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Comparing branches/new_design/OOPSE-4/src/brains/MoleculeCreator.cpp (file contents):
Revision 1732 by tim, Fri Nov 5 23:38:27 2004 UTC vs.
Revision 1733 by tim, Fri Nov 12 06:19:04 2004 UTC

# Line 37 | Line 37 | Molecule* MoleculeCreator::createMolecule(ForceField*
37   namespace oopse {
38  
39   Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
40 <    Molecule* mol = new Molecule(stampId, globalIndex);
40 >    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
41      
42      //create atoms
43      Atom* atom;
# Line 117 | Line 117 | Atom* MoleculeCreator::createAtom(ForceField* ff, Mole
117  
118      atomType =  ff->getAtomType(stamp->getType());
119  
120 +    if (bondType == NULL) {
121 +        sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
122 +                   stamp->getType());
123 +
124 +        painCave.isFatal = 1;
125 +        simError();
126 +    }
127 +    
128      //below code still have some kind of hard-coding smell
129      if (stamp->haveOrientation()){
130          DirectionalAtom* dAtom;
# Line 152 | Line 160 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
160      Vector3d refCoor;
161      AtomStamp* atomStamp;
162      
163 <    nAtoms = stamp->getNMembers();
163 >    nAtoms = molStamp->getNMembers();
164  
165      RigidBody* rb = new RigidBody();
166      
# Line 163 | Line 171 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
171          atomStamp= molStamp->molStamp->getAtom(rbStamp->getMember(i));    
172          rb->addAtom(atom, atomStamp);
173      }
174 <    
174 >
175 >    //after all of the atoms are added, we need to calculate the reference coordinates
176      rb->calcRefCoords();
177 +
178 +    //set the local index of this rigid body, global index will be set later
179      rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
180 <    rb->setType(mol->getType() + "_" + itoa(mol.getNRigidBodies()));
180 >
181 >    //the rule for naming rigidbody MoleculeName_RB_Integer
182 >    //The first part is the name of the molecule
183 >    //The second part is alway fixed as "RB"
184 >    //The third part is the index of the rigidbody defined in meta-data file
185 >    //For example, Butane_RB_0 is a valid rigid body name of butane molecule
186 >    rb->setType(mol->getType() + "_RB_" + itoa(mol.getNRigidBodies()));
187      
188      return rb;
189   }    
# Line 183 | Line 200 | Bond* MoleculeCreator::createBond(ForceField* ff, Mole
200      
201      bondType = ff->getBondType(atomA, atomB);
202  
203 +    if (bondType == NULL) {
204 +        sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
205 +                   atomA->getType().c_str(),
206 +                   atomB->getType().c_str());
207 +
208 +        painCave.isFatal = 1;
209 +        simError();
210 +    }
211      return new Bond(atomA, atomB, bondType);    
212   }    
213  
214   Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
215 <    BendType* benType;
215 >    BendType* bendType;
216      Atom* atomA;
217      Atom* atomB;
218      Atom* atomC;
# Line 199 | Line 224 | Bend* MoleculeCreator::createBend(ForceField* ff, Mole
224  
225      assert( atomA && atomB && atomC);
226      
227 <    benType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
227 >    bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
228  
229 <    return new Bond(atomA, atomB, benType);      
229 >    if (bendType == NULL) {
230 >        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
231 >                   atomA->getType().c_str(),
232 >                   atomB->getType().c_str(),
233 >                   atomC->getType().c_str());
234  
235 +        painCave.isFatal = 1;
236 +        simError();
237 +    }
238 +
239 +    return new Bond(atomA, atomB, bendType);      
240 +
241   }    
242  
243   Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
# Line 222 | Line 257 | Torsion* MoleculeCreator::createTorsion(ForceField* ff
257      torsionType = ff->getTosionType(atomA->getType(), atomB->getType(),
258                                                         atomC->getType(), atomD->getType());
259  
260 +    if (torsionType == NULL) {
261 +        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
262 +                   atomA->getType().c_str(),
263 +                   atomB->getType().c_str(),
264 +                   atomC->getType().c_str(),
265 +                   atomD->getType().c_str());
266 +
267 +        painCave.isFatal = 1;
268 +        simError();
269 +    }
270 +    
271      return new Torsion(atomA, atomB, torsionType);      
272   }    
273  

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