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#define _FILE_OFFSET_BITS 64 |
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mmeineke |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include "atom_parser.h" |
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mmeineke |
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#define MK_STR(s) # s |
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#define STR_DEFINE(t, s) t = MK_STR(s) |
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mmeineke |
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mmeineke |
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mmeineke |
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struct linked_atom *head_main; |
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struct linked_atom *head_inUse; |
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int n_inUse; |
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int findAtomType_internal(char *, struct atom *); |
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void initializeParser(){ |
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char *token; |
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char *delim = "\t ,;"; |
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struct linked_atom *temp_linked; |
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const int buffer_size = 300; |
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char lineBuffer[buffer_size]; |
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mmeineke |
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char in_filenameStd[500]; |
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char tempString[500]; |
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char *atPath; |
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char *in_filenameSet; |
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mmeineke |
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char *in_file_env = "_xyz2pov_AtomTypes_"; |
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FILE *in_file; |
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head_main = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
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head_main->next = NULL; |
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head_inUse = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
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head_inUse->next = NULL; |
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n_inUse = 0; |
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mmeineke |
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// generate the AtomTypes Name |
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strcpy( in_filenameStd, "AtomTypes" ); |
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// attempt to open the file in the current directory first. |
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in_file = fopen( in_filenameStd, "r" ); |
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if( in_file == NULL ){ |
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// next see if the force path enviorment variable is set |
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in_filenameSet = getenv( in_file_env ); |
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if( in_filenameSet != NULL ) { |
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in_file = fopen(in_filenameSet, "r"); |
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if(in_file == NULL){ |
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fprintf(stderr, |
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"Error reading AtomTypes file. The _xyz2pov_AtomTypes_\n" |
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"enviorment variable was set incorrectly.\n"); |
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exit(8); |
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} |
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} |
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else{ |
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STR_DEFINE(atPath, TYPES_PATH ); |
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strcpy( tempString, atPath ); |
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strcat( tempString, "/" ); |
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strcat( tempString, in_filenameStd ); |
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strcpy( in_filenameStd, tempString ); |
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in_file = fopen( in_filenameStd, "r" ); |
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if( in_file == NULL ){ |
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fprintf(stderr, |
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"Error opening the AtomTypes definition file: %s\n" |
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"Have you tried setting the _xyz2pov_AtomTypes_ environment " |
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"vairable?\n", |
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in_filenameStd ); |
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exit(8); |
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} |
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} |
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mmeineke |
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} |
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mmeineke |
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mmeineke |
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while(fgets(lineBuffer, sizeof(lineBuffer), in_file) != NULL){ |
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if(lineBuffer[0] == '#' || lineBuffer[0] == '\n'){ |
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continue; |
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} |
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token = strtok(lineBuffer, delim); |
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sscanf(token, "%s", head_main->myAtom.name); |
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strtok(NULL, delim); |
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strtok(NULL, delim); |
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strtok(NULL, delim); |
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token = strtok(NULL, delim); |
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sscanf(token, "%lf", &head_main->myAtom.vanDerWallRadii); |
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token = strtok(NULL, delim); |
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sscanf(token, "%lf", &head_main->myAtom.covalentRadii); |
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token = strtok(NULL, delim); |
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sscanf(token, "%d", &head_main->myAtom.red); |
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token = strtok(NULL, delim); |
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sscanf(token, "%d", &head_main->myAtom.green); |
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token = strtok(NULL, delim); |
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sscanf(token, "%d", &head_main->myAtom.blue); |
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temp_linked = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
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temp_linked->next = head_main; |
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head_main = temp_linked; |
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} |
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fclose(in_file); |
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return; |
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} |
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int findAtomType_internal(char *typeKey, struct atom *dummy_plug){ |
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struct linked_atom *link; |
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link = head_main->next; |
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while(link != NULL){ |
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if(!strcmp(link->myAtom.name, typeKey)){ |
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strcpy(dummy_plug->name, link->myAtom.name); |
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dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii; |
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dummy_plug->covalentRadii = link->myAtom.covalentRadii; |
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dummy_plug->red = link->myAtom.red; |
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dummy_plug->green = link->myAtom.green; |
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dummy_plug->blue = link->myAtom.blue; |
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return 1; |
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} |
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link = link->next; |
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} |
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return 0; |
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} |
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void update_types(char *new_key){ |
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int found = 0; |
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struct linked_atom *link; |
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link = head_inUse->next; |
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while(link != NULL){ |
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if(!strcmp(link->myAtom.name, new_key)){ |
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found = 1; |
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} |
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link = link->next; |
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} |
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if(!found){ |
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found = findAtomType_internal(new_key, &head_inUse->myAtom); |
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if(!found){ |
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fprintf(stderr, "Atom Type %s, not found!\n", |
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new_key); |
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exit(8); |
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} |
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link = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
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link->next = head_inUse; |
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head_inUse = link; |
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n_inUse++; |
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} |
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} |
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int get_n_inUse(void){ |
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return n_inUse; |
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} |
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int findAtomType(char *typeKey, struct atom *dummy_plug){ |
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struct linked_atom *link; |
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link = head_inUse->next; |
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while(link != NULL){ |
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if(!strcmp(link->myAtom.name, typeKey)){ |
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strcpy(dummy_plug->name, link->myAtom.name); |
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dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii; |
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dummy_plug->covalentRadii = link->myAtom.covalentRadii; |
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dummy_plug->red = link->myAtom.red; |
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dummy_plug->green = link->myAtom.green; |
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dummy_plug->blue = link->myAtom.blue; |
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return 1; |
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} |
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link = link->next; |
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} |
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return 0; |
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} |
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struct linked_atom *get_type_list(){ |
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return head_inUse; |
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} |
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void clean_type_list(){ |
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struct linked_atom *current_atom; |
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struct linked_atom *next_atom; /* place holders */ |
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current_atom = head_inUse->next; |
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while(current_atom != NULL){ |
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next_atom = current_atom->next; |
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free(current_atom); |
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current_atom = next_atom; |
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} |
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head_inUse->next = NULL; |
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} |