5 |
|
* non-exclusive, royalty free, license to use, modify and |
6 |
|
* redistribute this software in source and binary code form, provided |
7 |
|
* that the following conditions are met: |
8 |
– |
* |
8 |
|
* 1. Acknowledgement of the program authors must be made in any |
9 |
|
* publication of scientific results based in part on use of the |
10 |
|
* program. An acceptable form of acknowledgement is citation of |
289 |
|
return; |
290 |
|
} else |
291 |
|
return; |
292 |
+ |
|
293 |
+ |
AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType(); |
294 |
+ |
std::string bn = baseTypeName(at); |
295 |
|
|
296 |
|
if (posOnly_){ |
297 |
|
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
298 |
|
atomInfo = atomData->nextAtomInfo(i) ) { |
299 |
|
if (atomInfo->hasCharge) { |
300 |
|
sprintf(buffer, |
301 |
< |
"%s%15.8f%15.8f%15.8f%15.8f", |
302 |
< |
atomInfo->atomTypeName.c_str(), |
303 |
< |
atomInfo->pos[0], |
304 |
< |
atomInfo->pos[1], |
305 |
< |
atomInfo->pos[2], |
306 |
< |
atomInfo->charge); |
301 |
> |
"%s%15.8f%15.8f%15.8f%15.8f", |
302 |
> |
bn.c_str(), |
303 |
> |
atomInfo->pos[0], |
304 |
> |
atomInfo->pos[1], |
305 |
> |
atomInfo->pos[2], |
306 |
> |
atomInfo->charge); |
307 |
|
} else { |
308 |
|
sprintf(buffer, |
309 |
|
"%s%15.8f%15.8f%15.8f", |
310 |
< |
atomInfo->atomTypeName.c_str(), |
311 |
< |
atomInfo->pos[0], |
312 |
< |
atomInfo->pos[1], |
313 |
< |
atomInfo->pos[2]); |
310 |
> |
bn.c_str(), |
311 |
> |
atomInfo->pos[0], |
312 |
> |
atomInfo->pos[1], |
313 |
> |
atomInfo->pos[2]); |
314 |
|
} |
315 |
|
frame.push_back(buffer); |
316 |
|
} |
320 |
|
if (atomInfo->hasCharge) { |
321 |
|
sprintf(buffer, |
322 |
|
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
323 |
< |
atomInfo->atomTypeName.c_str(), |
323 |
> |
bn.c_str(), |
324 |
|
atomInfo->pos[0], |
325 |
|
atomInfo->pos[1], |
326 |
|
atomInfo->pos[2], |
331 |
|
} else { |
332 |
|
sprintf(buffer, |
333 |
|
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
334 |
< |
atomInfo->atomTypeName.c_str(), |
334 |
> |
bn.c_str(), |
335 |
|
atomInfo->pos[0], |
336 |
|
atomInfo->pos[1], |
337 |
|
atomInfo->pos[2], |
375 |
|
outStream << *i << std::endl; |
376 |
|
} |
377 |
|
|
378 |
+ |
std::string XYZVisitor::trimmedName(const std::string&atomTypeName) { |
379 |
+ |
return atomTypeName.substr(0, atomTypeName.find('-')); |
380 |
+ |
} |
381 |
+ |
|
382 |
+ |
std::string XYZVisitor::baseTypeName(AtomType* at) { |
383 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
384 |
+ |
return ayb[ayb.size()-1]->getName(); |
385 |
+ |
} |
386 |
+ |
|
387 |
|
const std::string XYZVisitor::toString() { |
388 |
|
char buffer[65535]; |
389 |
|
std::string result; |