src/types/MoleculeStamp.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <iostream>

#include "types/MoleculeStamp.hpp"

namespace oopse {
MoleculeStamp::MoleculeStamp() {
    DefineParameter(Name, "name");
    
    deprecatedKeywords_.insert("nAtoms");
    deprecatedKeywords_.insert("nBonds");
    deprecatedKeywords_.insert("nBends");
    deprecatedKeywords_.insert("nTorsions");
    deprecatedKeywords_.insert("nRigidBodies");
    deprecatedKeywords_.insert("nCutoffGroups");
    
}

MoleculeStamp::~MoleculeStamp() {

}

bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
    bool ret = addIndexSensitiveStamp(atomStamps_, atom);
    if (!ret) {
        std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName()  << " Molecule\n";
    }
    return ret;
    
}

bool MoleculeStamp::addBondStamp( BondStamp* bond) {
    bondStamps_.push_back(bond);
    return true;
}

bool MoleculeStamp::addBendStamp( BendStamp* bend) {
    bendStamps_.push_back(bend);
    return true;
}

bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) {
    torsionStamps_.push_back(torsion);
    return true;
}

bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) {
    bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody);
    if (!ret) {
        std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName()  << " Molecule\n";
    }
    return ret;
}

bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) {
    cutoffGroupStamps_.push_back(cutoffgroup);
    return true;
}

bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) {
    return addIndexSensitiveStamp(fragmentStamps_, fragment);
}
    
void MoleculeStamp::validate() {
    DataHolder::validate();

    std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL));
    if (ai != atomStamps_.end()) {
        std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n";
    }

     std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL));
     if (ri != rigidBodyStamps_.end()) {
         std::cout << "Error in Molecule " << getName() << ":rigidBody[" <<  ri - rigidBodyStamps_.begin()<< "] is missing\n";
     }
    
    std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL));
    if (fi != fragmentStamps_.end()) {
        std::cout << "Error in Molecule " << getName() << ":fragment[" <<  fi - fragmentStamps_.begin()<< "] is missing\n";
    }

    //make sure index is not out of range
    int natoms = getNAtoms();
    for(int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        if (bondStamp->getA() >=  natoms && bondStamp->getB() >= natoms) {
            std::cout << "Error in Molecule " << getName() <<  ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n";
        }
    }
    for(int i = 0; i < getNBends(); ++i) {
        BendStamp* bendStamp = getBendStamp(i);
        std::vector<int> bendAtoms =  bendStamp->getMembers();
        std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
        if (j != bendAtoms.end()) {
            std::cout << "Error in Molecule " << getName();
        }

        if (bendAtoms.size() == 2 && !bendStamp->haveGhostVectorSource()) {
            std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing";
        }
    }    
    for(int i = 0; i < getNBends(); ++i) {
        TorsionStamp* torsionStamp = getTorsionStamp(i);
        std::vector<int> torsionAtoms =  torsionStamp ->getMembers();
        std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
        if (j != torsionAtoms.end()) {
            std::cout << "Error in Molecule " << getName();
        }
    }
    for(int i = 0; i < getNCutoffGroups(); ++i) {
        CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i);
        std::vector<int> cutoffGroupAtoms =  cutoffGroupStamp ->getMembers();
        std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
        if (j != cutoffGroupAtoms.end()) {
            std::cout << "Error in Molecule " << getName();
        }
    }
        
    atom2Rigidbody.resize(natoms); 
    // negative number means atom is a free atom, does not belong to rigidbody
    //every element in atom2Rigidbody has unique negative number at the very beginning
    for(int i = 0; i < atom2Rigidbody.size(); ++i) {
        atom2Rigidbody[i] = -1 - i;
    }

    for (int i = 0; i < getNRigidBodies(); ++i) {
        RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
        std::vector<int> members = rbStamp->getMembers();
        for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) {
            atom2Rigidbody[*j] = i;                 
        }
    }
    //make sure atoms belong to same rigidbody do not bond to each other
    for(int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()])
            std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << "belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
        }
        
    for(int i = 0; i < getNBends(); ++i) {
        BendStamp* bendStamp = getBendStamp(i);
        std::vector<int> bendAtoms =  bendStamp->getMembers();
        std::vector<int> rigidSet(getNRigidBodies(), 0);
        std::vector<int>::iterator j;
        for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) {
            int rigidbodyIndex = atom2Rigidbody[*j];
            if (rigidbodyIndex >= 0) {
                ++rigidSet[rigidbodyIndex];
                if (rigidSet[rigidbodyIndex] > 1) {
                    std::cout << "Error in Molecule " << getName() << ": ";
                    //std::cout << "atoms of bend " <<  << "belong to same rigidbody " << rigidbodyIndex << "\n";                    
                }
            }
        }
    }      
    for(int i = 0; i < getNTorsions(); ++i) {
        TorsionStamp* torsionStamp = getTorsionStamp(i);
        std::vector<int> torsionAtoms =  torsionStamp->getMembers();
        std::vector<int> rigidSet(getNRigidBodies(), 0);
        std::vector<int>::iterator j;
        for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) {
            int rigidbodyIndex = atom2Rigidbody[*j];
            if (rigidbodyIndex >= 0) {
                ++rigidSet[rigidbodyIndex];
                if (rigidSet[rigidbodyIndex] > 1) {
                    std::cout << "Error in Molecule " << getName() << ": ";
                    //std::cout << "atoms of torsion " <<  << "belong to same rigidbody " << rigidbodyIndex << "\n";                    
                }
            }
        }
    } 


    //fill in bond information into atom
    fillBondInfo();
    findBends();
    findTorsions();

    int nrigidAtoms = 0;
    for (int i = 0; i < getNRigidBodies(); ++i) {
        RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
        nrigidAtoms += rbStamp->getNMembers();
    }
    nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms;

 }

void MoleculeStamp::fillBondInfo() {
}

void MoleculeStamp::findBends() {

}

void MoleculeStamp::findTorsions() {

}

//Function Name: isBondInSameRigidBody
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){
  int rbA;
  int rbB;
  int consAtomA;
  int consAtomB;

  if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA))
    return false;

  if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) )
    return false;

  if(rbB == rbA)
    return true;
  else
    return false;
}

// Function Name: isAtomInRigidBody 
//return false if atom does not belong to a rigid body, otherwise return true 
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
  int whichRigidBody;
  int consAtomIndex;

  return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex);
   
}

// Function Name: isAtomInRigidBody 
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody 
//and consAtomIndex
//atomIndex : the index of atom in component
//whichRigidBody: the index of rigidbody in component
//consAtomIndex:  the position of joint atom apears in  rigidbody's definition
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){
  RigidBodyStamp* rbStamp;
  int numRb;
  int numAtom;

  whichRigidBody = -1;
  consAtomIndex = -1;

  numRb = this->getNRigidBodies();
  
  for(int i = 0 ; i < numRb; i++){
    rbStamp = this->getRigidBodyStamp(i);
    numAtom = rbStamp->getNMembers();
    for(int j = 0; j < numAtom; j++)
      if (rbStamp->getMemberAt(j) == atomIndex){
        whichRigidBody = i;
        consAtomIndex = j;
        return true;
      }
  }

  return false;
   
}

//return the position of joint atom apears in  rigidbody's definition
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2)
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
  RigidBodyStamp* rbStamp1;
  RigidBodyStamp* rbStamp2;
  int natomInRb1;
  int natomInRb2;
  int atomIndex1;
  int atomIndex2;
  std::vector<std::pair<int, int> > jointAtomIndexPair;
  
  rbStamp1 = this->getRigidBodyStamp(rb1);
  natomInRb1 =rbStamp1->getNMembers();

  rbStamp2 = this->getRigidBodyStamp(rb2);
  natomInRb2 =rbStamp2->getNMembers();

  for(int i = 0; i < natomInRb1; i++){
    atomIndex1 = rbStamp1->getMemberAt(i);
      
    for(int j= 0; j < natomInRb1; j++){
      atomIndex2 = rbStamp2->getMemberAt(j);

      if(atomIndex1 == atomIndex2){
        jointAtomIndexPair.push_back(std::make_pair(i, j));
        break;
      }
      
    }

  }

  return jointAtomIndexPair;
}

}
Revision:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 7 months ago) by tim
File size:	12467 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
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	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include <stdlib.h>
43	#include <stdio.h>
44	#include <string.h>
45	#include <iostream>
46
47	#include "types/MoleculeStamp.hpp"
48
49	namespace oopse {
50	MoleculeStamp::MoleculeStamp() {
51	DefineParameter(Name, "name");
52
53	deprecatedKeywords_.insert("nAtoms");
54	deprecatedKeywords_.insert("nBonds");
55	deprecatedKeywords_.insert("nBends");
56	deprecatedKeywords_.insert("nTorsions");
57	deprecatedKeywords_.insert("nRigidBodies");
58	deprecatedKeywords_.insert("nCutoffGroups");
59
60	}
61
62	MoleculeStamp::~MoleculeStamp() {
63
64	}
65
66	bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
67	bool ret = addIndexSensitiveStamp(atomStamps_, atom);
68	if (!ret) {
69	std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName() << " Molecule\n";
70	}
71	return ret;
72
73	}
74
75	bool MoleculeStamp::addBondStamp( BondStamp* bond) {
76	bondStamps_.push_back(bond);
77	return true;
78	}
79
80	bool MoleculeStamp::addBendStamp( BendStamp* bend) {
81	bendStamps_.push_back(bend);
82	return true;
83	}
84
85	bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) {
86	torsionStamps_.push_back(torsion);
87	return true;
88	}
89
90	bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) {
91	bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody);
92	if (!ret) {
93	std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName() << " Molecule\n";
94	}
95	return ret;
96	}
97
98	bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) {
99	cutoffGroupStamps_.push_back(cutoffgroup);
100	return true;
101	}
102
103	bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) {
104	return addIndexSensitiveStamp(fragmentStamps_, fragment);
105	}
106
107	void MoleculeStamp::validate() {
108	DataHolder::validate();
109
110	std::vector<AtomStamp>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp>(NULL));
111	if (ai != atomStamps_.end()) {
112	std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n";
113	}
114
115	std::vector<RigidBodyStamp>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp>(NULL));
116	if (ri != rigidBodyStamps_.end()) {
117	std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n";
118	}
119
120	std::vector<FragmentStamp>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp>(NULL));
121	if (fi != fragmentStamps_.end()) {
122	std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n";
123	}
124
125	//make sure index is not out of range
126	int natoms = getNAtoms();
127	for(int i = 0; i < getNBonds(); ++i) {
128	BondStamp* bondStamp = getBondStamp(i);
129	if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) {
130	std::cout << "Error in Molecule " << getName() << ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n";
131	}
132	}
133	for(int i = 0; i < getNBends(); ++i) {
134	BendStamp* bendStamp = getBendStamp(i);
135	std::vector<int> bendAtoms = bendStamp->getMembers();
136	std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
137	if (j != bendAtoms.end()) {
138	std::cout << "Error in Molecule " << getName();
139	}
140
141	if (bendAtoms.size() == 2 && !bendStamp->haveGhostVectorSource()) {
142	std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing";
143	}
144	}
145	for(int i = 0; i < getNBends(); ++i) {
146	TorsionStamp* torsionStamp = getTorsionStamp(i);
147	std::vector<int> torsionAtoms = torsionStamp ->getMembers();
148	std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
149	if (j != torsionAtoms.end()) {
150	std::cout << "Error in Molecule " << getName();
151	}
152	}
153	for(int i = 0; i < getNCutoffGroups(); ++i) {
154	CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i);
155	std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers();
156	std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1));
157	if (j != cutoffGroupAtoms.end()) {
158	std::cout << "Error in Molecule " << getName();
159	}
160	}
161
162	atom2Rigidbody.resize(natoms);
163	// negative number means atom is a free atom, does not belong to rigidbody
164	//every element in atom2Rigidbody has unique negative number at the very beginning
165	for(int i = 0; i < atom2Rigidbody.size(); ++i) {
166	atom2Rigidbody[i] = -1 - i;
167	}
168
169	for (int i = 0; i < getNRigidBodies(); ++i) {
170	RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
171	std::vector<int> members = rbStamp->getMembers();
172	for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) {
173	atom2Rigidbody[*j] = i;
174	}
175	}
176	//make sure atoms belong to same rigidbody do not bond to each other
177	for(int i = 0; i < getNBonds(); ++i) {
178	BondStamp* bondStamp = getBondStamp(i);
179	if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()])
180	std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << "belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
181	}
182
183	for(int i = 0; i < getNBends(); ++i) {
184	BendStamp* bendStamp = getBendStamp(i);
185	std::vector<int> bendAtoms = bendStamp->getMembers();
186	std::vector<int> rigidSet(getNRigidBodies(), 0);
187	std::vector<int>::iterator j;
188	for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) {
189	int rigidbodyIndex = atom2Rigidbody[*j];
190	if (rigidbodyIndex >= 0) {
191	++rigidSet[rigidbodyIndex];
192	if (rigidSet[rigidbodyIndex] > 1) {
193	std::cout << "Error in Molecule " << getName() << ": ";
194	//std::cout << "atoms of bend " << << "belong to same rigidbody " << rigidbodyIndex << "\n";
195	}
196	}
197	}
198	}
199	for(int i = 0; i < getNTorsions(); ++i) {
200	TorsionStamp* torsionStamp = getTorsionStamp(i);
201	std::vector<int> torsionAtoms = torsionStamp->getMembers();
202	std::vector<int> rigidSet(getNRigidBodies(), 0);
203	std::vector<int>::iterator j;
204	for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) {
205	int rigidbodyIndex = atom2Rigidbody[*j];
206	if (rigidbodyIndex >= 0) {
207	++rigidSet[rigidbodyIndex];
208	if (rigidSet[rigidbodyIndex] > 1) {
209	std::cout << "Error in Molecule " << getName() << ": ";
210	//std::cout << "atoms of torsion " << << "belong to same rigidbody " << rigidbodyIndex << "\n";
211	}
212	}
213	}
214	}
215
216
217	//fill in bond information into atom
218	fillBondInfo();
219	findBends();
220	findTorsions();
221
222	int nrigidAtoms = 0;
223	for (int i = 0; i < getNRigidBodies(); ++i) {
224	RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
225	nrigidAtoms += rbStamp->getNMembers();
226	}
227	nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms;
228
229	}
230
231	void MoleculeStamp::fillBondInfo() {
232	}
233
234	void MoleculeStamp::findBends() {
235
236	}
237
238	void MoleculeStamp::findTorsions() {
239
240	}
241
242	//Function Name: isBondInSameRigidBody
243	//Return true is both atoms of the bond belong to the same rigid body, otherwise return false
244	bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){
245	int rbA;
246	int rbB;
247	int consAtomA;
248	int consAtomB;
249
250	if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA))
251	return false;
252
253	if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) )
254	return false;
255
256	if(rbB == rbA)
257	return true;
258	else
259	return false;
260	}
261
262	// Function Name: isAtomInRigidBody
263	//return false if atom does not belong to a rigid body, otherwise return true
264	bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
265	int whichRigidBody;
266	int consAtomIndex;
267
268	return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex);
269
270	}
271
272	// Function Name: isAtomInRigidBody
273	//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody
274	//and consAtomIndex
275	//atomIndex : the index of atom in component
276	//whichRigidBody: the index of rigidbody in component
277	//consAtomIndex: the position of joint atom apears in rigidbody's definition
278	bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){
279	RigidBodyStamp* rbStamp;
280	int numRb;
281	int numAtom;
282
283	whichRigidBody = -1;
284	consAtomIndex = -1;
285
286	numRb = this->getNRigidBodies();
287
288	for(int i = 0 ; i < numRb; i++){
289	rbStamp = this->getRigidBodyStamp(i);
290	numAtom = rbStamp->getNMembers();
291	for(int j = 0; j < numAtom; j++)
292	if (rbStamp->getMemberAt(j) == atomIndex){
293	whichRigidBody = i;
294	consAtomIndex = j;
295	return true;
296	}
297	}
298
299	return false;
300
301	}
302
303	//return the position of joint atom apears in rigidbody's definition
304	//for the time being, we will use the most inefficient algorithm, the complexity is O(N2)
305	//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first
306	std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
307	RigidBodyStamp* rbStamp1;
308	RigidBodyStamp* rbStamp2;
309	int natomInRb1;
310	int natomInRb2;
311	int atomIndex1;
312	int atomIndex2;
313	std::vector<std::pair<int, int> > jointAtomIndexPair;
314
315	rbStamp1 = this->getRigidBodyStamp(rb1);
316	natomInRb1 =rbStamp1->getNMembers();
317
318	rbStamp2 = this->getRigidBodyStamp(rb2);
319	natomInRb2 =rbStamp2->getNMembers();
320
321	for(int i = 0; i < natomInRb1; i++){
322	atomIndex1 = rbStamp1->getMemberAt(i);
323
324	for(int j= 0; j < natomInRb1; j++){
325	atomIndex2 = rbStamp2->getMemberAt(j);
326
327	if(atomIndex1 == atomIndex2){
328	jointAtomIndexPair.push_back(std::make_pair(i, j));
329	break;
330	}
331
332	}
333
334	}
335
336	return jointAtomIndexPair;
337	}
338
339	}