[ViewVC] Diff of: group/trunk/OOPSE/libBASS/MoleculeStamp.cpp

Comparing trunk/OOPSE/libBASS/MoleculeStamp.cpp (file contents):
Revision 1216 by gezelter, Tue Jun 1 21:44:54 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

+  return NULL;
-+
-+
-+
+//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 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;
-+
-+
+  numRb = this->getNRigidBodies();
-+
-+
+  for(int i = 0 ; i < numRb; i++){
-+
+    rbStamp = this->getRigidBody(i);
-+
+    numAtom = rbStamp->getNMembers();
-+
+    for(int j = 0; j < numAtom; j++)
-+
+      if (rbStamp->getMember(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
-+
+vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
-+
+  RigidBodyStamp* rbStamp1;
-+
+  RigidBodyStamp* rbStamp2;
-+
+  int natomInRb1;
-+
+  int natomInRb2;
-+
+  int atomIndex1;
-+
+  int atomIndex2;
-+
+  vector<pair<int, int> > jointAtomIndexPair;
-+
-+
+  rbStamp1 = this->getRigidBody(rb1);
-+
+  natomInRb1 =rbStamp1->getNMembers();
-+
-+
+  rbStamp2 = this->getRigidBody(rb2);
-+
+  natomInRb2 =rbStamp2->getNMembers();
-+
-+
+  for(int i = 0; i < natomInRb1; i++){
-+
+    atomIndex1 = rbStamp1->getMember(i);
-+
-+
+    for(int j= 0; j < natomInRb1; j++){
-+
+      atomIndex2 = rbStamp2->getMember(j);
-+
-+
+      if(atomIndex1 == atomIndex2){
-+
+        jointAtomIndexPair.push_back(make_pair(i, j));
-+
+        break;
-+
+      }
-+
-+
+    }//end for(j =0)
-+
-+
+  }//end for (i = 0)
-+
-+
+  return jointAtomIndexPair;
-+
+}

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Comparing trunk/OOPSE/libBASS/MoleculeStamp.cpp (file contents): Revision 1216 by gezelter, Tue Jun 1 21:44:54 2004 UTC vs. Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libBASS/MoleculeStamp.cpp (file contents):
Revision 1216 by gezelter, Tue Jun 1 21:44:54 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC