#include <stdio.h>#include <stdlib.h>#include <unistd.h>#include <string.h>#include "utils.h"Go to the source code of this file.
Functions | |
| void | write_visualization (char *pdb_name, char *pdb_out_name) |
| void | write_vmd (char *pdb_name, char *pdb_out_name) |
| void | write_pymol (char *pdb_name, char *pdb_out_name) |
| void write_pymol | ( | char * | pdb_name, | |
| char * | pdb_out_name | |||
| ) |
## FUNCTION: write_pymol
## SPECIFICATION: write visualization script for PyMol
## PARAMETERS: @ char *pdb_name : pdb code @ char *pdb_out_name : name of the pdb output file
## RETURN: void
Definition at line 196 of file write_visu.c.
References remove_ext(), and remove_path().
Referenced by write_visualization().
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 }
| void write_visualization | ( | char * | pdb_name, | |
| char * | pdb_out_name | |||
| ) |
## FUNCTION: write_visualization
## SPECIFICATION: Write visualization scripts for VMD and PyMol
## PARAMETERS: @ char *pdb_name : pdb code @ char *pdb_out_name : name of the pdb output file
## RETURN: void
Definition at line 76 of file write_visu.c.
References write_pymol(), and write_vmd().
Referenced by write_out_fpocket().
00077 { 00078 write_vmd(pdb_name,pdb_out_name); 00079 write_pymol(pdb_name,pdb_out_name); 00080 }
| void write_vmd | ( | char * | pdb_name, | |
| char * | pdb_out_name | |||
| ) |
## FUNCTION: write_vmd
## SPECIFICATION: Write visualization script for VMD
## PARAMETERS: @ char *pdb_name : pdb code @ char *pdb_out_name : name of the pdb output file
## RETURN: void
Definition at line 98 of file write_visu.c.
References remove_ext(), and remove_path().
Referenced by write_visualization().
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 }
1.5.6