146 |
|
compList(stamps, simParams, moleculeStampPairs); |
147 |
|
|
148 |
|
//create SimInfo |
149 |
< |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
150 |
< |
|
149 |
> |
SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
150 |
> |
|
151 |
|
//gather parameters (SimCreator only retrieves part of the parameters) |
152 |
|
gatherParameters(info, mdFileName); |
153 |
|
|
397 |
|
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
398 |
|
int i; |
399 |
|
char * id; |
400 |
– |
LinkedMolStamp* extractedStamp = NULL; |
400 |
|
MoleculeStamp * currentStamp; |
401 |
|
Component** the_components = simParams->getComponents(); |
402 |
|
int n_components = simParams->getNComponents(); |
417 |
|
} |
418 |
|
|
419 |
|
id = the_components[i]->getType(); |
420 |
< |
|
421 |
< |
extractedStamp = stamps->extractMolStamp(id); |
422 |
< |
if (extractedStamp == NULL) { |
420 |
> |
|
421 |
> |
currentStamp = stamps->getMolStamp(id); |
422 |
> |
if (currentStamp == NULL) { |
423 |
|
sprintf(painCave.errMsg, |
424 |
|
"SimCreator error: Component \"%s\" was not found in the " |
425 |
|
"list of declared molecules\n", id); |
428 |
|
simError(); |
429 |
|
} |
430 |
|
|
432 |
– |
currentStamp = extractedStamp->getStamp(); |
433 |
– |
|
434 |
– |
|
431 |
|
moleculeStampPairs.push_back( |
432 |
|
std::make_pair(currentStamp, the_components[i]->getNMol())); |
433 |
|
} //end for (i = 0; i < n_components; i++) |