| 43 |
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int main(int argc, char* argv[]){ |
| 44 |
|
|
| 45 |
|
gengetopt_args_info args_info; |
| 46 |
< |
vector<Atype*> vdwAtypes; |
| 47 |
< |
vector<Atype*>::iterator iter; |
| 46 |
> |
|
| 47 |
> |
vector<Atype*> vdwAtypes; |
| 48 |
> |
vector<Atype*>::iterator i; |
| 49 |
> |
Atype* at; |
| 50 |
> |
vector<VDWAtom*> theAtoms; |
| 51 |
> |
vector<VDWAtom*>::iterator j; |
| 52 |
> |
VDWAtom* atom; |
| 53 |
> |
|
| 54 |
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double mass, rpar, eps; |
| 55 |
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string fileName; |
| 56 |
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char vdwFileName[2002]; |
| 62 |
|
char* ffPath; |
| 63 |
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char* eof_test; |
| 64 |
|
char* foo; |
| 65 |
+ |
char* myType; |
| 66 |
+ |
char* vType; |
| 67 |
|
int lineNum; |
| 68 |
|
int nTokens; |
| 61 |
– |
Atype* at; |
| 69 |
|
int FF; |
| 70 |
< |
vector <VDWAtom*> theAtoms; |
| 70 |
> |
short int gotMatch; |
| 71 |
|
|
| 72 |
|
//parse the command line options |
| 73 |
|
if (cmdline_parser (argc, argv, &args_info) != 0) |
| 184 |
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PDBread->setPDBfile(structureFileName); |
| 185 |
|
theAtoms = PDBread->getAtomList(); |
| 186 |
|
printf("Found %d atoms\n", theAtoms.size()); |
| 187 |
< |
|
| 187 |
> |
|
| 188 |
> |
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 189 |
> |
atom = *j; |
| 190 |
> |
myType = atom->getType(); |
| 191 |
> |
gotMatch = 0; |
| 192 |
> |
|
| 193 |
> |
for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
| 194 |
> |
at = *i; |
| 195 |
> |
vType = at->getType(); |
| 196 |
> |
|
| 197 |
> |
if (!strcasecmp(myType, vType)) { |
| 198 |
> |
atom->setMass(at->getMass()); |
| 199 |
> |
atom->setRpar(at->getRpar()); |
| 200 |
> |
atom->setEps(at->getEps()); |
| 201 |
> |
gotMatch = 1; |
| 202 |
> |
} |
| 203 |
> |
} |
| 204 |
> |
if (!gotMatch) { |
| 205 |
> |
printf("No matches found for %s, ", myType); |
| 206 |
> |
myType = atom->getBase(); |
| 207 |
> |
printf("trying with BaseType %s\n", myType); |
| 208 |
> |
for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
| 209 |
> |
at = *i; |
| 210 |
> |
vType = at->getType(); |
| 211 |
> |
if (!strcasecmp(myType, vType)) { |
| 212 |
> |
atom->setMass(at->getMass()); |
| 213 |
> |
atom->setRpar(at->getRpar()); |
| 214 |
> |
atom->setEps(at->getEps()); |
| 215 |
> |
gotMatch = 1; |
| 216 |
> |
} |
| 217 |
> |
} |
| 218 |
> |
} |
| 219 |
> |
|
| 220 |
> |
if (!gotMatch) { |
| 221 |
> |
printf("No matches found with BaseType!\n"); |
| 222 |
> |
} |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
//GridBuilder gb = new GridBuilder(); |
| 226 |
> |
//gb->findAxesAndOrigin(theAtoms); |
| 227 |
> |
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 228 |
> |
|
| 229 |
> |
|
| 230 |
|
} |
| 231 |
|
|
| 232 |
|
int count_tokens(char *line, char *delimiters) { |
