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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "selection/NameFinder.hpp" |
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#include "utils/wildcards.hpp" |
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#include "utils/StringTokenizer.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace OpenMD { |
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|
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TreeNode::~TreeNode(){ |
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std::map<std::string, TreeNode*>::iterator i; |
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for ( i = children.begin(); i != children.end(); ++i) { |
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i->second->~TreeNode(); |
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} |
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children.clear(); |
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} |
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|
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NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
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nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies()); |
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nObjects_.push_back(info_->getNGlobalBonds()); |
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nObjects_.push_back(info_->getNGlobalBends()); |
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nObjects_.push_back(info_->getNGlobalTorsions()); |
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nObjects_.push_back(info_->getNGlobalInversions()); |
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loadNames(); |
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} |
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|
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NameFinder::~NameFinder(){ |
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delete root_; |
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} |
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|
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void NameFinder::loadNames() { |
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SimInfo::MoleculeIterator mi; |
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Molecule::AtomIterator ai; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::BondIterator bondIter; |
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Molecule::BendIterator bendIter; |
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Molecule::TorsionIterator torsionIter; |
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Molecule::InversionIterator inversionIter; |
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|
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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Inversion* inversion; |
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|
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root_ = new TreeNode; |
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root_->bs.resize(nObjects_); |
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root_->bs.setAll(); // |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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std::string molName = mol->getMoleculeName(); |
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TreeNode* molNode = createNode(root_, molName); |
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|
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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std::string atomName = atom->getType(); |
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TreeNode* atomNode = createNode(molNode, atomName); |
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|
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molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
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atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
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} |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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std::string rbName = rb->getType(); |
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TreeNode* rbNode = createNode(molNode, rbName); |
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|
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molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
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rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
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|
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// COMMENTED OUT because rigid bodies are IntegrableObjects |
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// (e.g. they are independently mobile, so selecting their |
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// member atoms will give some odd results if we are computing |
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// degrees of freedom elsewhere. |
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|
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// //create nodes for atoms belong to this rigidbody |
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// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
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// std::string rbAtomName = atom->getType(); |
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// TreeNode* rbAtomNode = createNode(rbNode, rbAtomName); |
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|
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// rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
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// } |
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} |
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|
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for (bond = mol->beginBond(bondIter); bond != NULL; |
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bond = mol->nextBond(bondIter)) { |
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|
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std::string bondName = bond->getName(); |
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TreeNode* bondNode = createNode(molNode, bondName); |
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|
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molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); |
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bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); |
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|
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std::vector<Atom*> atoms = bond->getAtoms(); |
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std::vector<Atom*>::iterator ai; |
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|
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for (ai = atoms.begin(); ai != atoms.end(); ++ai) { |
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std::string atomName = (*ai)->getType(); |
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TreeNode* atomNode = createNode(bondNode, atomName); |
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atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex()); |
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} |
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} |
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for (bend = mol->beginBend(bendIter); bend != NULL; |
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bend = mol->nextBend(bendIter)) { |
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|
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std::string bendName = bend->getName(); |
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TreeNode* bendNode = createNode(molNode, bendName); |
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|
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molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); |
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bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); |
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|
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std::vector<Atom*> atoms = bend->getAtoms(); |
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std::vector<Atom*>::iterator ai; |
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|
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for (ai = atoms.begin(); ai != atoms.end(); ++ai) { |
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std::string atomName = (*ai)->getType(); |
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TreeNode* atomNode = createNode(bendNode, atomName); |
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atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex()); |
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} |
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|
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} |
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for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
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torsion = mol->nextTorsion(torsionIter)) { |
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|
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std::string torsionName = torsion->getName(); |
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TreeNode* torsionNode = createNode(molNode, torsionName); |
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|
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molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); |
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torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); |
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|
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std::vector<Atom*> atoms = torsion->getAtoms(); |
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std::vector<Atom*>::iterator ai; |
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|
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for (ai = atoms.begin(); ai != atoms.end(); ++ai) { |
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std::string atomName = (*ai)->getType(); |
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TreeNode* atomNode = createNode(torsionNode, atomName); |
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atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex()); |
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} |
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|
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} |
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for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
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inversion = mol->nextInversion(inversionIter)) { |
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|
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std::string inversionName = inversion->getName(); |
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TreeNode* inversionNode = createNode(molNode, inversionName); |
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|
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molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); |
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inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); |
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std::vector<Atom*> atoms = inversion->getAtoms(); |
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std::vector<Atom*>::iterator ai; |
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|
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for (ai = atoms.begin(); ai != atoms.end(); ++ai) { |
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std::string atomName = (*ai)->getType(); |
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TreeNode* atomNode = createNode(inversionNode, atomName); |
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atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex()); |
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} |
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} |
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} |
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} |
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|
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TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
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TreeNode* node; |
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std::map<std::string, TreeNode*>::iterator foundIter; |
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foundIter = parent->children.find(name); |
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if ( foundIter == parent->children.end()) { |
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node = new TreeNode; |
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node->name = name; |
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node->bs.resize(nObjects_); |
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parent->children.insert(std::make_pair(name, node)); |
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}else { |
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node = foundIter->second; |
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} |
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return node; |
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} |
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|
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SelectionSet NameFinder::match(const std::string& name){ |
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SelectionSet bs(nObjects_); |
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|
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StringTokenizer tokenizer(name, "."); |
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|
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std::vector<std::string> names; |
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while(tokenizer.hasMoreTokens()) { |
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names.push_back(tokenizer.nextToken()); |
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} |
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|
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int size = names.size(); |
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|
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switch(size) { |
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case 1 : |
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//could be molecule name, atom name and rigidbody name |
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matchMolecule(names[0], bs); |
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matchStuntDouble("*", names[0], bs); |
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matchBond("*", names[0], bs); |
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matchBend("*", names[0], bs); |
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matchTorsion("*", names[0], bs); |
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matchInversion("*", names[0], bs); |
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|
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break; |
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case 2: |
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//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
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|
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if (!isInteger(names[1])){ |
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matchRigidAtoms("*", names[0], names[1], bs); |
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matchStuntDouble(names[0], names[1], bs); |
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} else { |
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int internalIndex = lexi_cast<int>(names[1]); |
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if (internalIndex < 0) { |
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std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl; |
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} else { |
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matchInternalIndex(names[0], internalIndex, bs); |
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} |
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} |
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|
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break; |
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case 3: |
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//must be molecule.rigidbody.* |
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matchRigidAtoms(names[0], names[1], names[2], bs); |
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break; |
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default: |
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std::cerr << "invalid name: " << name << std::endl; |
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break; |
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} |
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|
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return bs; |
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} |
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|
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void NameFinder::matchMolecule(const std::string& molName, SelectionSet& bs) { |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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bs |= (*i)->bs; |
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} |
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} |
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|
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void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = sdNodes.begin(); j != sdNodes.end(); ++j) { |
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bs |= (*j)->bs; |
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} |
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} |
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|
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} |
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|
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void NameFinder::matchBond(const std::string& molName, |
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const std::string& bondName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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std::vector<TreeNode*> bondNodes = getMatchedChildren(*i, bondName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = bondNodes.begin(); j != bondNodes.end(); ++j) { |
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bs |= (*j)->bs; |
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std::vector<TreeNode*> bondAtomNodes = getAllChildren(*j); |
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std::vector<TreeNode*>::iterator k; |
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for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){ |
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bs |= (*k)->bs; |
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} |
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} |
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} |
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} |
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|
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void NameFinder::matchBend(const std::string& molName, const std::string& bendName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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std::vector<TreeNode*> bendNodes = getMatchedChildren(*i, bendName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = bendNodes.begin(); j != bendNodes.end(); ++j) { |
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std::vector<TreeNode*> bendAtomNodes = getAllChildren(*j); |
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std::vector<TreeNode*>::iterator k; |
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for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){ |
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bs |= (*k)->bs; |
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} |
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} |
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} |
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} |
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void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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std::vector<TreeNode*> torsionNodes = getMatchedChildren(*i, torsionName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) { |
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std::vector<TreeNode*> torsionAtomNodes = getAllChildren(*j); |
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std::vector<TreeNode*>::iterator k; |
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for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){ |
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bs |= (*k)->bs; |
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} |
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} |
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} |
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} |
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void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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std::vector<TreeNode*> inversionNodes = getMatchedChildren(*i, inversionName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) { |
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std::vector<TreeNode*> inversionAtomNodes = getAllChildren(*j); |
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std::vector<TreeNode*>::iterator k; |
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for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){ |
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bs |= (*k)->bs; |
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} |
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} |
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} |
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} |
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|
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void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
| 357 |
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 358 |
std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName); |
| 359 |
std::vector<TreeNode*>::iterator j; |
| 360 |
for (j = rbNodes.begin(); j != rbNodes.end(); ++j) { |
| 361 |
std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
| 362 |
std::vector<TreeNode*>::iterator k; |
| 363 |
for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){ |
| 364 |
bs |= (*k)->bs; |
| 365 |
} |
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} |
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} |
| 368 |
|
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} |
| 370 |
|
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std::vector<TreeNode*> NameFinder::getAllChildren(TreeNode* node) { |
| 372 |
std::vector<TreeNode*> childNodes; |
| 373 |
std::map<std::string, TreeNode*>::iterator i; |
| 374 |
for (i = node->children.begin(); i != node->children.end(); ++i) { |
| 375 |
childNodes.push_back(i->second); |
| 376 |
} |
| 377 |
return childNodes; |
| 378 |
} |
| 379 |
|
| 380 |
std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) { |
| 381 |
std::vector<TreeNode*> matchedNodes; |
| 382 |
std::map<std::string, TreeNode*>::iterator i; |
| 383 |
for (i = node->children.begin(); i != node->children.end(); ++i) { |
| 384 |
if (isMatched( i->first, name)) { |
| 385 |
matchedNodes.push_back(i->second); |
| 386 |
} |
| 387 |
} |
| 388 |
|
| 389 |
return matchedNodes; |
| 390 |
} |
| 391 |
|
| 392 |
bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
| 393 |
return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false; |
| 394 |
} |
| 395 |
|
| 396 |
|
| 397 |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){ |
| 398 |
|
| 399 |
SimInfo::MoleculeIterator mi; |
| 400 |
Molecule* mol; |
| 401 |
|
| 402 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 403 |
mol = info_->nextMolecule(mi)) { |
| 404 |
|
| 405 |
if (isMatched(mol->getMoleculeName(), name) ) { |
| 406 |
int natoms = mol->getNAtoms(); |
| 407 |
int nrigidbodies = mol->getNRigidBodies(); |
| 408 |
if (internalIndex >= natoms + nrigidbodies) { |
| 409 |
continue; |
| 410 |
} else if (internalIndex < natoms) { |
| 411 |
bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex()); |
| 412 |
continue; |
| 413 |
} else if ( internalIndex < natoms + nrigidbodies) { |
| 414 |
bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
| 415 |
} |
| 416 |
} |
| 417 |
} |
| 418 |
} |
| 419 |
|
| 420 |
bool NameFinder::isInteger(const std::string &str) { |
| 421 |
for(unsigned int i = 0; i < str.size(); ++i){ |
| 422 |
if (!std::isdigit(str[i])) { |
| 423 |
return false; |
| 424 |
} |
| 425 |
} |
| 426 |
return true; |
| 427 |
} |
| 428 |
} |
