#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"Go to the source code of this file.
Data Structures | |
| struct | s_fparams |
Defines | |
| #define | M_MIN_ASHAPE_SIZE_DEFAULT 3.0 |
| #define | M_MAX_ASHAPE_SIZE_DEFAULT 6.0 |
| #define | M_CLUST_MAX_DIST 1.73 |
| #define | M_REFINE_DIST 4.5 |
| #define | M_REFINE_MIN_PROP_APOL_AS 0.0 |
| #define | M_SLCLUST_MAX_DIST 2.5 |
| #define | M_SLCLUST_MIN_NUM_NEIGH 2 |
| #define | M_MC_ITER 3000 |
| #define | M_BASIC_VOL_DIVISION -1 |
| #define | M_MIN_POCK_NB_ASPH 36 |
| #define | M__MIN_APOL_NEIGH_DEFAULT 3 |
| #define | M_DB_RUN 0 |
| #define | M_PAR_PDB_FILE 'f' |
| #define | M_PAR_PDB_LIST 'F' |
| #define | M_PAR_MAX_ASHAPE_SIZE 'M' |
| #define | M_PAR_MIN_ASHAPE_SIZE 'm' |
| #define | M_PAR_MIN_APOL_NEIGH 'A' |
| #define | M_PAR_CLUST_MAX_DIST 'D' |
| #define | M_PAR_SL_MAX_DIST 's' |
| #define | M_PAR_SL_MIN_NUM_NEIGH 'n' |
| #define | M_PAR_MC_ITER 'v' |
| #define | M_PAR_BASIC_VOL_DIVISION 'b' |
| #define | M_PAR_MIN_POCK_NB_ASPH 'i' |
| #define | M_PAR_REFINE_DIST 'r' |
| #define | M_PAR_REFINE_MIN_NAPOL_AS 'p' |
| #define | M_PAR_DB_RUN 'd' |
| #define | M_FP_USAGE "\n\***** USAGE (fpocket) *****\n\\n\Pocket finding on a pdb - list of pdb - file(s): \n\\t./bin/fpocket -f pdb \n\\t./bin/fpocket -F pdb_list \n\\nOPTIONS (find standard parameters in brackets) \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\\t-d flag : Put this flag if you want to run fpocket for \n\\t database creation \n\\nSee the manual (man fpocket), or the full documentation for\n\more information.\n\***************************\n" |
Functions | |
| s_fparams * | init_def_fparams (void) |
| s_fparams * | get_fpocket_args (int nargs, char **args) |
| int | parse_clust_max_dist (char *str, s_fparams *p) |
| int | parse_sclust_max_dist (char *str, s_fparams *p) |
| int | parse_sclust_min_nneigh (char *str, s_fparams *p) |
| int | parse_min_apol_neigh (char *str, s_fparams *p) |
| int | parse_asph_min_size (char *str, s_fparams *p) |
| int | parse_asph_max_size (char *str, s_fparams *p) |
| int | parse_mc_niter (char *str, s_fparams *p) |
| int | parse_basic_vol_div (char *str, s_fparams *p) |
| int | parse_refine_dist (char *str, s_fparams *p) |
| int | parse_refine_minaap (char *str, s_fparams *p) |
| int | parse_min_pock_nb_asph (char *str, s_fparams *p) |
| int | is_fpocket_opt (const char opt) |
| void | free_fparams (s_fparams *p) |
| void | print_pocket_usage (FILE *f) |
| void | print_fparams (s_fparams *p, FILE *f) |
| #define M__MIN_APOL_NEIGH_DEFAULT 3 |
Minimum number of atoms having a low electronegativity in order to declare an alpha sphere to be apolar 3
Definition at line 76 of file fparams.h.
Referenced by init_def_fparams().
| #define M_BASIC_VOL_DIVISION -1 |
Precision for "exact" volume integration, set to -1 if not used -1
Definition at line 72 of file fparams.h.
Referenced by init_def_fparams().
| #define M_CLUST_MAX_DIST 1.73 |
Use first connection distance (see report) : 2.0
Definition at line 60 of file fparams.h.
Referenced by init_def_fparams().
| #define M_DB_RUN 0 |
default value for running fpocket for populating a database, 0 default
Definition at line 78 of file fparams.h.
Referenced by init_def_fparams().
| #define M_FP_USAGE "\n\***** USAGE (fpocket) *****\n\\n\Pocket finding on a pdb - list of pdb - file(s): \n\\t./bin/fpocket -f pdb \n\\t./bin/fpocket -F pdb_list \n\\nOPTIONS (find standard parameters in brackets) \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\\t-d flag : Put this flag if you want to run fpocket for \n\\t database creation \n\\nSee the manual (man fpocket), or the full documentation for\n\more information.\n\***************************\n" |
the usage print content
Definition at line 95 of file fparams.h.
Referenced by print_pocket_usage().
| #define M_MAX_ASHAPE_SIZE_DEFAULT 6.0 |
Use max alpha sphere radius of : 6.0
Definition at line 58 of file fparams.h.
Referenced by init_def_fparams().
| #define M_MC_ITER 3000 |
Number of iterations for the Monte Carlo volume calculation 3000
Definition at line 70 of file fparams.h.
Referenced by init_def_fparams().
| #define M_MIN_ASHAPE_SIZE_DEFAULT 3.0 |
Use min alpha sphere radius of : 3.0
Definition at line 56 of file fparams.h.
Referenced by init_def_fparams().
| #define M_MIN_POCK_NB_ASPH 36 |
Minimum number of alpha spheres for a pocket to be kept
Definition at line 74 of file fparams.h.
Referenced by init_def_fparams().
| #define M_PAR_BASIC_VOL_DIVISION 'b' |
flag for the space approximation of the MC
Definition at line 89 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_CLUST_MAX_DIST 'D' |
flag for the first clustering distance
Definition at line 85 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_DB_RUN 'd' |
flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs
Definition at line 93 of file fparams.h.
Referenced by get_fpocket_args().
| #define M_PAR_MAX_ASHAPE_SIZE 'M' |
flag for the maximum alpha sphere size
Definition at line 82 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_MC_ITER 'v' |
flag for how many iterations for the monte carlo volume calculation algorithm
Definition at line 88 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_MIN_APOL_NEIGH 'A' |
flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar
Definition at line 84 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_MIN_ASHAPE_SIZE 'm' |
flag for the minimum alpha sphere size
Definition at line 83 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_MIN_POCK_NB_ASPH 'i' |
flag for the min number of alpha spheres in the pocket
Definition at line 90 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_PDB_FILE 'f' |
flag to give a single pdb input file
Definition at line 80 of file fparams.h.
Referenced by get_fpocket_args().
| #define M_PAR_PDB_LIST 'F' |
flag to give a txt file containing paths to multiple pdb files
Definition at line 81 of file fparams.h.
Referenced by get_fpocket_args().
| #define M_PAR_REFINE_DIST 'r' |
flag for the refining distance
Definition at line 91 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_REFINE_MIN_NAPOL_AS 'p' |
flag for minimum proportion of apolar alpha spheres
Definition at line 92 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_SL_MAX_DIST 's' |
flag for the distance crit. of the multiple linkage clustering algorithm
Definition at line 86 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_PAR_SL_MIN_NUM_NEIGH 'n' |
flag for the single linkage min neighbours
Definition at line 87 of file fparams.h.
Referenced by get_fpocket_args(), and is_fpocket_opt().
| #define M_REFINE_DIST 4.5 |
use second connection distance (see report) : 4.5
Definition at line 62 of file fparams.h.
Referenced by init_def_fparams().
| #define M_REFINE_MIN_PROP_APOL_AS 0.0 |
At least a proportion of M_REFINE_MIN_NAPOL_AS apolar alpha spheres in the pocket 0.0
Definition at line 64 of file fparams.h.
Referenced by init_def_fparams().
| #define M_SLCLUST_MAX_DIST 2.5 |
Single linkage clustering connection distance 2.5
Definition at line 66 of file fparams.h.
Referenced by init_def_fparams().
| #define M_SLCLUST_MIN_NUM_NEIGH 2 |
Minimum number of common neighbours for single linkage clustering 5
Definition at line 68 of file fparams.h.
Referenced by init_def_fparams().
| void free_fparams | ( | s_fparams * | p | ) |
## FUNCTION: free_fparams
## SPECIFICATION: Free parameters
## PARAMETRES: @ s_params *p: Pointer to the structure to free
## RETURN: void
Definition at line 562 of file fparams.c.
References my_free(), s_fparams::npdb, and s_fparams::pdb_lst.
Referenced by check_fpocket(), free_dparams(), free_mdparams(), free_tparams(), get_fpocket_args(), and main().
00563 { 00564 int i ; 00565 if(p) { 00566 if(p->npdb > 0 && p->pdb_lst != NULL) { 00567 for (i = 0 ; i < p->npdb ; i++) { 00568 if(p->pdb_lst[i] != NULL) my_free(p->pdb_lst[i]) ; 00569 } 00570 my_free(p->pdb_lst) ; 00571 } 00572 my_free(p) ; 00573 } 00574 }
| s_fparams* get_fpocket_args | ( | int | nargs, | |
| char ** | args | |||
| ) |
## FUNCTION: get_fpocket_args
## SPECIFICATION: This function analyse the user's command line and parse it to store parameters for the pocket finder programm.
## PARAMETRES: @ int nargs : Number of arguments @ char **args : Arguments of main program
## RETURN: s_params*: Pointer to parameters
Definition at line 88 of file fparams.c.
References s_fparams::db_run, free_fparams(), init_def_fparams(), M_MAX_PDB_NAME_LEN, M_PAR_BASIC_VOL_DIVISION, M_PAR_CLUST_MAX_DIST, M_PAR_DB_RUN, M_PAR_MAX_ASHAPE_SIZE, M_PAR_MC_ITER, M_PAR_MIN_APOL_NEIGH, M_PAR_MIN_ASHAPE_SIZE, M_PAR_MIN_POCK_NB_ASPH, M_PAR_PDB_FILE, M_PAR_PDB_LIST, M_PAR_REFINE_DIST, M_PAR_REFINE_MIN_NAPOL_AS, M_PAR_SL_MAX_DIST, M_PAR_SL_MIN_NUM_NEIGH, my_malloc(), s_fparams::npdb, parse_asph_max_size(), parse_asph_min_size(), parse_basic_vol_div(), parse_clust_max_dist(), parse_mc_niter(), parse_min_apol_neigh(), parse_min_pock_nb_asph(), parse_refine_dist(), parse_refine_minaap(), parse_sclust_max_dist(), parse_sclust_min_nneigh(), s_fparams::pdb_lst, s_fparams::pdb_path, and print_pocket_usage().
Referenced by check_fparams(), check_fpocket(), get_dpocket_args(), get_mdpocket_args(), get_tpocket_args(), and main().
00089 { 00090 int i, 00091 npdb = 0, 00092 status = 0 ; 00093 00094 s_fparams *par = init_def_fparams() ; 00095 char *pdb_lst = NULL ; 00096 00097 //read arguments by flags 00098 for (i = 1; i < nargs; i++) { 00099 if (strlen(args[i]) == 2 && args[i][0] == '-' && i <= (nargs-1)) { 00100 00101 switch (args[i][1]) { 00102 case M_PAR_MAX_ASHAPE_SIZE : 00103 status += parse_asph_max_size(args[++i], par) ; break ; 00104 case M_PAR_MIN_ASHAPE_SIZE : 00105 status += parse_asph_min_size(args[++i], par) ; break ; 00106 case M_PAR_MIN_APOL_NEIGH : 00107 status += parse_min_apol_neigh(args[++i], par) ; break ; 00108 case M_PAR_CLUST_MAX_DIST : 00109 status += parse_clust_max_dist(args[++i], par) ; break ; 00110 case M_PAR_SL_MAX_DIST : 00111 status += parse_sclust_max_dist(args[++i], par) ; break ; 00112 case M_PAR_SL_MIN_NUM_NEIGH : 00113 status += parse_sclust_min_nneigh(args[++i], par) ; break ; 00114 case M_PAR_MC_ITER : 00115 status += parse_mc_niter(args[++i], par) ; break ; 00116 case M_PAR_BASIC_VOL_DIVISION : 00117 status += parse_basic_vol_div(args[++i], par) ; break ; 00118 case M_PAR_MIN_POCK_NB_ASPH : 00119 status += parse_min_pock_nb_asph(args[++i], par) ; break ; 00120 case M_PAR_REFINE_DIST : 00121 status += parse_refine_dist(args[++i], par) ; break ; 00122 case M_PAR_REFINE_MIN_NAPOL_AS: 00123 status += parse_refine_minaap(args[++i], par) ; 00124 break ; 00125 case M_PAR_DB_RUN : 00126 par->db_run=1; 00127 break; 00128 00129 case M_PAR_PDB_LIST : 00130 pdb_lst = args[++i] ; 00131 break ; 00132 00133 case M_PAR_PDB_FILE : 00134 if(npdb >= 1) fprintf(stderr, 00135 "! Only first input pdb will be used.\n") ; 00136 else { 00137 strcpy(par->pdb_path, args[++i]) ; npdb++ ; 00138 } 00139 break ; 00140 default: break ; 00141 } 00142 } 00143 } 00144 00145 if(status > 0) { 00146 free_fparams(par) ; 00147 print_pocket_usage(stdout); 00148 return NULL ; 00149 } 00150 00151 par->npdb = npdb ; 00152 00153 /* Handle a file containing a list of PDB */ 00154 if(pdb_lst != NULL) { 00155 FILE *f = fopen(pdb_lst, "r") ; 00156 if(f != NULL) { 00157 /* Count the number of lines */ 00158 int n = 0 ; 00159 char cline [M_MAX_PDB_NAME_LEN + 1] ; 00160 00161 while(fgets(cline, M_MAX_PDB_NAME_LEN, f) != NULL) { 00162 if(strcmp("\n", cline) != 0) { 00163 n ++ ; 00164 } 00165 } 00166 fclose(f) ; 00167 if(n == 0) { 00168 return par ; 00169 } 00170 00171 /* Allocate memory and store each line */ 00172 par->pdb_lst = (char **)my_malloc(n*sizeof(char*)) ; 00173 00174 f = fopen (pdb_lst, "r") ; 00175 int i = 0, l = 0 ; 00176 char *line; 00177 while(fgets(cline, M_MAX_PDB_NAME_LEN, f) != NULL) { 00178 if(strcmp("\n", cline) != 0) { 00179 l = strlen(cline) ; 00180 if(cline[l-1] == '\n') { 00181 l-- ; 00182 cline[l] = '\0' ; 00183 } 00184 line = (char *) my_malloc((l+1)*sizeof(char)) ; 00185 memcpy (line, cline, l+1); 00186 00187 par->pdb_lst[i] = line ; 00188 i ++ ; 00189 } 00190 } 00191 00192 par->npdb = n ; 00193 } 00194 } 00195 00196 return par; 00197 }
| s_fparams* init_def_fparams | ( | void | ) |
## FUNCTION: init_def_fparams
## SPECIFICATION: Initialisation of default parameters
## PARAMETRES: void
## RETURN: s_fparams*: Pointer to allocated paramers.
Definition at line 48 of file fparams.c.
References s_fparams::asph_max_size, s_fparams::asph_min_size, s_fparams::basic_volume_div, s_fparams::clust_max_dist, s_fparams::db_run, s_fparams::flag_do_asa_and_volume_calculations, M__MIN_APOL_NEIGH_DEFAULT, M_BASIC_VOL_DIVISION, M_CLUST_MAX_DIST, M_DB_RUN, M_MAX_ASHAPE_SIZE_DEFAULT, M_MC_ITER, M_MIN_ASHAPE_SIZE_DEFAULT, M_MIN_POCK_NB_ASPH, M_REFINE_DIST, M_REFINE_MIN_PROP_APOL_AS, M_SLCLUST_MAX_DIST, M_SLCLUST_MIN_NUM_NEIGH, s_fparams::min_apol_neigh, s_fparams::min_pock_nb_asph, my_malloc(), s_fparams::nb_mcv_iter, s_fparams::npdb, s_fparams::pdb_lst, s_fparams::pdb_path, s_fparams::refine_clust_dist, s_fparams::refine_min_apolar_asphere_prop, s_fparams::sl_clust_max_dist, and s_fparams::sl_clust_min_nneigh.
Referenced by get_fpocket_args().
00049 { 00050 s_fparams *par = (s_fparams *) my_malloc(sizeof(s_fparams)) ; 00051 00052 par->min_apol_neigh = M__MIN_APOL_NEIGH_DEFAULT ; 00053 par->asph_min_size = M_MIN_ASHAPE_SIZE_DEFAULT ; 00054 par->asph_max_size = M_MAX_ASHAPE_SIZE_DEFAULT ; 00055 par->sl_clust_max_dist = M_SLCLUST_MAX_DIST ; 00056 par->sl_clust_min_nneigh = M_SLCLUST_MIN_NUM_NEIGH ; 00057 par->pdb_path[0] = 0 ; 00058 par->basic_volume_div = M_BASIC_VOL_DIVISION ; 00059 par->nb_mcv_iter = M_MC_ITER ; 00060 par->min_pock_nb_asph = M_MIN_POCK_NB_ASPH ; 00061 par->refine_clust_dist = M_REFINE_DIST ; 00062 par->refine_min_apolar_asphere_prop = M_REFINE_MIN_PROP_APOL_AS ; 00063 par->clust_max_dist = M_CLUST_MAX_DIST ; 00064 par->npdb = 0 ; 00065 par->pdb_lst = NULL ; 00066 par->flag_do_asa_and_volume_calculations=1; 00067 par->db_run=M_DB_RUN; 00068 00069 return par ; 00070 }
| int is_fpocket_opt | ( | const char | opt | ) |
## FUNCTION: is_fpocket_opt
## SPECIFICATION: Say either or not a single letter code is a fpocket option (excluding input file/list option.)
## PARAMETRES: @ const char opt: The one letter code option.
## RETURN: integer: 1 if it's a valid option parmeter, 0 if not.
Definition at line 529 of file fparams.c.
References M_PAR_BASIC_VOL_DIVISION, M_PAR_CLUST_MAX_DIST, M_PAR_MAX_ASHAPE_SIZE, M_PAR_MC_ITER, M_PAR_MIN_APOL_NEIGH, M_PAR_MIN_ASHAPE_SIZE, M_PAR_MIN_POCK_NB_ASPH, M_PAR_REFINE_DIST, M_PAR_REFINE_MIN_NAPOL_AS, M_PAR_SL_MAX_DIST, and M_PAR_SL_MIN_NUM_NEIGH.
Referenced by get_dpocket_args(), get_mdpocket_args(), and get_tpocket_args().
00530 { 00531 if( opt == M_PAR_MAX_ASHAPE_SIZE || 00532 opt == M_PAR_MIN_ASHAPE_SIZE || 00533 opt == M_PAR_MIN_APOL_NEIGH || 00534 opt == M_PAR_CLUST_MAX_DIST || 00535 opt == M_PAR_SL_MAX_DIST || 00536 opt == M_PAR_SL_MIN_NUM_NEIGH || 00537 opt == M_PAR_MC_ITER || 00538 opt == M_PAR_BASIC_VOL_DIVISION || 00539 opt == M_PAR_MIN_POCK_NB_ASPH || 00540 opt == M_PAR_REFINE_DIST || 00541 opt == M_PAR_REFINE_MIN_NAPOL_AS) { 00542 return 1 ; 00543 } 00544 00545 return 0 ; 00546 }
| int parse_asph_max_size | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_asph_max_size
## SPECIFICATION: Parsing function for the maximum radius of each alpha shpere
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 358 of file fparams.c.
References s_fparams::asph_max_size, M_NO_SIGN, and str_is_float().
Referenced by get_fpocket_args().
00359 { 00360 if(str_is_float(str, M_NO_SIGN)) { 00361 p->asph_max_size = (float) atof(str) ; 00362 } 00363 else { 00364 fprintf(stdout, "! Invalid value (%s) given for the max radius of alpha shperes.\n", str) ; 00365 return 1 ; 00366 } 00367 00368 return 0 ; 00369 }
| int parse_asph_min_size | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_asph_min_size
## SPECIFICATION: Parsing function for the minimum radius of each alpha shpere
## PARAMETERS: @ char *str: The string to parse @ s_fparams *p: The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 330 of file fparams.c.
References s_fparams::asph_min_size, M_NO_SIGN, and str_is_float().
Referenced by get_fpocket_args().
00331 { 00332 if(str_is_float(str, M_NO_SIGN)) { 00333 p->asph_min_size = (float) atof(str) ; 00334 } 00335 else { 00336 fprintf(stdout, "! Invalid value (%s) given for the min radius of alpha shperes.\n", str) ; 00337 return 1 ; 00338 } 00339 00340 return 0 ; 00341 }
| int parse_basic_vol_div | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_basic_vol_div
## SPECIFICATION: Parsing function for the number of iteration for the basic volume calculation.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
Definition at line 415 of file fparams.c.
References s_fparams::basic_volume_div, M_NO_SIGN, and str_is_number().
Referenced by get_fpocket_args().
00416 { 00417 if(str_is_number(str, M_NO_SIGN)) { 00418 p->basic_volume_div = (int) atoi(str) ; 00419 } 00420 else { 00421 fprintf(stdout, "! Invalid value (%s) given for the precision of the basic volume calculation.\n", str) ; 00422 return 1 ; 00423 } 00424 00425 return 0 ; 00426 }
| int parse_clust_max_dist | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_clust_max_dist
## SPECIFICATION: Parsing function for the distance criteria first clustering algorithm.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 214 of file fparams.c.
References s_fparams::clust_max_dist, M_NO_SIGN, and str_is_float().
Referenced by get_fpocket_args().
00215 { 00216 if(str_is_float(str, M_NO_SIGN)) { 00217 p->clust_max_dist = atof(str) ; 00218 } 00219 else { 00220 fprintf(stdout, "! Invalid value (%s) given for the single linkage max dist.\n", str) ; 00221 return 1 ; 00222 } 00223 00224 return 0 ; 00225 }
| int parse_mc_niter | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_mc_niter
## SPECIFICATION: Parsing function for the number of iteration for the Monte Carlo volume calculation.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 387 of file fparams.c.
References M_NO_SIGN, s_fparams::nb_mcv_iter, and str_is_float().
Referenced by get_fpocket_args().
00388 { 00389 if(str_is_float(str, M_NO_SIGN)) { 00390 p->nb_mcv_iter = (int) atoi(str) ; 00391 } 00392 else { 00393 fprintf(stdout, "! Invalid value (%s) given for the number of monte-carlo iteration for the volume.\n", str) ; 00394 return 1 ; 00395 } 00396 00397 return 0 ; 00398 }
| int parse_min_apol_neigh | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_min_apol_neigh
## SPECIFICATION: Parsing function for the minimum number of apolar contacted atom for an alpha sphere to be considered as apolar.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid int), 1 if not
Definition at line 300 of file fparams.c.
References M_NO_SIGN, s_fparams::min_apol_neigh, and str_is_number().
Referenced by get_fpocket_args().
00301 { 00302 if(str_is_number(str, M_NO_SIGN)) { 00303 p->min_apol_neigh = (int) atoi(str) ; 00304 if(p->min_apol_neigh < 0) p->min_apol_neigh = 0 ; 00305 if(p->min_apol_neigh > 4) p->min_apol_neigh = 4 ; 00306 } 00307 else { 00308 fprintf(stdout, "! Invalid value (%s) given for the min radius of alpha shperes.\n", str) ; 00309 return 1 ; 00310 } 00311 00312 return 0 ; 00313 }
| int parse_min_pock_nb_asph | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_min_pock_nb_asph
## SPECIFICATION: Parsing function for the minimum number of alpha sphere per pocket.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
Definition at line 499 of file fparams.c.
References M_NO_SIGN, s_fparams::min_pock_nb_asph, and str_is_number().
Referenced by get_fpocket_args().
00500 { 00501 if(str_is_number(str, M_NO_SIGN)) { 00502 p->min_pock_nb_asph = (int) atoi(str) ; 00503 } 00504 else { 00505 fprintf(stdout, "! Invalid value (%s) given for the refine distance.\n", str) ; 00506 return 1 ; 00507 } 00508 00509 return 0 ; 00510 }
| int parse_refine_dist | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_refine_dist
## SPECIFICATION: Parsing function for the distance in the refine algorithm
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 443 of file fparams.c.
References M_NO_SIGN, s_fparams::refine_clust_dist, and str_is_float().
Referenced by get_fpocket_args().
00444 { 00445 if(str_is_float(str, M_NO_SIGN)) { 00446 p->refine_clust_dist = (float) atof(str) ; 00447 } 00448 else { 00449 fprintf(stdout, "! Invalid value (%s) given for the refine distance.\n", str) ; 00450 return 1 ; 00451 } 00452 00453 return 0 ; 00454 }
| int parse_refine_minaap | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_refine_min_apol
## SPECIFICATION: Parsing function for the minimum number of apolar sphere per pocket.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
Definition at line 471 of file fparams.c.
References M_NO_SIGN, s_fparams::refine_min_apolar_asphere_prop, and str_is_float().
Referenced by get_fpocket_args().
00472 { 00473 if(str_is_float(str, M_NO_SIGN)) { 00474 p->refine_min_apolar_asphere_prop = (float) atof(str) ; 00475 } 00476 else { 00477 fprintf(stdout, "! Invalid value (%s) given for the refine distance.\n", str) ; 00478 return 1 ; 00479 } 00480 00481 return 0 ; 00482 }
| int parse_sclust_max_dist | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_sclust_max_dist
## SPECIFICATION: Parsing function for the distance criteria in the single linkage clustering.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
Definition at line 243 of file fparams.c.
References M_NO_SIGN, s_fparams::sl_clust_max_dist, and str_is_float().
Referenced by get_fpocket_args().
00244 { 00245 if(str_is_float(str, M_NO_SIGN)) { 00246 p->sl_clust_max_dist = atof(str) ; 00247 } 00248 else { 00249 fprintf(stdout, "! Invalid value (%s) given for the single linkage max dist.\n", str) ; 00250 return 1 ; 00251 } 00252 00253 return 0 ; 00254 }
| int parse_sclust_min_nneigh | ( | char * | str, | |
| s_fparams * | p | |||
| ) |
## FUNCTION: parse_sclust_min_nneigh
## SPECIFICATION: Parsing function for the number of neighbours in the single linkage clustering.
## PARAMETERS: @ char *str : The string to parse @ s_fparams *p : The structure than will contain the parsed parameter
## RETURN: int: 0 if the parameter is valid (here a valid int), 1 if not
Definition at line 271 of file fparams.c.
References M_NO_SIGN, s_fparams::sl_clust_min_nneigh, and str_is_number().
Referenced by get_fpocket_args().
00272 { 00273 if(str_is_number(str, M_NO_SIGN)) { 00274 p->sl_clust_min_nneigh = atoi(str) ; 00275 } 00276 else { 00277 fprintf(stdout, "! Invalid value (%s) given for the single linkage max dist.\n", str) ; 00278 return 1 ; 00279 } 00280 00281 return 0 ; 00282 }
| void print_fparams | ( | s_fparams * | p, | |
| FILE * | f | |||
| ) |
## FUNCTION: print_fparams
## SPECIFICATION: Print function
## PARAMETRES: @ s_fparams *p : Parameters to print @ FILE *f : Buffer to write in
## RETURN:
Definition at line 611 of file fparams.c.
References s_fparams::asph_max_size, s_fparams::asph_min_size, s_fparams::basic_volume_div, s_fparams::clust_max_dist, s_fparams::min_apol_neigh, s_fparams::nb_mcv_iter, s_fparams::pdb_path, s_fparams::refine_clust_dist, s_fparams::refine_min_apolar_asphere_prop, s_fparams::sl_clust_max_dist, and s_fparams::sl_clust_min_nneigh.
00612 { 00613 if(p) { 00614 fprintf(f, "==============\nParameters of fpocket: \n"); 00615 fprintf(f, "> Minimum alpha sphere radius: %f\n", p->asph_min_size); 00616 fprintf(f, "> Maximum alpha sphere radius: %f\n", p->asph_max_size); 00617 fprintf(f, "> Minimum number of apolar neighbor: %d\n", p->min_apol_neigh); 00618 fprintf(f, "> Maximum distance for first clustering algorithm: %f \n", p->clust_max_dist) ; 00619 fprintf(f, "> Single linkage clustering distance: %f\n", p->sl_clust_max_dist); 00620 fprintf(f, "> Single linkage clustering neighbor: %d\n", p->sl_clust_min_nneigh); 00621 fprintf(f, "> Refine clustering distance: %f\n", p->refine_clust_dist); 00622 fprintf(f, "> Min number of apolar sphere in refine to keep a pocket: %f\n", p->refine_min_apolar_asphere_prop) ; 00623 fprintf(f, "> Monte carlo iterations: %d\n", p->nb_mcv_iter); 00624 fprintf(f, "> Basic method for volume calculation: %d\n", p->basic_volume_div); 00625 fprintf(f, "> PDB file: %s\n", p->pdb_path); 00626 fprintf(f, "==============\n"); 00627 } 00628 else fprintf(f, "> No parameters detected\n"); 00629 }
| void print_pocket_usage | ( | FILE * | f | ) |
## FUNCTION: print_pocket_usage
## SPECIFICATION: Displaying usage of the programm in the given buffer
## PARAMETRES: @ FILE *f: buffer to print in
## RETURN: void
Definition at line 590 of file fparams.c.
References M_FP_USAGE.
Referenced by get_fpocket_args(), and main().
00591 { 00592 f = (f == NULL) ? stdout:f ; 00593 00594 fprintf(f, M_FP_USAGE) ; 00595 }
1.5.6