xyz2pov/src/atom_parser.c

#define _FILE_OFFSET_BITS 64

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "atom_parser.h"

#define MK_STR(s) # s
#define STR_DEFINE(t, s) t = MK_STR(s)


struct linked_atom *head_main;
struct linked_atom *head_inUse;
int n_inUse;

int findAtomType_internal(char *, struct atom *);

void initializeParser(){
  char *token;
  char *delim = "\t ,;";
  struct linked_atom *temp_linked;
  const int buffer_size = 300;
  char lineBuffer[buffer_size]; 
  
  char in_filenameStd[500];
  char tempString[500];
  char *atPath;
  char *in_filenameSet;
  char *in_file_env = "_xyz2pov_AtomTypes_";
  FILE *in_file;

  head_main = (struct linked_atom *)malloc(sizeof(struct linked_atom));
  head_main->next = NULL;
  
  head_inUse = (struct linked_atom *)malloc(sizeof(struct linked_atom));
  head_inUse->next = NULL;

  n_inUse = 0;

  // generate the AtomTypes Name
    
  strcpy( in_filenameStd, "AtomTypes" ); 
  
  // attempt to open the file in the current directory first.
  
  in_file = fopen( in_filenameStd, "r" );
  
  if( in_file == NULL ){
    
    // next see if the force path enviorment variable is set
    
    in_filenameSet = getenv( in_file_env );
    if( in_filenameSet != NULL ) {
      
      in_file = fopen(in_filenameSet, "r");
      
      if(in_file == NULL){
        
        fprintf(stderr,
                "Error reading AtomTypes file. The _xyz2pov_AtomTypes_\n"
                "enviorment variable was set incorrectly.\n");
        exit(8);
      }
    }
    else{
      STR_DEFINE(atPath, TYPES_PATH );      
      
      strcpy( tempString, atPath );
      strcat( tempString, "/" );
      strcat( tempString, in_filenameStd );
      strcpy( in_filenameStd, tempString );
      
      in_file = fopen( in_filenameStd, "r" );
      
      if( in_file == NULL ){
        
        fprintf(stderr,
                "Error opening the AtomTypes definition file: %s\n"
                "Have you tried setting the _xyz2pov_AtomTypes_ environment "
                "vairable?\n",
                in_filenameStd );
        exit(8);
      }
    }
  }
   
  
  while(fgets(lineBuffer, sizeof(lineBuffer), in_file) != NULL){
    
    if(lineBuffer[0] == '#' || lineBuffer[0] == '\n'){
      continue;
    }

    token = strtok(lineBuffer, delim);
    sscanf(token, "%s", head_main->myAtom.name);
    strtok(NULL, delim);
    strtok(NULL, delim);
    strtok(NULL, delim);
    token = strtok(NULL, delim);
    sscanf(token, "%lf", &head_main->myAtom.vanDerWallRadii);
    token = strtok(NULL, delim);
    sscanf(token, "%lf", &head_main->myAtom.covalentRadii);
    token = strtok(NULL, delim);
    sscanf(token, "%d", &head_main->myAtom.red);
    token = strtok(NULL, delim);
    sscanf(token, "%d", &head_main->myAtom.green);
    token = strtok(NULL, delim);
    sscanf(token, "%d", &head_main->myAtom.blue);
    
    temp_linked = (struct linked_atom *)malloc(sizeof(struct linked_atom));
    temp_linked->next = head_main;
    head_main = temp_linked;
  }

  fclose(in_file);
  return;
}
  

int findAtomType_internal(char *typeKey, struct atom *dummy_plug){

  struct linked_atom *link;

  link = head_main->next;

  while(link != NULL){

    if(!strcmp(link->myAtom.name, typeKey)){
      strcpy(dummy_plug->name, link->myAtom.name);
      dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii;
      dummy_plug->covalentRadii = link->myAtom.covalentRadii;
      dummy_plug->red = link->myAtom.red;
      dummy_plug->green = link->myAtom.green;
      dummy_plug->blue = link->myAtom.blue;
      
      return 1;
    }
    link = link->next;
  }
  return 0;
}


void update_types(char *new_key){
  
  int found = 0;
  
  struct linked_atom *link;
  
  link = head_inUse->next;
  
  while(link != NULL){
    
    if(!strcmp(link->myAtom.name, new_key)){
      found = 1;
    }
  
    link = link->next;
  }

  if(!found){
    found = findAtomType_internal(new_key, &head_inUse->myAtom);
    if(!found){
      fprintf(stderr, "Atom Type %s, not found!\n",
              new_key);
      exit(8);
    }
    
    link = (struct linked_atom *)malloc(sizeof(struct linked_atom));

    link->next = head_inUse;
    head_inUse = link;

    n_inUse++;
  }

  
}

int get_n_inUse(void){
  return n_inUse;
}


int findAtomType(char *typeKey, struct atom *dummy_plug){

  struct linked_atom *link;

  link = head_inUse->next;

  while(link != NULL){

    if(!strcmp(link->myAtom.name, typeKey)){
      strcpy(dummy_plug->name, link->myAtom.name);
      dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii;
      dummy_plug->covalentRadii = link->myAtom.covalentRadii;
      dummy_plug->red = link->myAtom.red;
      dummy_plug->green = link->myAtom.green;
      dummy_plug->blue = link->myAtom.blue;
      
      return 1;
    }
    link = link->next;
  }
  return 0;
}


struct linked_atom *get_type_list(){
  
  return head_inUse;
}

void clean_type_list(){

  struct linked_atom *current_atom;
  struct linked_atom *next_atom; /* place holders */
  
  
  current_atom = head_inUse->next;
  
  while(current_atom != NULL){
    
    next_atom = current_atom->next;
    free(current_atom);
    current_atom = next_atom;
  }
  
  head_inUse->next = NULL;
}
Revision:	1095
Committed:	Mon Apr 5 19:34:21 2004 UTC (21 years, 7 months ago) by mmeineke
Content type:	text/plain
File size:	5059 byte(s)
Log Message:	more gcc friendly configure script who knows
#	Content
1	#define _FILE_OFFSET_BITS 64
2
3	#include <stdio.h>
4	#include <stdlib.h>
5	#include <string.h>
6
7	#include "atom_parser.h"
8
9	#define MK_STR(s) # s
10	#define STR_DEFINE(t, s) t = MK_STR(s)
11
12
13	struct linked_atom *head_main;
14	struct linked_atom *head_inUse;
15	int n_inUse;
16
17	int findAtomType_internal(char , struct atom );
18
19	void initializeParser(){
20	char *token;
21	char *delim = "\t ,;";
22	struct linked_atom *temp_linked;
23	const int buffer_size = 300;
24	char lineBuffer[buffer_size];
25
26	char in_filenameStd[500];
27	char tempString[500];
28	char *atPath;
29	char *in_filenameSet;
30	char *in_file_env = "_xyz2pov_AtomTypes_";
31	FILE *in_file;
32
33	head_main = (struct linked_atom *)malloc(sizeof(struct linked_atom));
34	head_main->next = NULL;
35
36	head_inUse = (struct linked_atom *)malloc(sizeof(struct linked_atom));
37	head_inUse->next = NULL;
38
39	n_inUse = 0;
40
41	// generate the AtomTypes Name
42
43	strcpy( in_filenameStd, "AtomTypes" );
44
45	// attempt to open the file in the current directory first.
46
47	in_file = fopen( in_filenameStd, "r" );
48
49	if( in_file == NULL ){
50
51	// next see if the force path enviorment variable is set
52
53	in_filenameSet = getenv( in_file_env );
54	if( in_filenameSet != NULL ) {
55
56	in_file = fopen(in_filenameSet, "r");
57
58	if(in_file == NULL){
59
60	fprintf(stderr,
61	"Error reading AtomTypes file. The _xyz2pov_AtomTypes_\n"
62	"enviorment variable was set incorrectly.\n");
63	exit(8);
64	}
65	}
66	else{
67	STR_DEFINE(atPath, TYPES_PATH );
68
69	strcpy( tempString, atPath );
70	strcat( tempString, "/" );
71	strcat( tempString, in_filenameStd );
72	strcpy( in_filenameStd, tempString );
73
74	in_file = fopen( in_filenameStd, "r" );
75
76	if( in_file == NULL ){
77
78	fprintf(stderr,
79	"Error opening the AtomTypes definition file: %s\n"
80	"Have you tried setting the _xyz2pov_AtomTypes_ environment "
81	"vairable?\n",
82	in_filenameStd );
83	exit(8);
84	}
85	}
86	}
87
88
89	while(fgets(lineBuffer, sizeof(lineBuffer), in_file) != NULL){
90
91	if(lineBuffer[0] == '#' \|\| lineBuffer[0] == '\n'){
92	continue;
93	}
94
95	token = strtok(lineBuffer, delim);
96	sscanf(token, "%s", head_main->myAtom.name);
97	strtok(NULL, delim);
98	strtok(NULL, delim);
99	strtok(NULL, delim);
100	token = strtok(NULL, delim);
101	sscanf(token, "%lf", &head_main->myAtom.vanDerWallRadii);
102	token = strtok(NULL, delim);
103	sscanf(token, "%lf", &head_main->myAtom.covalentRadii);
104	token = strtok(NULL, delim);
105	sscanf(token, "%d", &head_main->myAtom.red);
106	token = strtok(NULL, delim);
107	sscanf(token, "%d", &head_main->myAtom.green);
108	token = strtok(NULL, delim);
109	sscanf(token, "%d", &head_main->myAtom.blue);
110
111	temp_linked = (struct linked_atom *)malloc(sizeof(struct linked_atom));
112	temp_linked->next = head_main;
113	head_main = temp_linked;
114	}
115
116	fclose(in_file);
117	return;
118	}
119
120
121	int findAtomType_internal(char typeKey, struct atom dummy_plug){
122
123	struct linked_atom *link;
124
125	link = head_main->next;
126
127	while(link != NULL){
128
129	if(!strcmp(link->myAtom.name, typeKey)){
130	strcpy(dummy_plug->name, link->myAtom.name);
131	dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii;
132	dummy_plug->covalentRadii = link->myAtom.covalentRadii;
133	dummy_plug->red = link->myAtom.red;
134	dummy_plug->green = link->myAtom.green;
135	dummy_plug->blue = link->myAtom.blue;
136
137	return 1;
138	}
139	link = link->next;
140	}
141	return 0;
142	}
143
144
145	void update_types(char *new_key){
146
147	int found = 0;
148
149	struct linked_atom *link;
150
151	link = head_inUse->next;
152
153	while(link != NULL){
154
155	if(!strcmp(link->myAtom.name, new_key)){
156	found = 1;
157	}
158
159	link = link->next;
160	}
161
162	if(!found){
163	found = findAtomType_internal(new_key, &head_inUse->myAtom);
164	if(!found){
165	fprintf(stderr, "Atom Type %s, not found!\n",
166	new_key);
167	exit(8);
168	}
169
170	link = (struct linked_atom *)malloc(sizeof(struct linked_atom));
171
172	link->next = head_inUse;
173	head_inUse = link;
174
175	n_inUse++;
176	}
177
178
179	}
180
181	int get_n_inUse(void){
182	return n_inUse;
183	}
184
185
186	int findAtomType(char typeKey, struct atom dummy_plug){
187
188	struct linked_atom *link;
189
190	link = head_inUse->next;
191
192	while(link != NULL){
193
194	if(!strcmp(link->myAtom.name, typeKey)){
195	strcpy(dummy_plug->name, link->myAtom.name);
196	dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii;
197	dummy_plug->covalentRadii = link->myAtom.covalentRadii;
198	dummy_plug->red = link->myAtom.red;
199	dummy_plug->green = link->myAtom.green;
200	dummy_plug->blue = link->myAtom.blue;
201
202	return 1;
203	}
204	link = link->next;
205	}
206	return 0;
207	}
208
209
210	struct linked_atom *get_type_list(){
211
212	return head_inUse;
213	}
214
215	void clean_type_list(){
216
217	struct linked_atom *current_atom;
218	struct linked_atom next_atom; / place holders */
219
220
221	current_atom = head_inUse->next;
222
223	while(current_atom != NULL){
224
225	next_atom = current_atom->next;
226	free(current_atom);
227	current_atom = next_atom;
228	}
229
230	head_inUse->next = NULL;
231	}