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root/group/trunk/OOPSE/libBASS/MoleculeStamp.cpp
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Comparing trunk/OOPSE/libBASS/MoleculeStamp.cpp (file contents):
Revision 988 by gezelter, Tue Jan 27 19:37:48 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 14 | Line 14 | MoleculeStamp::MoleculeStamp(){
14    n_bends = 0;
15    n_torsions = 0;
16    n_rigidbodies = 0;
17 +  n_cutoffgroups = 0;
18 +  n_integrable = 0;
19  
20    unhandled = NULL;
21    atoms = NULL;
# Line 21 | Line 23 | MoleculeStamp::MoleculeStamp(){
23    bends = NULL;
24    torsions = NULL;
25    rigidBodies = NULL;
26 +  cutoffGroups = NULL;
27  
28    have_name = 0;
29    have_atoms = 0;
# Line 28 | Line 31 | MoleculeStamp::MoleculeStamp(){
31    have_bends = 0;
32    have_torsions = 0;
33    have_rigidbodies = 0;
34 +  have_cutoffgroups = 0;
35  
36   }
37  
# Line 39 | Line 43 | MoleculeStamp::~MoleculeStamp(){
43    if( rigidBodies != NULL ) {
44      for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i];
45    }
46 +  delete[] rigidBodies;
47 +
48 +  if( cutoffGroups != NULL ) {
49 +    for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i];
50 +  }
51 +  delete[] cutoffGroups;
52    
53    if( atoms != NULL ){
54      for( i=0; i<n_atoms; i++ ) delete atoms[i];
55    }
56 +  delete[] atoms;
57    
58    if( bonds != NULL ){
59      for( i=0; i<n_bonds; i++ ) delete bonds[i];
60    }
61 +  delete[] bonds;
62    
63    if( bends != NULL ){
64      for( i=0; i<n_bends; i++ ) delete bends[i];
65    }
66 +  delete[] bends;
67    
68    if( torsions != NULL ){
69      for( i=0; i<n_torsions; i++ ) delete torsions[i];
70    }
71 +  delete[] torsions;
72    
73 +
74 +
75 +
76   }
77  
78   char* MoleculeStamp::assignString( char* lhs, char* rhs ){
# Line 150 | Line 167 | char* MoleculeStamp::assignDouble( char* lhs, double r
167      for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
168    }
169  
170 +  else if( !strcmp( lhs, "nCutoffGroups" ) ){
171 +    n_cutoffgroups = (int)rhs;
172 +
173 +    if( have_cutoffgroups ){
174 +      sprintf( errMsg,
175 +               "MoleculeStamp error, n_cutoffgroups already declared for"
176 +               " molecule: %s\n",
177 +               name );
178 +      return strdup( errMsg );
179 +    }
180 +    have_cutoffgroups = 1;
181 +    cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups];
182 +    for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL;
183 +  }
184 +  
185    else{
186      if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
187      else unhandled->add( lhs, rhs );
# Line 226 | Line 258 | char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
258  
259      if( have_rigidbodies ){
260        sprintf( errMsg,
261 <               "RigidBodyStamp error, n_rigidbodies already declared for"
261 >               "MoleculeStamp error, n_rigidbodies already declared for"
262                 " molecule: %s\n",
263                 name);
264        return strdup( errMsg );
# Line 234 | Line 266 | char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
266      have_rigidbodies = 1;
267      rigidBodies = new RigidBodyStamp*[n_rigidbodies];
268      for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
269 +  }
270 +  else if( !strcmp( lhs, "nCutoffGroups" ) ){
271 +    n_cutoffgroups = rhs;
272 +
273 +    if( have_cutoffgroups ){
274 +      sprintf( errMsg,
275 +               "MoleculeStamp error, n_cutoffgroups already declared for"
276 +               " molecule: %s\n",
277 +               name);
278 +      return strdup( errMsg );
279 +    }
280 +    have_cutoffgroups = 1;
281 +    cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups];
282 +    for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL;
283    }
284    else{
285      if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
# Line 246 | Line 292 | char* MoleculeStamp::addAtom( AtomStamp* the_atom, int
292   char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){
293    
294    if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom;
295 <  else{
295 >  else {
296      if( have_atoms ){
297        sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range",
298                 atomIndex );
# Line 264 | Line 310 | char* MoleculeStamp::addRigidBody( RigidBodyStamp* the
310    
311    if( have_rigidbodies && rigidBodyIndex < n_rigidbodies )
312      rigidBodies[rigidBodyIndex] = the_rigidbody;
313 <  else{
313 >  else {
314      if( have_rigidbodies ){
315        sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range",
316                 rigidBodyIndex );
# Line 277 | Line 323 | char* MoleculeStamp::addBond( BondStamp* the_bond, int
323    return NULL;
324   }
325  
326 + char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup,
327 +                                     int cutoffGroupIndex ){
328 +  
329 +  if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups )
330 +    cutoffGroups[cutoffGroupIndex] = the_cutoffgroup;
331 +  else {
332 +    if( have_cutoffgroups ){
333 +      sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range",
334 +               cutoffGroupIndex );
335 +      return strdup( errMsg );
336 +    }
337 +    else return strdup("MoleculeStamp error, nCutoffGroups not given before"
338 +                       " first CutoffGroup declaration." );
339 +  }
340 +  
341 +  return NULL;
342 + }
343 +
344   char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){
345    
346    
# Line 332 | Line 396 | char* MoleculeStamp::checkMe( void ){
396   char* MoleculeStamp::checkMe( void ){
397    
398    int i;
399 <  short int no_atom, no_rigidbody;
399 >  short int no_atom, no_rigidbody, no_cutoffgroup;
400  
401    if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
402                                    " was not given.\n" );
# Line 353 | Line 417 | char* MoleculeStamp::checkMe( void ){
417      return strdup( errMsg );
418    }
419  
420 +  no_cutoffgroup = 0;
421 +  for( i=0; i<n_cutoffgroups; i++ ){
422 +    if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1;
423 +  }
424 +
425 +  if( no_cutoffgroup ){
426 +    sprintf( errMsg,
427 +             "MoleculeStamp error. Not all of the CutoffGroups were"
428 +             " declared in molecule \"%s\".\n", name );
429 +    return strdup( errMsg );
430 +  }
431 +  
432    no_atom = 0;
433    for( i=0; i<n_atoms; i++ ){
434      if( atoms[i] == NULL ) no_atom = 1;
# Line 365 | Line 441 | char* MoleculeStamp::checkMe( void ){
441      return strdup( errMsg );
442    }
443  
444 +  n_integrable = n_atoms;
445 +  for (i = 0; i < n_rigidbodies; i++)
446 +    n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object
447 +  
448 +  if (n_integrable <= 0 || n_integrable > n_atoms) {
449 +    sprintf( errMsg,
450 +             "MoleculeStamp error. n_integrable is either <= 0 or"
451 +             " greater than n_atoms in molecule \"%s\".\n", name );
452 +    return strdup( errMsg );
453 +  }
454 +
455    return NULL;
456   }  
457 +
458 +
459 + //Function Name: isBondInSameRigidBody
460 + //Return true is both atoms of the bond belong to the same rigid body, otherwise return false
461 + bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){
462 +  int rbA;
463 +  int rbB;
464 +  int consAtomA;
465 +  int consAtomB;
466 +
467 +  if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA))
468 +    return false;
469 +
470 +  if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) )
471 +    return false;
472 +
473 +  if(rbB == rbA)
474 +    return true;
475 +  else
476 +    return false;
477 + }
478 +
479 +
480 + // Function Name isAtomInRigidBody
481 + //return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody
482 + //and consAtomIndex
483 + //atomIndex : the index of atom in component
484 + //whichRigidBody: the index of rigidbody in component
485 + //consAtomIndex:  the position of joint atom apears in  rigidbody's definition
486 + bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){
487 +  RigidBodyStamp* rbStamp;
488 +  int numRb;
489 +  int numAtom;
490 +
491 +  numRb = this->getNRigidBodies();
492 +  
493 +  for(int i = 0 ; i < numRb; i++){
494 +    rbStamp = this->getRigidBody(i);
495 +    numAtom = rbStamp->getNMembers();
496 +    for(int j = 0; j < numAtom; j++)
497 +      if (rbStamp->getMember(j) == atomIndex){
498 +        whichRigidBody = i;
499 +        consAtomIndex = j;
500 +        return true;
501 +      }
502 +  }
503 +
504 +  return false;
505 +  
506 + }
507 +
508 + //return the position of joint atom apears in  rigidbody's definition
509 + //for the time being, we will use the most inefficient algorithm, the complexity is O(N2)
510 + //actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first
511 + vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
512 +  RigidBodyStamp* rbStamp1;
513 +  RigidBodyStamp* rbStamp2;
514 +  int natomInRb1;
515 +  int natomInRb2;
516 +  int atomIndex1;
517 +  int atomIndex2;
518 +  vector<pair<int, int> > jointAtomIndexPair;
519 +  
520 +  rbStamp1 = this->getRigidBody(rb1);
521 +  natomInRb1 =rbStamp1->getNMembers();
522 +
523 +  rbStamp2 = this->getRigidBody(rb2);
524 +  natomInRb2 =rbStamp2->getNMembers();
525 +
526 +  for(int i = 0; i < natomInRb1; i++){
527 +    atomIndex1 = rbStamp1->getMember(i);
528 +      
529 +    for(int j= 0; j < natomInRb1; j++){
530 +      atomIndex2 = rbStamp2->getMember(j);
531 +
532 +      if(atomIndex1 == atomIndex2){
533 +        jointAtomIndexPair.push_back(make_pair(i, j));
534 +        break;
535 +      }
536 +      
537 +    }//end for(j =0)
538 +
539 +  }//end for (i = 0)
540 +
541 +  return jointAtomIndexPair;
542 + }

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