fpocket: write_visu.c Source File

00001 #include "../headers/write_visu.h"
00002 
00003 /*
00004 
00005 ## GENERAL INFORMATION
00006 ##
00007 ## FILE                                         write_visu.c
00008 ## AUTHORS                                      P. Schmidtke and V. Le Guilloux
00009 ## LAST MODIFIED                        02-12-08
00010 ##
00011 ## SPECIFICATIONS
00012 ##
00013 ##              Write output script to launch visualization of fpocket output using
00014 ##              pymol and VMD.
00015 ##
00016 ## MODIFICATIONS HISTORY
00017 ##
00018 ##  02-12-08    (v)  Comments UTD
00019 ##  29-11-08    (p)  Enhanced VMD output, corrected bug in pymol output
00020 ##  20-11-08    (p)  Just got rid of a memory issue (fflush after fclose) 
00021 ##      01-04-08        (v)  Added template for comments and creation of history
00022 ##      01-01-08        (vp) Created (random date...)
00023 ##      
00024 ## TODO or SUGGESTIONS
00025 ##
00026 ## (v) Handle system command failure
00027 ##
00028 */
00029 
00030  /*
00031     COPYRIGHT DISCLAIMER
00032 
00033     Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby
00034         disclaim all copyright interest in the program “fpocket” (which
00035         performs protein cavity detection) written by Vincent Le Guilloux and Peter
00036         Schmidtke.
00037 
00038     Vincent Le Guilloux  28 November 2008
00039     Peter Schmidtke      28 November 2008
00040     Pierre Tuffery       28 November 2008
00041 
00042     GNU GPL
00043 
00044     This file is part of the fpocket package.
00045 
00046     fpocket is free software: you can redistribute it and/or modify
00047     it under the terms of the GNU General Public License as published by
00048     the Free Software Foundation, either version 3 of the License, or
00049     (at your option) any later version.
00050 
00051     fpocket is distributed in the hope that it will be useful,
00052     but WITHOUT ANY WARRANTY; without even the implied warranty of
00053     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00054     GNU General Public License for more details.
00055 
00056     You should have received a copy of the GNU General Public License
00057     along with fpocket.  If not, see <http://www.gnu.org/licenses/>.
00058 
00059 **/
00060  
00061 /**
00062    ## FUNCTION: 
00063         write_visualization
00064   
00065    ## SPECIFICATION: 
00066         Write visualization scripts for VMD and PyMol
00067   
00068    ## PARAMETERS:
00069         @ char *pdb_name     : pdb code
00070         @ char *pdb_out_name : name of the pdb output file
00071   
00072    ## RETURN: void
00073   
00074 */
00075 
00076 void write_visualization(char *pdb_name,char *pdb_out_name)
00077 {
00078         write_vmd(pdb_name,pdb_out_name);
00079         write_pymol(pdb_name,pdb_out_name);
00080 }
00081 
00082 /**
00083    ## FUNCTION: 
00084         write_vmd
00085   
00086    ## SPECIFICATION: 
00087         Write visualization script for VMD
00088   
00089    ## PARAMETERS:
00090         @ char *pdb_name : pdb code
00091         @ char *pdb_out_name : name of the pdb output file
00092   
00093    ## RETURN: void
00094   
00095 */
00096 
00097 
00098 void write_vmd(char *pdb_name,char *pdb_out_name)
00099 {
00100         char fout[250] = "" ;
00101         char fout2[250] = "" ;
00102         char sys_cmd[250] ="";
00103         char c_tmp[255];
00104         int status ;
00105         
00106         strcpy(c_tmp,pdb_name);
00107         remove_ext(c_tmp) ;
00108         remove_path(c_tmp) ;
00109         FILE *f,*f_tcl;
00110         sprintf(fout,"%s_VMD.sh",pdb_name);
00111         f = fopen(fout, "w") ;
00112         if(f){
00113                 sprintf(fout2,"%s.tcl",pdb_name);
00114 
00115                 f_tcl=fopen(fout2,"w");
00116                 if(f_tcl){
00117                         /* Write bash script for visualization using VMD */
00118                         fprintf(f,"#!/bin/bash\nvmd %s -e %s.tcl\n",pdb_out_name,c_tmp);
00119                         fflush(f);
00120                         fclose(f);
00121                         
00122                         /* Make tcl script executable, and Write tcl script */
00123                         sprintf(sys_cmd,"chmod +x %s",fout);
00124                         status = system(sys_cmd);
00125 
00126                         
00127                         fprintf(f_tcl,"proc highlighting { colorId representation id selection } {\n");
00128                         fprintf(f_tcl,"   set id [[atomselect $id $selection] molid]\n");
00129                         fprintf(f_tcl,"   puts \"highlighting $id\"\n");
00130                         fprintf(f_tcl,"   mol delrep 0 $id\n");
00131                         fprintf(f_tcl,"   mol representation $representation\n");
00132                         fprintf(f_tcl,"   mol color $colorId\n");
00133                         fprintf(f_tcl,"   mol selection $selection\n");
00134                         fprintf(f_tcl,"   mol addrep $id\n}\n\n");
00135                         fprintf(f_tcl,"set repr \"Points 10\"\n");
00136                         fprintf(f_tcl,"highlighting ResID \"Points 10\" 0 \"resname STP\"\n");
00137                         fprintf(f_tcl,"set id [[atomselect 0 \"protein\"] molid]\n");
00138                         fprintf(f_tcl,"puts \"highlighting $id\"\n");
00139                         fprintf(f_tcl,"mol representation \"Lines\"\n");
00140                         fprintf(f_tcl,"mol material \"Transparent\"\n");
00141                         fprintf(f_tcl,"mol color Element\n");
00142                         fprintf(f_tcl,"mol selection \"protein\"\n");
00143                         fprintf(f_tcl,"mol addrep $id\n");
00144                         fprintf(f_tcl,"set id [[atomselect 0 \"not protein and not resname STP\"] molid]\n");
00145                         fprintf(f_tcl,"puts \"highlighting $id\"\n");
00146                         fprintf(f_tcl,"mol representation \"Bonds\"\n");
00147                         fprintf(f_tcl,"mol color Element\n");
00148                         fprintf(f_tcl,"mol selection \"not protein and not resname STP\"\n");
00149                         fprintf(f_tcl,"mol addrep $id\n\n");
00150                         
00151                         
00152                         fprintf(f_tcl,"mol new \"../%s.pdb\"\n",c_tmp);
00153                         fprintf(f_tcl,"mol selection \"not protein and not water\" \n \
00154                                 mol material \"Opaque\" \n \
00155                                 mol delrep 0 1 \n \
00156                                 mol representation \"Lines 10\" \n \
00157                                 mol addrep 1 \n \
00158                                 highlighting Element \"NewCartoon\" 1 \"protein\"\n \
00159                                 mol representation \"NewCartoon\" \n \
00160                                 mol addrep $id \n \
00161                                 mol new \"%s_pockets.pqr\"\n \
00162                                 mol selection \"all\" \n \
00163                                 mol material \"Glass1\" \n \
00164                                 mol delrep 0 2 \n \
00165                                 mol representation \"VDW\" \n \
00166                                 mol color ResID 2 \n \
00167                                 mol addrep 2 \n",c_tmp);
00168                         fclose(f_tcl);
00169 
00170                 }
00171                 else {
00172                         fprintf(stderr, "! The file %s could not be opened!\n", fout2);
00173                 }
00174                 
00175         }
00176         else{
00177                 fprintf(stderr, "! The file %s could not be opened!\n", fout);
00178         }
00179 
00180 }
00181 
00182 /**
00183    ## FUNCTION: 
00184         write_pymol
00185   
00186    ## SPECIFICATION: 
00187         write visualization script for PyMol
00188   
00189    ## PARAMETERS:
00190         @ char *pdb_name     : pdb code
00191         @ char *pdb_out_name : name of the pdb output file
00192   
00193    ## RETURN: void
00194   
00195 */
00196 void write_pymol(char *pdb_name,char *pdb_out_name)
00197 {
00198         char fout[250] = "" ;
00199         char fout2[250] = "" ;
00200         char sys_cmd[250] ="";
00201         FILE *f,*f_pml;
00202         char c_tmp[255];
00203         int status ;
00204         
00205         strcpy(c_tmp,pdb_name);
00206         remove_ext(c_tmp) ;
00207         remove_path(c_tmp) ;
00208         sprintf(fout,"%s_PYMOL.sh",pdb_name);
00209         f = fopen(fout, "w") ;
00210         if(f){
00211                 sprintf(fout2,"%s.pml",pdb_name);
00212                 f_pml=fopen(fout2,"w");
00213                 if(f_pml){
00214                         /* Write bash script for visualization using VMD */
00215                         fprintf(f,"#!/bin/bash\npymol %s.pml\n",c_tmp);
00216                         fflush(f);
00217                         fclose(f);
00218                         
00219                         sprintf(sys_cmd,"chmod +x %s",fout);
00220                         status = system(sys_cmd);
00221                         /* Write pml script */
00222                         fprintf(f_pml,"from pymol import cmd,stored\n");
00223                         fprintf(f_pml,"load %s\n",pdb_out_name);
00224                         fprintf(f_pml,"#select pockets, resn STP\n");
00225                         fprintf(f_pml,"stored.list=[]\n");
00226                         fprintf(f_pml,"cmd.iterate(\"(resn STP)\",\"stored.list.append(resi)\") #read info about residues STP\n");
00227                         fprintf(f_pml,"#print stored.list\n");
00228                         fprintf(f_pml,"lastSTP=stored.list[-1]  #get the index of the last residu\n");
00229                         fprintf(f_pml,"hide lines, resn STP\n\n");
00230                         fprintf(f_pml,"#show spheres, resn STP\n");
00231                         fprintf(f_pml,"for my_index in range(1,int(lastSTP)+1): cmd.select(\"pocket\"+str(my_index), \"resn STP and resi \"+str(my_index))\n");
00232                         fprintf(f_pml,"for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,\"pocket\"+str(my_index))\n");
00233                         fprintf(f_pml,"for my_index in range(1,int(lastSTP)+1): cmd.show(\"spheres\",\"pocket\"+str(my_index))\n");
00234                         fprintf(f_pml,"for my_index in range(1,int(lastSTP)+1): cmd.set(\"sphere_scale\",\"0.3\",\"pocket\"+str(my_index))\n");
00235                         fprintf(f_pml,"for my_index in range(1,int(lastSTP)+1): cmd.set(\"sphere_transparency\",\"0.1\",\"pocket\"+str(my_index))\n");
00236                         
00237                         fclose(f_pml);
00238                 }
00239                 else {
00240                         fprintf(stderr, "! The file %s could not be opened!\n", fout2);
00241                 }
00242         }
00243         else{
00244                 fprintf(stderr, "! The file %s could not be opened!\n", fout);
00245         }
00246 }