#include <string.h>#include <ctype.h>#include <stdio.h>#include <stdlib.h>#include "utils.h"Go to the source code of this file.
Functions | |
| float | pte_get_vdw_ray (const char *symbol) |
| float | pte_get_mass (const char *symbol) |
| float | pte_get_enegativity (const char *symbol) |
| int | is_valid_element (const char *str, int ignore_case) |
| int | element_in_std_res (char *res_name) |
| int | element_in_nucl_acid (char *res_name) |
| int | is_water (char *res_name) |
| int | is_valid_prot_element (const char *str, int ignore_case) |
| int | is_valid_nucl_acid_element (const char *str, int ignore_case) |
| int element_in_nucl_acid | ( | char * | res_name | ) |
----------------------------------------------------------------------------- ## FUNCTION: int element_in_nucl_acid(char *res_name) ----------------------------------------------------------------------------- ## SPECIFICATION: Compare resname to the list of standard nucleic acid residues. Return 1 if resname is in this list, 0 else. ----------------------------------------------------------------------------- ## PARAMETRES: @ char *res_name : The current residue name ----------------------------------------------------------------------------- ## RETURN: int -----------------------------------------------------------------------------
Definition at line 355 of file pertable.c.
References ST_n_standard_nucl_acid_names, and ST_standard_nucl_acid_names.
Referenced by guess_element(), and set_atom_based_descriptors().
00355 { 00356 int i; 00357 for(i=0;i<ST_n_standard_nucl_acid_names;i++){ 00358 if(!strncmp(res_name, ST_standard_nucl_acid_names[i],3)) return 1; 00359 } 00360 return 0; 00361 }
| int element_in_std_res | ( | char * | res_name | ) |
----------------------------------------------------------------------------- ## FUNCTION: int element_in_std_res(char *res_name) ----------------------------------------------------------------------------- ## SPECIFICATION: Compare resname to the list of standard protein resnames. Return 1 if resname is in this list, 0 else. ----------------------------------------------------------------------------- ## PARAMETRES: @ char *res_name : The current residue name ----------------------------------------------------------------------------- ## RETURN: int -----------------------------------------------------------------------------
Definition at line 333 of file pertable.c.
References ST_n_standard_res_names, and ST_standard_res_names.
Referenced by guess_element(), and set_atom_based_descriptors().
00333 { 00334 int i; 00335 for(i=0;i<ST_n_standard_res_names;i++){ 00336 if(!strncmp(res_name, ST_standard_res_names[i],3)) return 1; 00337 } 00338 return 0; 00339 }
| int is_valid_element | ( | const char * | str, | |
| int | ignore_case | |||
| ) |
## FUNCTION: is_valid_element
## SPECIFICATION: Check if a given string corresponds to an atom element.
## PARAMETERS: @ const char *str : The string to test @ int tcase : If = 1, dont take into account the case.
## RETURN: int: -1 if the strig is not an atom element, the index in the periodic table if so.
Definition at line 282 of file pertable.c.
References ST_nelem, ST_pte_symbol, and str_trim().
Referenced by check_is_valid_element(), and guess_element().
00283 { 00284 if(str == NULL) return -1 ; 00285 if(strlen(str) <= 0) return -1 ; 00286 00287 /* Use temporary variable to work on the string */ 00288 int i ; 00289 char str_tmp[strlen(str)+1] ; 00290 strcpy(str_tmp, str) ; 00291 00292 /* Remove spaces and case if asked*/ 00293 str_trim(str_tmp) ; 00294 if(ignore_case == 1) { 00295 str_tmp[0] = tolower(str_tmp[0]) ; 00296 str_tmp[1] = tolower(str_tmp[1]) ; 00297 } 00298 00299 /* Loop over */ 00300 for (i = 0; i < ST_nelem ; i++) { 00301 char tmp[3] ; 00302 tmp[0] = ST_pte_symbol[i][0] ; 00303 tmp[1] = ST_pte_symbol[i][1] ; 00304 00305 /* Remove case if asked */ 00306 if(ignore_case == 1) { 00307 tmp[0] = tolower(tmp[0]) ; 00308 tmp[1] = tolower(tmp[1]) ; 00309 } 00310 tmp[2] = '\0' ; 00311 00312 /* Do the comparison*/ 00313 if(strcmp(str_tmp, tmp) == 0) return i ; 00314 } 00315 00316 return -1 ; 00317 }
| int is_valid_nucl_acid_element | ( | const char * | str, | |
| int | ignore_case | |||
| ) |
----------------------------------------------------------------------------- ## FUNCTION: is_valid_nucl_acid_element ----------------------------------------------------------------------------- ## SPECIFICATION: Check if a given string corresponds to an atom element. ----------------------------------------------------------------------------- ## PARAMETERS: @ const char *str : The string to test @ int tcase : If = 1, dont take into account the case. ----------------------------------------------------------------------------- ## RETURN: int: -1 if the strig is not an atom element, the index in the periodic table if so. -----------------------------------------------------------------------------
Definition at line 437 of file pertable.c.
References ST_nucl_acid_nelem, ST_pte_nucl_acid_symbol, and str_trim().
Referenced by guess_element().
00438 { 00439 if(str == NULL) return -1 ; 00440 if(strlen(str) <= 0) return -1 ; 00441 /* Use temporary variable to work on the string */ 00442 int i ; 00443 char str_tmp[strlen(str)+1] ; 00444 strcpy(str_tmp, str) ; 00445 00446 00447 /* Remove spaces and case if asked*/ 00448 str_trim(str_tmp) ; 00449 if(ignore_case == 1) { 00450 str_tmp[0] = tolower(str_tmp[0]) ; 00451 str_tmp[1] = tolower(str_tmp[1]) ; 00452 } 00453 00454 /* Loop over standard protein element table*/ 00455 for (i = 0; i < ST_nucl_acid_nelem ; i++) { 00456 char tmp[3] ; 00457 tmp[0] = ST_pte_nucl_acid_symbol[i][0] ; 00458 tmp[1] = ST_pte_nucl_acid_symbol[i][1] ; 00459 00460 /* Remove case if asked */ 00461 if(ignore_case == 1) { 00462 tmp[0] = tolower(tmp[0]) ; 00463 tmp[1] = tolower(tmp[1]) ; 00464 } 00465 tmp[2] = '\0' ; 00466 00467 /* Do the comparison*/ 00468 if(strncmp(str_tmp, tmp,1) == 0) return i ; 00469 } 00470 00471 return -1 ; 00472 }
| int is_valid_prot_element | ( | const char * | str, | |
| int | ignore_case | |||
| ) |
----------------------------------------------------------------------------- ## FUNCTION: is_valid_prot_element ----------------------------------------------------------------------------- ## SPECIFICATION: Check if a given string corresponds to an atom element. ----------------------------------------------------------------------------- ## PARAMETERS: @ const char *str : The string to test @ int tcase : If = 1, dont take into account the case. ----------------------------------------------------------------------------- ## RETURN: int: -1 if the strig is not an atom element, the index in the periodic table if so. -----------------------------------------------------------------------------
Definition at line 384 of file pertable.c.
References ST_prot_nelem, ST_pte_prot_symbol, and str_trim().
Referenced by guess_element().
00385 { 00386 if(str == NULL) return -1 ; 00387 if(strlen(str) <= 0) return -1 ; 00388 /* Use temporary variable to work on the string */ 00389 int i ; 00390 char str_tmp[strlen(str)+1] ; 00391 strcpy(str_tmp, str) ; 00392 00393 00394 /* Remove spaces and case if asked*/ 00395 str_trim(str_tmp) ; 00396 if(ignore_case == 1) { 00397 str_tmp[0] = tolower(str_tmp[0]) ; 00398 str_tmp[1] = tolower(str_tmp[1]) ; 00399 } 00400 00401 /* Loop over standard protein element table*/ 00402 for (i = 0; i < ST_prot_nelem ; i++) { 00403 char tmp[3] ; 00404 tmp[0] = ST_pte_prot_symbol[i][0] ; 00405 tmp[1] = ST_pte_prot_symbol[i][1] ; 00406 00407 /* Remove case if asked */ 00408 if(ignore_case == 1) { 00409 tmp[0] = tolower(tmp[0]) ; 00410 tmp[1] = tolower(tmp[1]) ; 00411 } 00412 tmp[2] = '\0' ; 00413 00414 /* Do the comparison*/ 00415 if(strncmp(str_tmp, tmp,1) == 0) return i ; 00416 } 00417 00418 return -1 ; 00419 }
| int is_water | ( | char * | res_name | ) |
Definition at line 363 of file pertable.c.
00363 { 00364 if(!strncmp(res_name, "HOH",3)||!strncmp(res_name, "WAT",3)) return 1; 00365 return 0; 00366 }
| float pte_get_enegativity | ( | const char * | symbol | ) |
## FUNCTION: pte_get_enegativity
## SPECIFICATION: Returns the electronegativity (Pauling) value for a given element
## PARAMETERS: @ const char *symbol: The symbol of the element in the periodic table
## RETURN: float: electrobegativity of Pauling corresponding to symbol
Definition at line 247 of file pertable.c.
References ST_nelem, ST_pte_electronegativity, and ST_pte_symbol.
Referenced by rpdb_read().
00248 { 00249 char atom[3] = "" ; 00250 00251 if (symbol != NULL) { 00252 atom[0] = (char) toupper((int) symbol[0]); 00253 atom[1] = (char) tolower((int) symbol[1]); 00254 atom[2] = '\0' ; 00255 00256 int i ; 00257 for (i = 0; i < ST_nelem ; i++) { 00258 if ( (ST_pte_symbol[i][0] == atom[0]) && (ST_pte_symbol[i][1] == atom[1]) ) { 00259 return ST_pte_electronegativity[i] ; 00260 } 00261 } 00262 } 00263 00264 return -1 ; 00265 }
| float pte_get_mass | ( | const char * | symbol | ) |
## FUNCTION: pte_get_mass
## SPECIFICATION: Returns the mass for a given element
## PARAMETERS: @ const char *symbol: The symbol of the element in the periodic table
## RETURN: float: mass corresponding to symbol
Definition at line 178 of file pertable.c.
References ST_nelem, ST_pte_mass, and ST_pte_symbol.
Referenced by rpdb_read().
00179 { 00180 char atom[3] ; 00181 if (symbol != NULL) { 00182 atom[0] = (char) toupper((int) symbol[0]); 00183 atom[1] = (char) tolower((int) symbol[1]); 00184 atom[2] = '\0' ; 00185 00186 int i ; 00187 for (i = 0; i < ST_nelem ; i++) { 00188 if ( (ST_pte_symbol[i][0] == atom[0]) && (ST_pte_symbol[i][1] == atom[1]) ) { 00189 00190 return ST_pte_mass[i] ; 00191 } 00192 } 00193 } 00194 00195 00196 return -1 ; 00197 }
| float pte_get_vdw_ray | ( | const char * | symbol | ) |
## FUNCTION: pte_get_vdw_ray
## SPECIFICATION: Returns the van der walls radius for a given element
## PARAMETERS: @ const char *symbol: The symbol of the element in the periodic table
## RETURN: float: vdw radius corresponding to symbol
Definition at line 213 of file pertable.c.
References ST_nelem, ST_pte_rvdw, and ST_pte_symbol.
Referenced by rpdb_read().
00214 { 00215 char atom[3] ; 00216 00217 if (symbol != NULL) { 00218 atom[0] = (char) toupper((int) symbol[0]); 00219 atom[1] = (char) tolower((int) symbol[1]); 00220 atom[2] = '\0' ; 00221 00222 int i ; 00223 for (i = 0; i < ST_nelem ; i++) { 00224 if ( (ST_pte_symbol[i][0] == atom[0]) && (ST_pte_symbol[i][1] == atom[1]) ) { 00225 return ST_pte_rvdw[i] ; 00226 } 00227 } 00228 } 00229 00230 return -1 ; 00231 }
1.5.6