#include <stdio.h>#include <stdlib.h>#include <unistd.h>#include <string.h>#include <ctype.h>#include <limits.h>#include <assert.h>#include "utils.h"#include "memhandler.h"#include "fparams.h"Go to the source code of this file.
Data Structures | |
| struct | s_dparams |
Defines | |
| #define | M_DPAR_INTERFACE_METHOD1 'e' |
| #define | M_DPAR_INTERFACE_METHOD2 'E' |
| #define | M_DPAR_DISTANCE_CRITERIA 'd' |
| #define | M_DPAR_INPUT_FILE 'f' |
| #define | M_DPAR_OUTPUT_FILE 'o' |
| #define | M_INTERFACE_METHOD1 1 |
| #define | M_VERT_LIG_NEIG_DIST 4.0 |
| #define | M_INTERFACE_METHOD2 2 |
| #define | M_LIG_NEIG_DIST 4.0 |
| #define | M_OUTPUT_FILE1_DEFAULT "dpout_explicitp.txt" |
| #define | M_OUTPUT_FILE2_DEFAULT "dpout_fpocketp.txt" |
| #define | M_OUTPUT_FILE3_DEFAULT "dpout_fpocketnp.txt" |
| #define | M_MAX_FILE_NAME_LENGTH 300 |
| #define | M_NB_MC_ITER 2500 |
| #define | M_MIN_ASPH_RAY 2.8 |
| #define | M_MAX_ASPH_RAY 10.0 |
| #define | M_DP_USAGE "\\n***** USAGE (dpocket) *****\n\\n\The program needs as input a file containing at each \n\line a pdb file name and a ligand code (3 letters). \n\The format of each line must be: \n\n\{PATH/}2fej.pdb LIG \n\n\The ligand code is the resname of the ligand atoms in \n\the pdb file and has to separated by a tab from the \n\pdb structure in the input file. \n\n\See the manual for more information. \n\n\Example of command using default parameters: \n\\t./bin/dpocket -f file_path \n\n\Options: \n\\t-o string : Prefix of the output file. (./dpout_*) \n\\t-e : Use the first protein-ligand explicit \n\\t interface definition (default). \n\\t-E : Use the second protein-ligand explicit \n\\t interface definition. \n\\t-d float : Distance criteria for the choosen \n\\t interface definition. (4.0) \n\n\Options specific to fpocket are usable too. \n\See the manual/tutorial for mor information. \n\***************************\n" |
Functions | |
| s_dparams * | init_def_dparams (void) |
| s_dparams * | get_dpocket_args (int nargs, char **args) |
| int | add_list_complexes (char *str_list_file, s_dparams *par) |
| int | add_complexe (char *complex, char *ligand, s_dparams *par) |
| int | parse_dist_crit (char *str, s_dparams *p) |
| void | print_dparams (s_dparams *p, FILE *f) |
| void | print_dpocket_usage (FILE *f) |
| void | free_dparams (s_dparams *p) |
| #define M_DP_USAGE "\\n***** USAGE (dpocket) *****\n\\n\The program needs as input a file containing at each \n\line a pdb file name and a ligand code (3 letters). \n\The format of each line must be: \n\n\{PATH/}2fej.pdb LIG \n\n\The ligand code is the resname of the ligand atoms in \n\the pdb file and has to separated by a tab from the \n\pdb structure in the input file. \n\n\See the manual for more information. \n\n\Example of command using default parameters: \n\\t./bin/dpocket -f file_path \n\n\Options: \n\\t-o string : Prefix of the output file. (./dpout_*) \n\\t-e : Use the first protein-ligand explicit \n\\t interface definition (default). \n\\t-E : Use the second protein-ligand explicit \n\\t interface definition. \n\\t-d float : Distance criteria for the choosen \n\\t interface definition. (4.0) \n\n\Options specific to fpocket are usable too. \n\See the manual/tutorial for mor information. \n\***************************\n" |
| #define M_DPAR_DISTANCE_CRITERIA 'd' |
| #define M_DPAR_INPUT_FILE 'f' |
| #define M_DPAR_INTERFACE_METHOD1 'e' |
COPYRIGHT DISCLAIMER
Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby disclaim all copyright interest in the program “fpocket” (which performs protein cavity detection) written by Vincent Le Guilloux and Peter Schmidtke.
Vincent Le Guilloux 28 November 2008 Peter Schmidtke 28 November 2008 Pierre Tuffery 28 November 2008
GNU GPL
This file is part of the fpocket package.
fpocket is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
fpocket is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with fpocket. If not, see <http://www.gnu.org/licenses/>.
Definition at line 54 of file dparams.h.
Referenced by get_dpocket_args().
| #define M_DPAR_INTERFACE_METHOD2 'E' |
| #define M_DPAR_OUTPUT_FILE 'o' |
| #define M_INTERFACE_METHOD1 1 |
Definition at line 63 of file dparams.h.
Referenced by get_dpocket_args(), init_def_dparams(), and print_dparams().
| #define M_INTERFACE_METHOD2 2 |
| #define M_LIG_NEIG_DIST 4.0 |
| #define M_MAX_FILE_NAME_LENGTH 300 |
Definition at line 73 of file dparams.h.
Referenced by get_dpocket_args(), get_mdpocket_args(), get_tpocket_args(), init_def_dparams(), init_def_mdparams(), and init_def_tparams().
| #define M_OUTPUT_FILE1_DEFAULT "dpout_explicitp.txt" |
| #define M_OUTPUT_FILE2_DEFAULT "dpout_fpocketp.txt" |
| #define M_OUTPUT_FILE3_DEFAULT "dpout_fpocketnp.txt" |
| #define M_VERT_LIG_NEIG_DIST 4.0 |
| int add_complexe | ( | char * | complex, | |
| char * | ligand, | |||
| s_dparams * | par | |||
| ) |
## FUNCTION: add_complexe
## SPECIFICATION: Add a set of data to the list of set of data in the parameters. this function is used for the tpocket program only.
The function will try to open the file, and data will be stored only if the file exists, and if the name of the ligand is valid.
## PARAMETERS: @ char *apo : The apo path @ char *complex : The complex path @ char *ligan : The ligand resname: a 4 letter (max!) @ s_dparams *par: The structure than contains parameters.
## RETURN: int: 1 if everything is OK, 0 if not.
Definition at line 301 of file dparams.c.
References s_dparams::fcomplex, fopen_pdb_check_case(), s_dparams::ligs, my_malloc(), my_realloc(), and s_dparams::nfiles.
Referenced by add_list_complexes().
00302 { 00303 int nm1, i, l ; 00304 00305 FILE *f = fopen_pdb_check_case(complex, "r") ; 00306 if(f) { 00307 l = strlen(ligand) ; 00308 if(strlen(ligand) >= 2) { 00309 for(i = 0 ; i < l ; i++) ligand[i] = toupper(ligand[i]) ; 00310 00311 nm1 = par->nfiles ; 00312 par->nfiles += 1 ; 00313 00314 par->ligs = (char**) my_realloc(par->ligs, (par->nfiles)*sizeof(char*)) ; 00315 par->fcomplex = (char**) my_realloc(par->fcomplex, (par->nfiles)*sizeof(char*)) ; 00316 00317 par->fcomplex[nm1] = (char *)my_malloc((strlen(complex)+1)*sizeof(char)) ; 00318 par->ligs[nm1] = (char *)my_malloc((strlen(ligand)+1)*sizeof(char)) ; 00319 00320 strcpy(par->fcomplex[nm1], complex) ; 00321 strcpy(par->ligs[nm1], ligand) ; 00322 00323 fclose(f) ; 00324 } 00325 else { 00326 fprintf(stdout, "! The name given for the ligand is invalid or absent.\n") ; 00327 fclose(f) ; 00328 return 0 ; 00329 } 00330 00331 } 00332 else { 00333 fprintf(stdout, "! The pdb file '%s' doesn't exists.\n", complex) ; 00334 return 0 ; 00335 } 00336 00337 return 1 ; 00338 }
| int add_list_complexes | ( | char * | str_list_file, | |
| s_dparams * | par | |||
| ) |
## FUNCTION: add_list_complexes
## SPECIFICATION: Load a list of protein-ligand pdb file path. This file should have the following format:
complex_pdb_file ligand_code complex_pdb_file2 ligand_code2 complex_pdb_file3 ligand_code3 (...)
Each complexe-ligand set will be stored in the parameters structure.
## PARAMETRES: @ char *str_list_file : Path of the file containing all data @ s_dparams *par : Structures that stores all thoses files
## RETURN: int: Number of file read.
Definition at line 234 of file dparams.c.
References add_complexe(), M_MAX_PDB_NAME_LEN, and s_dparams::nfiles.
Referenced by get_dpocket_args().
00235 { 00236 FILE *f; 00237 int n, 00238 nread = 0, 00239 status ; 00240 00241 char buf[M_MAX_PDB_NAME_LEN*2 + 6], 00242 complexbuf[M_MAX_PDB_NAME_LEN], 00243 ligbuf[5]; 00244 00245 /* Loading data. */ 00246 f = fopen(str_list_file, "r") ; 00247 /* 00248 printf(str_list_file); 00249 */ 00250 if(f) { 00251 while(fgets(buf, 210, f)) { 00252 /* 00253 printf("B: %s\n" , buf); 00254 */ 00255 n = par->nfiles ; 00256 status = sscanf(buf, "%s\t%s", complexbuf, ligbuf) ; 00257 00258 if(status < 2) { 00259 /* 00260 fprintf(stderr, "! Skipping row '%s' with bad format (status %d).\n", 00261 buf, status) ; 00262 */ 00263 } 00264 else { 00265 /* 00266 printf("%s %s\n", complexbuf, ligbuf ); 00267 */ 00268 nread += add_complexe(complexbuf, ligbuf, par) ; 00269 } 00270 00271 } 00272 } 00273 else { 00274 fprintf(stderr, "! File %s doesn't exists\n", str_list_file) ; 00275 } 00276 00277 return nread ; 00278 }
| void free_dparams | ( | s_dparams * | p | ) |
## FUNCTION: free_params
## SPECIFICATION: Free parameters
## PARAMETRES: @ s_dparams *p: Pointer to the structure to free
## RETURN: void
Definition at line 440 of file dparams.c.
References s_dparams::f_exp, s_dparams::f_fpcknp, s_dparams::f_fpckp, s_dparams::fcomplex, s_dparams::fpar, free_fparams(), s_dparams::ligs, and my_free().
Referenced by get_dpocket_args(), and main().
00441 { 00442 if(p) { 00443 if(p->ligs) { 00444 my_free(p->ligs) ; 00445 p->ligs = NULL ; 00446 } 00447 00448 if(p->fcomplex) { 00449 my_free(p->fcomplex) ; 00450 p->fcomplex = NULL ; 00451 } 00452 00453 if(p->f_exp) { 00454 my_free(p->f_exp) ; 00455 p->f_exp = NULL ; 00456 } 00457 00458 if(p->f_fpckp) { 00459 my_free(p->f_fpckp) ; 00460 p->f_fpckp = NULL ; 00461 } 00462 00463 if(p->f_fpcknp) { 00464 my_free(p->f_fpcknp) ; 00465 p->f_fpcknp = NULL ; 00466 } 00467 00468 free_fparams(p->fpar) ; 00469 00470 my_free(p) ; 00471 } 00472 }
| s_dparams* get_dpocket_args | ( | int | nargs, | |
| char ** | args | |||
| ) |
## FUNCTION: get_dpocket_args
## SPECIFICATION: This function analyse the user's command line and parse it to store parameters for the descriptor calculator programm.
## PARAMETRES: @ int nargs : Number of arguments @ char **args : Arguments of main program
## RETURN: s_dparams*: Pointer to parameters
Definition at line 113 of file dparams.c.
References add_list_complexes(), s_dparams::f_exp, s_dparams::f_fpcknp, s_dparams::f_fpckp, s_dparams::fpar, free_dparams(), get_fpocket_args(), init_def_dparams(), s_dparams::interface_dist_crit, s_dparams::interface_method, is_fpocket_opt(), M_DPAR_DISTANCE_CRITERIA, M_DPAR_INPUT_FILE, M_DPAR_INTERFACE_METHOD1, M_DPAR_INTERFACE_METHOD2, M_DPAR_OUTPUT_FILE, M_INTERFACE_METHOD1, M_INTERFACE_METHOD2, M_LIG_NEIG_DIST, M_MAX_FILE_NAME_LENGTH, M_VERT_LIG_NEIG_DIST, parse_dist_crit(), print_dpocket_usage(), and remove_ext().
Referenced by main().
00114 { 00115 int i, 00116 status = 0, 00117 nstats = 0, 00118 res; 00119 00120 char *str_list_file = NULL ; 00121 00122 s_dparams *par = init_def_dparams() ; 00123 par->fpar = get_fpocket_args(nargs, args) ; 00124 00125 /* Read arguments by flags */ 00126 for (i = 1; i < nargs; i++) { 00127 if (strlen(args[i]) == 2 && args[i][0] == '-') { 00128 switch (args[i][1]) { 00129 case M_DPAR_DISTANCE_CRITERIA : 00130 if(i < nargs-1) status += parse_dist_crit(args[++i], par) ; 00131 else { 00132 fprintf(stdout, "! Distance criteria defining the protein-ligand interface is missing.\n") ; 00133 status += 1 ; 00134 } 00135 break ; 00136 00137 case M_DPAR_INTERFACE_METHOD1 : 00138 par->interface_method = M_INTERFACE_METHOD1 ; 00139 par->interface_dist_crit = M_VERT_LIG_NEIG_DIST ; 00140 break ; 00141 00142 case M_DPAR_INTERFACE_METHOD2 : 00143 par->interface_method = M_INTERFACE_METHOD2 ; 00144 par->interface_dist_crit = M_LIG_NEIG_DIST ; 00145 break ; 00146 00147 case M_DPAR_OUTPUT_FILE : 00148 if(nstats >= 1) fprintf(stdout, "! More than one single file for the stats output file has been given. Ignoring this one.\n") ; 00149 else { 00150 if(i < nargs-1) { 00151 if(strlen(args[++i]) < M_MAX_FILE_NAME_LENGTH) { 00152 remove_ext(args[i]) ; 00153 sprintf(par->f_exp, "%s_exp.txt", args[i]) ; 00154 sprintf(par->f_fpckp, "%s_fp.txt", args[i]) ; 00155 sprintf(par->f_fpcknp, "%s_fpn.txt", args[i]) ; 00156 } 00157 else fprintf(stdout, "! Output file name is too long... Keeping default.") ; 00158 } 00159 else { 00160 fprintf(stdout, "! Invalid output file name argument missing.\n") ; 00161 status += 1 ; 00162 } 00163 } 00164 break ; 00165 00166 case M_DPAR_INPUT_FILE : 00167 if(i < nargs-1) str_list_file = args[++i] ; 00168 else { 00169 fprintf(stdout, "! Input file name argument missing.\n") ; 00170 status += 1 ; 00171 } 00172 break ; 00173 00174 default: 00175 // Check fpocket parameters! 00176 if(!is_fpocket_opt(args[i][1])) { 00177 fprintf(stdout, "> Unknown option '%s'. Ignoring it.\n", 00178 args[i]) ; 00179 } 00180 break ; 00181 } 00182 } 00183 } 00184 00185 if(status > 0) { 00186 free_dparams(par) ; 00187 par = NULL ; 00188 print_dpocket_usage(stdout); 00189 } 00190 else { 00191 if(str_list_file) { 00192 res = add_list_complexes(str_list_file, par) ; 00193 if(res <= 0) { 00194 fprintf(stdout, "! No data has been read.\n") ; 00195 free_dparams(par) ; 00196 par = NULL ; 00197 print_dpocket_usage(stdout); 00198 } 00199 } 00200 else { 00201 fprintf(stdout, "! No input file given... Try again :).\n") ; 00202 free_dparams(par) ; 00203 par = NULL ; 00204 print_dpocket_usage(stdout); 00205 } 00206 } 00207 00208 return par; 00209 }
| s_dparams* init_def_dparams | ( | void | ) |
## GENERAL INFORMATION ## ## FILE dparams.c ## AUTHORS P. Schmidtke and V. Le Guilloux ## LAST MODIFIED 28-11-08 ## ## SPECIFICATIONS ## ## Handle parameters (parse the command line and sore values) ## for the dpocket programm. ## ## MODIFICATIONS HISTORY ## ## 28-11-08 (v) Comments UTD + relooking ## 27-11-08 (v) Minor Relooking ## 01-04-08 (v) Added comments and creation of history ## 01-01-08 (vp) Created (random date...) ## ## TODO or SUGGESTIONS ## ## (v) Check and update if necessary comments of each function!! ## (v) Review the main function and handle all possible crashes. ## COPYRIGHT DISCLAIMER
Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby disclaim all copyright interest in the program “fpocket” (which performs protein cavity detection) written by Vincent Le Guilloux and Peter Schmidtke.
Vincent Le Guilloux 28 November 2008 Peter Schmidtke 28 November 2008 Pierre Tuffery 28 November 2008
GNU GPL
This file is part of the fpocket package.
fpocket is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
fpocket is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with fpocket. If not, see <http://www.gnu.org/licenses/>. ## FUNCTION: init_def_dparams
## SPECIFICATION: Initialisation of default parameters.
## PARAMETRES: void
## RETURN: s_dparams*: Pointer to allocated paramers.
Definition at line 76 of file dparams.c.
References s_dparams::f_exp, s_dparams::f_fpcknp, s_dparams::f_fpckp, s_dparams::fcomplex, s_dparams::interface_dist_crit, s_dparams::interface_method, s_dparams::ligs, M_INTERFACE_METHOD1, M_MAX_FILE_NAME_LENGTH, M_OUTPUT_FILE1_DEFAULT, M_OUTPUT_FILE2_DEFAULT, M_OUTPUT_FILE3_DEFAULT, M_VERT_LIG_NEIG_DIST, my_malloc(), and s_dparams::nfiles.
Referenced by get_dpocket_args().
00077 { 00078 s_dparams *par = (s_dparams*) my_malloc(sizeof(s_dparams)) ; 00079 00080 par->f_exp = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ; 00081 par->f_fpckp = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ; 00082 par->f_fpcknp = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ; 00083 00084 strcpy(par->f_exp, M_OUTPUT_FILE1_DEFAULT) ; 00085 strcpy(par->f_fpckp, M_OUTPUT_FILE2_DEFAULT) ; 00086 strcpy(par->f_fpcknp, M_OUTPUT_FILE3_DEFAULT) ; 00087 00088 par->fcomplex = NULL ; 00089 par->ligs = NULL ; 00090 par->nfiles = 0 ; 00091 par->interface_dist_crit = M_VERT_LIG_NEIG_DIST ; 00092 par->interface_method = M_INTERFACE_METHOD1 ; 00093 00094 return par ; 00095 }
| int parse_dist_crit | ( | char * | str, | |
| s_dparams * | p | |||
| ) |
## FUNCTION: parse_dist_crit
## SPECIFICATION: Parsing function for the distance criteria defining the protein-ligand interface.
## PARAMETERS: @ char *str : The string to parse @ s_dparams *p : The structure than will contain the parsed parameter
## RETURN: 0 if the parameter is valid (here a valid integer), 1 if not
Definition at line 356 of file dparams.c.
References s_dparams::interface_dist_crit, M_NO_SIGN, and str_is_float().
Referenced by get_dpocket_args().
00357 { 00358 if(str_is_float(str, M_NO_SIGN)) { 00359 p->interface_dist_crit = (float) atof(str) ; 00360 } 00361 else { 00362 fprintf(stdout, "! Invalid value (%s) given for the distance criteria defining the protein-ligand interface.\n", str) ; 00363 return 1 ; 00364 } 00365 00366 return 0 ; 00367 }
| void print_dparams | ( | s_dparams * | p, | |
| FILE * | f | |||
| ) |
## FUNCTION: print_dparams
## SPECIFICATION: Print function, usefull to debug
## PARAMETRES: @ s_dparams *p : The structure than will contain the parsed parameter @ FILE *f : The file to write in
## RETURN: void
Definition at line 384 of file dparams.c.
References s_dparams::fcomplex, s_dparams::interface_dist_crit, s_dparams::interface_method, s_dparams::ligs, M_INTERFACE_METHOD1, and s_dparams::nfiles.
00385 { 00386 00387 if(p) { 00388 fprintf(f, "==============\nParameters of the program: \n"); 00389 int i ; 00390 for(i = 0 ; i < p->nfiles ; i++) { 00391 fprintf(f, "> Protein %d: '%s', '%s'\n", i+1, p->fcomplex[i], p->ligs[i]) ; 00392 } 00393 00394 if(p->interface_method == M_INTERFACE_METHOD1) 00395 fprintf(f, "> Method used to define explicitely the interface atoms: contacted atom by alpha spheres.\n") ; 00396 else fprintf(f, "> Method used to define explicitely the interface atoms: ligand's neighbors.\n") ; 00397 00398 fprintf(f, "> Distance used to define explicitely the interface: %f.\n", 00399 p->interface_dist_crit) ; 00400 00401 fprintf(f, "==============\n"); 00402 } 00403 else fprintf(f, "> No parameters detected\n"); 00404 }
| void print_dpocket_usage | ( | FILE * | f | ) |
## FUNCTION: print_dparams_usage
## SPECIFICATION: Displaying usage of the programm in the given buffer
## PARAMETRES: @ FILE *f: buffer to print in
## RETURN:
Definition at line 419 of file dparams.c.
References M_DP_USAGE.
Referenced by get_dpocket_args().
00420 { 00421 f = (f == NULL) ? stdout:f ; 00422 00423 fprintf(f, M_DP_USAGE) ; 00424 }
1.5.6