| 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 |
+ |
return isAtomInRigidBody(bond->getA(),rbA, consAtomA) && |
| 468 |
+ |
isAtomInRigidBody(bond->getB(),rbB, consAtomB); |
| 469 |
+ |
} |
| 470 |
+ |
|
| 471 |
+ |
|
| 472 |
+ |
// Function Name isAtomInRigidBody |
| 473 |
+ |
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
| 474 |
+ |
//and consAtomIndex |
| 475 |
+ |
//atomIndex : the index of atom in component |
| 476 |
+ |
//whichRigidBody: the index of rigidbody in component |
| 477 |
+ |
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
| 478 |
+ |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
| 479 |
+ |
RigidBodyStamp* rbStamp; |
| 480 |
+ |
int numRb; |
| 481 |
+ |
int numAtom; |
| 482 |
+ |
|
| 483 |
+ |
numRb = this->getNRigidBodies(); |
| 484 |
+ |
|
| 485 |
+ |
for(int i = 0 ; i < numRb; i++){ |
| 486 |
+ |
rbStamp = this->getRigidBody(i); |
| 487 |
+ |
numAtom = rbStamp->getNMembers(); |
| 488 |
+ |
for(int j = 0; j < numAtom; j++) |
| 489 |
+ |
if (rbStamp->getMember(j) == atomIndex){ |
| 490 |
+ |
whichRigidBody = i; |
| 491 |
+ |
consAtomIndex = j; |
| 492 |
+ |
return true; |
| 493 |
+ |
} |
| 494 |
+ |
} |
| 495 |
+ |
|
| 496 |
+ |
return false; |
| 497 |
+ |
|
| 498 |
+ |
} |
| 499 |
+ |
|
| 500 |
+ |
//return the position of joint atom apears in rigidbody's definition |
| 501 |
+ |
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
| 502 |
+ |
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
| 503 |
+ |
vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
| 504 |
+ |
RigidBodyStamp* rbStamp1; |
| 505 |
+ |
RigidBodyStamp* rbStamp2; |
| 506 |
+ |
int natomInRb1; |
| 507 |
+ |
int natomInRb2; |
| 508 |
+ |
int atomIndex1; |
| 509 |
+ |
int atomIndex2; |
| 510 |
+ |
vector<pair<int, int> > jointAtomIndexPair; |
| 511 |
+ |
|
| 512 |
+ |
rbStamp1 = this->getRigidBody(rb1); |
| 513 |
+ |
natomInRb1 =rbStamp1->getNMembers(); |
| 514 |
+ |
|
| 515 |
+ |
rbStamp2 = this->getRigidBody(rb2); |
| 516 |
+ |
natomInRb2 =rbStamp2->getNMembers(); |
| 517 |
+ |
|
| 518 |
+ |
for(int i = 0; i < natomInRb1; i++){ |
| 519 |
+ |
atomIndex1 = rbStamp1->getMember(i); |
| 520 |
+ |
|
| 521 |
+ |
for(int j= 0; j < natomInRb1; j++){ |
| 522 |
+ |
atomIndex2 = rbStamp2->getMember(j); |
| 523 |
+ |
|
| 524 |
+ |
if(atomIndex1 == atomIndex2){ |
| 525 |
+ |
jointAtomIndexPair.push_back(make_pair(i, j)); |
| 526 |
+ |
break; |
| 527 |
+ |
} |
| 528 |
+ |
|
| 529 |
+ |
}//end for(j =0) |
| 530 |
+ |
|
| 531 |
+ |
}//end for (i = 0) |
| 532 |
+ |
|
| 533 |
+ |
return jointAtomIndexPair; |
| 534 |
+ |
} |
