| 226 |
|
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
| 227 |
|
|
| 228 |
|
if (molInfo.nBonds > 0) |
| 229 |
< |
molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
| 229 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
| 230 |
|
else |
| 231 |
|
molInfo.myBonds = NULL; |
| 232 |
|
|
| 233 |
|
if (molInfo.nBends > 0) |
| 234 |
< |
molInfo.myBends = new (Bend *) [molInfo.nBends]; |
| 234 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
| 235 |
|
else |
| 236 |
|
molInfo.myBends = NULL; |
| 237 |
|
|
| 238 |
|
if (molInfo.nTorsions > 0) |
| 239 |
< |
molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
| 239 |
> |
molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
| 240 |
|
else |
| 241 |
|
molInfo.myTorsions = NULL; |
| 242 |
|
|
| 948 |
|
|
| 949 |
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
| 950 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 951 |
< |
|
| 951 |
> |
|
| 952 |
> |
// check for thermodynamic integration |
| 953 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 954 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 955 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 956 |
> |
info[i].useThermInt = 1; |
| 957 |
> |
|
| 958 |
> |
Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
| 959 |
> |
info[i].restraint = myRestraint; |
| 960 |
> |
} |
| 961 |
|
} |
| 962 |
|
|
| 963 |
|
//setup seed for random number generator |
| 1270 |
|
} |
| 1271 |
|
} |
| 1272 |
|
|
| 1273 |
+ |
strcpy(info[k].rawPotName, inFileName); |
| 1274 |
+ |
nameLength = strlen(info[k].rawPotName); |
| 1275 |
+ |
endTest = &(info[k].rawPotName[nameLength - 5]); |
| 1276 |
+ |
if (!strcmp(endTest, ".bass")){ |
| 1277 |
+ |
strcpy(endTest, ".raw"); |
| 1278 |
+ |
} |
| 1279 |
+ |
else if (!strcmp(endTest, ".BASS")){ |
| 1280 |
+ |
strcpy(endTest, ".raw"); |
| 1281 |
+ |
} |
| 1282 |
+ |
else{ |
| 1283 |
+ |
endTest = &(info[k].rawPotName[nameLength - 4]); |
| 1284 |
+ |
if (!strcmp(endTest, ".bss")){ |
| 1285 |
+ |
strcpy(endTest, ".raw"); |
| 1286 |
+ |
} |
| 1287 |
+ |
else if (!strcmp(endTest, ".mdl")){ |
| 1288 |
+ |
strcpy(endTest, ".raw"); |
| 1289 |
+ |
} |
| 1290 |
+ |
else{ |
| 1291 |
+ |
strcat(info[k].rawPotName, ".raw"); |
| 1292 |
+ |
} |
| 1293 |
+ |
} |
| 1294 |
+ |
|
| 1295 |
|
#ifdef IS_MPI |
| 1296 |
|
|
| 1297 |
|
} |
