mdparams.h File Reference

#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_mdparams

Defines

#define M_MDPAR_INPUT_FILE   'L'
#define M_MDPAR_INPUT_FILE2   'f'
#define M_MDPAR_OUTPUT_FILE   'o'
#define M_MDPAR_SCORING_MODE   'S'
#define M_MDPAR_OUTPUT_ALL_SNAPSHOTS   'a'
#define M_MDP_OUTPUT_FILE1_DEFAULT   "mdpout_snapshots_concat.pqr"
#define M_MDP_OUTPUT_FILE2_DEFAULT   "mdpout_freq_grid.dx"
#define M_MDP_OUTPUT_FILE3_DEFAULT   "mdpout_freq_iso_0_5.pdb"
#define M_MDP_OUTPUT_FILE4_DEFAULT   "mdpout_descriptors.txt"
#define M_MDP_OUTPUT_FILE5_DEFAULT   "mdpout_mdpocket.pdb"
#define M_MDP_OUTPUT_FILE6_DEFAULT   "mdpout_mdpocket_atoms.pdb"
#define M_MDP_OUTPUT_FILE7_DEFAULT   "mdpout_all_atom_pdensities.pdb"
#define M_MDP_OUTPUT_FILE8_DEFAULT   "mdpout_dens_grid.dx"
#define M_MDP_OUTPUT_FILE9_DEFAULT   "mdpout_dens_iso_8.pdb"
#define M_MDP_DEFAULT_ISO_VALUE_FREQ   0.5
#define M_MDP_DEFAULT_ISO_VALUE_DENS   8.0
#define M_MAX_FILE_NAME_LENGTH   300
#define M_NB_MC_ITER   2500
#define M_MDP_USAGE   "\***** USAGE (mdpocket) *****\n\\n\1 : Pocket finding on a MD trajectory -> list of pre-aligned pdb ordered by time file:\n\\t./bin/mdpocket -L pdb_list \n\2 : Pocket characterization on a MD trajectory -> list of pre-aligned pdb ordered by \n\ time file and wanted pocket pdb file \n\\t./bin/mdpocket -L pdb_list -f wanted_pocket.pdb \n\\t an example of a wanted pocket file can be obtained by running (1) \n\\t (mdpout_iso_8.pdb) and non wanted grid points should be deleted by hand (i.e. PyMOL).\n\\nOPTIONS (find standard parameters in brackets) \n\n\\t-o (char *) : common prefix of output file (mdpout_snapshots) \n\n\\t-S : if you put this flag, the pocket score is matched to the \n\\t density grid \n\\t-a : output all bfactor colored snapshots\n\n\\t-m (float) : Minimum radius of an alpha-sphere. (3.0)\n\\t-M (float) : Maximum radius of an alpha-sphere. (6.0)\n\\t-A (int) : Minimum number of apolar neighbor for \n\\t an a-sphere to be considered as apolar. (3)\n\\t-i (int) : Minimum number of a-sphere per pocket. (30)\n\\t-D (float) : Maximum distance for first clustering \n\\t algorithm. (1.73)\n\\t-s (float) : Maximum distance for single linkage \n\\t clustering (2.5)\n\\t-n (integer): Minimum number of neighbor close from \n\\t each other (not merged otherwise). (3)\n\\t-r (float) : Maximum distance between two pockets \n\\t barycenter (merged otherwise). (4.5)\n\\t-p (float) : Minimum proportion of apolar sphere in \n\\t a pocket (remove otherwise) (0.0)\n\\t-v (integer): Number of Monte-Carlo iteration for the \n\\t calculation of each pocket volume. (2500)\n\\t-b (integer): Space approximation for the basic method \n\\t of the volume calculation. Not used by \n\\t default (Monte Carlo approximation is) \n\\nSee the manual (man fpocket), or the full documentation for\n\more information.\n\***************************\n"

Functions

s_mdparamsinit_def_mdparams (void)
s_mdparamsget_mdpocket_args (int nargs, char **args)
int add_list_snapshots (char *str_list_file, s_mdparams *par)
int add_snapshot (char *snapbuf, s_mdparams *par)
void print_mdparams (s_mdparams *p, FILE *f)
void print_mdpocket_usage (FILE *f)
void free_mdparams (s_mdparams *p)


Define Documentation

#define M_MAX_FILE_NAME_LENGTH   300

Definition at line 73 of file mdparams.h.

#define M_MDP_DEFAULT_ISO_VALUE_DENS   8.0

Definition at line 71 of file mdparams.h.

Referenced by mdpocket_detect().

#define M_MDP_DEFAULT_ISO_VALUE_FREQ   0.5

Definition at line 70 of file mdparams.h.

Referenced by mdpocket_detect().

#define M_MDP_OUTPUT_FILE1_DEFAULT   "mdpout_snapshots_concat.pqr"

Definition at line 61 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE2_DEFAULT   "mdpout_freq_grid.dx"

Definition at line 62 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE3_DEFAULT   "mdpout_freq_iso_0_5.pdb"

Definition at line 63 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE4_DEFAULT   "mdpout_descriptors.txt"

Definition at line 64 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE5_DEFAULT   "mdpout_mdpocket.pdb"

Definition at line 65 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE6_DEFAULT   "mdpout_mdpocket_atoms.pdb"

Definition at line 66 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE7_DEFAULT   "mdpout_all_atom_pdensities.pdb"

Definition at line 67 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE8_DEFAULT   "mdpout_dens_grid.dx"

Definition at line 68 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_OUTPUT_FILE9_DEFAULT   "mdpout_dens_iso_8.pdb"

Definition at line 69 of file mdparams.h.

Referenced by init_def_mdparams().

#define M_MDP_USAGE   "\***** USAGE (mdpocket) *****\n\\n\1 : Pocket finding on a MD trajectory -> list of pre-aligned pdb ordered by time file:\n\\t./bin/mdpocket -L pdb_list \n\2 : Pocket characterization on a MD trajectory -> list of pre-aligned pdb ordered by \n\ time file and wanted pocket pdb file \n\\t./bin/mdpocket -L pdb_list -f wanted_pocket.pdb \n\\t an example of a wanted pocket file can be obtained by running (1) \n\\t (mdpout_iso_8.pdb) and non wanted grid points should be deleted by hand (i.e. PyMOL).\n\\nOPTIONS (find standard parameters in brackets) \n\n\\t-o (char *) : common prefix of output file (mdpout_snapshots) \n\n\\t-S : if you put this flag, the pocket score is matched to the \n\\t density grid \n\\t-a : output all bfactor colored snapshots\n\n\\t-m (float) : Minimum radius of an alpha-sphere. (3.0)\n\\t-M (float) : Maximum radius of an alpha-sphere. (6.0)\n\\t-A (int) : Minimum number of apolar neighbor for \n\\t an a-sphere to be considered as apolar. (3)\n\\t-i (int) : Minimum number of a-sphere per pocket. (30)\n\\t-D (float) : Maximum distance for first clustering \n\\t algorithm. (1.73)\n\\t-s (float) : Maximum distance for single linkage \n\\t clustering (2.5)\n\\t-n (integer): Minimum number of neighbor close from \n\\t each other (not merged otherwise). (3)\n\\t-r (float) : Maximum distance between two pockets \n\\t barycenter (merged otherwise). (4.5)\n\\t-p (float) : Minimum proportion of apolar sphere in \n\\t a pocket (remove otherwise) (0.0)\n\\t-v (integer): Number of Monte-Carlo iteration for the \n\\t calculation of each pocket volume. (2500)\n\\t-b (integer): Space approximation for the basic method \n\\t of the volume calculation. Not used by \n\\t default (Monte Carlo approximation is) \n\\nSee the manual (man fpocket), or the full documentation for\n\more information.\n\***************************\n"

the usage print content

Definition at line 79 of file mdparams.h.

Referenced by print_mdpocket_usage().

#define M_MDPAR_INPUT_FILE   'L'

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 mdparams.h.

Referenced by get_mdpocket_args().

#define M_MDPAR_INPUT_FILE2   'f'

Definition at line 55 of file mdparams.h.

Referenced by get_mdpocket_args().

#define M_MDPAR_OUTPUT_ALL_SNAPSHOTS   'a'

Definition at line 58 of file mdparams.h.

Referenced by get_mdpocket_args().

#define M_MDPAR_OUTPUT_FILE   'o'

Definition at line 56 of file mdparams.h.

Referenced by get_mdpocket_args().

#define M_MDPAR_SCORING_MODE   'S'

Definition at line 57 of file mdparams.h.

Referenced by get_mdpocket_args().

#define M_NB_MC_ITER   2500

Definition at line 74 of file mdparams.h.


Function Documentation

int add_list_snapshots ( char *  str_list_file,
s_mdparams par 
)

## FUNCTION: add_list_snapshots

## SPECIFICATION: Load a list of snapshot pdb file path. This file should have the following format:

snapshot_pdb_file snapshot_pdb_file2 snapshot_pdb_file3 (...)

Each snapshot file will be stored in the parameters structure.

## PARAMETRES: @ char *str_list_file : Path of the file containing all data @ s_mdparams *par : Structures that stores all thoses files

## RETURN: int: Number of file read.

Definition at line 244 of file mdparams.c.

References add_snapshot(), M_MAX_PDB_NAME_LEN, and s_mdparams::nfiles.

Referenced by get_mdpocket_args().

00245 {
00246         FILE *f;
00247         int n,
00248                 nread = 0,
00249                 status ;
00250 
00251         char buf[M_MAX_PDB_NAME_LEN*2 + 6],
00252                  snapbuf[M_MAX_PDB_NAME_LEN];
00253 
00254         /* Loading data. */
00255         f = fopen(str_list_file, "r") ;
00256 /*
00257         printf(str_list_file);
00258 */
00259         if(f) {
00260                 while(fgets(buf, 210, f)) {
00261 /*
00262                         printf("B: %s\n" , buf);
00263 */
00264                         n = par->nfiles ;
00265                         status = sscanf(buf, "%s", snapbuf) ;
00266                         if(status < 1) {
00267 
00268                                 fprintf(stderr, "! Skipping row '%s' with bad format (status %d).\n",
00269                                                                 buf, status) ;
00270                         }
00271                         else {
00272                                 nread += add_snapshot(snapbuf, par) ;
00273                         }
00274 
00275                 }
00276         }
00277         else {
00278                 fprintf(stderr, "! File %s doesn't exists\n", str_list_file) ;
00279         }
00280         fclose(f);
00281         return nread ;
00282 }

int add_snapshot ( char *  snapbuf,
s_mdparams par 
)

## FUNCTION: add_snapshot

## SPECIFICATION: Add a set of data to the list of set of data in the parameters. this function is used for the mdpocket 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 *snapbuf : The snapshots path @ s_mdparams *par: The structure than contains parameters.

## RETURN: int: 1 if everything is OK, 0 if not.

Definition at line 303 of file mdparams.c.

References fopen_pdb_check_case(), s_mdparams::fsnapshot, my_malloc(), my_realloc(), and s_mdparams::nfiles.

Referenced by add_list_snapshots().

00304 {
00305         int nm1 ;
00306 
00307         FILE *f = fopen_pdb_check_case(snapbuf, "r") ;
00308         if(f) {
00309                 nm1 = par->nfiles ;
00310                 par->nfiles += 1 ;
00311 
00312                 
00313                 par->fsnapshot = (char**) my_realloc(par->fsnapshot, (par->nfiles)*sizeof(char*)) ;
00314 
00315                 par->fsnapshot[nm1] = (char *)my_malloc((strlen(snapbuf)+1)*sizeof(char)) ;
00316 
00317                 strcpy(par->fsnapshot[nm1], snapbuf) ;
00318 
00319                 fclose(f) ;
00320 
00321         }
00322         else {
00323                 fprintf(stdout, "! The pdb file '%s' doesn't exists.\n", snapbuf) ;
00324                 return 0 ;
00325         }
00326 
00327         return 1 ;
00328 }

void free_mdparams ( s_mdparams p  ) 

## FUNCTION: free_params

## SPECIFICATION: Free parameters

## PARAMETRES: @ s_mdparams *p: Pointer to the structure to free

## RETURN: void

Definition at line 397 of file mdparams.c.

References s_mdparams::f_densdx, s_mdparams::f_desc, s_mdparams::f_freqdx, s_mdparams::f_pqr, s_mdparams::fpar, free_fparams(), s_mdparams::fsnapshot, and my_free().

Referenced by get_mdpocket_args(), and main().

00398 {
00399         if(p) {
00400                 
00401                 if(p->fsnapshot) {
00402                         my_free(p->fsnapshot);
00403                         p->fsnapshot = NULL;
00404                 }
00405                 if(p->f_pqr) {
00406                         my_free(p->f_pqr);
00407                         p->f_pqr = NULL;
00408                 }
00409                 if(p->f_densdx) {
00410                         my_free(p->f_densdx);
00411                         p->f_densdx = NULL ;
00412                 }
00413                 if(p->f_freqdx) {
00414                         my_free(p->f_freqdx);
00415                         p->f_freqdx = NULL ;
00416                 }
00417                 if(p->f_desc) {
00418                         my_free(p->f_desc);
00419                         p->f_desc = NULL;
00420                 }
00421                 free_fparams(p->fpar);
00422                 my_free(p) ;
00423         }
00424 }

s_mdparams* get_mdpocket_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_mdparams*: Pointer to parameters

Definition at line 123 of file mdparams.c.

References add_list_snapshots(), s_mdparams::bfact_on_all, s_mdparams::f_apdb, s_mdparams::f_appdb, s_mdparams::f_densdx, s_mdparams::f_densiso, s_mdparams::f_desc, s_mdparams::f_freqdx, s_mdparams::f_freqiso, s_mdparams::f_ppdb, s_mdparams::f_pqr, s_mdparams::flag_scoring, s_mdparams::fpar, free_mdparams(), s_mdparams::fwantedpocket, get_fpocket_args(), init_def_mdparams(), is_fpocket_opt(), M_MAX_FILE_NAME_LENGTH, M_MDPAR_INPUT_FILE, M_MDPAR_INPUT_FILE2, M_MDPAR_OUTPUT_ALL_SNAPSHOTS, M_MDPAR_OUTPUT_FILE, M_MDPAR_SCORING_MODE, print_mdpocket_usage(), and remove_ext().

Referenced by main().

00124 {
00125         int i,
00126                 status = 0,
00127                 nstats = 0,
00128                 npdb=0;
00129 
00130         char *str_list_file = NULL ;
00131 
00132         s_mdparams *par = init_def_mdparams() ;
00133         par->fpar = get_fpocket_args(nargs, args) ;
00134 
00135         /* Read arguments by flags */
00136         for (i = 1; i < nargs; i++) {
00137                 if (strlen(args[i]) == 2 && args[i][0] == '-') {
00138                         switch (args[i][1]) {
00139                                 case M_MDPAR_OUTPUT_FILE :
00140                                                 if(nstats >= 1) fprintf(stdout, "! More than one single file for the stats output file has been given. Ignoring this one.\n") ;
00141                                                 else {
00142                                                         if(i < nargs-1) {
00143                                                                 if(strlen(args[++i]) < M_MAX_FILE_NAME_LENGTH) {
00144                                                                         remove_ext(args[i]) ;
00145                                                                         sprintf(par->f_pqr, "%s.pqr", args[i]) ;
00146                                                                         sprintf(par->f_freqdx, "%s.dx", args[i]) ;
00147                                                                         sprintf(par->f_densdx, "%s.dx", args[i]) ;
00148                                                                         sprintf(par->f_freqiso, "%s_freq_iso_0_5.pdb", args[i]) ;
00149                                                                         sprintf(par->f_densiso, "%s_dens_iso_8.pdb", args[i]) ;
00150                                                                         sprintf(par->f_desc, "%s_descriptors.txt", args[i]) ;
00151                                                                         sprintf(par->f_ppdb, "%s_mdpocket.pdb", args[i]) ;
00152                                                                         sprintf(par->f_apdb, "%s_mdpocket_atoms.pdb", args[i]) ;
00153                                                                         sprintf(par->f_appdb, "%s_all_atom_pdensities.pdb", args[i]) ;
00154                                                                 }
00155                                                                 else fprintf(stdout, "! Output file name is too long... Keeping default.") ;
00156                                                         }
00157                                                         else {
00158                                                                 fprintf(stdout, "! Invalid output file name argument missing.\n") ;
00159                                                                 status += 1 ;
00160                                                         }
00161                                                 }
00162                                                 break ;
00163 
00164                                 case M_MDPAR_INPUT_FILE :
00165                                                 if(i < nargs-1) str_list_file = args[++i] ;
00166                                                 else {
00167                                                         fprintf(stdout, "! Input file name argument missing.\n") ;
00168                                                         status += 1 ;
00169                                                 }
00170                                                  break ;
00171                                 case M_MDPAR_INPUT_FILE2 :
00172                                                 if(npdb >= 1) fprintf(stderr,
00173                                                         "! Only first input pdb will be used.\n") ;
00174                                                 else {
00175                                                         strcpy(par->fwantedpocket, args[++i]) ; npdb++ ;
00176                                                 }
00177                                                 break ;
00178                                 case M_MDPAR_SCORING_MODE :
00179                                                 par->flag_scoring=1;
00180                                                 break;
00181                                 case M_MDPAR_OUTPUT_ALL_SNAPSHOTS :
00182                                                 par->bfact_on_all=1;
00183                                                 break;
00184                                 default:
00185                                         //  Check fpocket parameters!
00186                                         if(!is_fpocket_opt(args[i][1])) {
00187                                                 fprintf(stdout, "> Unknown option '%s'. Ignoring it.\n",
00188                                                                 args[i]) ;
00189                                         }
00190                                         break ;
00191                         }
00192                 }
00193         }
00194 
00195         if(status > 0) {
00196                 free_mdparams(par) ;
00197                 par = NULL ;
00198                 print_mdpocket_usage(stdout);
00199         }
00200         else {
00201                 if(str_list_file) {
00202                         int res = add_list_snapshots(str_list_file, par) ;
00203                         if(res <= 0) {
00204                                 fprintf(stdout, "! No data has been read.\n") ;
00205                                 free_mdparams(par) ;
00206                                 par = NULL ;
00207                                 print_mdpocket_usage(stdout);
00208                         }
00209                 }
00210                 else {
00211                         fprintf(stdout, "! No input file given... Try again :).\n") ;
00212                         free_mdparams(par) ;
00213                         par = NULL ;
00214                         print_mdpocket_usage(stdout);
00215                 }
00216         }
00217 
00218         return par;
00219 }

s_mdparams* init_def_mdparams ( void   ) 

## GENERAL INFORMATION ## ## FILE mdparams.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 mdpocket 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_mdparams

## SPECIFICATION: Initialisation of default parameters.

## PARAMETRES: void

## RETURN: s_mdparams*: Pointer to allocated paramers.

Definition at line 76 of file mdparams.c.

References s_mdparams::bfact_on_all, s_mdparams::f_apdb, s_mdparams::f_appdb, s_mdparams::f_densdx, s_mdparams::f_densiso, s_mdparams::f_desc, s_mdparams::f_freqdx, s_mdparams::f_freqiso, s_mdparams::f_ppdb, s_mdparams::f_pqr, s_mdparams::flag_scoring, s_mdparams::fsnapshot, s_mdparams::fwantedpocket, M_MAX_FILE_NAME_LENGTH, M_MDP_OUTPUT_FILE1_DEFAULT, M_MDP_OUTPUT_FILE2_DEFAULT, M_MDP_OUTPUT_FILE3_DEFAULT, M_MDP_OUTPUT_FILE4_DEFAULT, M_MDP_OUTPUT_FILE5_DEFAULT, M_MDP_OUTPUT_FILE6_DEFAULT, M_MDP_OUTPUT_FILE7_DEFAULT, M_MDP_OUTPUT_FILE8_DEFAULT, M_MDP_OUTPUT_FILE9_DEFAULT, my_malloc(), and s_mdparams::nfiles.

Referenced by get_mdpocket_args().

00077 {
00078         s_mdparams *par = (s_mdparams*) my_malloc(sizeof(s_mdparams)) ;
00079 
00080         par->f_pqr = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00081         par->f_freqdx = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00082         par->f_densdx = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00083         par->f_freqiso = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00084         par->f_densiso = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00085         par->f_desc = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00086         par->f_ppdb = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00087         par->f_apdb = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char)) ;
00088         par->f_appdb = (char *)my_malloc(M_MAX_FILE_NAME_LENGTH*sizeof(char));
00089         strcpy(par->f_pqr, M_MDP_OUTPUT_FILE1_DEFAULT) ;
00090         strcpy(par->f_freqdx, M_MDP_OUTPUT_FILE2_DEFAULT) ;
00091         strcpy(par->f_freqiso, M_MDP_OUTPUT_FILE3_DEFAULT) ;
00092         strcpy(par->f_desc, M_MDP_OUTPUT_FILE4_DEFAULT) ;
00093         strcpy(par->f_ppdb, M_MDP_OUTPUT_FILE5_DEFAULT) ;
00094         strcpy(par->f_apdb, M_MDP_OUTPUT_FILE6_DEFAULT) ;
00095         strcpy(par->f_appdb, M_MDP_OUTPUT_FILE7_DEFAULT);
00096         strcpy(par->f_densdx, M_MDP_OUTPUT_FILE8_DEFAULT) ;
00097         strcpy(par->f_densiso, M_MDP_OUTPUT_FILE9_DEFAULT) ;
00098         par->fsnapshot = NULL ;
00099         par->fwantedpocket[0] = 0 ;
00100         par->nfiles = 0 ;
00101         par->flag_scoring=0;
00102         par->bfact_on_all=0;
00103 
00104         return par ;
00105 }

void print_mdparams ( s_mdparams p,
FILE *  f 
)

## FUNCTION: print_mdparams

## SPECIFICATION: Print function, usefull to debug

## PARAMETRES: @ s_mdparams *p : The structure than will contain the parsed parameter @ FILE *f : The file to write in

## RETURN: void

Definition at line 345 of file mdparams.c.

References s_mdparams::fsnapshot, s_mdparams::fwantedpocket, and s_mdparams::nfiles.

Referenced by main().

00346 {
00347 
00348         if(p) {
00349                 fprintf(f, "==============\nParameters of the program: \n");
00350                 int i ;
00351                 for(i = 0 ; i < p->nfiles ; i++) {
00352                         fprintf(f, "> Snaphot %d: '%s'\n", i+1, p->fsnapshot[i]) ;
00353                 }
00354                 fprintf(f, "==============\n");
00355                 if(p->fwantedpocket[0]!=0){
00356                     fprintf(f,"Wanted pocket given in file : %s\n",p->fwantedpocket);
00357                     fprintf(f, "==============\n");
00358                 }
00359         }
00360         else fprintf(f, "> No parameters detected\n");
00361 }

void print_mdpocket_usage ( FILE *  f  ) 

## FUNCTION: print_mdparams_usage

## SPECIFICATION: Displaying usage of the programm in the given buffer

## PARAMETRES: @ FILE *f: buffer to print in

## RETURN:

Definition at line 376 of file mdparams.c.

References M_MDP_USAGE.

Referenced by get_mdpocket_args().

00377 {
00378         f = (f == NULL) ? stdout:f ;
00379 
00380         fprintf(f, M_MDP_USAGE) ;
00381 }


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