fixed typo and deleted mod 2POR

lilely not working

.gitattributes

@@ -0,0 +1,2 @@
+*.tcl linguist-detectable=false
+*.c linguist-detectable=true

.github/workflows/c-cpp.yml

@@ -0,0 +1,23 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build-and-test-linux:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: netcdf
+      run: sudo apt-get install libnetcdf-dev
+    - name: make
+      run: make fpocket
+    - name: create conda environment
+      run: conda env update -f ./tests/environment.yml
+    - name: activate conda environment
+      run: conda activate fpocket_test
+    - name: Run pytest
+      run: pytest

README.md

@@ -2,8 +2,7 @@
 ![fpocket logo](doc/images/fpocket_logo.png) 
 
 [![Build Status](https://dev.azure.com/3decision/fpocket/_apis/build/status/Discngine.fpocket?branchName=master)](https://dev.azure.com/3decision/fpocket/_build/latest?definitionId=2&branchName=master)
-[![Join the chat at https://gitter.im/fpocket/community](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/fpocket/community?utm_source=badge&utm_medium=badge&utm_content=badge)
-
+[![Join the chat at https://gitter.im/fpocket/community](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/fpocket-official/community?utm_source=badge&utm_medium=badge&utm_content=badge)
 
 The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
 

doc/GETTINGSTARTED.md

@@ -457,7 +457,11 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
     
     -x None: (None) EXPERIMENTAL: specify this flag if you want to run energy calculations on calculated pockets. That's not fully functional and only one or two probes are currently generated and output density grids written. Use with caution
     
-    -c char : (Default is none): Use this flag to chose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
+    -c char : (Default is none): Use this flag to choose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
+    
+    -k char : (Default is none): Use this flag to choose which chains you want to keep before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-k A,B,E' or '-k A:B:E'. You can keep up to 20 different chains.
+    
+    -a char : (Default is none): With this flag you can select a chain you want to be considered as a ligand. Works the same way as the "-r" flag but with a whole chain. Only a single chain can be chosen, for example '-a D'.
 
 
 ###  Output files description

headers/fparams.h

@@ -111,6 +111,13 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_DROP_CHAINS 'c' /**flag, to define which chain are dropped before the pocket detection*/
 #define M_PAR_DROP_CHAINS_LONG "drop_chains"
 
+#define M_PAR_KEEP_CHAINS 'k' /**flag, to define which chains are kept before the pocket detection*/
+#define M_PAR_KEEP_CHAINS_LONG "keep_chains"
+
+#define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
+#define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
+
+
 
 #define M_FP_USAGE "\n\
 ***** USAGE (fpocket) *****\n\
@@ -194,7 +201,8 @@ typedef struct s_fparams
                 min_as_density,                 /**<Minimum alpha sphere density for a pocket to be retained*/
 		  asph_max_size ;		/**< Maximum size of alpha spheres to keep */
 	char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
-
+	char chain_as_ligand[M_MAX_CHAINS_DELETE];
+	int chain_is_kept;/* To choose if we keep the chains or not*/
 
 } s_fparams ;
 

headers/rpdb.h

@@ -141,5 +141,5 @@ s_atom_ptr_list *init_atom_ptr_list(void);
 
 
 short get_mm_type_from_element(char *symbol);
-int chains_to_delete(char *chains_selected, char *current_line_chain);
+int chains_to_delete(char *chains_selected, char *current_line_chain, int is_chain_kept);
 #endif

src/fparams.c

@@ -80,6 +80,7 @@ s_fparams* init_def_fparams(void) {
     par->topology_path[0] = 0;
     par->fpocket_running = 0;
     par->xlig_resnumber = - 1;
+    par->chain_is_kept = 0;
     return par;
 }
 
@@ -108,6 +109,7 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
     opterr = 0;
     char *pt;
     short custom_ligand_i=0;
+    
     static struct option fplong_options[] = {  /*long options args located in fparams.h*/
         {"file", required_argument, 0, M_PAR_PDB_FILE},
         {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
@@ -125,6 +127,8 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
         {"model_number", required_argument, 0, M_PAR_MODEL_FLAG},
         {"custom_ligand", required_argument, 0, M_PAR_CUSTOM_LIGAND},
         {M_PAR_DROP_CHAINS_LONG, required_argument, 0, M_PAR_DROP_CHAINS}, /*drop chains*/
+        {M_PAR_CHAIN_AS_LIGAND_LONG, required_argument, 0, M_PAR_CHAIN_AS_LIGAND}, /*chain as ligand*/
+        {M_PAR_KEEP_CHAINS_LONG, required_argument, 0, M_PAR_KEEP_CHAINS}, /*chain as ligand*/
         {0, 0, 0, 0}
     };
 
@@ -133,7 +137,7 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
         /* getopt_long stores the option index here. */
         int option_index = 0;
         optarg = 0;
-        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:c:",
+        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:c:a:k:",
                 fplong_options, &option_index);
         //        printf("C: %d nargs : %d optindex:%d\n", c, nargs, option_index);
 
@@ -141,6 +145,24 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
             case 0:
                 break;
 
+            case M_PAR_CHAIN_AS_LIGAND :
+                /*select the chains as ligand*/
+                status++;
+                strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
+                const char  *separatorss  = ",:"; /* defining separators*/
+                pt = strtok( par->chain_as_ligand, separatorss);
+                int nn = 0;
+                while (pt != NULL) {
+                    strncpy(&(par->chain_as_ligand[nn]), pt, 1);
+                    nn++;
+                    pt = strtok(NULL, separatorss);
+                }
+                par->xlig_resnumber = 0;
+                //printf("lig %s\n",par->chain_as_ligand);
+                
+                
+                break;
+
             case M_PAR_DROP_CHAINS :
             /*drop the selected chains from the pdb file*/
                 strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
@@ -153,7 +175,26 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
                     n++;
                     pt = strtok(NULL, separators);
                 }
-                printf("%s\n",par->chain_delete);
+                par->chain_is_kept = 0;
+                //printf("%s\n",par->chain_delete);
+                status++;
+                break;
+                
+            case M_PAR_KEEP_CHAINS :
+            /*drop the selected chains from the pdb file*/
+                
+                strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
+                //printf("%s and %s",par->custom_ligand,optarg);
+                const char  *separator  = ",:"; /* defining separators for drop chains args*/
+                pt = strtok( par->chain_delete, separator);
+                int nk = 0;
+                while (pt != NULL) {
+                    strncpy(&(par->chain_delete[nk]), pt, 1);
+                    nk++;
+                    pt = strtok(NULL, separator);
+                }
+                //printf("%s\n",par->chain_delete);
+                par->chain_is_kept = 1;
                 status++;
                 break;
 
@@ -168,8 +209,6 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
                 strcpy(par->custom_ligand, optarg);
                 //printf("%s and %s",par->custom_ligand,optarg);
                 pt = strtok( par->custom_ligand, ":");
-                
-                
 
                 while (pt != NULL) {
                     custom_ligand_i++;
@@ -750,6 +789,7 @@ void print_pocket_usage(FILE *f) {
     fprintf(f, "\t-%c --%s (int)\t\t\t: Number of Model to analyze.\t\n", M_PAR_MODEL_FLAG, M_PAR_MODEL_FLAG_LONG);
     fprintf(f, "\t-%c --%s (string)\t\t: File name of a topology file (Amber prmtop).\t\n", M_PAR_TOPOLOGY, M_PAR_LONG_TOPOLOGY);
     fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n", M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
+    fprintf(f, "\t-%c --%s (char)\t\t: Character specifying a chain as a ligand\t\n", M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG);
 
     fprintf(f, "\n\n\033[1mOptional pocket detection parameters\033[0m (default parameters)           \n\
 \t-%c --%s (float)\t\t: Minimum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
@@ -773,6 +813,8 @@ void print_pocket_usage(FILE *f) {
 \t\t\t\t\t\t  calculation of each pocket volume.(%d)\n", M_PAR_MC_ITER, M_PAR_LONG_MC_ITER, M_MC_ITER);
 fprintf(f, "\t-%c --%s (char)\t\t\t: Name of the chains to be deleted before pocket detection,      \n\
 \t\t\t\t\t\t  able to delete up to (%d) chains (ie : -c A,B,E)\n", M_PAR_DROP_CHAINS, M_PAR_DROP_CHAINS_LONG, M_MAX_CHAINS_DELETE);
+fprintf(f, "\t-%c --%s (char)\t\t\t: Name of the chains to be kept before pocket detection,      \n\
+\t\t\t\t\t\t  able to keep up to (%d) chains (ie : -k A,B,C,E)\n", M_PAR_KEEP_CHAINS, M_PAR_KEEP_CHAINS_LONG, M_MAX_CHAINS_DELETE);
     fprintf(f, "\n\033[1mFor more information: http://fpocket.sourceforge.net\033[0m\n");
 
 }

src/rpdb.c

@@ -841,24 +841,24 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         if (model_flag == 0 || model_read == 1)
         {
 
-            if (!strncmp(buf, "ATOM ", 5))
+            if (!strncmp(buf, "ATOM ", 5) && buf[21] != par->chain_as_ligand[0])
             {
 
                 //printf("%s",par->chain_delete ); // deleting the chains we want to delete from pdb file
-                if (chains_to_delete(par->chain_delete, buf[21]))
+                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
                 {
-
                     /* Check if this is the first occurence of this atom*/
                     rpdb_extract_atm_resname(buf, resb);
                     rpdb_extract_atom_coordinates(buf, &x, &y, &z); /*extract and double check coordinates to avoid issues with wrong coordinates*/
                     resnbuf = rpdb_extract_atm_resumber(buf);
-
-                    if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
+                }
+                if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
+                {
+                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
                     {
                         /* Atom entry: check if there is a ligand in there (just in case)... */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
-
                             if (keep_lig)
                             {
                                 natm_lig++;
@@ -874,38 +874,49 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                                 natoms++;
                             }
                         }
+
                         else
                         {
                             natoms++;
                         }
-                        /*handle explicit ligand input here*/
-                        if (par->xlig_resnumber > -1)
+                    }
+                    /*handle explicit ligand input here*/
+                    if (par->xlig_resnumber > -1)
+                    {
+
+                        //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
+                        //fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
+
+                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
                         {
-
-                            //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
-                            //fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
-
-                            if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                            {
-                                pdb->n_xlig_atoms++;
-                                fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
-                            }
+                            pdb->n_xlig_atoms++;
+                            fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
                         }
                     }
+
+                    if (buf[21] == par->chain_as_ligand[0])
+                    {
+                        pdb->n_xlig_atoms++;
+                        //fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
+                    }
                 }
             }
-            else if (!strncmp(buf, "HETATM", 6))
+            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && buf[21] == par->chain_as_ligand[0]))
             {
-                if (chains_to_delete(par->chain_delete, buf[21]))
+                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
                 {
 
                     /*Check again for the first occurence*/
                     rpdb_extract_atom_coordinates(buf, &x, &y, &z); /*extract and double check coordinates to avoid issues with wrong coordinates*/
                     resnbuf = rpdb_extract_atm_resumber(buf);
-                    if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
+                }
+                if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
+                {
+                    /* Hetatom entry: check if there is a ligand in there too... */
+                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
                     {
-                        /* Hetatom entry: check if there is a ligand in there too... */
                         rpdb_extract_atm_resname(buf, resb);
+
                         //printf("%s ",ligan);
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
@@ -921,12 +932,13 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         else
                         {
                             /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                            if (keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && buf[21] == par->chain_as_ligand[0]))
                             {
+                                //printf("%s|%c ",resb,buf[21]);
                                 natoms++;
                                 nhetatm++;
                             }
-                            else
+                            else if (buf[21] != par->chain_as_ligand[0])
                             {
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
                                 {
@@ -939,17 +951,22 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                                 }
                             }
                         }
+                    }
 
-                        /*handle explicit ligand input here*/
+                    /*handle explicit ligand input here*/
 
-                        if (par->xlig_resnumber > -1)
+                    if (par->xlig_resnumber > -1)
+                    {
+                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
                         {
-                            if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                            {
-                                pdb->n_xlig_atoms++;
-                            }
+                            pdb->n_xlig_atoms++;
                         }
                     }
+                    if (buf[21] == par->chain_as_ligand[0])
+                    {
+                        pdb->n_xlig_atoms++;
+                        //fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
+                    }
                 }
             }
 
@@ -1077,34 +1094,46 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         }
         if (model_flag == 0 || model_read == 1)
         {
-            if (strncmp(pdb_line, "ATOM ", 5) == 0)
+
+            if (strncmp(pdb_line, "ATOM ", 5) == 0 && pdb_line[21] != params->chain_as_ligand[0])
             {
 
-                if (chains_to_delete(params->chain_delete, pdb_line[21])) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
                 {
                     //printf("%s\n",params->chain_delete);
 
                     rpdb_extract_atom_coordinates(pdb_line, &tmpx, &tmpy, &tmpz); /*extract and double check coordinates to avoid issues with wrong coordinates*/
+                }
 
-                    //printf("%c ",pdb_line[16]); /* column 16 check for configuration of the residue e.g A,B */
-                    if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
-                    { /*if within first occurence*/
-                        /* Store ATOM entry */
+                //printf("%c ",pdb_line[16]); /* column 16 check for configuration of the residue e.g A,B */
+                if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
+                { /*if within first occurence*/
+                    /* Store ATOM entry */
+                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    {
                         rpdb_extract_atm_resname(pdb_line, resb);
 
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
-
-                        /* Enter this if when arg in command line is -r */
-                        if (pdb->n_xlig_atoms)
+                    }
+                    /* Enter this if when arg in command line is -r */
+                    if (pdb->n_xlig_atoms)
+                    {
+                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
                         {
 
-                            if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                            {
-                                rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-                                i_explicit_ligand_atom++;
-                            }
+                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                            i_explicit_ligand_atom++;
                         }
+                    }
 
+                    /* Enter this if when arg in command line is -a */
+                    if (pdb_line[21] == params->chain_as_ligand[0])
+                    {
+                        rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                        i_explicit_ligand_atom++;
+                    }
+                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    {
                         /* Check if the desired ligand is in such an entry */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
@@ -1162,6 +1191,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 ligfound = 1;
                             }
                         }
+
                         else
                         {
 
@@ -1185,33 +1215,45 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
-            else if (strncmp(pdb_line, "HETATM", 6) == 0)
+            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && pdb_line[21] == params->chain_as_ligand[0]))
             {
-                if (chains_to_delete(params->chain_delete, pdb_line[21])) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
                 {
                     rpdb_extract_atom_coordinates(pdb_line, &tmpx, &tmpy, &tmpz); /*extract and double check coordinates to avoid issues with wrong coordinates*/
-                    if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
-                    { /*first occurence*/
-                        /* Check HETATM entry */
+                }
+                if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
+                { /*first occurence*/
+                    /* Check HETATM entry */
+                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    {
                         rpdb_extract_atm_resname(pdb_line, resb);
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
+                    }
 
-                        if (pdb->n_xlig_atoms)
+                    if (pdb->n_xlig_atoms)
+                    {
+                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
                         {
-                            if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                            {
-                                //if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
+                            //if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
 
-                                rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                            rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
 
-                                i_explicit_ligand_atom++;
-                            }
+                            i_explicit_ligand_atom++;
                         }
-                        //fflush(stdout);
+                    }
+                    if (pdb_line[21] == params->chain_as_ligand[0])
+                    {
+
+                        rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
+                        //printf("%d\n", i_explicit_ligand_atom);
+                        i_explicit_ligand_atom++;
+                    }
+                    //fflush(stdout);
+                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    {
                         /* Check if the desired ligand is in HETATM entry */
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
-
                             atom = atoms + iatoms;
                             rpdb_extract_pdb_atom(pdb_line, atom->type, &(atom->id),
                                                   atom->name, &(atom->pdb_aloc), atom->res_name,
@@ -1234,6 +1276,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                         else if (ligan && strlen(ligan) == 1 && ligan[0] == pdb_line[21])
                         {
+
                             if (keep_lig)
                             {
 
@@ -1262,8 +1305,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         {
 
                             /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                            if (keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && pdb_line[21] == params->chain_as_ligand[0]))
                             {
+
                                 atom = atoms + iatoms;
                                 rpdb_extract_pdb_atom(pdb_line, atom->type, &(atom->id),
                                                       atom->name, &(atom->pdb_aloc), atom->res_name,
@@ -1283,12 +1327,14 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 ihetatm++;
                                 iatoms++;
                             }
-                            else
+                            else if (pdb_line[21] != params->chain_as_ligand[0])
                             {
+
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
                                 {
                                     if (ST_keep_hetatm[i][0] == resb[0] && ST_keep_hetatm[i][1] == resb[1] && ST_keep_hetatm[i][2] == resb[2])
                                     {
+
                                         atom = atoms + iatoms;
                                         rpdb_extract_pdb_atom(pdb_line, atom->type, &(atom->id),
                                                               atom->name, &(atom->pdb_aloc), atom->res_name,
@@ -1452,18 +1498,37 @@ void free_pdb_atoms(s_pdb *pdb)
         int
 
  */
-int chains_to_delete(char *chains_selected, char *current_line_chain)
+int chains_to_delete(char *chains_selected, char *current_line_chain, int is_chain_kept)
 { /*deletes the chains selected by command -c, returns true if the chain correspond false if not*/
-    int is_deleted = 1;
-    int i = 0;
-    for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+    
+    if (is_chain_kept == 0)
     {
-        if (chains_selected[i] == current_line_chain)
+        int is_deleted = 1;
+        int i = 0;
+        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
         {
-            //printf("%c_%c ", chains_selected[i],current_line_chain);
-            is_deleted = 0;
+            if (chains_selected[i] == current_line_chain)
+            {
+                //printf("%c_%c ", chains_selected[i],current_line_chain);
+                is_deleted = 0;
+            }
         }
+        //printf("\n");
+        return is_deleted;
+    }
+    else
+    {      
+            int is_deleted = 0;
+            int i = 0;
+            for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+            {
+                if (chains_selected[i] == current_line_chain)
+                {
+                    //printf("%c_%c ", chains_selected[i],current_line_chain);
+                    is_deleted = 1;
+                }
+            }
+            //printf("\n");
+            return is_deleted;
     }
-    //printf("\n");
-    return is_deleted;
 }

src/voronoi.c

@@ -93,10 +93,12 @@ s_lst_vvertice* load_vvertices_DEPRECATED(s_pdb *pdb, int min_apol_neigh, float
     FILE *fvoro = fopen(tmpn1, "w+");
     FILE *ftmp = fopen(tmpn2, "w");
 
+    
     if (fvoro != NULL) {
         lvvert = (s_lst_vvertice *) my_malloc(sizeof (s_lst_vvertice));
         lvvert->h_tr = NULL;
         /* Loop a first time to get out how many heavy atoms are in the file */
+        
         for (i = 0; i < pdb->natoms; i++) {
             ca = (pdb->latoms) + i;
             if (strcmp(ca->symbol, "H") != 0) {
@@ -181,7 +183,6 @@ s_lst_vvertice* load_vvertices(s_pdb *pdb, int min_apol_neigh, float asph_min_si
 
     pid_t pid = getpid();
 
-
     sprintf(tmpn1, "/tmp/qvoro_in_fpocket_%d.dat", pid);
     sprintf(tmpn2, "/tmp/qvoro_out_fpocket_%d.dat", pid);
 //    fprintf(stdout, tmpn1);
@@ -601,7 +602,9 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
                     else v->type = M_POLAR_AS;
 
                     v->qhullId = i; /* Set index in the qhull file */
-                    if(pdb->n_xlig_atoms>0) v->resid=1;
+                    if(pdb->n_xlig_atoms>0) {
+                        v->resid=1;
+                    }
                     
                     else v->resid = -1; /* Initialize internal index */
 
@@ -1080,9 +1083,12 @@ float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
                     printf("here %d\n",dist(xlig_x,xlig_y,xlig_z, x,y,z));*/
                     if(dist(xlig_x, xlig_y, xlig_z, x,y,z)<=(distVatom1)){
                         /*TODO, debug why not working here*/
+                        //printf("xl:%.2f|yl:%.2f|zl:%.2f\t x:%.2f|y:%.2f|z:%.2f\n", xlig_x, xlig_y, xlig_z,x,y,z);
+                        //printf("here %f\t %f\n",dist(xlig_x,xlig_y,xlig_z, x,y,z),distVatom1);
                         /*TODO: add manual clustering for explicit pockets*/
                         return distVatom1;
                     };
+                    
                 }
                 return(-1.0);
             }

tests/reference_output/2P0R_mod_out/2P0R_mod.pml

@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 2P0R_mod_out.pdb
+#select pockets, resn STP
+stored.list=[]
+cmd.iterate("(resn STP)","stored.list.append(resi)")	#read info about residues STP
+#print stored.list
+lastSTP=stored.list[-1]	#get the index of the last residu
+hide lines, resn STP
+
+#show spheres, resn STP
+for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
+for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.3","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))

tests/reference_output/2P0R_mod_out/2P0R_mod.tcl

@@ -0,0 +1,24 @@
+proc highlighting { colorId representation id selection } {
+   puts "highlighting $id"
+   mol representation $representation
+   mol material "Diffuse" 
+    mol color $colorId
+   mol selection $selection
+   mol addrep $id
+}
+
+set id [mol new 2P0R_mod_out.pdb type pdb]
+mol delrep top $id
+highlighting Name "Lines" $id "protein"
+highlighting Name "Licorice" $id "not protein and not resname STP"
+highlighting Element "NewCartoon" $id "protein"
+highlighting "ColorID 7" "VdW 0.4" $id "protein and occupancy>0.95"
+set id [mol new 2P0R_mod_pockets.pqr type pqr]
+                        mol selection "all" 
+                         mol material "Glass3" 
+                         mol delrep top $id 
+                         mol representation "QuickSurf 0.3" 
+                         mol color ResId $id 
+                         mol addrep $id 
+highlighting Index "Points 1" $id "resname STP"
+display rendermode GLSL

tests/reference_output/2P0R_mod_out/2P0R_mod_PYMOL.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 2P0R_mod.pml

tests/reference_output/2P0R_mod_out/2P0R_mod_VMD.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 2P0R_mod_out.pdb -e 2P0R_mod.tcl

tests/reference_output/2P0R_mod_out/2P0R_mod_info.txt

@@ -0,0 +1,21 @@
+Pocket 1 :
+	Score : 	0.156
+	Druggability Score : 	0.421
+	Number of Alpha Spheres : 	100
+	Total SASA : 	195.984
+	Polar SASA : 	87.297
+	Apolar SASA : 	108.687
+	Volume : 	1933.883
+	Mean local hydrophobic density : 	19.643
+	Mean alpha sphere radius :	4.224
+	Mean alp. sph. solvent access : 	0.508
+	Apolar alpha sphere proportion : 	0.280
+	Hydrophobicity score:	12.962
+	Volume score: 	 3.462
+	Polarity score:	 15
+	Charge score :	 -2
+	Proportion of polar atoms: 	46.970
+	Alpha sphere density : 	7.636
+	Cent. of mass - Alpha Sphere max dist: 	20.089
+	Flexibility : 	0.000
+

tests/reference_output/2P0R_mod_out/2P0R_mod_pockets.pqr

@@ -0,0 +1,105 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It contains all the pocket vertices found by fpocket.                    
+ATOM      1    O STP     1      -7.927  25.710  29.491    0.00     5.17
+ATOM      2    O STP     1      -0.944  21.557  24.346    0.00     3.44
+ATOM      3    C STP     1      -0.390  21.119  25.163    0.00     3.64
+ATOM      4    C STP     1      -0.497  19.750  26.137    0.00     3.65
+ATOM      5    O STP     1      -1.505  21.560  24.468    0.00     3.47
+ATOM      6    O STP     1      -7.006  23.099  31.939    0.00     4.34
+ATOM      7    C STP     1      -2.421  19.598  26.681    0.00     4.15
+ATOM      8    O STP     1      -1.904  20.950  25.868    0.00     3.94
+ATOM      9    O STP     1      -1.138  19.994  26.698    0.00     4.16
+ATOM     10    O STP     1      -0.610  21.340  26.848    0.00     3.56
+ATOM     11    O STP     1      -1.105  20.703  26.217    0.00     4.05
+ATOM     12    C STP     1      -2.450  19.593  26.684    0.00     4.15
+ATOM     13    C STP     1      -0.703  20.660  31.637    0.00     3.51
+ATOM     14    O STP     1      -0.812  20.704  31.050    0.00     3.49
+ATOM     15    C STP     1      -0.219  20.522  28.381    0.00     3.59
+ATOM     16    O STP     1      -0.246  20.464  28.365    0.00     3.61
+ATOM     17    O STP     1       2.253  18.734  33.805    0.00     3.49
+ATOM     18    O STP     1       2.716  18.560  34.058    0.00     3.45
+ATOM     19    O STP     1      -2.017  21.009  25.831    0.00     3.92
+ATOM     20    C STP     1      -7.684  25.074  29.391    0.00     4.87
+ATOM     21    C STP     1      -5.738  21.726  22.846    0.00     4.15
+ATOM     22    O STP     1      -4.802  20.822  26.086    0.00     4.22
+ATOM     23    O STP     1      -3.784  20.874  25.890    0.00     3.98
+ATOM     24    O STP     1      -2.002  21.755  24.422    0.00     3.47
+ATOM     25    O STP     1      -3.770  21.486  26.150    0.00     3.48
+ATOM     26    O STP     1      -3.053  21.034  25.802    0.00     3.86
+ATOM     27    O STP     1      -2.286  21.303  25.452    0.00     3.76
+ATOM     28    C STP     1      -2.467  19.582  26.696    0.00     4.15
+ATOM     29    C STP     1      -3.065  18.013  27.593    0.00     4.08
+ATOM     30    O STP     1      -4.069  15.575  26.940    0.00     3.56
+ATOM     31    O STP     1      -3.587  13.987  38.073    0.00     4.16
+ATOM     32    O STP     1      -3.704  14.174  38.166    0.00     4.28
+ATOM     33    O STP     1      -5.656  15.984  36.278    0.00     4.39
+ATOM     34    O STP     1      -5.504  16.518  38.204    0.00     5.63
+ATOM     35    C STP     1      -6.227  18.398  36.193    0.00     6.02
+ATOM     36    O STP     1      -3.847  18.514  36.288    0.00     4.85
+ATOM     37    O STP     1      -5.712  16.109  39.065    0.00     5.80
+ATOM     38    O STP     1      -3.819  14.133  38.275    0.00     4.27
+ATOM     39    O STP     1      -4.642  15.555  38.606    0.00     5.18
+ATOM     40    O STP     1      -4.979  16.043  38.743    0.00     5.59
+ATOM     41    O STP     1      -4.914  16.042  38.749    0.00     5.56
+ATOM     42    O STP     1      -4.641  18.226  28.432    0.00     5.06
+ATOM     43    C STP     1      -3.129  18.059  27.644    0.00     4.13
+ATOM     44    O STP     1      -2.825  18.832  27.555    0.00     4.37
+ATOM     45    C STP     1      -3.030  18.141  27.600    0.00     4.12
+ATOM     46    O STP     1      -1.764  19.741  31.334    0.00     3.95
+ATOM     47    O STP     1      -1.278  19.903  31.356    0.00     3.93
+ATOM     48    O STP     1      -1.286  19.922  31.268    0.00     3.93
+ATOM     49    O STP     1      -0.653  19.833  28.635    0.00     3.77
+ATOM     50    O STP     1      -1.291  18.558  33.444    0.00     4.21
+ATOM     51    O STP     1       0.141  18.540  33.212    0.00     3.88
+ATOM     52    O STP     1      -0.337  17.740  33.506    0.00     3.75
+ATOM     53    O STP     1      -0.856  18.760  27.475    0.00     3.57
+ATOM     54    O STP     1      -2.728  14.181  37.978    0.00     3.82
+ATOM     55    O STP     1      -0.221  17.529  33.664    0.00     3.59
+ATOM     56    C STP     1      -3.437  18.918  36.407    0.00     4.47
+ATOM     57    O STP     1      -2.278  19.673  36.184    0.00     3.62
+ATOM     58    C STP     1      -4.398  20.219  36.733    0.00     4.08
+ATOM     59    O STP     1      -1.215  19.866  26.768    0.00     4.18
+ATOM     60    C STP     1      -2.296  19.575  26.726    0.00     4.15
+ATOM     61    C STP     1      -0.463  19.697  26.108    0.00     3.61
+ATOM     62    O STP     1      -0.646  18.417  26.693    0.00     3.44
+ATOM     63    O STP     1      -1.504  19.313  27.220    0.00     4.28
+ATOM     64    O STP     1      -1.799  19.199  27.242    0.00     4.28
+ATOM     65    O STP     1      -1.195  18.862  27.071    0.00     3.93
+ATOM     66    C STP     1      -1.255  18.277  26.909    0.00     3.58
+ATOM     67    O STP     1      -1.374  19.085  27.170    0.00     4.12
+ATOM     68    C STP     1      -1.665  18.991  27.195    0.00     4.13
+ATOM     69    C STP     1       0.538  20.926  24.251    0.00     3.40
+ATOM     70    O STP     1      -4.253  16.196  38.650    0.00     5.21
+ATOM     71    C STP     1      -0.660  17.674  41.151    0.00     3.82
+ATOM     72    O STP     1      -0.665  17.381  41.718    0.00     4.21
+ATOM     73    O STP     1      -2.320  14.385  37.937    0.00     3.72
+ATOM     74    O STP     1      -3.527  17.299  37.574    0.00     4.60
+ATOM     75    O STP     1       1.896  18.908  33.762    0.00     3.44
+ATOM     76    C STP     1      -0.502  20.722  31.885    0.00     3.42
+ATOM     77    O STP     1      -0.828  18.820  33.297    0.00     4.14
+ATOM     78    O STP     1      -0.715  19.279  32.645    0.00     3.96
+ATOM     79    O STP     1      -0.068  18.700  33.204    0.00     3.95
+ATOM     80    O STP     1       2.761  18.546  34.093    0.00     3.44
+ATOM     81    O STP     1       2.783  18.567  34.049    0.00     3.45
+ATOM     82    C STP     1      -4.983  18.148  28.557    0.00     5.25
+ATOM     83    C STP     1      -6.697  18.281  32.723    0.00     6.16
+ATOM     84    O STP     1      -6.877  15.226  26.592    0.00     3.64
+ATOM     85    O STP     1      -5.571  16.002  26.870    0.00     3.92
+ATOM     86    O STP     1      -4.952  18.143  28.746    0.00     5.22
+ATOM     87    C STP     1      -4.516  15.952  27.324    0.00     3.90
+ATOM     88    C STP     1      -6.455  17.186  32.808    0.00     5.30
+ATOM     89    C STP     1      -6.466  17.333  32.806    0.00     5.42
+ATOM     90    O STP     1      -5.335  18.346  31.496    0.00     5.69
+ATOM     91    O STP     1      -5.324  18.315  31.552    0.00     5.68
+ATOM     92    O STP     1      -3.887  15.796  31.076    0.00     3.86
+ATOM     93    C STP     1      -3.831  15.614  31.082    0.00     3.77
+ATOM     94    O STP     1      -5.263  16.341  42.194    0.00     5.12
+ATOM     95    O STP     1      -4.438  16.373  40.937    0.00     4.86
+ATOM     96    O STP     1      -4.111  16.415  42.058    0.00     4.74
+ATOM     97    O STP     1      -6.809  16.200  40.052    0.00     6.13
+ATOM     98    O STP     1      -6.390  16.221  39.684    0.00     6.00
+ATOM     99    O STP     1       2.836  18.727  33.815    0.00     3.49
+ATOM    100    O STP     1       2.888  18.613  33.980    0.00     3.47
+TER
+END

tests/reference_output/2P0R_mod_out/pockets/pocket1_atm.pdb

@@ -0,0 +1,88 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.1562
+HEADER 1  - Drug Score                        : 0.4209
+HEADER 2  - Number of alpha spheres           :   100
+HEADER 3  - Mean alpha-sphere radius          : 4.2242
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5076
+HEADER 5  - Mean B-factor of pocket residues  : 0.0000
+HEADER 6  - Hydrophobicity Score              : 12.9615
+HEADER 7  - Polarity Score                    :    15
+HEADER 8  - Amino Acid based volume Score     : 3.4615
+HEADER 9  - Pocket volume (Monte Carlo)       : 1933.8832
+HEADER 10  -Pocket volume (convex hull)       : 700.1219
+HEADER 11 - Charge Score                      :    -2
+HEADER 12 - Local hydrophobic density Score   : 19.6429
+HEADER 13 - Number of apolar alpha sphere     :    28
+HEADER 14 - Proportion of apolar alpha sphere : 0.2800
+ATOM   1378   CA GLY A 190      -3.069  24.572  30.848  0.00  0.00           C 0
+ATOM   1385   CB SER A 191      -3.958  24.958  26.264  0.00  0.00           C 0
+ATOM   1407  OE1 GLU A 194      -3.709  28.683  29.816  0.00  0.00           O 0
+ATOM   1381    N SER A 191      -2.905  25.010  28.479  0.00  0.00           N 0
+ATOM   1387    N ALA A 192      -0.717  24.707  25.707  0.00  0.00           N 0
+ATOM   1708  CD1 PHE A 233      -1.372  18.506  22.820  0.00  0.00           C 0
+ATOM   2514  OE2 GLU A 332      -1.745  20.996  21.050  0.94  2.14           O 0
+ATOM   1391   CB ALA A 192       1.169  24.266  24.193  0.00  0.00           C 0
+ATOM   1875   CB ALA A 255       2.918  20.919  26.678  0.00  0.00           C 0
+ATOM   1871    N ALA A 255       2.705  18.589  27.448  0.00  0.00           N 0
+ATOM   1872   CA ALA A 255       3.134  19.444  26.343  0.00  0.00           C 0
+ATOM   1710  CE1 PHE A 233      -2.716  18.891  22.605  0.00  0.00           C 0
+ATOM   1375    C GLY A 189      -2.873  23.712  33.124  0.00  0.00           C 0
+ATOM   1377    N GLY A 190      -2.688  23.547  31.816  0.00  0.00           N 0
+ATOM   1376    O GLY A 189      -3.355  24.744  33.620  0.59  1.07           O 0
+ATOM   1380    O GLY A 190      -2.803  22.883  29.185  0.00  0.00           O 0
+ATOM   1709  CD2 PHE A 233      -2.136  16.521  23.915  0.00  0.00           C 0
+ATOM    629   CB TRP A  98       1.005  23.879  28.745  0.00  0.00           C 0
+ATOM   1712   CZ PHE A 233      -3.744  18.091  23.041  0.00  0.00           C 0
+ATOM    624   SG CYS A  97       2.577  20.007  30.576  0.00  0.00           S 0
+ATOM   1374   CA GLY A 189      -2.458  22.559  34.008  0.00  0.00           C 0
+ATOM    631  CD1 TRP A  98       0.531  23.921  31.248  0.00  0.00           C 0
+ATOM    608   CA GLY A  95       2.503  21.248  36.208  0.00  0.00           C 0
+ATOM   2906  NE2 GLN B  62       0.939  18.225  36.994  0.00  0.00           N 0
+ATOM   1786  OE2 GLU A 243       2.492  15.584  32.332  0.00  0.00           O 0
+ATOM   1784   CD GLU A 243       2.694  15.158  33.499  0.00  0.00           C 0
+ATOM   1382   CA SER A 191      -2.701  24.663  27.080  0.00  0.00           C 0
+ATOM   1379    C GLY A 190      -2.921  24.081  29.426  0.00  0.00           C 0
+ATOM   1386   OG SER A 191      -3.724  24.727  24.886  0.57  6.43           O 0
+ATOM   1399  CD1 ILE A 193      -4.273  25.106  20.935  0.00  0.00           C 0
+ATOM   1711  CE2 PHE A 233      -3.457  16.897  23.692  0.00  0.00           C 0
+ATOM   1859    C GLY A 253      -0.072  15.654  29.040  0.00  0.00           C 0
+ATOM   1858   CA GLY A 253      -1.116  14.599  28.671  0.00  0.00           C 0
+ATOM   1716    O ILE A 234      -1.778  13.371  25.339  0.00  0.00           O 0
+ATOM   1729    N THR A 236      -4.945  12.140  26.625  0.51  2.19           N 0
+ATOM   2873    C GLU B  59      -0.834  12.124  40.583  0.00  0.00           C 0
+ATOM   1777   OG SER A 242      -2.074  14.501  34.227  0.55  6.43           O 0
+ATOM   1776   CB SER A 242      -2.940  13.400  34.001  0.00  0.00           C 0
+ATOM   1756    O ALA A 239      -5.685  11.711  35.287  0.52  7.50           O 0
+ATOM   2874    O GLU B  59      -0.742  13.219  41.098  0.45  8.57           O 0
+ATOM   1757   CB ALA A 239      -8.655  12.980  35.171  0.00  0.00           C 0
+ATOM   1371   CE LYS A 188      -2.628  20.847  40.357  0.00  0.00           C 0
+ATOM   2871    N GLU B  59      -2.827  11.860  41.757  0.00  0.00           N 0
+ATOM   1860    O GLY A 253      -0.215  16.355  30.028  0.00  0.00           O 0
+ATOM   1861    N HIS A 254       0.956  15.779  28.210  0.00  0.00           N 0
+ATOM   2880    N ARG B  60      -0.178  11.767  39.486  0.41  4.37           N 0
+ATOM   1783   CG GLU A 243       1.575  14.473  34.258  0.00  0.00           C 0
+ATOM   1369   CG LYS A 188      -1.361  22.226  38.580  0.00  0.00           C 0
+ATOM   1373    N GLY A 189      -1.500  23.000  34.991  0.00  0.00           N 0
+ATOM   1367    O LYS A 188      -3.008  24.033  36.303  0.50  3.21           O 0
+ATOM   1707   CG PHE A 233      -1.075  17.309  23.466  0.00  0.00           C 0
+ATOM   1706   CB PHE A 233       0.351  16.918  23.763  0.00  0.00           C 0
+ATOM   2513  OE1 GLU A 332       0.238  22.000  21.040  0.69  2.14           O 0
+ATOM   2905  OE1 GLN B  62       0.920  16.211  37.999  0.65  3.21           O 0
+ATOM   2903   CG GLN B  62       2.406  17.910  38.889  0.00  0.00           C 0
+ATOM   2904   CD GLN B  62       1.349  17.373  37.919  0.00  0.00           C 0
+ATOM    610    O GLY A  95       1.251  22.223  34.411  0.00  0.00           O 0
+ATOM   1785  OE1 GLU A 243       3.783  15.261  34.092  0.00  0.00           O 0
+ATOM   1735  CG2 THR A 236      -6.115  13.099  29.447  0.00  0.00           C 0
+ATOM   1727  OD1 ASP A 235      -5.761  14.755  23.158  0.70  4.29           O 0
+ATOM   1732    O THR A 236      -7.509  11.799  27.646  0.44  5.36           O 0
+ATOM   1754   CA ALA A 239      -7.769  12.233  34.170  0.00  0.00           C 0
+ATOM   2868    O SER B  58      -2.600  12.325  43.922  0.61  4.29           O 0
+ATOM   1372   NZ LYS A 188      -3.438  21.085  41.590  0.00  0.00           N 0
+ATOM   2869   CB SER B  58      -5.491  11.456  43.707  0.00  0.00           C 0
+ATOM    585  NE2 GLN A  91       5.950  20.196  34.395  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_mod_out/pockets/pocket1_vert.pqr

@@ -0,0 +1,122 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.1562
+HEADER 1  - Drug Score                        : 0.4209
+HEADER 2  - Number of V. Vertices             :   100
+HEADER 3  - Mean alpha-sphere radius          : 4.2242
+HEADER 4  - Mean alpha-sphere SA              : 0.5076
+HEADER 5  - Mean B-factor                     : 0.0000
+HEADER 6  - Hydrophobicity Score              : 12.9615
+HEADER 7  - Polarity Score                    :    15
+HEADER 8  - Volume Score                      : 3.4615
+HEADER 9  - Real volume (approximation)       : 1933.8832
+HEADER 10 - Charge Score                      :    -2
+HEADER 11 - Local hydrophobic density Score   : 19.6429
+HEADER 12 - Number of apolar alpha sphere     :    28
+HEADER 13 - Proportion of apolar alpha sphere : 0.2800
+ATOM      1    O STP     1      -7.927  25.710  29.491    0.00     5.17
+ATOM      2    O STP     1      -0.944  21.557  24.346    0.00     3.44
+ATOM      3    C STP     1      -0.390  21.119  25.163    0.00     3.64
+ATOM      4    C STP     1      -0.497  19.750  26.137    0.00     3.65
+ATOM      5    O STP     1      -1.505  21.560  24.468    0.00     3.47
+ATOM      6    O STP     1      -7.006  23.099  31.939    0.00     4.34
+ATOM      7    C STP     1      -2.421  19.598  26.681    0.00     4.15
+ATOM      8    O STP     1      -1.904  20.950  25.868    0.00     3.94
+ATOM      9    O STP     1      -1.138  19.994  26.698    0.00     4.16
+ATOM     10    O STP     1      -0.610  21.340  26.848    0.00     3.56
+ATOM     11    O STP     1      -1.105  20.703  26.217    0.00     4.05
+ATOM     12    C STP     1      -2.450  19.593  26.684    0.00     4.15
+ATOM     13    C STP     1      -0.703  20.660  31.637    0.00     3.51
+ATOM     14    O STP     1      -0.812  20.704  31.050    0.00     3.49
+ATOM     15    C STP     1      -0.219  20.522  28.381    0.00     3.59
+ATOM     16    O STP     1      -0.246  20.464  28.365    0.00     3.61
+ATOM     17    O STP     1       2.253  18.734  33.805    0.00     3.49
+ATOM     18    O STP     1       2.716  18.560  34.058    0.00     3.45
+ATOM     19    O STP     1      -2.017  21.009  25.831    0.00     3.92
+ATOM     20    C STP     1      -7.684  25.074  29.391    0.00     4.87
+ATOM     21    C STP     1      -5.738  21.726  22.846    0.00     4.15
+ATOM     22    O STP     1      -4.802  20.822  26.086    0.00     4.22
+ATOM     23    O STP     1      -3.784  20.874  25.890    0.00     3.98
+ATOM     24    O STP     1      -2.002  21.755  24.422    0.00     3.47
+ATOM     25    O STP     1      -3.770  21.486  26.150    0.00     3.48
+ATOM     26    O STP     1      -3.053  21.034  25.802    0.00     3.86
+ATOM     27    O STP     1      -2.286  21.303  25.452    0.00     3.76
+ATOM     28    C STP     1      -2.467  19.582  26.696    0.00     4.15
+ATOM     29    C STP     1      -3.065  18.013  27.593    0.00     4.08
+ATOM     30    O STP     1      -4.069  15.575  26.940    0.00     3.56
+ATOM     31    O STP     1      -3.587  13.987  38.073    0.00     4.16
+ATOM     32    O STP     1      -3.704  14.174  38.166    0.00     4.28
+ATOM     33    O STP     1      -5.656  15.984  36.278    0.00     4.39
+ATOM     34    O STP     1      -5.504  16.518  38.204    0.00     5.63
+ATOM     35    C STP     1      -6.227  18.398  36.193    0.00     6.02
+ATOM     36    O STP     1      -3.847  18.514  36.288    0.00     4.85
+ATOM     37    O STP     1      -5.712  16.109  39.065    0.00     5.80
+ATOM     38    O STP     1      -3.819  14.133  38.275    0.00     4.27
+ATOM     39    O STP     1      -4.642  15.555  38.606    0.00     5.18
+ATOM     40    O STP     1      -4.979  16.043  38.743    0.00     5.59
+ATOM     41    O STP     1      -4.914  16.042  38.749    0.00     5.56
+ATOM     42    O STP     1      -4.641  18.226  28.432    0.00     5.06
+ATOM     43    C STP     1      -3.129  18.059  27.644    0.00     4.13
+ATOM     44    O STP     1      -2.825  18.832  27.555    0.00     4.37
+ATOM     45    C STP     1      -3.030  18.141  27.600    0.00     4.12
+ATOM     46    O STP     1      -1.764  19.741  31.334    0.00     3.95
+ATOM     47    O STP     1      -1.278  19.903  31.356    0.00     3.93
+ATOM     48    O STP     1      -1.286  19.922  31.268    0.00     3.93
+ATOM     49    O STP     1      -0.653  19.833  28.635    0.00     3.77
+ATOM     50    O STP     1      -1.291  18.558  33.444    0.00     4.21
+ATOM     51    O STP     1       0.141  18.540  33.212    0.00     3.88
+ATOM     52    O STP     1      -0.337  17.740  33.506    0.00     3.75
+ATOM     53    O STP     1      -0.856  18.760  27.475    0.00     3.57
+ATOM     54    O STP     1      -2.728  14.181  37.978    0.00     3.82
+ATOM     55    O STP     1      -0.221  17.529  33.664    0.00     3.59
+ATOM     56    C STP     1      -3.437  18.918  36.407    0.00     4.47
+ATOM     57    O STP     1      -2.278  19.673  36.184    0.00     3.62
+ATOM     58    C STP     1      -4.398  20.219  36.733    0.00     4.08
+ATOM     59    O STP     1      -1.215  19.866  26.768    0.00     4.18
+ATOM     60    C STP     1      -2.296  19.575  26.726    0.00     4.15
+ATOM     61    C STP     1      -0.463  19.697  26.108    0.00     3.61
+ATOM     62    O STP     1      -0.646  18.417  26.693    0.00     3.44
+ATOM     63    O STP     1      -1.504  19.313  27.220    0.00     4.28
+ATOM     64    O STP     1      -1.799  19.199  27.242    0.00     4.28
+ATOM     65    O STP     1      -1.195  18.862  27.071    0.00     3.93
+ATOM     66    C STP     1      -1.255  18.277  26.909    0.00     3.58
+ATOM     67    O STP     1      -1.374  19.085  27.170    0.00     4.12
+ATOM     68    C STP     1      -1.665  18.991  27.195    0.00     4.13
+ATOM     69    C STP     1       0.538  20.926  24.251    0.00     3.40
+ATOM     70    O STP     1      -4.253  16.196  38.650    0.00     5.21
+ATOM     71    C STP     1      -0.660  17.674  41.151    0.00     3.82
+ATOM     72    O STP     1      -0.665  17.381  41.718    0.00     4.21
+ATOM     73    O STP     1      -2.320  14.385  37.937    0.00     3.72
+ATOM     74    O STP     1      -3.527  17.299  37.574    0.00     4.60
+ATOM     75    O STP     1       1.896  18.908  33.762    0.00     3.44
+ATOM     76    C STP     1      -0.502  20.722  31.885    0.00     3.42
+ATOM     77    O STP     1      -0.828  18.820  33.297    0.00     4.14
+ATOM     78    O STP     1      -0.715  19.279  32.645    0.00     3.96
+ATOM     79    O STP     1      -0.068  18.700  33.204    0.00     3.95
+ATOM     80    O STP     1       2.761  18.546  34.093    0.00     3.44
+ATOM     81    O STP     1       2.783  18.567  34.049    0.00     3.45
+ATOM     82    C STP     1      -4.983  18.148  28.557    0.00     5.25
+ATOM     83    C STP     1      -6.697  18.281  32.723    0.00     6.16
+ATOM     84    O STP     1      -6.877  15.226  26.592    0.00     3.64
+ATOM     85    O STP     1      -5.571  16.002  26.870    0.00     3.92
+ATOM     86    O STP     1      -4.952  18.143  28.746    0.00     5.22
+ATOM     87    C STP     1      -4.516  15.952  27.324    0.00     3.90
+ATOM     88    C STP     1      -6.455  17.186  32.808    0.00     5.30
+ATOM     89    C STP     1      -6.466  17.333  32.806    0.00     5.42
+ATOM     90    O STP     1      -5.335  18.346  31.496    0.00     5.69
+ATOM     91    O STP     1      -5.324  18.315  31.552    0.00     5.68
+ATOM     92    O STP     1      -3.887  15.796  31.076    0.00     3.86
+ATOM     93    C STP     1      -3.831  15.614  31.082    0.00     3.77
+ATOM     94    O STP     1      -5.263  16.341  42.194    0.00     5.12
+ATOM     95    O STP     1      -4.438  16.373  40.937    0.00     4.86
+ATOM     96    O STP     1      -4.111  16.415  42.058    0.00     4.74
+ATOM     97    O STP     1      -6.809  16.200  40.052    0.00     6.13
+ATOM     98    O STP     1      -6.390  16.221  39.684    0.00     6.00
+ATOM     99    O STP     1       2.836  18.727  33.815    0.00     3.49
+ATOM    100    O STP     1       2.888  18.613  33.980    0.00     3.47
+TER
+END

tests/test_fpocket.py

@@ -109,6 +109,7 @@ def test_drop_chain():
     for pdb_code in pdb_list:
         fpocket_out_test_default_equal(pdb_code,params="-c D")
         fpocket_out_test_default_equal(pdb_code,params="--drop_chains D")
+        fpocket_out_test_default_equal(pdb_code,params="-k A,B,C,E")
 
     
     
@@ -119,5 +120,13 @@ def test_explicit_pocket_detection():
     pdb_list=['1UYD']
     for pdb_code in pdb_list:
         fpocket_out_test_default_equal(pdb_code,params="-r 1224:PU8:A",explicit=True)
+
+def test_chain_as_ligand():
+    """
+    Test fpocket explicit pocket detection of the PU8 binding site.
+    """
+    pdb_list=['2P0R_mod']
+    for pdb_code in pdb_list:
+        fpocket_out_test_default_equal(pdb_code,params="-a D")