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root/group/trunk/OOPSE-2.0/src/types/MoleculeStamp.cpp
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Comparing trunk/OOPSE-2.0/src/types/MoleculeStamp.cpp (file contents):
Revision 2483 by tim, Mon Dec 5 18:23:30 2005 UTC vs.
Revision 2507 by tim, Sat Dec 10 16:54:40 2005 UTC

# Line 38 | Line 38
38   * University of Notre Dame has been advised of the possibility of
39   * such damages.
40   */
41 <
41 >
42 > #include <functional>
43   #include <iostream>
44 < #include <functional>
44 > #include <sstream>
45   #include "types/MoleculeStamp.hpp"
46   #include "utils/Tuple.hpp"
47  
48   namespace oopse {
49 +
50 + template<class ContainerType>
51 + std::string containerToString(ContainerType& cont) {
52 +    std::ostringstream oss;
53 +    oss << "(";
54 +    typename ContainerType::iterator i = cont.begin();
55 +    if (i != cont.end()) {
56 +        oss << *i;
57 +        ++i;
58 +    }
59 +    for (; i != cont.end();++i) {
60 +        oss << ", ";
61 +        oss << *i;
62 +    }
63 +    oss << ")";
64 +    return oss.str();
65 + }
66 +
67   MoleculeStamp::MoleculeStamp() {
68      DefineParameter(Name, "name");
69      
# Line 64 | Line 83 | bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
83   bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
84      bool ret = addIndexSensitiveStamp(atomStamps_, atom);
85      if (!ret) {
86 <        std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName()  << " Molecule\n";
86 >         std::cout<< "Error in Molecule " << getName()  << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n";
87      }
88      return ret;
89      
# Line 88 | Line 107 | bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp*
107   bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) {
108      bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody);
109      if (!ret) {
110 <        std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName()  << " Molecule\n";
110 >        std::cout<< "Error in Molecule " << getName()  << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n";
111      }
112      return ret;
113   }
# Line 143 | Line 162 | void MoleculeStamp::checkAtoms() {
162          std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n";
163      }
164  
165 + }
166 +
167 + void MoleculeStamp::checkBonds() {
168      //make sure index is not out of range
169      int natoms = getNAtoms();
170      for(int i = 0; i < getNBonds(); ++i) {
171          BondStamp* bondStamp = getBondStamp(i);
172          if (bondStamp->getA() >=  natoms && bondStamp->getB() >= natoms) {
173 <            std::cout << "Error in Molecule " << getName() <<  ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n";
173 >            std::cout << "Error in Molecule " << getName() <<  ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n";
174          }
175      }
176 < }
155 <
156 < void MoleculeStamp::checkBonds() {
176 >    
177      //make sure bonds are unique
178      std::set<std::pair<int, int> > allBonds;
179      for(int i = 0; i < getNBonds(); ++i) {
# Line 166 | Line 186 | void MoleculeStamp::checkBonds() {
186          
187          std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair);
188          if ( iter != allBonds.end()) {
189 <            std::cout << "Error in Molecule " << getName() << ": " << "Bond appears multiple times\n";
189 >            std::cout << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ")appears multiple times\n";
190          } else {
191              allBonds.insert(bondPair);
192          }
# Line 176 | Line 196 | void MoleculeStamp::checkBonds() {
196      for(int i = 0; i < getNBonds(); ++i) {
197          BondStamp* bondStamp = getBondStamp(i);
198          if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) {
199 <            std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
199 >            std::cout << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
200          }
201      }
202      
203   }
204  
185 – struct BendLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> {
186 –    bool operator()(IntTuple3 b1, IntTuple3 b2) {
187 –        return b1.first < b2.first
188 –             || (!(b2.first < b1.first) && b1.second < b2.second)
189 –             || (!(b2.first < b1.first) && !(b2.second < b2.second) && b1.third < b2.third);
190 –    }
191 – };
192 –
205   void MoleculeStamp::checkBends() {
206      for(int i = 0; i < getNBends(); ++i) {
207          BendStamp* bendStamp = getBendStamp(i);
208          std::vector<int> bendAtoms =  bendStamp->getMembers();
209          std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
210          if (j != bendAtoms.end()) {
211 <            std::cout << "Error in Molecule " << getName();
211 >            std::cout << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << "have invalid indices\n";
212          }
213  
214          if (bendAtoms.size() == 2 ) {
# Line 230 | Line 242 | void MoleculeStamp::checkBends() {
242              if (rigidbodyIndex >= 0) {
243                  ++rigidSet[rigidbodyIndex];
244                  if (rigidSet[rigidbodyIndex] > 1) {
245 <                    std::cout << "Error in Molecule " << getName() << ": ";
234 <                    //std::cout << "atoms of bend " <<  << "belong to same rigidbody " << rigidbodyIndex << "\n";                    
245 >                    std::cout << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n";                    
246                  }
247              }
248          }
249      }
250      
251      
252 <    std::set<IntTuple3, BendLessThan> allBends;
253 <    std::set<IntTuple3, BendLessThan>::iterator iter;
252 >    std::set<IntTuple3> allBends;
253 >    std::set<IntTuple3>::iterator iter;
254      for(int i = 0; i < getNBends(); ++i) {
255          BendStamp* bendStamp= getBendStamp(i);
256          std::vector<int> bend = bendStamp->getMembers();
# Line 326 | Line 337 | struct TorsionLessThan : public std::binary_function<I
337  
338   }
339  
329 – struct TorsionLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> {
330 –    bool operator()(IntTuple4 t1, IntTuple4 t2) {
331 –
332 –        return t1.first < t2.first
333 –             || (!(t2.first < t1.first) && t1.second < t2.second)
334 –             || (!(t2.first < t1.first) && !(t2.second < t2.second) && t1.third < t2.third)
335 –             ||(!(t2.first < t1.first) && !(t2.second < t2.second) && !(t2.third < t1.third) && t1.fourth < t2.fourth);
336 –    }
337 –
338 –
339 –
340 – };
341 –
342 –
340   void MoleculeStamp::checkTorsions() {
341      for(int i = 0; i < getNTorsions(); ++i) {
342          TorsionStamp* torsionStamp = getTorsionStamp(i);
343 +        std::vector<int> torsionAtoms =  torsionStamp ->getMembers();
344 +        std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
345 +        if (j != torsionAtoms.end()) {
346 +            std::cout << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n";
347 +        }
348 +    }
349 +    
350 +    for(int i = 0; i < getNTorsions(); ++i) {
351 +        TorsionStamp* torsionStamp = getTorsionStamp(i);
352          std::vector<int> torsionAtoms =  torsionStamp->getMembers();
353          std::vector<int> rigidSet(getNRigidBodies(), 0);
354          std::vector<int>::iterator j;
# Line 351 | Line 357 | void MoleculeStamp::checkTorsions() {
357              if (rigidbodyIndex >= 0) {
358                  ++rigidSet[rigidbodyIndex];
359                  if (rigidSet[rigidbodyIndex] > 1) {
360 <                    std::cout << "Error in Molecule " << getName() << ": ";
355 <                    //std::cout << "atoms of torsion " <<  << "belong to same rigidbody " << rigidbodyIndex << "\n";                    
360 >                    std::cout << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n";                  
361                  }
362              }
363          }
364      }    
365  
366 <    std::set<IntTuple4, TorsionLessThan> allTorsions;
367 <    std::set<IntTuple4, TorsionLessThan>::iterator iter;
366 >    std::set<IntTuple4> allTorsions;
367 >    std::set<IntTuple4>::iterator iter;
368       for(int i = 0; i < getNTorsions(); ++i) {
369           TorsionStamp* torsionStamp= getTorsionStamp(i);
370           std::vector<int> torsion = torsionStamp->getMembers();
# Line 503 | Line 508 | bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
508   // Function Name: isAtomInRigidBody
509   //return false if atom does not belong to a rigid body, otherwise return true
510   bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
511 <  int whichRigidBody;
507 <  int consAtomIndex;
508 <
509 <  return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex);
511 >  return atom2Rigidbody[atomIndex] >=0 ;
512    
513   }
514  
# Line 517 | Line 519 | bool MoleculeStamp::isAtomInRigidBody(int atomIndex, i
519   //whichRigidBody: the index of rigidbody in component
520   //consAtomIndex:  the position of joint atom apears in  rigidbody's definition
521   bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){
520 –  RigidBodyStamp* rbStamp;
521 –  int numRb;
522 –  int numAtom;
522  
523 +  
524 +
525    whichRigidBody = -1;
526    consAtomIndex = -1;
527  
528 <  numRb = this->getNRigidBodies();
529 <  
530 <  for(int i = 0 ; i < numRb; i++){
531 <    rbStamp = this->getRigidBodyStamp(i);
532 <    numAtom = rbStamp->getNMembers();
532 <    for(int j = 0; j < numAtom; j++)
528 >  if (atom2Rigidbody[atomIndex] >=0) {
529 >    whichRigidBody = atom2Rigidbody[atomIndex];
530 >    RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody);
531 >    int numAtom = rbStamp->getNMembers();
532 >    for(int j = 0; j < numAtom; j++) {
533        if (rbStamp->getMemberAt(j) == atomIndex){
534 –        whichRigidBody = i;
534          consAtomIndex = j;
535          return true;
536        }
537 +    }
538    }
539  
540    return false;

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