1 |
mmeineke |
60 |
#include <stdio.h> |
2 |
|
|
#include <stdlib.h> |
3 |
|
|
#include <string.h> |
4 |
|
|
|
5 |
|
|
#include "atom_parser.h" |
6 |
|
|
|
7 |
mmeineke |
638 |
#define MK_STR(s) # s |
8 |
|
|
#define STR_DEFINE(t, s) t = MK_STR(s) |
9 |
mmeineke |
60 |
|
10 |
mmeineke |
638 |
|
11 |
mmeineke |
60 |
struct linked_atom *head_main; |
12 |
|
|
struct linked_atom *head_inUse; |
13 |
|
|
int n_inUse; |
14 |
|
|
|
15 |
|
|
int findAtomType_internal(char *, struct atom *); |
16 |
|
|
|
17 |
|
|
void initializeParser(){ |
18 |
|
|
char *token; |
19 |
|
|
char *delim = "\t ,;"; |
20 |
|
|
struct linked_atom *temp_linked; |
21 |
|
|
const int buffer_size = 300; |
22 |
|
|
char lineBuffer[buffer_size]; |
23 |
|
|
|
24 |
mmeineke |
638 |
char in_filenameStd[500]; |
25 |
|
|
char tempString[500]; |
26 |
|
|
char *atPath; |
27 |
|
|
char *in_filenameSet; |
28 |
mmeineke |
60 |
char *in_file_env = "_xyz2pov_AtomTypes_"; |
29 |
|
|
FILE *in_file; |
30 |
|
|
|
31 |
|
|
head_main = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
32 |
|
|
head_main->next = NULL; |
33 |
|
|
|
34 |
|
|
head_inUse = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
35 |
|
|
head_inUse->next = NULL; |
36 |
|
|
|
37 |
|
|
n_inUse = 0; |
38 |
|
|
|
39 |
mmeineke |
638 |
// generate the AtomTypes Name |
40 |
|
|
|
41 |
|
|
strcpy( in_filenameStd, "AtomTypes" ); |
42 |
|
|
|
43 |
|
|
// attempt to open the file in the current directory first. |
44 |
|
|
|
45 |
|
|
in_file = fopen( in_filenameStd, "r" ); |
46 |
|
|
|
47 |
|
|
if( in_file == NULL ){ |
48 |
|
|
|
49 |
|
|
// next see if the force path enviorment variable is set |
50 |
|
|
|
51 |
|
|
in_filenameSet = getenv( in_file_env ); |
52 |
|
|
if( in_filenameSet != NULL ) { |
53 |
|
|
|
54 |
|
|
in_file = fopen(in_filenameSet, "r"); |
55 |
|
|
|
56 |
|
|
if(in_file == NULL){ |
57 |
|
|
|
58 |
|
|
fprintf(stderr, |
59 |
|
|
"Error reading AtomTypes file. The _xyz2pov_AtomTypes_\n" |
60 |
|
|
"enviorment variable was set incorrectly.\n"); |
61 |
|
|
exit(8); |
62 |
|
|
} |
63 |
|
|
} |
64 |
|
|
else{ |
65 |
|
|
STR_DEFINE(atPath, TYPES_PATH ); |
66 |
|
|
|
67 |
|
|
strcpy( tempString, atPath ); |
68 |
|
|
strcat( tempString, "/" ); |
69 |
|
|
strcat( tempString, in_filenameStd ); |
70 |
|
|
strcpy( in_filenameStd, tempString ); |
71 |
|
|
|
72 |
|
|
in_file = fopen( in_filenameStd, "r" ); |
73 |
|
|
|
74 |
|
|
if( in_file == NULL ){ |
75 |
|
|
|
76 |
|
|
fprintf(stderr, |
77 |
|
|
"Error opening the AtomTypes definition file: %s\n" |
78 |
|
|
"Have you tried setting the _xyz2pov_AtomTypes_ environment " |
79 |
|
|
"vairable?\n", |
80 |
|
|
in_filenameStd ); |
81 |
|
|
exit(8); |
82 |
|
|
} |
83 |
|
|
} |
84 |
mmeineke |
60 |
} |
85 |
mmeineke |
638 |
|
86 |
mmeineke |
60 |
|
87 |
|
|
while(fgets(lineBuffer, sizeof(lineBuffer), in_file) != NULL){ |
88 |
|
|
|
89 |
|
|
if(lineBuffer[0] == '#' || lineBuffer[0] == '\n'){ |
90 |
|
|
continue; |
91 |
|
|
} |
92 |
|
|
|
93 |
|
|
token = strtok(lineBuffer, delim); |
94 |
|
|
sscanf(token, "%s", head_main->myAtom.name); |
95 |
|
|
strtok(NULL, delim); |
96 |
|
|
strtok(NULL, delim); |
97 |
|
|
strtok(NULL, delim); |
98 |
|
|
token = strtok(NULL, delim); |
99 |
|
|
sscanf(token, "%lf", &head_main->myAtom.vanDerWallRadii); |
100 |
|
|
token = strtok(NULL, delim); |
101 |
|
|
sscanf(token, "%lf", &head_main->myAtom.covalentRadii); |
102 |
|
|
token = strtok(NULL, delim); |
103 |
|
|
sscanf(token, "%d", &head_main->myAtom.red); |
104 |
|
|
token = strtok(NULL, delim); |
105 |
|
|
sscanf(token, "%d", &head_main->myAtom.green); |
106 |
|
|
token = strtok(NULL, delim); |
107 |
|
|
sscanf(token, "%d", &head_main->myAtom.blue); |
108 |
|
|
|
109 |
|
|
temp_linked = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
110 |
|
|
temp_linked->next = head_main; |
111 |
|
|
head_main = temp_linked; |
112 |
|
|
} |
113 |
|
|
|
114 |
|
|
fclose(in_file); |
115 |
|
|
return; |
116 |
|
|
} |
117 |
|
|
|
118 |
|
|
|
119 |
|
|
int findAtomType_internal(char *typeKey, struct atom *dummy_plug){ |
120 |
|
|
|
121 |
|
|
struct linked_atom *link; |
122 |
|
|
|
123 |
|
|
link = head_main->next; |
124 |
|
|
|
125 |
|
|
while(link != NULL){ |
126 |
|
|
|
127 |
|
|
if(!strcmp(link->myAtom.name, typeKey)){ |
128 |
|
|
strcpy(dummy_plug->name, link->myAtom.name); |
129 |
|
|
dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii; |
130 |
|
|
dummy_plug->covalentRadii = link->myAtom.covalentRadii; |
131 |
|
|
dummy_plug->red = link->myAtom.red; |
132 |
|
|
dummy_plug->green = link->myAtom.green; |
133 |
|
|
dummy_plug->blue = link->myAtom.blue; |
134 |
|
|
|
135 |
|
|
return 1; |
136 |
|
|
} |
137 |
|
|
link = link->next; |
138 |
|
|
} |
139 |
|
|
return 0; |
140 |
|
|
} |
141 |
|
|
|
142 |
|
|
|
143 |
|
|
void update_types(char *new_key){ |
144 |
|
|
|
145 |
|
|
int found = 0; |
146 |
|
|
|
147 |
|
|
struct linked_atom *link; |
148 |
|
|
|
149 |
|
|
link = head_inUse->next; |
150 |
|
|
|
151 |
|
|
while(link != NULL){ |
152 |
|
|
|
153 |
|
|
if(!strcmp(link->myAtom.name, new_key)){ |
154 |
|
|
found = 1; |
155 |
|
|
} |
156 |
|
|
|
157 |
|
|
link = link->next; |
158 |
|
|
} |
159 |
|
|
|
160 |
|
|
if(!found){ |
161 |
|
|
found = findAtomType_internal(new_key, &head_inUse->myAtom); |
162 |
|
|
if(!found){ |
163 |
|
|
fprintf(stderr, "Atom Type %s, not found!\n", |
164 |
|
|
new_key); |
165 |
|
|
exit(8); |
166 |
|
|
} |
167 |
|
|
|
168 |
|
|
link = (struct linked_atom *)malloc(sizeof(struct linked_atom)); |
169 |
|
|
|
170 |
|
|
link->next = head_inUse; |
171 |
|
|
head_inUse = link; |
172 |
|
|
|
173 |
|
|
n_inUse++; |
174 |
|
|
} |
175 |
|
|
|
176 |
|
|
|
177 |
|
|
} |
178 |
|
|
|
179 |
|
|
int get_n_inUse(void){ |
180 |
|
|
return n_inUse; |
181 |
|
|
} |
182 |
|
|
|
183 |
|
|
|
184 |
|
|
int findAtomType(char *typeKey, struct atom *dummy_plug){ |
185 |
|
|
|
186 |
|
|
struct linked_atom *link; |
187 |
|
|
|
188 |
|
|
link = head_inUse->next; |
189 |
|
|
|
190 |
|
|
while(link != NULL){ |
191 |
|
|
|
192 |
|
|
if(!strcmp(link->myAtom.name, typeKey)){ |
193 |
|
|
strcpy(dummy_plug->name, link->myAtom.name); |
194 |
|
|
dummy_plug->vanDerWallRadii = link->myAtom.vanDerWallRadii; |
195 |
|
|
dummy_plug->covalentRadii = link->myAtom.covalentRadii; |
196 |
|
|
dummy_plug->red = link->myAtom.red; |
197 |
|
|
dummy_plug->green = link->myAtom.green; |
198 |
|
|
dummy_plug->blue = link->myAtom.blue; |
199 |
|
|
|
200 |
|
|
return 1; |
201 |
|
|
} |
202 |
|
|
link = link->next; |
203 |
|
|
} |
204 |
|
|
return 0; |
205 |
|
|
} |
206 |
|
|
|
207 |
|
|
|
208 |
|
|
struct linked_atom *get_type_list(){ |
209 |
|
|
|
210 |
|
|
return head_inUse; |
211 |
|
|
} |
212 |
|
|
|
213 |
|
|
void clean_type_list(){ |
214 |
|
|
|
215 |
|
|
struct linked_atom *current_atom; |
216 |
|
|
struct linked_atom *next_atom; /* place holders */ |
217 |
|
|
|
218 |
|
|
|
219 |
|
|
current_atom = head_inUse->next; |
220 |
|
|
|
221 |
|
|
while(current_atom != NULL){ |
222 |
|
|
|
223 |
|
|
next_atom = current_atom->next; |
224 |
|
|
free(current_atom); |
225 |
|
|
current_atom = next_atom; |
226 |
|
|
} |
227 |
|
|
|
228 |
|
|
head_inUse->next = NULL; |
229 |
|
|
} |