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root/group/trunk/OOPSE-2.0/src/brains/MoleculeCreator.cpp
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Comparing trunk/OOPSE-2.0/src/brains/MoleculeCreator.cpp (file contents):
Revision 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2087 by gezelter, Tue Mar 8 21:06:49 2005 UTC

# Line 52 | Line 52
52  
53   #include "brains/MoleculeCreator.hpp"
54   #include "primitives/GhostBend.hpp"
55 + #include "primitives/GhostTorsion.hpp"
56   #include "types/DirectionalAtomType.hpp"
57   #include "types/FixedBondType.hpp"
58   #include "utils/simError.h"
# Line 252 | Line 253 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
253      //The third part is the index of the rigidbody defined in meta-data file
254      //For example, Butane_RB_0 is a valid rigid body name of butane molecule
255      /**@todo replace itoa by lexi_cast */
256 <    rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
257 <    
256 >    std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
257 >    rb->setType(mol->getType() + "_RB_" + s.c_str());
258 >
259      return rb;
260   }    
261  
# Line 376 | Line 378 | Torsion* MoleculeCreator::createTorsion(ForceField* ff
378   }    
379  
380   Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
379 –    TorsionType* torsionType;
380 –    Atom* atomA;
381 –    Atom* atomB;
382 –    Atom* atomC;
383 –    Atom* atomD;
381  
382 <    atomA = mol->getAtomAt(stamp->getA());
383 <    atomB = mol->getAtomAt(stamp->getB());
384 <    atomC = mol->getAtomAt(stamp->getC());
385 <    atomD = mol->getAtomAt(stamp->getD());
389 <
390 <    assert(atomA && atomB && atomC && atomD);
391 <    
392 <    torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
393 <                                                       atomC->getType(), atomD->getType());
382 >    Atom* atomA = mol->getAtomAt(stamp->getA());
383 >    Atom* atomB = mol->getAtomAt(stamp->getB());
384 >    Atom* atomC = mol->getAtomAt(stamp->getC());
385 >    Torsion* torsion;
386  
387 <    if (torsionType == NULL) {
388 <        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
397 <                   atomA->getType().c_str(),
398 <                   atomB->getType().c_str(),
399 <                   atomC->getType().c_str(),
400 <                   atomD->getType().c_str());
387 >    if (stamp->getD() != -1) {
388 >        Atom* atomD = mol->getAtomAt(stamp->getD());
389  
390 <        painCave.isFatal = 1;
391 <        simError();
390 >        assert(atomA && atomB && atomC && atomD);
391 >        
392 >        TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
393 >                                                           atomC->getType(), atomD->getType());
394 >
395 >        if (torsionType == NULL) {
396 >            sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
397 >                       atomA->getType().c_str(),
398 >                       atomB->getType().c_str(),
399 >                       atomC->getType().c_str(),
400 >                       atomD->getType().c_str());
401 >
402 >            painCave.isFatal = 1;
403 >            simError();
404 >        }
405 >        
406 >        torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);      
407      }
408 <    
409 <    return new Torsion(atomA, atomB, atomC, atomD, torsionType);      
408 >    else {
409 >
410 >        DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
411 >        if (dAtom == NULL) {
412 >            sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
413 >            painCave.isFatal = 1;
414 >            simError();
415 >        }        
416 >
417 >        TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
418 >                                                           atomC->getType(), "GHOST");
419 >
420 >        if (torsionType == NULL) {
421 >            sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
422 >                       atomA->getType().c_str(),
423 >                       atomB->getType().c_str(),
424 >                       atomC->getType().c_str(),
425 >                       "GHOST");
426 >
427 >            painCave.isFatal = 1;
428 >            simError();
429 >        }
430 >        
431 >        torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);              
432 >    }
433 >
434 >    return torsion;
435   }    
436  
437   CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {

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