ?   66.372   48.924   15.249   0.00  0 248 C
+ATOM    4822     C  CD1 ?  PHE    Cxp 90 ?   68.357   49.652   19.357   0.00  0 317 C
+ATOM    4827     N    N ?  MET    Cxp 91 ?   65.600   51.395   21.975   0.00  0 318 C
+ATOM    4587     C   CB ?  GLU    Cxp 59 ?   59.660   61.810    8.754   0.00  0 286 C
+ATOM    4584     C   CA ?  GLU    Cxp 59 ?   59.760   63.312    8.983   0.00  0 286 C
+ATOM    4348     O   OH ?  TYR    Cxp 26 ?   59.736   46.661   17.066  -2.14  0 253 C
+ATOM    4335     O  OE1 ?  GLN    Cxp 25 ?   58.998   43.247   14.898  -4.69  0 252 C
+ATOM    4886     C   CB ?  ASP    Cxp 98 ?   56.203   41.956   20.500   0.00  0 325 C
+ATOM    4929     O  OE2 ?  GLU    Cxp 102 ?   57.083   38.222   21.105  -0.54  0 329 C
+ATOM    4316     N    N ?  GLY    Cxp 22 ?   64.012   43.884   14.345  -6.98  0 249 C
+ATOM    4315     C  CD2 ?  LEU    Cxp 21 ?   67.339   46.763   16.058   0.00  0 248 C
+ATOM    4312     C   CB ?  LEU    Cxp 21 ?   65.502   46.661   14.421   0.00  0 248 C
+ATOM    4893     O    O ?  TYR    Cxp 99 ?   55.173   41.873   26.595   0.00  0 326 C
+ATOM    5331     C    C ?  ALA    Cxp 153 ?   55.953   56.313   16.712   0.00  0 380 C
+ATOM    5332     O    O ?  ALA    Cxp 153 ?   54.761   56.347   16.907   0.00  0 380 C
+ATOM    4485     N    N ?  LYS    Cxp 44 ?   66.985   54.643   10.662   0.00  0 271 C
+ATOM    4317     C   CA ?  GLY    Cxp 22 ?   62.747   43.150   14.231   0.00  0 249 C
+ATOM    4343     C  CD1 ?  TYR    Cxp 26 ?   61.357   47.296   13.808   0.00  0 253 C
+ATOM    4830     O    O ?  MET    Cxp 91 ?   64.488   48.834   22.426   0.00  0 318 C
+ATOM    4824     C  CE1 ?  PHE    Cxp 90 ?   68.165   48.287   19.279   0.00  0 317 C
+ATOM    5258     C  CD1 ?  LEU    Cxp 143 ?   60.801   52.853   19.522   0.00  0 370 C
+ATOM    4810     O    O ?  GLU    Cxp 89 ?   66.226   54.641   19.567   0.00  0 316 C
+ATOM    4590     O  OE1 ?  GLU    Cxp 59 ?   60.143   59.180    8.562   0.00  0 286 C
+ATOM    4560     C   CA ?  PHE    Cxp 56 ?   61.727   61.139    4.612   0.00  0 283 C
+ATOM    4552     C    C ?  GLU    Cxp 55 ?   59.443   61.938    4.041   0.00  0 282 C
+ATOM    4553     O    O ?  GLU    Cxp 55 ?   59.074   62.152    5.210  -0.40  0 282 C
+ATOM    4559     N    N ?  PHE    Cxp 56 ?   60.677   61.556    3.690   0.00  0 283 C
+ATOM    5354     C   CA ?  GLY    Cxp 156 ?   55.185   54.289    9.070   0.00  0 383 C
+ATOM    5340     O  OD1 ?  ASP    Cxp 154 ?   54.160   56.484   12.072  -0.40  0 381 C
+ATOM    4588     C   CG ?  GLU    Cxp 59 ?   59.879   61.018   10.009   0.00  0 286 C
+ATOM    4586     O    O ?  GLU    Cxp 59 ?   60.890   64.044   10.965   0.00  0 286 C
+ATOM    4554     C   CB ?  GLU    Cxp 55 ?   57.705   60.840    2.562   0.00  0 282 C
+ATOM    5356     O    O ?  GLY    Cxp 156 ?   55.311   52.499    7.563  -3.62  0 383 C
+ATOM    5376     C   CG ?  ARG    Cxp 159 ?   54.486   53.056    3.655   0.00  0 386 C
+ATOM    5259     C  CD2 ?  LEU    Cxp 143 ?   60.391   50.436   19.544   0.00  0 370 C
+ATOM    4346     C  CE2 ?  TYR    Cxp 26 ?   59.090   48.126   15.277   0.00  0 253 C
+ATOM    4347     C   CZ ?  TYR    Cxp 26 ?   59.971   47.200   15.806   0.00  0 253 C
+ATOM    4345     C  CE1 ?  TYR    Cxp 26 ?   61.109   46.769   15.049   0.00  0 253 C
+ATOM    4790     C  CG2 ?  ILE    Cxp 86 ?   65.267   59.719   11.684   0.00  0 313 C
+ATOM    5343     C   CA ?  PHE    Cxp 155 ?   57.162   53.520   12.244   0.00  0 382 C
+ATOM    5345     O    O ?  PHE    Cxp 155 ?   57.545   52.974    9.992  -1.07  0 382 C
+ATOM    4476     O    O ?  ALA    Cxp 42 ?   68.283   54.987   14.590   0.00  0 269 C
+ATOM    4497     O    O ?  THR    Cxp 45 ?   65.625   53.907    4.664  -2.55  0 272 C
+ATOM    4368     C  CG2 ?  VAL    Cxp 29 ?   63.667   51.380   10.691   0.00  0 256 C
+ATOM    5346     C   CB ?  PHE    Cxp 155 ?   57.304   52.068   12.736   0.00  0 382 C
+ATOM    5353     N    N ?  GLY    Cxp 156 ?   55.685   54.235   10.437   0.00  0 383 C
+ATOM    5330     C   CA ?  ALA    Cxp 153 ?   56.928   56.348   17.874   0.00  0 380 C
+ATOM    5325     O    O ?  VAL    Cxp 152 ?   57.290   57.718   20.233   0.00  0 379 C
+ATOM    4589     C   CD ?  GLU    Cxp 59 ?   60.082   59.588    9.746   0.00  0 286 C
+ATOM    5339     C   CG ?  ASP    Cxp 154 ?   54.313   57.558   12.649   0.00  0 381 C
+ATOM    4787     O    O ?  ILE    Cxp 86 ?   67.579   57.024   11.540   0.00  0 313 C
+ATOM    4532     O    O ?  GLU    Cxp 52 ?   60.629   60.058    1.220  -1.07  0 279 C
+ATOM    4563     C   CB ?  PHE    Cxp 56 ?   62.803   60.407    3.827   0.00  0 283 C
+ATOM    4555     C   CG ?  GLU    Cxp 55 ?   56.341   60.714    3.218   0.00  0 282 C
+ATOM    4557     O  OE1 ?  GLU    Cxp 55 ?   54.968   62.335    4.361   0.00  0 282 C
+# 

tests/reference_output/123abc_out/pocket1_env_atm.cif

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

tests/reference_output/123abc_out/pocket1_vert.pqr

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

tests/reference_output/123abc_out/pocket20_atm.cif

@@ -0,0 +1,66 @@
+data_pocket20_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    20:
+0  - Pocket Score                      : -0.0058
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    37
+3  - Mean alpha-sphere radius          : 3.7789
+4  - Mean alpha-sphere Solvent Acc.    : 0.4544
+5  - Mean B-factor of pocket residues  : 0.2229
+6  - Hydrophobicity Score              : 11.7857
+7  - Polarity Score                    :    10
+8  - Amino Acid based volume Score     : 4.4286
+9  - Pocket volume (Monte Carlo)       : 419.1526
+10  -Pocket volume (convex hull)       : 54.0760
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 7.4000
+13 - Number of apolar alpha sphere     :    10
+14 - Proportion of apolar alpha sphere : 0.2703
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1578     C   CA ?  SER    Axp 211 ?   28.519   31.580   13.536   0.00  0 438 A
+ATOM    729      N  NH2 ?  ARG    Axp 101 ?   29.744   27.079   13.417  -2.19  0 328 A
+ATOM    1582     O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM    1531     O  OE1 ?  GLU    Axp 204 ?   23.660   27.646   12.432  -1.07  0 431 A
+ATOM    1572     O    O ?  MET    Axp 210 ?   27.392   30.484   11.286  -2.14  0 437 A
+ATOM    1589     C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM    1321     C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM    1192     C   CE ?  MET    Axp 161 ?   25.473   22.258   20.061   0.00  0 388 A
+ATOM    1193     N    N ?  THR    Axp 162 ?   27.717   23.001   24.543  -3.28  0 389 A
+ATOM    1196     O    O ?  THR    Axp 162 ?   30.318   24.681   23.653  -0.54  0 389 A
+ATOM    1190     C   CG ?  MET    Axp 161 ?   25.693   23.794   22.437   0.00  0 388 A
+ATOM    1191     S   SD ?  MET    Axp 161 ?   25.108   23.914   20.726   0.00  0 388 A
+ATOM    1214     O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM    1197     C   CB ?  THR    Axp 162 ?   30.043   22.165   24.907   0.00  0 389 A
+ATOM    728      N  NH1 ?  ARG    Axp 101 ?   30.641   25.059   14.054   0.00  0 328 A
+ATOM    1319     C  CZ2 ?  TRP    Axp 178 ?   23.312   29.778   15.389   0.00  0 405 A
+ATOM    690      C  CD2 ?  LEU    Axp 97 ?   26.615   24.712   14.130   0.00  0 324 A
+ATOM    1039     N  NH1 ?  ARG    Axp 140 ?   22.161   27.219   17.402  -2.19  0 367 A
+ATOM    1036     C   CD ?  ARG    Axp 140 ?   22.384   24.464   18.025   0.00  0 367 A
+ATOM    697      O  OD1 ?  ASP    Axp 98 ?   29.383   20.437   13.443   0.00  0 325 A
+ATOM    136      N  NE2 ?  GLN    Axp 25 ?   26.655   17.754   17.106  -1.51  0 252 A
+ATOM    1034     C   CB ?  ARG    Axp 140 ?   22.854   23.046   15.953   0.00  0 367 A
+ATOM    674      N  ND2 ?  ASN    Axp 95 ?   25.138   19.957   12.965  -2.19  0 322 A
+ATOM    1198     O  OG1 ?  THR    Axp 162 ?   29.373   20.894   24.874  -2.55  0 389 A
+# 

tests/reference_output/123abc_out/pocket20_env_atm.cif

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

tests/reference_output/123abc_out/pocket20_vert.pqr

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

tests/reference_output/123abc_out/pocket21_atm.cif

@@ -0,0 +1,74 @@
+data_pocket21_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    21:
+0  - Pocket Score                      : -0.0129
+1  - Drug Score                        : 0.0844
+2  - Number of alpha spheres           :    48
+3  - Mean alpha-sphere radius          : 3.7739
+4  - Mean alpha-sphere Solvent Acc.    : 0.4618
+5  - Mean B-factor of pocket residues  : 0.0755
+6  - Hydrophobicity Score              : 51.7143
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 3.8571
+9  - Pocket volume (Monte Carlo)       : 337.7557
+10  -Pocket volume (convex hull)       : 33.9441
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 32.5294
+13 - Number of apolar alpha sphere     :    34
+14 - Proportion of apolar alpha sphere : 0.7083
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    5013     C  CD1 ?  LEU    Cxp 113 ?   47.637   45.537   32.420   0.00  0 340 C
+ATOM    5969     O    O ?  GLY    Cxp 236 ?   41.436   44.926   35.683  -1.88  0 463 C
+ATOM    5742     C  CE2 ?  TYR    Cxp 208 ?   47.578   41.887   31.506   0.00  0 435 C
+ATOM    5744     O   OH ?  TYR    Cxp 208 ?   49.149   42.483   33.247   0.00  0 435 C
+ATOM    5967     C   CA ?  GLY    Cxp 236 ?   40.408   42.885   35.092   0.00  0 463 C
+ATOM    5960     O    O ?  GLU    Cxp 235 ?   40.959   41.746   32.508  -6.17  0 462 C
+ATOM    5724     O    O ?  ALA    Cxp 206 ?   44.035   43.617   29.804  -4.29  0 433 C
+ATOM    4992     C   CB ?  ALA    Cxp 110 ?   46.896   45.998   37.907   0.00  0 337 C
+ATOM    4989     C   CA ?  ALA    Cxp 110 ?   48.023   46.286   36.893   0.00  0 337 C
+ATOM    4988     N    N ?  ALA    Cxp 110 ?   49.019   45.250   37.006  -1.09  0 337 C
+ATOM    5722     C   CA ?  ALA    Cxp 206 ?   44.400   45.936   29.263   0.00  0 433 C
+ATOM    5011     C   CB ?  LEU    Cxp 113 ?   48.507   47.814   32.706   0.00  0 340 C
+ATOM    5725     C   CB ?  ALA    Cxp 206 ?   43.007   46.611   29.412   0.00  0 433 C
+ATOM    5971     C   CA ?  CYS    Cxp 237 ?   40.269   46.381   33.554   0.00  0 464 C
+ATOM    5968     C    C ?  GLY    Cxp 236 ?   40.655   44.362   34.916   0.00  0 463 C
+ATOM    5009     C    C ?  LEU    Cxp 113 ?   49.262   50.208   32.866   0.00  0 340 C
+ATOM    6002     C  CG1 ?  VAL    Cxp 241 ?   41.927   51.680   31.567   0.00  0 468 C
+ATOM    5010     O    O ?  LEU    Cxp 113 ?   49.304   50.941   31.905   0.00  0 340 C
+ATOM    5982     C   CD ?  PRO    Cxp 238 ?   41.741   48.427   35.286   0.00  0 465 C
+ATOM    5975     S   SG ?  CYS    Cxp 237 ?   39.866   48.440   31.675   0.00  0 464 C
+ATOM    4991     O    O ?  ALA    Cxp 110 ?   48.119   48.581   36.365  -4.29  0 337 C
+ATOM    5021     C  CD1 ?  LEU    Cxp 114 ?   45.548   52.723   35.306   0.00  0 341 C
+ATOM    6003     C  CG2 ?  VAL    Cxp 241 ?   42.161   52.318   34.092   0.00  0 468 C
+ATOM    5981     C   CG ?  PRO    Cxp 238 ?   41.902   49.346   36.487   0.00  0 465 C
+ATOM    5015     N    N ?  LEU    Cxp 114 ?   48.853   50.629   34.038  -1.09  0 341 C
+ATOM    5016     C   CA ?  LEU    Cxp 114 ?   48.437   52.025   34.290   0.00  0 341 C
+ATOM    5047     C   CB ?  ALA    Cxp 117 ?   47.619   53.976   30.267   0.00  0 344 C
+ATOM    5689     C  CD2 ?  LEU    Cxp 202 ?   44.675   53.384   28.357   0.00  0 429 C
+ATOM    6210     C  CE1 ?  PHE    Cxp 266 ?   44.724   55.322   32.190   0.00  0 493 C
+ATOM    5719     C  CG2 ?  ILE    Cxp 205 ?   48.010   48.643   29.034   0.00  0 432 C
+ATOM    5685     O    O ?  LEU    Cxp 202 ?   43.911   49.067   27.179  -2.14  0 429 C
+ATOM    5721     N    N ?  ALA    Cxp 206 ?   45.181   46.650   28.250   0.00  0 433 C
+# 

tests/reference_output/123abc_out/pocket21_env_atm.cif

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

tests/reference_output/123abc_out/pocket21_vert.pqr

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

tests/reference_output/123abc_out/pocket22_atm.cif

@@ -0,0 +1,77 @@
+data_pocket22_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    22:
+0  - Pocket Score                      : -0.0139
+1  - Drug Score                        : 0.0034
+2  - Number of alpha spheres           :    36
+3  - Mean alpha-sphere radius          : 3.9913
+4  - Mean alpha-sphere Solvent Acc.    : 0.6555
+5  - Mean B-factor of pocket residues  : 0.2200
+6  - Hydrophobicity Score              : 9.7857
+7  - Polarity Score                    :     8
+8  - Amino Acid based volume Score     : 4.0714
+9  - Pocket volume (Monte Carlo)       : 672.5394
+10  -Pocket volume (convex hull)       : 117.8604
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 17.8095
+13 - Number of apolar alpha sphere     :    21
+14 - Proportion of apolar alpha sphere : 0.5833
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    4048     O    O ?  ARG    Bxp 256 ?    5.584   39.776   52.007  -0.40  0 483 B
+ATOM    4034     O    O ?  SER    Bxp 254 ?    3.034   36.722   50.663  -3.35  0 481 B
+ATOM    4092     O  OE1 ?  GLU    Bxp 261 ?    4.400   40.941   57.227   0.00  0 488 B
+ATOM    4093     O  OE2 ?  GLU    Bxp 261 ?    2.933   42.122   56.184   0.00  0 488 B
+ATOM    4040     O    O ?  ASP    Bxp 255 ?    6.559   36.007   52.815   0.00  0 482 B
+ATOM    4057     C   CA ?  PRO    Bxp 257 ?    6.624   40.819   54.353   0.00  0 484 B
+ATOM    4143     C   CB ?  THR    Bxp 268 ?   10.227   46.401   67.772   0.00  0 495 B
+ATOM    4118     C   CA ?  ALA    Bxp 265 ?    9.929   45.031   63.065   0.00  0 492 B
+ATOM    4145     C  CG2 ?  THR    Bxp 268 ?   10.384   45.639   69.065   0.00  0 495 B
+ATOM    4144     O  OG1 ?  THR    Bxp 268 ?    8.840   46.564   67.429   0.00  0 495 B
+ATOM    4120     O    O ?  ALA    Bxp 265 ?   11.641   45.676   64.603  -1.48  0 492 B
+ATOM    4089     C   CB ?  GLU    Bxp 261 ?    5.421   43.577   58.123   0.00  0 488 B
+ATOM    4060     C   CB ?  PRO    Bxp 257 ?    7.583   41.016   55.523   0.00  0 484 B
+ATOM    3947     C  CD1 ?  LEU    Bxp 244 ?   11.916   41.124   59.300   0.00  0 471 B
+ATOM    4047     C    C ?  ARG    Bxp 256 ?    6.658   39.348   52.433   0.00  0 483 B
+ATOM    3972     C   CB ?  ALA    Bxp 247 ?   11.015   37.196   55.846   0.00  0 474 B
+ATOM    3937     C   CG ?  GLU    Bxp 243 ?   13.561   35.641   61.217   0.00  0 470 B
+ATOM    3940     O  OE2 ?  GLU    Bxp 243 ?   11.836   34.934   62.719   0.00  0 470 B
+ATOM    3935     O    O ?  GLU    Bxp 243 ?   13.956   36.736   57.962  -1.48  0 470 B
+ATOM    4062     C   CD ?  PRO    Bxp 257 ?    8.652   39.555   53.954   0.00  0 484 B
+ATOM    3938     C   CD ?  GLU    Bxp 243 ?   12.975   35.501   62.669   0.00  0 470 B
+ATOM    3911     O    O ?  LYS    Bxp 240 ?   15.567   39.731   61.909  -3.21  0 467 B
+ATOM    3939     O  OE1 ?  GLU    Bxp 243 ?   13.626   35.936   63.713   0.00  0 470 B
+ATOM    4152     S   SD ?  MET    Bxp 269 ?   15.508   43.520   64.899   0.00  0 496 B
+ATOM    4153     C   CE ?  MET    Bxp 269 ?   14.440   43.776   63.513   0.00  0 496 B
+ATOM    3912     C   CB ?  LYS    Bxp 240 ?   15.915   39.653   65.197   0.00  0 467 B
+ATOM    4151     C   CG ?  MET    Bxp 269 ?   14.602   44.443   66.216   0.00  0 496 B
+ATOM    4121     C   CB ?  ALA    Bxp 265 ?   10.310   43.906   62.117   0.00  0 492 B
+ATOM    4088     O    O ?  GLU    Bxp 261 ?    7.481   45.179   60.241  -3.62  0 488 B
+ATOM    3528     N   NZ ?  LYS    Bxp 192 ?    4.513   41.805   50.925   0.00  0 419 B
+ATOM    4056     N    N ?  PRO    Bxp 257 ?    7.275   39.856   53.515  -1.09  0 484 B
+ATOM    4061     C   CG ?  PRO    Bxp 257 ?    8.908   40.517   55.032   0.00  0 484 B
+ATOM    3948     C  CD2 ?  LEU    Bxp 244 ?   13.574   42.584   60.502   0.00  0 471 B
+ATOM    4087     C    C ?  GLU    Bxp 261 ?    7.103   45.132   59.045   0.00  0 488 B
+ATOM    4094     N    N ?  ILE    Bxp 262 ?    7.932   45.257   57.985   0.00  0 489 B
+# 

tests/reference_output/123abc_out/pocket22_env_atm.cif

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

tests/reference_output/123abc_out/pocket22_vert.pqr

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

tests/reference_output/123abc_out/pocket23_atm.cif

@@ -0,0 +1,59 @@
+data_pocket23_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    23:
+0  - Pocket Score                      : -0.0164
+1  - Drug Score                        : 0.0005
+2  - Number of alpha spheres           :    21
+3  - Mean alpha-sphere radius          : 3.6900
+4  - Mean alpha-sphere Solvent Acc.    : 0.4917
+5  - Mean B-factor of pocket residues  : 0.2299
+6  - Hydrophobicity Score              : 10.2857
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 249.0322
+10  -Pocket volume (convex hull)       : 9.4367
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 6.0000
+13 - Number of apolar alpha sphere     :     7
+14 - Proportion of apolar alpha sphere : 0.3333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    8199     C   CG ?  ASN    Dxp 252 ?   27.586    9.214   42.829   0.00  0 479 D
+ATOM    8186     C  CD1 ?  TRP    Dxp 251 ?   26.276   14.665   45.063   0.00  0 478 D
+ATOM    8201     N  ND2 ?  ASN    Dxp 252 ?   28.367    8.903   43.871   0.00  0 479 D
+ATOM    8198     C   CB ?  ASN    Dxp 252 ?   27.436   10.710   42.437   0.00  0 479 D
+ATOM    8195     C   CA ?  ASN    Dxp 252 ?   28.576   11.606   42.953   0.00  0 479 D
+ATOM    8188     N  NE1 ?  TRP    Dxp 251 ?   26.256   14.921   46.406  -0.17  0 478 D
+ATOM    8183     O    O ?  TRP    Dxp 251 ?   29.606   13.897   44.157  -1.07  0 478 D
+ATOM    8208     C   CD ?  PRO    Dxp 253 ?   30.672   10.672   44.713   0.00  0 480 D
+ATOM    7945     O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM    8191     C  CZ2 ?  TRP    Dxp 251 ?   27.038   16.816   47.830   0.00  0 478 D
+ATOM    7656     C  CE1 ?  TYR    Dxp 186 ?   28.922   12.123   52.576   0.00  0 413 D
+ATOM    7659     O   OH ?  TYR    Dxp 186 ?   26.735   12.867   53.246   0.00  0 413 D
+ATOM    7620     N    N ?  GLU    Dxp 182 ?   32.487   14.873   49.114   0.00  0 409 D
+ATOM    8189     C  CE2 ?  TRP    Dxp 251 ?   26.844   16.141   46.643   0.00  0 478 D
+ATOM    7617     C   CB ?  PRO    Dxp 181 ?   30.988   17.092   47.631   0.00  0 408 D
+ATOM    7624     C   CB ?  GLU    Dxp 182 ?   32.311   12.417   49.315   0.00  0 409 D
+ATOM    7621     C   CA ?  GLU    Dxp 182 ?   32.543   13.747   50.045   0.00  0 409 D
+# 

tests/reference_output/123abc_out/pocket23_env_atm.cif

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

tests/reference_output/123abc_out/pocket23_vert.pqr

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

tests/reference_output/123abc_out/pocket24_atm.cif

@@ -0,0 +1,73 @@
+data_pocket24_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    24:
+0  - Pocket Score                      : -0.0278
+1  - Drug Score                        : 0.0029
+2  - Number of alpha spheres           :    41
+3  - Mean alpha-sphere radius          : 3.9593
+4  - Mean alpha-sphere Solvent Acc.    : 0.5927
+5  - Mean B-factor of pocket residues  : 0.1915
+6  - Hydrophobicity Score              : 10.6364
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.7273
+9  - Pocket volume (Monte Carlo)       : 460.9563
+10  -Pocket volume (convex hull)       : 89.6285
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 10.0000
+13 - Number of apolar alpha sphere     :    14
+14 - Proportion of apolar alpha sphere : 0.3415
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1634     C   CG ?  LEU    Axp 218 ?   26.546   36.235   23.630   0.00  0 445 A
+ATOM    1635     C  CD1 ?  LEU    Axp 218 ?   26.663   34.961   24.461   0.00  0 445 A
+ATOM    1625     C   CB ?  ASP    Axp 217 ?   29.707   40.718   23.735   0.00  0 444 A
+ATOM    1633     C   CB ?  LEU    Axp 218 ?   25.982   37.405   24.438   0.00  0 445 A
+ATOM    1616     O    O ?  ILE    Axp 216 ?   28.714   38.833   20.120  -0.40  0 443 A
+ATOM    1208     C   CB ?  ASP    Axp 164 ?   29.178   31.688   24.167   0.00  0 391 A
+ATOM    1307     N   NZ ?  LYS    Axp 177 ?   28.045   36.395   18.402  -5.21  0 404 A
+ATOM    1636     C  CD2 ?  LEU    Axp 218 ?   25.660   35.987   22.435   0.00  0 445 A
+ATOM    1207     O    O ?  ASP    Axp 164 ?   26.463   31.466   23.365  -2.55  0 391 A
+ATOM    1306     C   CE ?  LYS    Axp 177 ?   26.638   36.392   18.974   0.00  0 404 A
+ATOM    1305     C   CD ?  LYS    Axp 177 ?   25.713   35.218   18.453   0.00  0 404 A
+ATOM    1212     O    O ?  THR    Axp 165 ?   23.541   30.232   22.305  -2.14  0 392 A
+ATOM    1299     N    N ?  LYS    Axp 177 ?   21.604   34.670   19.815   0.00  0 404 A
+ATOM    1586     O    O ?  PRO    Axp 212 ?   27.163   35.309   15.349  -2.14  0 439 A
+ATOM    1581     C   CB ?  SER    Axp 211 ?   29.357   31.629   14.802   0.00  0 438 A
+ATOM    1320     C  CZ3 ?  TRP    Axp 178 ?   23.462   30.785   17.625   0.00  0 405 A
+ATOM    1637     N    N ?  SER    Axp 219 ?   25.769   40.519   25.023   0.00  0 446 A
+ATOM    1642     O   OG ?  SER    Axp 219 ?   26.959   42.469   26.857   0.00  0 446 A
+ATOM    1641     C   CB ?  SER    Axp 219 ?   25.796   41.724   27.105   0.00  0 446 A
+ATOM    1629     N    N ?  LEU    Axp 218 ?   27.266   38.964   23.188   0.00  0 445 A
+ATOM    1622     C   CA ?  ASP    Axp 217 ?   29.148   40.081   22.440   0.00  0 444 A
+ATOM    1582     O   OG ?  SER    Axp 211 ?   29.670   30.318   15.225   0.00  0 438 A
+ATOM    1321     C  CH2 ?  TRP    Axp 178 ?   24.064   30.155   16.482   0.00  0 405 A
+ATOM    1214     O  OG1 ?  THR    Axp 165 ?   26.599   27.686   20.315   0.00  0 392 A
+ATOM    1206     C    C ?  ASP    Axp 164 ?   27.100   30.422   23.545   0.00  0 391 A
+ATOM    1589     C   CD ?  PRO    Axp 212 ?   25.953   32.242   14.398   0.00  0 439 A
+ATOM    1204     N    N ?  ASP    Axp 164 ?   29.062   29.235   24.428  -0.84  0 391 A
+ATOM    1209     N    N ?  THR    Axp 165 ?   26.804   29.250   22.931   0.00  0 392 A
+ATOM    1210     C   CA ?  THR    Axp 165 ?   25.644   29.125   21.999   0.00  0 392 A
+ATOM    1611     C    C ?  GLY    Axp 215 ?   31.790   39.345   18.361   0.00  0 442 A
+ATOM    1610     C   CA ?  GLY    Axp 215 ?   32.619   38.349   17.567   0.00  0 442 A
+# 

tests/reference_output/123abc_out/pocket24_env_atm.cif

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

tests/reference_output/123abc_out/pocket24_vert.pqr

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

tests/reference_output/123abc_out/pocket25_atm.cif

@@ -0,0 +1,56 @@
+data_pocket25_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    25:
+0  - Pocket Score                      : -0.0372
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 4.0910
+4  - Mean alpha-sphere Solvent Acc.    : 0.5844
+5  - Mean B-factor of pocket residues  : 0.6654
+6  - Hydrophobicity Score              : 5.1667
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 272.5095
+10  -Pocket volume (convex hull)       : 4.5972
+11 - Charge Score                      :    -2
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.1333
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    6291     O    O ?  GLU    Dxp 9 ?   72.604    3.890   48.729   0.00  0 236 D
+ATOM    6300     O    O ?  MET    Dxp 10 ?   74.107    7.374   51.316  -2.14  0 237 D
+ATOM    6293     C   CG ?  GLU    Dxp 9 ?   71.423    4.039   52.375   0.00  0 236 D
+ATOM    6312     O  OE1 ?  GLU    Dxp 11 ?   77.808    6.551   52.358   0.00  0 238 D
+ATOM    6299     C    C ?  MET    Dxp 10 ?   74.371    7.293   50.096   0.00  0 237 D
+ATOM    6305     N    N ?  GLU    Dxp 11 ?   75.439    7.869   49.548  -2.19  0 238 D
+ATOM    6309     C   CB ?  GLU    Dxp 11 ?   77.861    8.128   49.916   0.00  0 238 D
+ATOM    6510     C   CE ?  LYS    Dxp 36 ?   78.782    6.894   42.671   0.00  0 263 D
+ATOM    6511     N   NZ ?  LYS    Dxp 36 ?   78.219    5.612   42.198   0.00  0 263 D
+ATOM    6301     C   CB ?  MET    Dxp 10 ?   73.225    7.186   47.771   0.00  0 237 D
+ATOM    6335     O  OD2 ?  ASP    Dxp 14 ?   78.726    9.496   45.541  -2.55  0 241 D
+ATOM    6298     C   CA ?  MET    Dxp 10 ?   73.486    6.472   49.131   0.00  0 237 D
+ATOM    6491     C  CZ2 ?  TRP    Dxp 34 ?   73.535    8.757   43.118   0.00  0 261 D
+ATOM    6488     N  NE1 ?  TRP    Dxp 34 ?   75.151   10.418   44.105  -1.09  0 261 D
+# 

tests/reference_output/123abc_out/pocket25_env_atm.cif

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

tests/reference_output/123abc_out/pocket25_vert.pqr

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

tests/reference_output/123abc_out/pocket26_atm.cif

@@ -0,0 +1,69 @@
+data_pocket26_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    26:
+0  - Pocket Score                      : -0.0384
+1  - Drug Score                        : 0.0846
+2  - Number of alpha spheres           :    45
+3  - Mean alpha-sphere radius          : 3.7304
+4  - Mean alpha-sphere Solvent Acc.    : 0.4267
+5  - Mean B-factor of pocket residues  : 0.1353
+6  - Hydrophobicity Score              : 57.6667
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.5833
+9  - Pocket volume (Monte Carlo)       : 229.2369
+10  -Pocket volume (convex hull)       : 15.0678
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 38.0000
+13 - Number of apolar alpha sphere     :    39
+14 - Proportion of apolar alpha sphere : 0.8667
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1821     C  CG1 ?  VAL    Axp 241 ?   18.722   33.273    0.801   0.00  0 468 A
+ATOM    824      N    N ?  LEU    Axp 114 ?   19.877   26.311   -1.669   0.00  0 341 A
+ATOM    818      C    C ?  LEU    Axp 113 ?   20.351   26.072   -0.464   0.00  0 340 A
+ATOM    825      C   CA ?  LEU    Axp 114 ?   18.529   26.785   -1.887   0.00  0 341 A
+ATOM    798      C   CA ?  ALA    Axp 110 ?   24.131   27.516   -4.659   0.00  0 337 A
+ATOM    1805     C   CD ?  PRO    Axp 238 ?   21.822   33.590   -2.836   0.00  0 465 A
+ATOM    1792     O    O ?  GLY    Axp 236 ?   25.501   33.661   -3.290  -6.17  0 463 A
+ATOM    801      C   CB ?  ALA    Axp 110 ?   24.277   28.499   -5.862   0.00  0 337 A
+ATOM    819      O    O ?  LEU    Axp 113 ?   19.663   26.116    0.542  -1.07  0 340 A
+ATOM    856      C   CB ?  ALA    Axp 117 ?   16.641   27.654    2.208   0.00  0 344 A
+ATOM    1539     C  CG2 ?  ILE    Axp 205 ?   21.953   27.141    3.249   0.00  0 432 A
+ATOM    1509     C  CD2 ?  LEU    Axp 202 ?   16.995   30.754    4.286   0.00  0 429 A
+ATOM    1505     O    O ?  LEU    Axp 202 ?   21.436   31.217    5.146  -3.21  0 429 A
+ATOM    820      C   CB ?  LEU    Axp 113 ?   22.728   26.946   -0.496   0.00  0 340 A
+ATOM    830      C  CD1 ?  LEU    Axp 114 ?   17.000   29.244   -2.786   0.00  0 341 A
+ATOM    2030     C  CE1 ?  PHE    Axp 266 ?   15.255   30.669    0.284   0.00  0 493 A
+ATOM    828      C   CB ?  LEU    Axp 114 ?   18.476   27.301   -3.305   0.00  0 341 A
+ATOM    1804     C   CG ?  PRO    Axp 238 ?   21.078   33.317   -4.111   0.00  0 465 A
+ATOM    1822     C  CG2 ?  VAL    Axp 241 ?   17.795   32.913   -1.514   0.00  0 468 A
+ATOM    800      O    O ?  ALA    Axp 110 ?   21.862   27.166   -3.931  -1.07  0 337 A
+ATOM    1545     C   CB ?  ALA    Axp 206 ?   24.087   32.253    2.900   0.00  0 433 A
+ATOM    1541     N    N ?  ALA    Axp 206 ?   24.014   29.985    3.998   0.00  0 433 A
+ATOM    1798     S   SG ?  CYS    Axp 237 ?   22.030   35.316    0.634   0.00  0 464 A
+ATOM    1794     C   CA ?  CYS    Axp 237 ?   24.026   34.922   -1.329   0.00  0 464 A
+ATOM    1544     O    O ?  ALA    Axp 206 ?   26.983   31.382    2.492  -3.21  0 433 A
+ATOM    1542     C   CA ?  ALA    Axp 206 ?   24.748   30.821    3.023   0.00  0 433 A
+ATOM    822      C  CD1 ?  LEU    Axp 113 ?   25.012   27.872   -0.209   0.00  0 340 A
+# 

tests/reference_output/123abc_out/pocket26_env_atm.cif

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

tests/reference_output/123abc_out/pocket26_vert.pqr

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

tests/reference_output/123abc_out/pocket27_atm.cif

@@ -0,0 +1,58 @@
+data_pocket27_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    27:
+0  - Pocket Score                      : -0.0425
+1  - Drug Score                        : 0.0001
+2  - Number of alpha spheres           :    17
+3  - Mean alpha-sphere radius          : 3.8983
+4  - Mean alpha-sphere Solvent Acc.    : 0.5210
+5  - Mean B-factor of pocket residues  : 0.3129
+6  - Hydrophobicity Score              : -21.2500
+7  - Polarity Score                    :     3
+8  - Amino Acid based volume Score     : 3.7500
+9  - Pocket volume (Monte Carlo)       : 242.5227
+10  -Pocket volume (convex hull)       : 8.0231
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 8.0000
+13 - Number of apolar alpha sphere     :     9
+14 - Proportion of apolar alpha sphere : 0.5294
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1256     C   CA ?  GLY    Axp 171 ?   17.074   29.084   34.902   0.00  0 398 A
+ATOM    3772     C   CB ?  GLU    Bxp 223 ?   20.899   28.443   38.451   0.00  0 450 B
+ATOM    3769     C   CA ?  GLU    Bxp 223 ?   19.756   29.026   39.321   0.00  0 450 B
+ATOM    3800     O  OE1 ?  GLU    Bxp 226 ?   14.870   27.408   38.360  -0.81  0 453 B
+ATOM    1258     O    O ?  GLY    Axp 171 ?   17.211   27.237   33.384   0.00  0 398 A
+ATOM    3810     N   NZ ?  LYS    Bxp 227 ?   18.871   22.046   40.724   0.00  0 454 B
+ATOM    3799     C   CD ?  GLU    Bxp 226 ?   13.993   27.306   39.282   0.00  0 453 B
+ATOM    3798     C   CG ?  GLU    Bxp 226 ?   14.425   27.213   40.755   0.00  0 453 B
+ATOM    3809     C   CE ?  LYS    Bxp 227 ?   19.628   23.270   41.089   0.00  0 454 B
+ATOM    3774     C   CD ?  GLU    Bxp 223 ?   21.775   28.184   36.070   0.00  0 450 B
+ATOM    3775     O  OE1 ?  GLU    Bxp 223 ?   22.737   27.521   36.550   0.00  0 450 B
+ATOM    3771     O    O ?  GLU    Bxp 223 ?   19.336   27.833   41.335   0.00  0 450 B
+ATOM    3797     C   CB ?  GLU    Bxp 226 ?   15.576   28.210   41.069   0.00  0 453 B
+ATOM    3773     C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM    3808     C   CD ?  LYS    Bxp 227 ?   19.254   23.527   42.569   0.00  0 454 B
+ATOM    3796     O    O ?  GLU    Bxp 226 ?   15.035   26.681   43.850   0.00  0 453 B
+# 

tests/reference_output/123abc_out/pocket27_env_atm.cif

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

tests/reference_output/123abc_out/pocket27_vert.pqr

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

tests/reference_output/123abc_out/pocket28_atm.cif

@@ -0,0 +1,54 @@
+data_pocket28_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    28:
+0  - Pocket Score                      : -0.0435
+1  - Drug Score                        : 0.0002
+2  - Number of alpha spheres           :    15
+3  - Mean alpha-sphere radius          : 3.8178
+4  - Mean alpha-sphere Solvent Acc.    : 0.5111
+5  - Mean B-factor of pocket residues  : 0.2583
+6  - Hydrophobicity Score              : 47.8000
+7  - Polarity Score                    :     2
+8  - Amino Acid based volume Score     : 4.6000
+9  - Pocket volume (Monte Carlo)       : 152.2791
+10  -Pocket volume (convex hull)       : 1.1933
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.4000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    5155     C    C ?  ASN    Cxp 131 ?   49.791   69.967   16.216   0.00  0 358 C
+ATOM    5164     O    O ?  PHE    Cxp 132 ?   48.967   66.829   17.018   0.00  0 359 C
+ATOM    5154     C   CA ?  ASN    Cxp 131 ?   49.335   70.969   17.293   0.00  0 358 C
+ATOM    5156     O    O ?  ASN    Cxp 131 ?   49.458   70.110   15.000  -2.55  0 358 C
+ATOM    5177     C  CG1 ?  ILE    Cxp 133 ?   46.547   66.252   14.171   0.00  0 360 C
+ATOM    5179     C  CD1 ?  ILE    Cxp 133 ?   45.747   66.718   12.918   0.00  0 360 C
+ATOM    5159     O  OD1 ?  ASN    Cxp 131 ?   46.848   72.862   17.330   0.00  0 358 C
+ATOM    5600     C  CG1 ?  ILE    Cxp 191 ?   45.611   66.019   19.250   0.00  0 418 C
+ATOM    5129     O    O ?  GLU    Cxp 128 ?   48.054   70.332   20.849  -1.48  0 355 C
+ATOM    5595     N    N ?  ILE    Cxp 191 ?   43.539   65.578   16.244   0.00  0 418 C
+ATOM    5599     C   CB ?  ILE    Cxp 191 ?   44.408   66.418   18.397   0.00  0 418 C
+ATOM    5601     C  CG2 ?  ILE    Cxp 191 ?   43.280   67.132   19.172   0.00  0 418 C
+# 

tests/reference_output/123abc_out/pocket28_env_atm.cif

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

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)       : 287.3492
+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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    633      C  CE1 ?  PHE    Axp 90 ?   23.219    7.620   12.523   0.00  0 317 A
+ATOM    115      C  CD2 ?  LEU    Axp 21 ?   23.833    8.296   15.998   0.00  0 248 A
+ATOM    116      N    N ?  GLY    Axp 22 ?   26.977   10.989   17.772   0.00  0 249 A
+ATOM    664      C   CA ?  GLY    Axp 94 ?   24.159   13.940   10.732   0.00  0 321 A
+ATOM    148      O   OH ?  TYR    Axp 26 ?   24.138   15.654   15.314   0.00  0 253 A
+ATOM    667      N    N ?  ASN    Axp 95 ?   23.996   16.143   11.694   0.00  0 322 A
+ATOM    673      O  OD1 ?  ASN    Axp 95 ?   25.880   18.114   13.960  -2.14  0 322 A
+ATOM    135      O  OE1 ?  GLN    Axp 25 ?   27.558   15.740   17.545  -2.14  0 252 A
+ATOM    117      C   CA ?  GLY    Axp 22 ?   27.711   12.259   17.704   0.00  0 249 A
+ATOM    635      C   CZ ?  PHE    Axp 90 ?   23.754    7.359   11.279   0.00  0 317 A
+ATOM    639      O    O ?  MET    Axp 91 ?   22.317   10.826    9.705   0.00  0 318 A
+ATOM    647      O    O ?  THR    Axp 92 ?   25.377   10.176    8.230   0.00  0 319 A
+ATOM    698      O  OD2 ?  ASP    Axp 98 ?   28.581   18.421   13.874   0.00  0 325 A
+ATOM    695      C   CB ?  ASP    Axp 98 ?   28.818   18.983   11.564   0.00  0 325 A
+ATOM    654      O    O ?  TYR    Axp 93 ?   25.886   14.436    8.543  -2.95  0 320 A
+ATOM    737      O  OE1 ?  GLU    Axp 102 ?   31.683   16.733    9.180   0.00  0 329 A
+ATOM    738      O  OE2 ?  GLU    Axp 102 ?   32.646   17.951   10.762  -1.88  0 329 A
+ATOM    145      C  CE1 ?  TYR    Axp 26 ?   24.215   14.118   17.108   0.00  0 253 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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    109      C   CA ?  LEU    Axp 21 ?   25.411    9.365   18.618   0.00  0 248 A
+ATOM    110      C    C ?  LEU    Axp 21 ?   26.217   10.637   18.809   0.00  0 248 A
+ATOM    112      C   CB ?  LEU    Axp 21 ?   24.055    9.763   18.043   0.00  0 248 A
+ATOM    113      C   CG ?  LEU    Axp 21 ?   23.240    8.692   17.348   0.00  0 248 A
+ATOM    115      C  CD2 ?  LEU    Axp 21 ?   23.833    8.296   15.998   0.00  0 248 A
+ATOM    116      N    N ?  GLY    Axp 22 ?   26.977   10.989   17.772   0.00  0 249 A
+ATOM    117      C   CA ?  GLY    Axp 22 ?   27.711   12.259   17.704   0.00  0 249 A
+ATOM    134      C   CD ?  GLN    Axp 25 ?   26.983   16.776   17.929   0.00  0 252 A
+ATOM    135      O  OE1 ?  GLN    Axp 25 ?   27.558   15.740   17.545  -2.14  0 252 A
+ATOM    136      N  NE2 ?  GLN    Axp 25 ?   26.655   17.754   17.106  -1.51  0 252 A
+ATOM    143      C  CD1 ?  TYR    Axp 26 ?   23.817   13.724   18.368   0.00  0 253 A
+ATOM    145      C  CE1 ?  TYR    Axp 26 ?   24.215   14.118   17.108   0.00  0 253 A
+ATOM    147      C   CZ ?  TYR    Axp 26 ?   23.727   15.310   16.576   0.00  0 253 A
+ATOM    148      O   OH ?  TYR    Axp 26 ?   24.138   15.654   15.314   0.00  0 253 A
+ATOM    633      C  CE1 ?  PHE    Axp 90 ?   23.219    7.620   12.523   0.00  0 317 A
+ATOM    635      C   CZ ?  PHE    Axp 90 ?   23.754    7.359   11.279   0.00  0 317 A
+ATOM    639      O    O ?  MET    Axp 91 ?   22.317   10.826    9.705   0.00  0 318 A
+ATOM    646      C    C ?  THR    Axp 92 ?   24.325   10.445    7.647   0.00  0 319 A
+ATOM    647      O    O ?  THR    Axp 92 ?   25.377   10.176    8.230   0.00  0 319 A
+ATOM    653      C    C ?  TYR    Axp 93 ?   25.046   13.581    8.441   0.00  0 320 A
+ATOM    654      O    O ?  TYR    Axp 93 ?   25.886   14.436    8.543  -2.95  0 320 A
+ATOM    663      N    N ?  GLY    Axp 94 ?   24.175   13.288    9.414   0.00  0 321 A
+ATOM    664      C   CA ?  GLY    Axp 94 ?   24.159   13.940   10.732   0.00  0 321 A
+ATOM    665      C    C ?  GLY    Axp 94 ?   23.592   15.331   10.711   0.00  0 321 A
+ATOM    667      N    N ?  ASN    Axp 95 ?   23.996   16.143   11.694   0.00  0 322 A
+ATOM    668      C   CA ?  ASN    Axp 95 ?   23.482   17.523   11.792   0.00  0 322 A
+ATOM    670      O    O ?  ASN    Axp 95 ?   25.129   18.291   10.166   0.00  0 322 A
+ATOM    672      C   CG ?  ASN    Axp 95 ?   24.977   18.738   13.399   0.00  0 322 A
+ATOM    673      O  OD1 ?  ASN    Axp 95 ?   25.880   18.114   13.960  -2.14  0 322 A
+ATOM    695      C   CB ?  ASP    Axp 98 ?   28.818   18.983   11.564   0.00  0 325 A
+ATOM    696      C   CG ?  ASP    Axp 98 ?   28.941   19.302   13.063   0.00  0 325 A
+ATOM    698      O  OD2 ?  ASP    Axp 98 ?   28.581   18.421   13.874   0.00  0 325 A
+ATOM    736      C   CD ?  GLU    Axp 102 ?   32.361   17.729    9.573   0.00  0 329 A
+ATOM    737      O  OE1 ?  GLU    Axp 102 ?   31.683   16.733    9.180   0.00  0 329 A
+ATOM    738      O  OE2 ?  GLU    Axp 102 ?   32.646   17.951   10.762  -1.88  0 329 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)       : 1485.1832
+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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    6631     O  OE1 ?  GLU    Dxp 55 ?   52.035   10.097   57.244   0.00  0 282 D
+ATOM    6656     C   CB ?  LYS    Dxp 58 ?   55.399    5.853   55.510   0.00  0 285 D
+ATOM    6682     C  CG2 ?  VAL    Dxp 62 ?   54.426    5.381   50.458   0.00  0 289 D
+ATOM    6657     N    N ?  GLU    Dxp 59 ?   57.037    7.697   53.496   0.00  0 286 D
+ATOM    6663     C   CD ?  GLU    Dxp 59 ?   57.497   12.310   51.368   0.00  0 286 D
+ATOM    7425     C   CA ?  GLY    Dxp 156 ?   53.352   17.790   52.036   0.00  0 383 D
+ATOM    7412     O  OD2 ?  ASP    Dxp 154 ?   51.451   13.986   48.870  -1.62  0 381 D
+ATOM    6664     O  OE1 ?  GLU    Dxp 59 ?   57.674   12.906   52.458  -2.28  0 286 D
+ATOM    6658     C   CA ?  GLU    Dxp 59 ?   57.186    8.499   52.273   0.00  0 286 D
+ATOM    7239     C  CD2 ?  PHE    Dxp 132 ?   50.695    4.565   46.284   0.00  0 359 D
+ATOM    6713     C  CD1 ?  ILE    Dxp 66 ?   54.653    7.398   44.141   0.00  0 293 D
+ATOM    7196     C  CD2 ?  LEU    Dxp 127 ?   50.885    7.312   42.017   0.00  0 354 D
+ATOM    7236     C   CB ?  PHE    Dxp 132 ?   48.964    5.452   44.735   0.00  0 359 D
+ATOM    6926     C   CA ?  GLY    Dxp 94 ?   60.034   24.932   39.574   0.00  0 321 D
+ATOM    6395     N    N ?  GLY    Dxp 22 ?   63.445   27.361   46.787  -2.19  0 249 D
+ATOM    6396     C   CA ?  GLY    Dxp 22 ?   62.352   28.355   46.720   0.00  0 249 D
+ATOM    6424     C  CE1 ?  TYR    Dxp 26 ?   59.877   24.854   46.075   0.00  0 253 D
+ATOM    6897     C   CZ ?  PHE    Dxp 90 ?   66.475   23.808   40.403   0.00  0 317 D
+ATOM    6909     O    O ?  THR    Dxp 92 ?   63.997   25.572   36.851   0.00  0 319 D
+ATOM    6925     N    N ?  GLY    Dxp 94 ?   60.701   24.762   38.280   0.00  0 321 D
+ATOM    7409     C   CB ?  ASP    Dxp 154 ?   52.864   14.692   47.175   0.00  0 381 D
+ATOM    6751     C  CD2 ?  LEU    Dxp 71 ?   53.389   10.979   40.449   0.00  0 298 D
+ATOM    7258     C  CD2 ?  HIS    Dxp 134 ?   49.543   13.548   43.730   0.00  0 361 D
+ATOM    6654     C    C ?  LYS    Dxp 58 ?   56.799    6.379   53.467   0.00  0 285 D
+ATOM    7424     N    N ?  GLY    Dxp 156 ?   53.836   17.822   50.662   0.00  0 383 D
+ATOM    7408     O    O ?  ASP    Dxp 154 ?   55.352   15.791   48.188   0.00  0 381 D
+ATOM    6572     N   NZ ?  LYS    Dxp 44 ?   57.996   15.644   52.375  -3.28  0 271 D
+ATOM    6662     C   CG ?  GLU    Dxp 59 ?   57.119   10.830   51.310   0.00  0 286 D
+ATOM    6661     C   CB ?  GLU    Dxp 59 ?   57.413    9.994   52.562   0.00  0 286 D
+ATOM    6629     C   CG ?  GLU    Dxp 55 ?   54.143   11.051   57.889   0.00  0 282 D
+ATOM    6665     O  OE2 ?  GLU    Dxp 59 ?   57.595   12.886   50.275   0.00  0 286 D
+ATOM    6570     C   CD ?  LYS    Dxp 44 ?   60.499   15.433   51.975   0.00  0 271 D
+ATOM    6689     S   SD ?  MET    Dxp 63 ?   59.342   10.341   47.098   0.00  0 290 D
+ATOM    6447     C  CG2 ?  VAL    Dxp 29 ?   61.867   19.746   50.754   0.00  0 256 D
+ATOM    7414     C   CA ?  PHE    Dxp 155 ?   55.356   18.410   48.844   0.00  0 382 D
+ATOM    7416     O    O ?  PHE    Dxp 155 ?   55.635   19.113   51.089  -1.07  0 382 D
+ATOM    6571     C   CE ?  LYS    Dxp 44 ?   59.381   16.004   52.877   0.00  0 271 D
+ATOM    6681     C  CG1 ?  VAL    Dxp 62 ?   53.788    5.636   48.109   0.00  0 289 D
+ATOM    7329     C  CD1 ?  LEU    Dxp 143 ?   59.244   18.841   41.193   0.00  0 370 D
+ATOM    6758     C  CG2 ?  VAL    Dxp 72 ?   60.178   15.150   41.326   0.00  0 299 D
+ATOM    6876     O  OG1 ?  THR    Dxp 88 ?   63.295   15.440   44.108   0.00  0 315 D
+ATOM    7422     C  CE2 ?  PHE    Dxp 155 ?   57.327   18.902   44.964   0.00  0 382 D
+ATOM    7402     C    C ?  ALA    Dxp 153 ?   53.826   15.699   44.308   0.00  0 380 D
+ATOM    7401     C   CA ?  ALA    Dxp 153 ?   54.851   15.556   43.189   0.00  0 380 D
+ATOM    6757     C  CG1 ?  VAL    Dxp 72 ?   58.423   13.974   42.618   0.00  0 299 D
+ATOM    7195     C  CD1 ?  LEU    Dxp 127 ?   49.551    9.478   41.993   0.00  0 354 D
+ATOM    6755     O    O ?  VAL    Dxp 72 ?   59.541   11.227   41.576  -7.50  0 299 D
+ATOM    6748     C   CB ?  LEU    Dxp 71 ?   55.487   10.215   39.179   0.00  0 298 D
+ATOM    6711     C  CG1 ?  ILE    Dxp 66 ?   55.748    6.675   43.366   0.00  0 293 D
+ATOM    6752     N    N ?  VAL    Dxp 72 ?   57.585   12.696   39.928  -1.09  0 299 D
+ATOM    6627     O    O ?  GLU    Dxp 55 ?   56.504    9.379   56.126  -3.21  0 282 D
+ATOM    6427     O   OH ?  TYR    Dxp 26 ?   58.288   24.914   44.228  -2.14  0 253 D
+ATOM    6414     O  OE1 ?  GLN    Dxp 25 ?   58.455   28.443   46.071  -5.09  0 252 D
+ATOM    6929     N    N ?  ASN    Dxp 95 ?   57.778   24.953   40.502  -2.19  0 322 D
+ATOM    6935     O  OD1 ?  ASN    Dxp 95 ?   56.159   26.889   42.866  -2.14  0 322 D
+ATOM    6960     O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM    6957     C   CB ?  ASP    Dxp 98 ?   55.535   30.185   40.403   0.00  0 325 D
+ATOM    6916     O    O ?  TYR    Dxp 93 ?   59.826   26.639   37.454   0.00  0 320 D
+ATOM    7420     C  CD2 ?  PHE    Dxp 155 ?   56.995   18.870   46.332   0.00  0 382 D
+ATOM    6446     C  CG1 ?  VAL    Dxp 29 ?   63.424   19.965   48.777   0.00  0 256 D
+ATOM    6420     C   CB ?  TYR    Dxp 26 ?   59.704   22.984   49.387   0.00  0 253 D
+ATOM    7404     C   CB ?  ALA    Dxp 153 ?   55.891   16.596   43.353   0.00  0 380 D
+ATOM    6555     O    O ?  ALA    Dxp 42 ?   66.250   15.967   46.440   0.00  0 269 D
+ATOM    6564     N    N ?  LYS    Dxp 44 ?   65.071   16.285   50.374   0.00  0 271 D
+ATOM    6688     C   CG ?  MET    Dxp 63 ?   58.233    8.978   46.901   0.00  0 290 D
+ATOM    6680     C   CB ?  VAL    Dxp 62 ?   54.934    5.664   49.113   0.00  0 289 D
+ATOM    6660     O    O ?  GLU    Dxp 59 ?   57.982    7.657   50.173   0.00  0 286 D
+ATOM    6556     C   CB ?  ALA    Dxp 42 ?   64.982   18.340   44.987   0.00  0 269 D
+ATOM    6881     O    O ?  GLU    Dxp 89 ?   64.168   16.713   41.645   0.00  0 316 D
+ATOM    6898     N    N ?  MET    Dxp 91 ?   63.736   19.963   39.260   0.00  0 318 D
+ATOM    6393     C  CD1 ?  LEU    Dxp 21 ?   64.675   22.066   45.945   0.00  0 248 D
+ATOM    6888     C   CA ?  PHE    Dxp 90 ?   65.499   18.836   40.501   0.00  0 317 D
+ATOM    6394     C  CD2 ?  LEU    Dxp 21 ?   66.139   23.878   45.329   0.00  0 248 D
+ATOM    6376     C  CE1 ?  HIS    Dxp 19 ?   68.713   27.227   46.138   0.00  0 246 D
+ATOM    6893     C  CD1 ?  PHE    Dxp 90 ?   66.360   21.823   41.727   0.00  0 317 D
+ATOM    6901     O    O ?  MET    Dxp 91 ?   63.034   22.679   38.496   0.00  0 318 D
+ATOM    6877     C  CG2 ?  THR    Dxp 88 ?   62.489   13.239   44.727   0.00  0 315 D
+ATOM    6861     C  CG2 ?  ILE    Dxp 86 ?   62.965   11.227   49.042   0.00  0 313 D
+ATOM    7405     N    N ?  ASP    Dxp 154 ?   54.325   15.719   45.523   0.00  0 381 D
+ATOM    6426     C   CZ ?  TYR    Dxp 26 ?   58.649   24.458   45.487   0.00  0 253 D
+ATOM    7330     C  CD2 ?  LEU    Dxp 143 ?   58.782   21.410   41.356   0.00  0 370 D
+ATOM    6421     C   CG ?  TYR    Dxp 26 ?   59.341   23.509   48.032   0.00  0 253 D
+ATOM    6423     C  CD2 ?  TYR    Dxp 26 ?   58.135   23.117   47.412   0.00  0 253 D
+ATOM    6422     C  CD1 ?  TYR    Dxp 26 ?   60.183   24.385   47.362   0.00  0 253 D
+ATOM    6425     C  CE2 ?  TYR    Dxp 26 ?   57.795   23.589   46.140   0.00  0 253 D
+ATOM    7423     C   CZ ?  PHE    Dxp 155 ?   56.783   19.883   44.153   0.00  0 382 D
+ATOM    7417     C   CB ?  PHE    Dxp 155 ?   55.748   19.792   48.329   0.00  0 382 D
+ATOM    7396     O    O ?  VAL    Dxp 152 ?   55.001   14.074   40.818   0.00  0 379 D
+ATOM    6690     C   CE ?  MET    Dxp 63 ?   59.360   10.409   48.847   0.00  0 290 D
+ATOM    6915     C    C ?  TYR    Dxp 93 ?   60.588   25.697   37.338   0.00  0 320 D
+ATOM    6391     C   CB ?  LEU    Dxp 21 ?   64.362   24.273   46.981   0.00  0 248 D
+ATOM    6895     C  CE1 ?  PHE    Dxp 90 ?   66.251   23.209   41.616   0.00  0 317 D
+ATOM    6467     O  OE1 ?  GLU    Dxp 31 ?   70.105   25.647   44.001   0.00  0 258 D
+ATOM    7246     O    O ?  ILE    Dxp 133 ?   47.623    9.183   47.095   0.00  0 360 D
+ATOM    6858     O    O ?  ILE    Dxp 86 ?   65.641   13.840   49.353   0.00  0 313 D
+ATOM    7252     C   CA ?  HIS    Dxp 134 ?   47.370   11.498   45.668   0.00  0 361 D
+ATOM    7254     O    O ?  HIS    Dxp 134 ?   47.812   12.555   47.804   0.00  0 361 D
+ATOM    7403     O    O ?  ALA    Dxp 153 ?   52.619   15.769   44.076   0.00  0 380 D
+ATOM    6568     C   CB ?  LYS    Dxp 44 ?   62.898   15.688   51.283   0.00  0 271 D
+ATOM    7260     N  NE2 ?  HIS    Dxp 134 ?   50.218   14.635   44.230   0.00  0 361 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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    6374     N  ND1 ?  HIS    Dxp 19 ?   68.624   27.394   47.446   0.00  0 246 D
+ATOM    6376     C  CE1 ?  HIS    Dxp 19 ?   68.713   27.227   46.138   0.00  0 246 D
+ATOM    6377     N  NE2 ?  HIS    Dxp 19 ?   69.990   27.294   45.797   0.00  0 246 D
+ATOM    6388     C   CA ?  LEU    Dxp 21 ?   64.781   25.564   47.694   0.00  0 248 D
+ATOM    6389     C    C ?  LEU    Dxp 21 ?   63.581   26.477   47.783   0.00  0 248 D
+ATOM    6391     C   CB ?  LEU    Dxp 21 ?   64.362   24.273   46.981   0.00  0 248 D
+ATOM    6392     C   CG ?  LEU    Dxp 21 ?   65.376   23.265   46.446   0.00  0 248 D
+ATOM    6393     C  CD1 ?  LEU    Dxp 21 ?   64.675   22.066   45.945   0.00  0 248 D
+ATOM    6394     C  CD2 ?  LEU    Dxp 21 ?   66.139   23.878   45.329   0.00  0 248 D
+ATOM    6395     N    N ?  GLY    Dxp 22 ?   63.445   27.361   46.787  -2.19  0 249 D
+ATOM    6396     C   CA ?  GLY    Dxp 22 ?   62.352   28.355   46.720   0.00  0 249 D
+ATOM    6413     C   CD ?  GLN    Dxp 25 ?   57.407   27.989   46.515   0.00  0 252 D
+ATOM    6414     O  OE1 ?  GLN    Dxp 25 ?   58.455   28.443   46.071  -5.09  0 252 D
+ATOM    6415     N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM    6419     O    O ?  TYR    Dxp 26 ?   59.073   21.717   51.991  -1.07  0 253 D
+ATOM    6420     C   CB ?  TYR    Dxp 26 ?   59.704   22.984   49.387   0.00  0 253 D
+ATOM    6421     C   CG ?  TYR    Dxp 26 ?   59.341   23.509   48.032   0.00  0 253 D
+ATOM    6422     C  CD1 ?  TYR    Dxp 26 ?   60.183   24.385   47.362   0.00  0 253 D
+ATOM    6423     C  CD2 ?  TYR    Dxp 26 ?   58.135   23.117   47.412   0.00  0 253 D
+ATOM    6424     C  CE1 ?  TYR    Dxp 26 ?   59.877   24.854   46.075   0.00  0 253 D
+ATOM    6425     C  CE2 ?  TYR    Dxp 26 ?   57.795   23.589   46.140   0.00  0 253 D
+ATOM    6426     C   CZ ?  TYR    Dxp 26 ?   58.649   24.458   45.487   0.00  0 253 D
+ATOM    6427     O   OH ?  TYR    Dxp 26 ?   58.288   24.914   44.228  -2.14  0 253 D
+ATOM    6445     C   CB ?  VAL    Dxp 29 ?   62.944   20.625   50.067   0.00  0 256 D
+ATOM    6446     C  CG1 ?  VAL    Dxp 29 ?   63.424   19.965   48.777   0.00  0 256 D
+ATOM    6447     C  CG2 ?  VAL    Dxp 29 ?   61.867   19.746   50.754   0.00  0 256 D
+ATOM    6466     C   CD ?  GLU    Dxp 31 ?   70.736   24.607   43.729   0.00  0 258 D
+ATOM    6467     O  OE1 ?  GLU    Dxp 31 ?   70.105   25.647   44.001   0.00  0 258 D
+ATOM    6553     C   CA ?  ALA    Dxp 42 ?   66.460   18.078   45.473   0.00  0 269 D
+ATOM    6554     C    C ?  ALA    Dxp 42 ?   66.467   17.150   46.611   0.00  0 269 D
+ATOM    6555     O    O ?  ALA    Dxp 42 ?   66.250   15.967   46.440   0.00  0 269 D
+ATOM    6556     C   CB ?  ALA    Dxp 42 ?   64.982   18.340   44.987   0.00  0 269 D
+ATOM    6557     N    N ?  VAL    Dxp 43 ?   66.710   17.707   47.791   0.00  0 270 D
+ATOM    6558     C   CA ?  VAL    Dxp 43 ?   66.934   16.896   48.965   0.00  0 270 D
+ATOM    6559     C    C ?  VAL    Dxp 43 ?   65.965   17.202   50.086   0.00  0 270 D
+ATOM    6564     N    N ?  LYS    Dxp 44 ?   65.071   16.285   50.374   0.00  0 271 D
+ATOM    6565     C   CA ?  LYS    Dxp 44 ?   64.214   16.433   51.505   0.00  0 271 D
+ATOM    6568     C   CB ?  LYS    Dxp 44 ?   62.898   15.688   51.283   0.00  0 271 D
+ATOM    6569     C   CG ?  LYS    Dxp 44 ?   61.806   16.127   52.262   0.00  0 271 D
+ATOM    6570     C   CD ?  LYS    Dxp 44 ?   60.499   15.433   51.975   0.00  0 271 D
+ATOM    6571     C   CE ?  LYS    Dxp 44 ?   59.381   16.004   52.877   0.00  0 271 D
+ATOM    6572     N   NZ ?  LYS    Dxp 44 ?   57.996   15.644   52.375  -3.28  0 271 D
+ATOM    6626     C    C ?  GLU    Dxp 55 ?   56.900    9.604   57.277   0.00  0 282 D
+ATOM    6627     O    O ?  GLU    Dxp 55 ?   56.504    9.379   56.126  -3.21  0 282 D
+ATOM    6629     C   CG ?  GLU    Dxp 55 ?   54.143   11.051   57.889   0.00  0 282 D
+ATOM    6630     C   CD ?  GLU    Dxp 55 ?   52.863   10.284   58.185   0.00  0 282 D
+ATOM    6631     O  OE1 ?  GLU    Dxp 55 ?   52.035   10.097   57.244   0.00  0 282 D
+ATOM    6653     C   CA ?  LYS    Dxp 58 ?   56.760    5.661   54.816   0.00  0 285 D
+ATOM    6654     C    C ?  LYS    Dxp 58 ?   56.799    6.379   53.467   0.00  0 285 D
+ATOM    6655     O    O ?  LYS    Dxp 58 ?   56.637    5.732   52.412   0.00  0 285 D
+ATOM    6656     C   CB ?  LYS    Dxp 58 ?   55.399    5.853   55.510   0.00  0 285 D
+ATOM    6657     N    N ?  GLU    Dxp 59 ?   57.037    7.697   53.496   0.00  0 286 D
+ATOM    6658     C   CA ?  GLU    Dxp 59 ?   57.186    8.499   52.273   0.00  0 286 D
+ATOM    6659     C    C ?  GLU    Dxp 59 ?   58.269    7.947   51.334   0.00  0 286 D
+ATOM    6660     O    O ?  GLU    Dxp 59 ?   57.982    7.657   50.173   0.00  0 286 D
+ATOM    6661     C   CB ?  GLU    Dxp 59 ?   57.413    9.994   52.562   0.00  0 286 D
+ATOM    6662     C   CG ?  GLU    Dxp 59 ?   57.119   10.830   51.310   0.00  0 286 D
+ATOM    6663     C   CD ?  GLU    Dxp 59 ?   57.497   12.310   51.368   0.00  0 286 D
+ATOM    6664     O  OE1 ?  GLU    Dxp 59 ?   57.674   12.906   52.458  -2.28  0 286 D
+ATOM    6665     O  OE2 ?  GLU    Dxp 59 ?   57.595   12.886   50.275   0.00  0 286 D
+ATOM    6680     C   CB ?  VAL    Dxp 62 ?   54.934    5.664   49.113   0.00  0 289 D
+ATOM    6681     C  CG1 ?  VAL    Dxp 62 ?   53.788    5.636   48.109   0.00  0 289 D
+ATOM    6682     C  CG2 ?  VAL    Dxp 62 ?   54.426    5.381   50.458   0.00  0 289 D
+ATOM    6683     N    N ?  MET    Dxp 63 ?   57.661    5.982   47.544   0.00  0 290 D
+ATOM    6684     C   CA ?  MET    Dxp 63 ?   58.332    6.530   46.387   0.00  0 290 D
+ATOM    6687     C   CB ?  MET    Dxp 63 ?   59.097    7.770   46.788   0.00  0 290 D
+ATOM    6688     C   CG ?  MET    Dxp 63 ?   58.233    8.978   46.901   0.00  0 290 D
+ATOM    6689     S   SD ?  MET    Dxp 63 ?   59.342   10.341   47.098   0.00  0 290 D
+ATOM    6690     C   CE ?  MET    Dxp 63 ?   59.360   10.409   48.847   0.00  0 290 D
+ATOM    6711     C  CG1 ?  ILE    Dxp 66 ?   55.748    6.675   43.366   0.00  0 293 D
+ATOM    6713     C  CD1 ?  ILE    Dxp 66 ?   54.653    7.398   44.141   0.00  0 293 D
+ATOM    6745     C   CA ?  LEU    Dxp 71 ?   56.003   11.469   38.527   0.00  0 298 D
+ATOM    6746     C    C ?  LEU    Dxp 71 ?   57.426   11.851   38.922   0.00  0 298 D
+ATOM    6748     C   CB ?  LEU    Dxp 71 ?   55.487   10.215   39.179   0.00  0 298 D
+ATOM    6749     C   CG ?  LEU    Dxp 71 ?   53.967   10.145   39.248   0.00  0 298 D
+ATOM    6750     C  CD1 ?  LEU    Dxp 71 ?   53.599    8.721   39.390   0.00  0 298 D
+ATOM    6751     C  CD2 ?  LEU    Dxp 71 ?   53.389   10.979   40.449   0.00  0 298 D
+ATOM    6752     N    N ?  VAL    Dxp 72 ?   57.585   12.696   39.928  -1.09  0 299 D
+ATOM    6753     C   CA ?  VAL    Dxp 72 ?   58.931   13.215   40.228   0.00  0 299 D
+ATOM    6754     C    C ?  VAL    Dxp 72 ?   59.856   12.001   40.654   0.00  0 299 D
+ATOM    6755     O    O ?  VAL    Dxp 72 ?   59.541   11.227   41.576  -7.50  0 299 D
+ATOM    6756     C   CB ?  VAL    Dxp 72 ?   58.870   14.428   41.240   0.00  0 299 D
+ATOM    6757     C  CG1 ?  VAL    Dxp 72 ?   58.423   13.974   42.618   0.00  0 299 D
+ATOM    6758     C  CG2 ?  VAL    Dxp 72 ?   60.178   15.150   41.326   0.00  0 299 D
+ATOM    6856     C   CA ?  ILE    Dxp 86 ?   65.111   11.772   50.324   0.00  0 313 D
+ATOM    6857     C    C ?  ILE    Dxp 86 ?   65.591   12.642   49.200   0.00  0 313 D
+ATOM    6858     O    O ?  ILE    Dxp 86 ?   65.641   13.840   49.353   0.00  0 313 D
+ATOM    6859     C   CB ?  ILE    Dxp 86 ?   63.580   11.714   50.371   0.00  0 313 D
+ATOM    6861     C  CG2 ?  ILE    Dxp 86 ?   62.965   11.227   49.042   0.00  0 313 D
+ATOM    6863     N    N ?  ILE    Dxp 87 ?   66.006   12.036   48.105   0.00  0 314 D
+ATOM    6871     N    N ?  THR    Dxp 88 ?   65.495   13.640   45.119   0.00  0 315 D
+ATOM    6875     C   CB ?  THR    Dxp 88 ?   63.341   14.038   43.772   0.00  0 315 D
+ATOM    6876     O  OG1 ?  THR    Dxp 88 ?   63.295   15.440   44.108   0.00  0 315 D
+ATOM    6877     C  CG2 ?  THR    Dxp 88 ?   62.489   13.239   44.727   0.00  0 315 D
+ATOM    6880     C    C ?  GLU    Dxp 89 ?   65.113   16.493   40.871   0.00  0 316 D
+ATOM    6881     O    O ?  GLU    Dxp 89 ?   64.168   16.713   41.645   0.00  0 316 D
+ATOM    6887     N    N ?  PHE    Dxp 90 ?   65.755   17.460   40.261  -1.09  0 317 D
+ATOM    6888     C   CA ?  PHE    Dxp 90 ?   65.499   18.836   40.501   0.00  0 317 D
+ATOM    6889     C    C ?  PHE    Dxp 90 ?   64.882   19.302   39.199   0.00  0 317 D
+ATOM    6891     C   CB ?  PHE    Dxp 90 ?   66.817   19.555   40.732   0.00  0 317 D
+ATOM    6892     C   CG ?  PHE    Dxp 90 ?   66.705   21.047   40.608   0.00  0 317 D
+ATOM    6893     C  CD1 ?  PHE    Dxp 90 ?   66.360   21.823   41.727   0.00  0 317 D
+ATOM    6895     C  CE1 ?  PHE    Dxp 90 ?   66.251   23.209   41.616   0.00  0 317 D
+ATOM    6896     C  CE2 ?  PHE    Dxp 90 ?   66.827   23.019   39.259   0.00  0 317 D
+ATOM    6897     C   CZ ?  PHE    Dxp 90 ?   66.475   23.808   40.403   0.00  0 317 D
+ATOM    6898     N    N ?  MET    Dxp 91 ?   63.736   19.963   39.260   0.00  0 318 D
+ATOM    6899     C   CA ?  MET    Dxp 91 ?   63.043   20.365   38.022   0.00  0 318 D
+ATOM    6900     C    C ?  MET    Dxp 91 ?   63.336   21.794   37.710   0.00  0 318 D
+ATOM    6901     O    O ?  MET    Dxp 91 ?   63.034   22.679   38.496   0.00  0 318 D
+ATOM    6902     C   CB ?  MET    Dxp 91 ?   61.552   20.075   38.131   0.00  0 318 D
+ATOM    6908     C    C ?  THR    Dxp 92 ?   63.568   24.501   36.393   0.00  0 319 D
+ATOM    6909     O    O ?  THR    Dxp 92 ?   63.997   25.572   36.851   0.00  0 319 D
+ATOM    6914     C   CA ?  TYR    Dxp 93 ?   61.441   25.543   36.069   0.00  0 320 D
+ATOM    6915     C    C ?  TYR    Dxp 93 ?   60.588   25.697   37.338   0.00  0 320 D
+ATOM    6916     O    O ?  TYR    Dxp 93 ?   59.826   26.639   37.454   0.00  0 320 D
+ATOM    6925     N    N ?  GLY    Dxp 94 ?   60.701   24.762   38.280   0.00  0 321 D
+ATOM    6926     C   CA ?  GLY    Dxp 94 ?   60.034   24.932   39.574   0.00  0 321 D
+ATOM    6927     C    C ?  GLY    Dxp 94 ?   58.584   24.495   39.537   0.00  0 321 D
+ATOM    6929     N    N ?  ASN    Dxp 95 ?   57.778   24.953   40.502  -2.19  0 322 D
+ATOM    6930     C   CA ?  ASN    Dxp 95 ?   56.386   24.517   40.572   0.00  0 322 D
+ATOM    6932     O    O ?  ASN    Dxp 95 ?   55.729   26.285   39.010   0.00  0 322 D
+ATOM    6934     C   CG ?  ASN    Dxp 95 ?   55.423   26.157   42.216   0.00  0 322 D
+ATOM    6935     O  OD1 ?  ASN    Dxp 95 ?   56.159   26.889   42.866  -2.14  0 322 D
+ATOM    6957     C   CB ?  ASP    Dxp 98 ?   55.535   30.185   40.403   0.00  0 325 D
+ATOM    6958     C   CG ?  ASP    Dxp 98 ?   55.143   30.209   41.861   0.00  0 325 D
+ATOM    6960     O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM    7194     C   CG ?  LEU    Dxp 127 ?   49.824    8.196   41.228   0.00  0 354 D
+ATOM    7195     C  CD1 ?  LEU    Dxp 127 ?   49.551    9.478   41.993   0.00  0 354 D
+ATOM    7196     C  CD2 ?  LEU    Dxp 127 ?   50.885    7.312   42.017   0.00  0 354 D
+ATOM    7236     C   CB ?  PHE    Dxp 132 ?   48.964    5.452   44.735   0.00  0 359 D
+ATOM    7237     C   CG ?  PHE    Dxp 132 ?   50.048    4.498   45.077   0.00  0 359 D
+ATOM    7239     C  CD2 ?  PHE    Dxp 132 ?   50.695    4.565   46.284   0.00  0 359 D
+ATOM    7241     C  CE2 ?  PHE    Dxp 132 ?   51.716    3.665   46.583   0.00  0 359 D
+ATOM    7243     N    N ?  ILE    Dxp 133 ?   46.537    6.891   46.024  -1.93  0 360 D
+ATOM    7245     C    C ?  ILE    Dxp 133 ?   46.737    9.259   46.259   0.00  0 360 D
+ATOM    7246     O    O ?  ILE    Dxp 133 ?   47.623    9.183   47.095   0.00  0 360 D
+ATOM    7251     N    N ?  HIS    Dxp 134 ?   46.595   10.297   45.460   0.00  0 361 D
+ATOM    7252     C   CA ?  HIS    Dxp 134 ?   47.370   11.498   45.668   0.00  0 361 D
+ATOM    7253     C    C ?  HIS    Dxp 134 ?   46.953   12.278   46.936   0.00  0 361 D
+ATOM    7254     O    O ?  HIS    Dxp 134 ?   47.812   12.555   47.804   0.00  0 361 D
+ATOM    7255     C   CB ?  HIS    Dxp 134 ?   47.334   12.399   44.428   0.00  0 361 D
+ATOM    7256     C   CG ?  HIS    Dxp 134 ?   48.415   13.421   44.453   0.00  0 361 D
+ATOM    7257     N  ND1 ?  HIS    Dxp 134 ?   48.485   14.377   45.431   0.00  0 361 D
+ATOM    7258     C  CD2 ?  HIS    Dxp 134 ?   49.543   13.548   43.730   0.00  0 361 D
+ATOM    7259     C  CE1 ?  HIS    Dxp 134 ?   49.558   15.116   45.253   0.00  0 361 D
+ATOM    7260     N  NE2 ?  HIS    Dxp 134 ?   50.218   14.635   44.230   0.00  0 361 D
+ATOM    7328     C   CG ?  LEU    Dxp 143 ?   58.274   20.017   40.820   0.00  0 370 D
+ATOM    7329     C  CD1 ?  LEU    Dxp 143 ?   59.244   18.841   41.193   0.00  0 370 D
+ATOM    7330     C  CD2 ?  LEU    Dxp 143 ?   58.782   21.410   41.356   0.00  0 370 D
+ATOM    7395     C    C ?  VAL    Dxp 152 ?   54.278   15.041   40.879   0.00  0 379 D
+ATOM    7396     O    O ?  VAL    Dxp 152 ?   55.001   14.074   40.818   0.00  0 379 D
+ATOM    7398     C  CG1 ?  VAL    Dxp 152 ?   51.341   14.429   40.809   0.00  0 379 D
+ATOM    7400     N    N ?  ALA    Dxp 153 ?   54.162   15.769   41.970   0.00  0 380 D
+ATOM    7401     C   CA ?  ALA    Dxp 153 ?   54.851   15.556   43.189   0.00  0 380 D
+ATOM    7402     C    C ?  ALA    Dxp 153 ?   53.826   15.699   44.308   0.00  0 380 D
+ATOM    7403     O    O ?  ALA    Dxp 153 ?   52.619   15.769   44.076   0.00  0 380 D
+ATOM    7404     C   CB ?  ALA    Dxp 153 ?   55.891   16.596   43.353   0.00  0 380 D
+ATOM    7405     N    N ?  ASP    Dxp 154 ?   54.325   15.719   45.523   0.00  0 381 D
+ATOM    7406     C   CA ?  ASP    Dxp 154 ?   53.526   15.970   46.675   0.00  0 381 D
+ATOM    7407     C    C ?  ASP    Dxp 154 ?   54.490   16.514   47.699   0.00  0 381 D
+ATOM    7408     O    O ?  ASP    Dxp 154 ?   55.352   15.791   48.188   0.00  0 381 D
+ATOM    7409     C   CB ?  ASP    Dxp 154 ?   52.864   14.692   47.175   0.00  0 381 D
+ATOM    7410     C   CG ?  ASP    Dxp 154 ?   51.982   14.931   48.357   0.00  0 381 D
+ATOM    7411     O  OD1 ?  ASP    Dxp 154 ?   51.809   16.053   48.830  -4.29  0 381 D
+ATOM    7412     O  OD2 ?  ASP    Dxp 154 ?   51.451   13.986   48.870  -1.62  0 381 D
+ATOM    7413     N    N ?  PHE    Dxp 155 ?   54.377   17.799   47.998   0.00  0 382 D
+ATOM    7414     C   CA ?  PHE    Dxp 155 ?   55.356   18.410   48.844   0.00  0 382 D
+ATOM    7415     C    C ?  PHE    Dxp 155 ?   54.936   18.484   50.300   0.00  0 382 D
+ATOM    7416     O    O ?  PHE    Dxp 155 ?   55.635   19.113   51.089  -1.07  0 382 D
+ATOM    7417     C   CB ?  PHE    Dxp 155 ?   55.748   19.792   48.329   0.00  0 382 D
+ATOM    7418     C   CG ?  PHE    Dxp 155 ?   56.120   19.814   46.868   0.00  0 382 D
+ATOM    7420     C  CD2 ?  PHE    Dxp 155 ?   56.995   18.870   46.332   0.00  0 382 D
+ATOM    7421     C  CE1 ?  PHE    Dxp 155 ?   55.921   20.831   44.680   0.00  0 382 D
+ATOM    7422     C  CE2 ?  PHE    Dxp 155 ?   57.327   18.902   44.964   0.00  0 382 D
+ATOM    7423     C   CZ ?  PHE    Dxp 155 ?   56.783   19.883   44.153   0.00  0 382 D
+ATOM    7424     N    N ?  GLY    Dxp 156 ?   53.836   17.822   50.662   0.00  0 383 D
+ATOM    7425     C   CA ?  GLY    Dxp 156 ?   53.352   17.790   52.036   0.00  0 383 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)       : 362.2673
+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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3308     O    O ?  ASP    Bxp 164 ?   27.151   43.554   37.600  -1.21  0 391 B
+ATOM    3313     O    O ?  THR    Bxp 165 ?   24.462   45.035   38.384  -2.14  0 392 B
+ATOM    3405     C   CG ?  LYS    Bxp 177 ?   24.464   39.615   42.306   0.00  0 404 B
+ATOM    3406     C   CD ?  LYS    Bxp 177 ?   25.964   39.772   42.543   0.00  0 404 B
+ATOM    3422     C  CH2 ?  TRP    Bxp 178 ?   24.948   45.190   44.295   0.00  0 405 B
+ATOM    3678     C   CB ?  SER    Bxp 211 ?   30.018   43.102   45.878   0.00  0 438 B
+ATOM    3686     C   CD ?  PRO    Bxp 212 ?   26.363   42.775   46.525   0.00  0 439 B
+ATOM    3683     O    O ?  PRO    Bxp 212 ?   27.502   39.687   45.538  -1.07  0 439 B
+ATOM    3408     N   NZ ?  LYS    Bxp 177 ?   28.079   38.314   42.470   0.00  0 404 B
+ATOM    3315     O  OG1 ?  THR    Bxp 165 ?   27.785   47.295   40.411  -2.69  0 392 B
+ATOM    3679     O   OG ?  SER    Bxp 211 ?   30.571   44.344   45.570   0.00  0 438 B
+ATOM    3421     C  CZ3 ?  TRP    Bxp 178 ?   24.294   44.617   43.200   0.00  0 405 B
+ATOM    3733     C  CD2 ?  LEU    Bxp 218 ?   25.994   39.197   38.463   0.00  0 445 B
+ATOM    3407     C   CE ?  LYS    Bxp 177 ?   26.663   38.511   41.999   0.00  0 404 B
+ATOM    3309     C   CB ?  ASP    Bxp 164 ?   29.556   43.103   36.104   0.00  0 391 B
+ATOM    3731     C   CG ?  LEU    Bxp 218 ?   26.746   38.765   37.215   0.00  0 445 B
+ATOM    3732     C  CD1 ?  LEU    Bxp 218 ?   26.904   39.928   36.336   0.00  0 445 B
+ATOM    3400     N    N ?  LYS    Bxp 177 ?   22.059   41.042   41.095   0.00  0 404 B
+ATOM    3404     C   CB ?  LYS    Bxp 177 ?   23.625   40.732   42.913   0.00  0 404 B
+ATOM    3311     C   CA ?  THR    Bxp 165 ?   26.568   46.000   38.856   0.00  0 392 B
+ATOM    3310     N    N ?  THR    Bxp 165 ?   27.717   45.708   37.984  -1.09  0 392 B
+ATOM    3307     C    C ?  ASP    Bxp 164 ?   27.840   44.547   37.321   0.00  0 391 B
+ATOM    3713     O    O ?  ILE    Bxp 216 ?   28.851   36.052   40.595  -4.02  0 443 B
+ATOM    3707     C   CA ?  GLY    Bxp 215 ?   32.598   35.981   43.265   0.00  0 442 B
+ATOM    3709     O    O ?  GLY    Bxp 215 ?   32.021   34.395   41.605   0.00  0 442 B
+ATOM    3708     C    C ?  GLY    Bxp 215 ?   31.630   35.052   42.556   0.00  0 442 B
+ATOM    3706     N    N ?  GLY    Bxp 215 ?   31.992   36.921   44.159   0.00  0 442 B
+ATOM    3700     C   CA ?  PRO    Bxp 214 ?   30.804   37.638   46.187   0.00  0 441 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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3305     N    N ?  ASP    Bxp 164 ?   29.908   45.575   36.198   0.00  0 391 B
+ATOM    3306     C   CA ?  ASP    Bxp 164 ?   28.891   44.496   36.165   0.00  0 391 B
+ATOM    3307     C    C ?  ASP    Bxp 164 ?   27.840   44.547   37.321   0.00  0 391 B
+ATOM    3308     O    O ?  ASP    Bxp 164 ?   27.151   43.554   37.600  -1.21  0 391 B
+ATOM    3309     C   CB ?  ASP    Bxp 164 ?   29.556   43.103   36.104   0.00  0 391 B
+ATOM    3310     N    N ?  THR    Bxp 165 ?   27.717   45.708   37.984  -1.09  0 392 B
+ATOM    3311     C   CA ?  THR    Bxp 165 ?   26.568   46.000   38.856   0.00  0 392 B
+ATOM    3312     C    C ?  THR    Bxp 165 ?   25.293   45.859   38.052   0.00  0 392 B
+ATOM    3313     O    O ?  THR    Bxp 165 ?   24.462   45.035   38.384  -2.14  0 392 B
+ATOM    3314     C   CB ?  THR    Bxp 165 ?   26.698   47.367   39.497   0.00  0 392 B
+ATOM    3315     O  OG1 ?  THR    Bxp 165 ?   27.785   47.295   40.411  -2.69  0 392 B
+ATOM    3392     N    N ?  ILE    Bxp 176 ?   21.472   42.362   38.641   0.00  0 403 B
+ATOM    3393     C   CA ?  ILE    Bxp 176 ?   21.108   40.929   38.881   0.00  0 403 B
+ATOM    3394     C    C ?  ILE    Bxp 176 ?   21.071   40.558   40.347   0.00  0 403 B
+ATOM    3396     C   CB ?  ILE    Bxp 176 ?   21.966   39.989   38.044   0.00  0 403 B
+ATOM    3400     N    N ?  LYS    Bxp 177 ?   22.059   41.042   41.095   0.00  0 404 B
+ATOM    3401     C   CA ?  LYS    Bxp 177 ?   22.185   40.603   42.480   0.00  0 404 B
+ATOM    3404     C   CB ?  LYS    Bxp 177 ?   23.625   40.732   42.913   0.00  0 404 B
+ATOM    3405     C   CG ?  LYS    Bxp 177 ?   24.464   39.615   42.306   0.00  0 404 B
+ATOM    3406     C   CD ?  LYS    Bxp 177 ?   25.964   39.772   42.543   0.00  0 404 B
+ATOM    3407     C   CE ?  LYS    Bxp 177 ?   26.663   38.511   41.999   0.00  0 404 B
+ATOM    3408     N   NZ ?  LYS    Bxp 177 ?   28.079   38.314   42.470   0.00  0 404 B
+ATOM    3419     C  CE3 ?  TRP    Bxp 178 ?   22.913   44.513   43.164   0.00  0 405 B
+ATOM    3421     C  CZ3 ?  TRP    Bxp 178 ?   24.294   44.617   43.200   0.00  0 405 B
+ATOM    3422     C  CH2 ?  TRP    Bxp 178 ?   24.948   45.190   44.295   0.00  0 405 B
+ATOM    3675     C   CA ?  SER    Bxp 211 ?   29.156   43.225   47.157   0.00  0 438 B
+ATOM    3676     C    C ?  SER    Bxp 211 ?   28.502   41.873   47.480   0.00  0 438 B
+ATOM    3677     O    O ?  SER    Bxp 211 ?   29.157   40.946   47.931  -1.07  0 438 B
+ATOM    3678     C   CB ?  SER    Bxp 211 ?   30.018   43.102   45.878   0.00  0 438 B
+ATOM    3679     O   OG ?  SER    Bxp 211 ?   30.571   44.344   45.570   0.00  0 438 B
+ATOM    3680     N    N ?  PRO    Bxp 212 ?   27.212   41.746   47.193   0.00  0 439 B
+ATOM    3683     O    O ?  PRO    Bxp 212 ?   27.502   39.687   45.538  -1.07  0 439 B
+ATOM    3685     C   CG ?  PRO    Bxp 212 ?   25.063   42.030   46.210   0.00  0 439 B
+ATOM    3686     C   CD ?  PRO    Bxp 212 ?   26.363   42.775   46.525   0.00  0 439 B
+ATOM    3689     C    C ?  TYR    Bxp 213 ?   28.452   37.120   45.720   0.00  0 440 B
+ATOM    3690     O    O ?  TYR    Bxp 213 ?   28.681   37.094   44.519   0.00  0 440 B
+ATOM    3699     N    N ?  PRO    Bxp 214 ?   29.411   37.369   46.621   0.00  0 441 B
+ATOM    3700     C   CA ?  PRO    Bxp 214 ?   30.804   37.638   46.187   0.00  0 441 B
+ATOM    3701     C    C ?  PRO    Bxp 214 ?   31.439   36.545   45.323   0.00  0 441 B
+ATOM    3703     C   CB ?  PRO    Bxp 214 ?   31.573   37.783   47.505   0.00  0 441 B
+ATOM    3706     N    N ?  GLY    Bxp 215 ?   31.992   36.921   44.159   0.00  0 442 B
+ATOM    3707     C   CA ?  GLY    Bxp 215 ?   32.598   35.981   43.265   0.00  0 442 B
+ATOM    3708     C    C ?  GLY    Bxp 215 ?   31.630   35.052   42.556   0.00  0 442 B
+ATOM    3709     O    O ?  GLY    Bxp 215 ?   32.021   34.395   41.605   0.00  0 442 B
+ATOM    3710     N    N ?  ILE    Bxp 216 ?   30.363   34.987   42.973   0.00  0 443 B
+ATOM    3712     C    C ?  ILE    Bxp 216 ?   29.102   34.842   40.748   0.00  0 443 B
+ATOM    3713     O    O ?  ILE    Bxp 216 ?   28.851   36.052   40.595  -4.02  0 443 B
+ATOM    3731     C   CG ?  LEU    Bxp 218 ?   26.746   38.765   37.215   0.00  0 445 B
+ATOM    3732     C  CD1 ?  LEU    Bxp 218 ?   26.904   39.928   36.336   0.00  0 445 B
+ATOM    3733     C  CD2 ?  LEU    Bxp 218 ?   25.994   39.197   38.463   0.00  0 445 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)       : 321.3664
+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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    578      C  CE1 ?  PHE    Axp 84 ?    9.022    7.022   32.326   0.00  0 311 A
+ATOM    347      C   CB ?  VAL    Axp 53 ?    9.518   11.423   34.079   0.00  0 280 A
+ATOM    318      C   CB ?  ASP    Axp 49 ?   15.460    8.001   36.408   0.00  0 276 A
+ATOM    576      C  CD1 ?  PHE    Axp 84 ?   10.020    7.279   31.353   0.00  0 311 A
+ATOM    325      O    O ?  THR    Axp 50 ?   13.753   11.886   36.017  -0.54  0 277 A
+ATOM    321      O  OD2 ?  ASP    Axp 49 ?   14.516    5.990   37.244  -0.95  0 276 A
+ATOM    349      C  CG2 ?  VAL    Axp 53 ?    8.506   10.392   33.534   0.00  0 280 A
+ATOM    561      C   CG ?  PRO    Axp 82 ?   10.732    3.280   34.195   0.00  0 309 A
+ATOM    348      C  CG1 ?  VAL    Axp 53 ?    9.081   12.091   35.427   0.00  0 280 A
+ATOM    319      C   CG ?  ASP    Axp 49 ?   15.469    6.493   36.614   0.00  0 276 A
+ATOM    560      C   CB ?  PRO    Axp 82 ?   12.030    2.927   33.492   0.00  0 309 A
+ATOM    564      C   CA ?  PRO    Axp 83 ?   14.000    2.962   30.575   0.00  0 310 A
+ATOM    320      O  OD1 ?  ASP    Axp 49 ?   16.422    5.816   36.164  -0.95  0 276 A
+ATOM    568      C   CG ?  PRO    Axp 83 ?   15.808    1.347   30.237   0.00  0 310 A
+ATOM    563      N    N ?  PRO    Axp 83 ?   13.592    1.581   30.904   0.00  0 310 A
+ATOM    304      O    O ?  LEU    Axp 46 ?   16.573    7.011   31.379  -2.14  0 273 A
+ATOM    570      N    N ?  PHE    Axp 84 ?   12.779    4.833   29.577   0.00  0 311 A
+ATOM    567      C   CB ?  PRO    Axp 83 ?   15.457    2.812   30.082   0.00  0 310 A
+ATOM    312      O    O ?  LYS    Axp 47 ?   19.128    6.617   33.897   0.00  0 274 A
+ATOM    308      C  CD2 ?  LEU    Axp 46 ?   12.808   10.745   31.273   0.00  0 273 A
+ATOM    306      C   CG ?  LEU    Axp 46 ?   14.285   10.407   31.218   0.00  0 273 A
+ATOM    305      C   CB ?  LEU    Axp 46 ?   14.483    9.154   30.366   0.00  0 273 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_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    302      C   CA ?  LEU    Axp 46 ?   15.918    8.854   29.945   0.00  0 273 A
+ATOM    303      C    C ?  LEU    Axp 46 ?   16.720    8.211   31.087   0.00  0 273 A
+ATOM    304      O    O ?  LEU    Axp 46 ?   16.573    7.011   31.379  -2.14  0 273 A
+ATOM    305      C   CB ?  LEU    Axp 46 ?   14.483    9.154   30.366   0.00  0 273 A
+ATOM    306      C   CG ?  LEU    Axp 46 ?   14.285   10.407   31.218   0.00  0 273 A
+ATOM    308      C  CD2 ?  LEU    Axp 46 ?   12.808   10.745   31.273   0.00  0 273 A
+ATOM    311      C    C ?  LYS    Axp 47 ?   18.202    7.333   33.490   0.00  0 274 A
+ATOM    312      O    O ?  LYS    Axp 47 ?   19.128    6.617   33.897   0.00  0 274 A
+ATOM    318      C   CB ?  ASP    Axp 49 ?   15.460    8.001   36.408   0.00  0 276 A
+ATOM    319      C   CG ?  ASP    Axp 49 ?   15.469    6.493   36.614   0.00  0 276 A
+ATOM    320      O  OD1 ?  ASP    Axp 49 ?   16.422    5.816   36.164  -0.95  0 276 A
+ATOM    321      O  OD2 ?  ASP    Axp 49 ?   14.516    5.990   37.244  -0.95  0 276 A
+ATOM    325      O    O ?  THR    Axp 50 ?   13.753   11.886   36.017  -0.54  0 277 A
+ATOM    344      C   CA ?  VAL    Axp 53 ?    9.902   12.497   32.989   0.00  0 280 A
+ATOM    347      C   CB ?  VAL    Axp 53 ?    9.518   11.423   34.079   0.00  0 280 A
+ATOM    348      C  CG1 ?  VAL    Axp 53 ?    9.081   12.091   35.427   0.00  0 280 A
+ATOM    349      C  CG2 ?  VAL    Axp 53 ?    8.506   10.392   33.534   0.00  0 280 A
+ATOM    557      C   CA ?  PRO    Axp 82 ?   11.584    2.421   32.113   0.00  0 309 A
+ATOM    558      C    C ?  PRO    Axp 82 ?   12.478    1.262   31.610   0.00  0 309 A
+ATOM    560      C   CB ?  PRO    Axp 82 ?   12.030    2.927   33.492   0.00  0 309 A
+ATOM    561      C   CG ?  PRO    Axp 82 ?   10.732    3.280   34.195   0.00  0 309 A
+ATOM    563      N    N ?  PRO    Axp 83 ?   13.592    1.581   30.904   0.00  0 310 A
+ATOM    564      C   CA ?  PRO    Axp 83 ?   14.000    2.962   30.575   0.00  0 310 A
+ATOM    565      C    C ?  PRO    Axp 83 ?   13.073    3.538   29.477   0.00  0 310 A
+ATOM    567      C   CB ?  PRO    Axp 83 ?   15.457    2.812   30.082   0.00  0 310 A
+ATOM    568      C   CG ?  PRO    Axp 83 ?   15.808    1.347   30.237   0.00  0 310 A
+ATOM    569      C   CD ?  PRO    Axp 83 ?   14.509    0.587   30.313   0.00  0 310 A
+ATOM    570      N    N ?  PHE    Axp 84 ?   12.779    4.833   29.577   0.00  0 311 A
+ATOM    571      C   CA ?  PHE    Axp 84 ?   11.890    5.469   28.614   0.00  0 311 A
+ATOM    574      C   CB ?  PHE    Axp 84 ?   11.248    6.723   29.215   0.00  0 311 A
+ATOM    575      C   CG ?  PHE    Axp 84 ?   10.188    6.434   30.264   0.00  0 311 A
+ATOM    576      C  CD1 ?  PHE    Axp 84 ?   10.020    7.279   31.353   0.00  0 311 A
+ATOM    578      C  CE1 ?  PHE    Axp 84 ?    9.022    7.022   32.326   0.00  0 311 A
+ATOM    580      C   CZ ?  PHE    Axp 84 ?    8.195    5.904   32.211   0.00  0 311 A
+#

tests/reference_output/123abc_out/pocket31_vert.pqr

@@ -0,0 +1,31 @@
+ATOM      1    C STP    31      11.941   8.349  34.639    0.00     3.95
+ATOM      2    O STP    31      11.350   8.533  36.417    0.00     4.14
+ATOM      3    C STP    31      10.851   7.890  36.101    0.00     4.28
+ATOM      4    C STP    31      11.466   8.078  35.454    0.00     4.11
+ATOM      5    C STP    31      12.140   6.767  34.425    0.00     3.77
+ATOM      6    C STP    31      12.124   7.405  34.577    0.00     3.85
+ATOM      7    C STP    31      10.334   7.929  36.985    0.00     4.62
+ATOM      8    O STP    31      11.119   8.605  36.905    0.00     4.30
+ATOM      9    C STP    31      12.720   6.889  34.009    0.00     3.81
+ATOM     10    C STP    31      15.929   2.551  33.997    0.00     3.95
+ATOM     11    C STP    31      12.489   6.616  34.126    0.00     3.77
+ATOM     12    C STP    31      12.783   6.645  33.908    0.00     3.82
+ATOM     13    C STP    31      15.809   2.433  33.914    0.00     3.83
+ATOM     14    O STP    31      14.207   5.626  33.503    0.00     3.47
+ATOM     15    C STP    31      13.275   6.812  33.423    0.00     3.89
+ATOM     16    O STP    31      14.877   4.783  33.313    0.00     3.40
+ATOM     17    C STP    31      13.267   6.620  33.403    0.00     3.90
+ATOM     18    O STP    31      13.259   6.376  32.913    0.00     3.71
+ATOM     19    C STP    31      15.934   2.557  33.992    0.00     3.95
+ATOM     20    O STP    31      15.834   4.198  33.197    0.00     3.43
+ATOM     21    O STP    31      17.535   2.896  33.570    0.00     4.06
+ATOM     22    O STP    31      16.888   3.928  33.163    0.00     3.58
+ATOM     23    C STP    31      12.216   8.719  34.482    0.00     3.84
+ATOM     24    C STP    31      12.122   8.514  34.421    0.00     3.92
+ATOM     25    C STP    31      12.996   7.792  33.583    0.00     3.75
+ATOM     26    C STP    31      13.056   7.708  33.531    0.00     3.76
+ATOM     27    C STP    31      13.286   7.078  33.373    0.00     3.85
+ATOM     28    O STP    31      13.272   6.667  32.533    0.00     3.51
+ATOM     29    C STP    31      12.989   7.793  33.391    0.00     3.64
+TER
+END

tests/reference_output/123abc_out/pocket32_atm.cif

@@ -0,0 +1,60 @@
+data_pocket32_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    32:
+0  - Pocket Score                      : -0.0556
+1  - Drug Score                        : 0.0003
+2  - Number of alpha spheres           :    28
+3  - Mean alpha-sphere radius          : 3.9447
+4  - Mean alpha-sphere Solvent Acc.    : 0.4561
+5  - Mean B-factor of pocket residues  : 0.1854
+6  - Hydrophobicity Score              : 37.2000
+7  - Polarity Score                    :     5
+8  - Amino Acid based volume Score     : 5.0000
+9  - Pocket volume (Monte Carlo)       : 350.9174
+10  -Pocket volume (convex hull)       : 14.9179
+11 - Charge Score                      :     3
+12 - Local hydrophobic density Score   : 8.0000
+13 - Number of apolar alpha sphere     :     9
+14 - Proportion of apolar alpha sphere : 0.3214
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    2552     O    O ?  HIS    Bxp 68 ?   11.190   62.764   53.093  -4.69  0 295 B
+ATOM    2594     C   CG ?  GLN    Bxp 73 ?   13.080   68.321   50.358   0.00  0 300 B
+ATOM    2548     C   CB ?  LYS    Bxp 67 ?    6.504   65.116   50.895   0.00  0 294 B
+ATOM    2597     N  NE2 ?  GLN    Bxp 73 ?   12.729   70.253   51.868   0.00  0 300 B
+ATOM    2549     N    N ?  HIS    Bxp 68 ?    8.770   62.722   52.136   0.00  0 295 B
+ATOM    2100     C  CH2 ?  TRP    Bxp 8 ?    8.021   70.120   46.212   0.00  0 235 B
+ATOM    2601     O    O ?  LEU    Bxp 74 ?   11.642   69.555   47.135  -1.48  0 301 B
+ATOM    2595     C   CD ?  GLN    Bxp 73 ?   13.604   69.305   51.438   0.00  0 300 B
+ATOM    3222     N   NZ ?  LYS    Bxp 151 ?   15.951   64.984   53.909   0.00  0 378 B
+ATOM    2596     O  OE1 ?  GLN    Bxp 73 ?   14.783   69.222   51.879  -1.88  0 300 B
+ATOM    2560     C   CA ?  PRO    Bxp 69 ?   11.828   62.498   55.801   0.00  0 296 B
+ATOM    2545     C   CA ?  LYS    Bxp 67 ?    7.422   63.917   50.500   0.00  0 294 B
+ATOM    2590     C   CA ?  GLN    Bxp 73 ?   13.804   66.159   48.996   0.00  0 300 B
+ATOM    2539     O    O ?  ILE    Bxp 66 ?    7.780   64.424   47.789  -7.50  0 293 B
+ATOM    2585     O    O ?  VAL    Bxp 72 ?   13.589   63.555   47.823  -6.43  0 299 B
+ATOM    2598     N    N ?  LEU    Bxp 74 ?   12.978   66.960   46.855  -1.09  0 301 B
+ATOM    2577     O    O ?  LEU    Bxp 71 ?   13.536   62.679   50.816   0.00  0 298 B
+ATOM    2593     C   CB ?  GLN    Bxp 73 ?   13.894   67.022   50.290   0.00  0 300 B
+# 

tests/reference_output/123abc_out/pocket32_env_atm.cif

@@ -0,0 +1,57 @@
+data_pocket32_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    2098     C  CZ2 ?  TRP    Bxp 8 ?    6.790   69.994   45.595   0.00  0 235 B
+ATOM    2099     C  CZ3 ?  TRP    Bxp 8 ?    9.064   70.864   45.620   0.00  0 235 B
+ATOM    2100     C  CH2 ?  TRP    Bxp 8 ?    8.021   70.120   46.212   0.00  0 235 B
+ATOM    2538     C    C ?  ILE    Bxp 66 ?    7.161   63.422   48.167   0.00  0 293 B
+ATOM    2539     O    O ?  ILE    Bxp 66 ?    7.780   64.424   47.789  -7.50  0 293 B
+ATOM    2544     N    N ?  LYS    Bxp 67 ?    6.861   63.173   49.437   0.00  0 294 B
+ATOM    2545     C   CA ?  LYS    Bxp 67 ?    7.422   63.917   50.500   0.00  0 294 B
+ATOM    2546     C    C ?  LYS    Bxp 67 ?    7.553   62.953   51.657   0.00  0 294 B
+ATOM    2548     C   CB ?  LYS    Bxp 67 ?    6.504   65.116   50.895   0.00  0 294 B
+ATOM    2549     N    N ?  HIS    Bxp 68 ?    8.770   62.722   52.136   0.00  0 295 B
+ATOM    2550     C   CA ?  HIS    Bxp 68 ?    8.991   61.888   53.306   0.00  0 295 B
+ATOM    2551     C    C ?  HIS    Bxp 68 ?   10.325   62.284   53.850   0.00  0 295 B
+ATOM    2552     O    O ?  HIS    Bxp 68 ?   11.190   62.764   53.093  -4.69  0 295 B
+ATOM    2559     N    N ?  PRO    Bxp 69 ?   10.515   62.185   55.179   0.00  0 296 B
+ATOM    2560     C   CA ?  PRO    Bxp 69 ?   11.828   62.498   55.801   0.00  0 296 B
+ATOM    2561     C    C ?  PRO    Bxp 69 ?   13.029   61.650   55.401   0.00  0 296 B
+ATOM    2562     O    O ?  PRO    Bxp 69 ?   14.205   62.058   55.580  -3.21  0 296 B
+ATOM    2563     C   CB ?  PRO    Bxp 69 ?   11.564   62.397   57.308   0.00  0 296 B
+ATOM    2576     C    C ?  LEU    Bxp 71 ?   13.846   61.648   50.258   0.00  0 298 B
+ATOM    2577     O    O ?  LEU    Bxp 71 ?   13.536   62.679   50.816   0.00  0 298 B
+ATOM    2578     C   CB ?  LEU    Bxp 71 ?   11.847   60.163   50.003   0.00  0 298 B
+ATOM    2584     C    C ?  VAL    Bxp 72 ?   14.568   63.839   48.524   0.00  0 299 B
+ATOM    2585     O    O ?  VAL    Bxp 72 ?   13.589   63.555   47.823  -6.43  0 299 B
+ATOM    2589     N    N ?  GLN    Bxp 73 ?   14.804   65.056   49.026   0.00  0 300 B
+ATOM    2590     C   CA ?  GLN    Bxp 73 ?   13.804   66.159   48.996   0.00  0 300 B
+ATOM    2591     C    C ?  GLN    Bxp 73 ?   13.976   67.021   47.738   0.00  0 300 B
+ATOM    2593     C   CB ?  GLN    Bxp 73 ?   13.894   67.022   50.290   0.00  0 300 B
+ATOM    2594     C   CG ?  GLN    Bxp 73 ?   13.080   68.321   50.358   0.00  0 300 B
+ATOM    2595     C   CD ?  GLN    Bxp 73 ?   13.604   69.305   51.438   0.00  0 300 B
+ATOM    2596     O  OE1 ?  GLN    Bxp 73 ?   14.783   69.222   51.879  -1.88  0 300 B
+ATOM    2597     N  NE2 ?  GLN    Bxp 73 ?   12.729   70.253   51.868   0.00  0 300 B
+ATOM    2598     N    N ?  LEU    Bxp 74 ?   12.978   66.960   46.855  -1.09  0 301 B
+ATOM    2599     C   CA ?  LEU    Bxp 74 ?   12.751   67.909   45.778   0.00  0 301 B
+ATOM    2600     C    C ?  LEU    Bxp 74 ?   12.544   69.318   46.298   0.00  0 301 B
+ATOM    2601     O    O ?  LEU    Bxp 74 ?   11.642   69.555   47.135  -1.48  0 301 B
+ATOM    2602     C   CB ?  LEU    Bxp 74 ?   11.545   67.505   44.911   0.00  0 301 B
+ATOM    3222     N   NZ ?  LYS    Bxp 151 ?   15.951   64.984   53.909   0.00  0 378 B
+#

tests/reference_output/123abc_out/pocket32_vert.pqr

@@ -0,0 +1,30 @@
+ATOM      1    O STP    32       9.834  67.069  53.237    0.00     4.52
+ATOM      2    O STP    32       9.989  66.615  52.422    0.00     4.09
+ATOM      3    C STP    32       8.667  69.004  50.490    0.00     4.47
+ATOM      4    O STP    32       8.762  69.085  50.409    0.00     4.39
+ATOM      5    C STP    32       8.744  68.816  50.313    0.00     4.36
+ATOM      6    O STP    32      12.655  67.582  55.455    0.00     4.47
+ATOM      7    O STP    32      11.072  66.898  53.744    0.00     4.19
+ATOM      8    O STP    32      11.668  66.953  54.834    0.00     4.56
+ATOM      9    O STP    32      12.028  67.109  55.223    0.00     4.65
+ATOM     10    O STP    32      11.987  66.813  54.745    0.00     4.45
+ATOM     11    C STP    32      10.039  66.443  51.999    0.00     3.93
+ATOM     12    O STP    32      10.715  65.348  50.642    0.00     3.59
+ATOM     13    O STP    32      10.498  65.826  51.169    0.00     3.68
+ATOM     14    O STP    32      10.757  64.549  49.632    0.00     3.50
+ATOM     15    O STP    32       8.845  67.882  49.348    0.00     3.94
+ATOM     16    O STP    32      10.088  66.899  48.980    0.00     3.59
+ATOM     17    O STP    32      10.288  66.538  49.115    0.00     3.54
+ATOM     18    C STP    32      10.276  66.069  49.853    0.00     3.63
+ATOM     19    O STP    32       9.288  67.580  49.598    0.00     3.94
+ATOM     20    C STP    32       9.672  66.847  49.918    0.00     3.74
+ATOM     21    O STP    32      10.852  64.851  50.318    0.00     3.49
+ATOM     22    O STP    32      10.802  64.764  50.143    0.00     3.50
+ATOM     23    O STP    32      10.778  64.525  49.682    0.00     3.51
+ATOM     24    C STP    32      10.708  65.383  50.667    0.00     3.60
+ATOM     25    C STP    32      10.502  65.796  50.405    0.00     3.61
+ATOM     26    C STP    32      10.532  65.779  51.099    0.00     3.67
+ATOM     27    O STP    32      12.297  66.474  53.857    0.00     3.95
+ATOM     28    C STP    32      11.962  66.542  53.637    0.00     3.89
+TER
+END

tests/reference_output/123abc_out/pocket33_atm.cif

@@ -0,0 +1,71 @@
+data_pocket33_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    33:
+0  - Pocket Score                      : -0.0559
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    39
+3  - Mean alpha-sphere radius          : 3.7737
+4  - Mean alpha-sphere Solvent Acc.    : 0.3632
+5  - Mean B-factor of pocket residues  : 0.1546
+6  - Hydrophobicity Score              : 21.2500
+7  - Polarity Score                    :    12
+8  - Amino Acid based volume Score     : 4.6875
+9  - Pocket volume (Monte Carlo)       : 440.8528
+10  -Pocket volume (convex hull)       : 79.9433
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 8.0000
+13 - Number of apolar alpha sphere     :    12
+14 - Proportion of apolar alpha sphere : 0.3077
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    5991     O  OE2 ?  GLU    Cxp 239 ?   33.082   48.141   38.837  -4.43  0 466 C
+ATOM    2820     N  NH1 ?  ARG    Bxp 101 ?   32.415   49.637   46.867   0.00  0 328 B
+ATOM    3315     O  OG1 ?  THR    Bxp 165 ?   27.785   47.295   40.411  -2.69  0 392 B
+ATOM    3679     O   OG ?  SER    Bxp 211 ?   30.571   44.344   45.570   0.00  0 438 B
+ATOM    3628     O  OE1 ?  GLU    Bxp 204 ?   25.049   47.777   48.346   0.00  0 431 B
+ATOM    3675     C   CA ?  SER    Bxp 211 ?   29.156   43.225   47.157   0.00  0 438 B
+ATOM    3422     C  CH2 ?  TRP    Bxp 178 ?   24.948   45.190   44.295   0.00  0 405 B
+ATOM    3420     C  CZ2 ?  TRP    Bxp 178 ?   24.271   45.652   45.407   0.00  0 405 B
+ATOM    2821     N  NH2 ?  ARG    Bxp 101 ?   31.115   47.833   47.466  -2.61  0 328 B
+ATOM    3669     O    O ?  MET    Bxp 210 ?   28.182   44.516   49.518   0.00  0 437 B
+ATOM    2242     C  CE2 ?  TYR    Bxp 26 ?   25.430   59.279   43.261   0.00  0 253 B
+ATOM    3293     C   CE ?  MET    Bxp 161 ?   26.781   52.972   40.791   0.00  0 388 B
+ATOM    3264     C  CD1 ?  LEU    Bxp 157 ?   23.447   54.265   41.302   0.00  0 384 B
+ATOM    3265     C  CD2 ?  LEU    Bxp 157 ?   24.047   56.043   39.564   0.00  0 384 B
+ATOM    5990     O  OE1 ?  GLU    Cxp 239 ?   33.030   50.320   38.639  -1.62  0 466 C
+ATOM    3291     C   CG ?  MET    Bxp 161 ?   27.612   51.526   38.485   0.00  0 388 B
+ATOM    3292     S   SD ?  MET    Bxp 161 ?   26.854   51.297   40.129   0.00  0 388 B
+ATOM    3299     O  OG1 ?  THR    Bxp 162 ?   32.015   51.934   37.284  -1.21  0 389 B
+ATOM    2229     C   CG ?  GLN    Bxp 25 ?   29.480   57.926   41.503   0.00  0 252 B
+ATOM    2232     N  NE2 ?  GLN    Bxp 25 ?   29.244   57.286   43.822  -1.93  0 252 B
+ATOM    3131     O    O ?  ARG    Bxp 140 ?   23.457   55.144   45.161  -1.07  0 367 B
+ATOM    3132     C   CB ?  ARG    Bxp 140 ?   24.715   52.271   44.626   0.00  0 367 B
+ATOM    2764     C   CG ?  ASN    Bxp 95 ?   27.203   56.454   47.356   0.00  0 322 B
+ATOM    2782     C  CD2 ?  LEU    Bxp 97 ?   28.304   50.650   46.399   0.00  0 324 B
+ATOM    2781     C  CD1 ?  LEU    Bxp 97 ?   27.928   49.668   48.729   0.00  0 324 B
+ATOM    3137     N  NH1 ?  ARG    Bxp 140 ?   23.339   48.032   43.234  -2.19  0 367 B
+ATOM    3134     C   CD ?  ARG    Bxp 140 ?   24.061   50.742   42.718   0.00  0 367 B
+ATOM    2789     O  OD1 ?  ASP    Bxp 98 ?   31.430   54.227   47.147  -5.09  0 325 B
+ATOM    2766     N  ND2 ?  ASN    Bxp 95 ?   27.312   55.250   47.801  -2.19  0 322 B
+# 

tests/reference_output/123abc_out/pocket33_env_atm.cif

@@ -0,0 +1,78 @@
+data_pocket33_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    2226     C    C ?  GLN    Bxp 25 ?   27.939   59.013   38.921   0.00  0 252 B
+ATOM    2227     O    O ?  GLN    Bxp 25 ?   27.350   57.919   38.806  -3.21  0 252 B
+ATOM    2229     C   CG ?  GLN    Bxp 25 ?   29.480   57.926   41.503   0.00  0 252 B
+ATOM    2230     C   CD ?  GLN    Bxp 25 ?   29.674   58.204   42.986   0.00  0 252 B
+ATOM    2232     N  NE2 ?  GLN    Bxp 25 ?   29.244   57.286   43.822  -1.93  0 252 B
+ATOM    2240     C  CD2 ?  TYR    Bxp 26 ?   25.035   59.577   41.953   0.00  0 253 B
+ATOM    2242     C  CE2 ?  TYR    Bxp 26 ?   25.430   59.279   43.261   0.00  0 253 B
+ATOM    2243     C   CZ ?  TYR    Bxp 26 ?   26.444   59.997   43.875   0.00  0 253 B
+ATOM    2763     C   CB ?  ASN    Bxp 95 ?   25.931   57.078   47.584   0.00  0 322 B
+ATOM    2764     C   CG ?  ASN    Bxp 95 ?   27.203   56.454   47.356   0.00  0 322 B
+ATOM    2765     O  OD1 ?  ASN    Bxp 95 ?   28.158   57.076   46.868  -2.14  0 322 B
+ATOM    2766     N  ND2 ?  ASN    Bxp 95 ?   27.312   55.250   47.801  -2.19  0 322 B
+ATOM    2779     C   CB ?  LEU    Bxp 97 ?   27.381   52.063   48.248   0.00  0 324 B
+ATOM    2780     C   CG ?  LEU    Bxp 97 ?   28.312   50.918   47.888   0.00  0 324 B
+ATOM    2781     C  CD1 ?  LEU    Bxp 97 ?   27.928   49.668   48.729   0.00  0 324 B
+ATOM    2782     C  CD2 ?  LEU    Bxp 97 ?   28.304   50.650   46.399   0.00  0 324 B
+ATOM    2788     C   CG ?  ASP    Bxp 98 ?   31.168   55.392   47.561   0.00  0 325 B
+ATOM    2789     O  OD1 ?  ASP    Bxp 98 ?   31.430   54.227   47.147  -5.09  0 325 B
+ATOM    2790     O  OD2 ?  ASP    Bxp 98 ?   30.977   56.310   46.763  -0.54  0 325 B
+ATOM    2819     C   CZ ?  ARG    Bxp 101 ?   31.855   48.898   47.794   0.00  0 328 B
+ATOM    2820     N  NH1 ?  ARG    Bxp 101 ?   32.415   49.637   46.867   0.00  0 328 B
+ATOM    2821     N  NH2 ?  ARG    Bxp 101 ?   31.115   47.833   47.466  -2.61  0 328 B
+ATOM    3129     C   CA ?  ARG    Bxp 140 ?   24.210   52.962   45.918   0.00  0 367 B
+ATOM    3130     C    C ?  ARG    Bxp 140 ?   23.149   54.033   45.618   0.00  0 367 B
+ATOM    3131     O    O ?  ARG    Bxp 140 ?   23.457   55.144   45.161  -1.07  0 367 B
+ATOM    3132     C   CB ?  ARG    Bxp 140 ?   24.715   52.271   44.626   0.00  0 367 B
+ATOM    3133     C   CG ?  ARG    Bxp 140 ?   23.643   51.417   43.981   0.00  0 367 B
+ATOM    3134     C   CD ?  ARG    Bxp 140 ?   24.061   50.742   42.718   0.00  0 367 B
+ATOM    3135     N   NE ?  ARG    Bxp 140 ?   22.920   50.005   42.161   0.00  0 367 B
+ATOM    3136     C   CZ ?  ARG    Bxp 140 ?   22.618   48.746   42.421   0.00  0 367 B
+ATOM    3137     N  NH1 ?  ARG    Bxp 140 ?   23.339   48.032   43.234  -2.19  0 367 B
+ATOM    3249     C  CD1 ?  PHE    Bxp 155 ?   22.205   57.740   43.459   0.00  0 382 B
+ATOM    3263     C   CG ?  LEU    Bxp 157 ?   23.028   54.917   40.029   0.00  0 384 B
+ATOM    3264     C  CD1 ?  LEU    Bxp 157 ?   23.447   54.265   41.302   0.00  0 384 B
+ATOM    3265     C  CD2 ?  LEU    Bxp 157 ?   24.047   56.043   39.564   0.00  0 384 B
+ATOM    3291     C   CG ?  MET    Bxp 161 ?   27.612   51.526   38.485   0.00  0 388 B
+ATOM    3292     S   SD ?  MET    Bxp 161 ?   26.854   51.297   40.129   0.00  0 388 B
+ATOM    3293     C   CE ?  MET    Bxp 161 ?   26.781   52.972   40.791   0.00  0 388 B
+ATOM    3299     O  OG1 ?  THR    Bxp 162 ?   32.015   51.934   37.284  -1.21  0 389 B
+ATOM    3314     C   CB ?  THR    Bxp 165 ?   26.698   47.367   39.497   0.00  0 392 B
+ATOM    3315     O  OG1 ?  THR    Bxp 165 ?   27.785   47.295   40.411  -2.69  0 392 B
+ATOM    3316     C  CG2 ?  THR    Bxp 165 ?   25.446   47.756   40.272   0.00  0 392 B
+ATOM    3420     C  CZ2 ?  TRP    Bxp 178 ?   24.271   45.652   45.407   0.00  0 405 B
+ATOM    3421     C  CZ3 ?  TRP    Bxp 178 ?   24.294   44.617   43.200   0.00  0 405 B
+ATOM    3422     C  CH2 ?  TRP    Bxp 178 ?   24.948   45.190   44.295   0.00  0 405 B
+ATOM    3627     C   CD ?  GLU    Bxp 204 ?   24.079   47.170   48.858   0.00  0 431 B
+ATOM    3628     O  OE1 ?  GLU    Bxp 204 ?   25.049   47.777   48.346   0.00  0 431 B
+ATOM    3665     O    O ?  GLY    Bxp 209 ?   30.493   47.107   49.961  -2.14  0 436 B
+ATOM    3668     C    C ?  MET    Bxp 210 ?   29.396   44.197   49.395   0.00  0 437 B
+ATOM    3669     O    O ?  MET    Bxp 210 ?   28.182   44.516   49.518   0.00  0 437 B
+ATOM    3674     N    N ?  SER    Bxp 211 ?   29.944   43.690   48.275  -1.51  0 438 B
+ATOM    3675     C   CA ?  SER    Bxp 211 ?   29.156   43.225   47.157   0.00  0 438 B
+ATOM    3678     C   CB ?  SER    Bxp 211 ?   30.018   43.102   45.878   0.00  0 438 B
+ATOM    3679     O   OG ?  SER    Bxp 211 ?   30.571   44.344   45.570   0.00  0 438 B
+ATOM    3686     C   CD ?  PRO    Bxp 212 ?   26.363   42.775   46.525   0.00  0 439 B
+ATOM    5989     C   CD ?  GLU    Cxp 239 ?   33.542   49.209   38.357   0.00  0 466 C
+ATOM    5990     O  OE1 ?  GLU    Cxp 239 ?   33.030   50.320   38.639  -1.62  0 466 C
+ATOM    5991     O  OE2 ?  GLU    Cxp 239 ?   33.082   48.141   38.837  -4.43  0 466 C
+#

tests/reference_output/123abc_out/pocket33_vert.pqr

@@ -0,0 +1,41 @@
+ATOM      1    O STP    33      31.401  47.826  42.938    0.00     4.44
+ATOM      2    O STP    33      27.700  46.421  46.293    0.00     3.62
+ATOM      3    C STP    33      27.673  46.391  46.313    0.00     3.60
+ATOM      4    O STP    33      31.089  47.886  43.141    0.00     4.33
+ATOM      5    O STP    33      27.819  46.823  46.033    0.00     3.73
+ATOM      6    O STP    33      27.897  46.532  46.547    0.00     3.59
+ATOM      7    O STP    33      27.899  46.530  46.566    0.00     3.58
+ATOM      8    C STP    33      26.249  56.073  42.237    0.00     3.46
+ATOM      9    O STP    33      31.025  49.532  42.589    0.00     4.50
+ATOM     10    C STP    33      30.519  52.114  40.920    0.00     3.84
+ATOM     11    O STP    33      30.562  52.296  40.822    0.00     3.84
+ATOM     12    O STP    33      30.050  49.940  40.401    0.00     3.48
+ATOM     13    C STP    33      26.499  56.243  41.995    0.00     3.46
+ATOM     14    C STP    33      26.463  56.191  42.054    0.00     3.47
+ATOM     15    C STP    33      26.513  56.209  41.987    0.00     3.46
+ATOM     16    C STP    33      26.249  55.934  42.594    0.00     3.51
+ATOM     17    O STP    33      26.140  55.831  42.968    0.00     3.53
+ATOM     18    O STP    33      26.209  55.668  43.005    0.00     3.54
+ATOM     19    O STP    33      26.760  54.989  44.301    0.00     3.42
+ATOM     20    O STP    33      26.579  55.040  43.598    0.00     3.49
+ATOM     21    O STP    33      27.805  46.966  45.942    0.00     3.75
+ATOM     22    O STP    33      27.847  47.120  46.240    0.00     3.56
+ATOM     23    O STP    33      28.279  47.299  44.322    0.00     3.94
+ATOM     24    O STP    33      27.920  46.989  45.700    0.00     3.75
+ATOM     25    O STP    33      29.266  47.694  44.015    0.00     3.92
+ATOM     26    O STP    33      26.977  48.264  43.895    0.00     3.70
+ATOM     27    O STP    33      30.326  48.538  43.451    0.00     4.15
+ATOM     28    C STP    33      26.417  48.272  44.767    0.00     3.45
+ATOM     29    C STP    33      27.338  47.340  45.715    0.00     3.51
+ATOM     30    O STP    33      26.905  48.666  43.675    0.00     3.65
+ATOM     31    C STP    33      27.369  49.511  43.162    0.00     3.56
+ATOM     32    O STP    33      30.597  50.215  42.488    0.00     4.55
+ATOM     33    O STP    33      30.776  49.974  42.607    0.00     4.58
+ATOM     34    C STP    33      30.816  51.476  42.567    0.00     4.66
+ATOM     35    C STP    33      28.167  53.704  44.209    0.00     3.76
+ATOM     36    O STP    33      29.688  53.256  43.611    0.00     4.06
+ATOM     37    O STP    33      27.127  54.680  44.440    0.00     3.41
+ATOM     38    O STP    33      28.090  53.814  44.465    0.00     3.71
+ATOM     39    O STP    33      28.725  53.851  44.792    0.00     3.61
+TER
+END