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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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#include "selection/NameFinder.hpp" |
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#include "utils/wildcards.hpp" |
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namespace oopse { |
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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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|
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NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
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nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies() |
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loadNames(); |
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} |
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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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|
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std::map<std::string, TreeNode*>::iterator foundIter; |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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|
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root_ = new TreeNode; |
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root_->bs.resize(nStuntDobule_); |
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root_->bs.setAll(); // |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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TreeNode* currentMolNode; |
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std::string molName = mol->getMoleculeName(); |
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|
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foundIter = root_->children.find(molName); |
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if ( foundIter == root_->children.end()) { |
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currentMolNode = new TreeNode; |
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currentMolNode->name = molName; |
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currentMolNode->bs.resize(nStuntDouble_); |
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}else { |
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currentMolNode = i->second; |
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} |
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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* currentAtomNode; |
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foundIter = currentMolNode->children.find(molName); |
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if (foundIter == currentMolNode->children.end()) { |
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currentAtomNode = new TreeNode; |
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currentAtomNode->name = atomName; |
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currentAtomNode->bs.resize(nStuntDouble_); |
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} else { |
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currentAtomNode = foundIter->second; |
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} |
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currentMolNode->bs.setBitOn(atom->getGlobalIndex()); |
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currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
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} |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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std::string rbName = atom->getType(); |
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TreeNode* currentRbNode; |
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foundIter = currentMolNode->children.find(molName); |
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if (foundIter == currentMolNode->children.end()) { |
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currentRbNode = new TreeNode; |
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currentRbNode->name = rbName; |
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currentRbNode->bs.resize(nStuntDouble_); |
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} else { |
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currentRbNode = foundIter->second; |
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} |
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|
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currentMolNode->bs.setBitOn(rb->getGlobalIndex()); |
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currentRbNode->bs.setBitOn(rb->getGlobalIndex()); |
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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); rb != NULL; atom = rb->nextAtom(ai)) { |
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std::string rbAtomName = atom->getType(); |
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TreeNode* currentRbAtomNode; |
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foundIter = currentRbNode->children.find(molName); |
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if (foundIter == currentRbNode->children.end()) { |
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currentRbAtomNode = new TreeNode; |
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currentRbAtomNode->name = rbAtomName; |
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currentRbAtomNode->bs.resize(nStuntDouble_); |
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} else { |
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currentRbAtomNode = foundIter->second; |
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} |
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currentRbAtomNode->bs.setBitOn(atom->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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|
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std::map<std::string, TreeNode*>::iterator i; |
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for( i = root_->children.begin(); i != ; ++i){ |
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i->bs = |
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} |
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} |
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|
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bool NameFinder::match(const std::string& name, BitSet& bs){ |
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|
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bool error = true; |
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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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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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if (names[0] == "*"){ |
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//if all molecules are selected, we don't need to do the matching, just set all of the bits |
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bs.setAll(); |
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} else{ |
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matchMolecule(name[0]); |
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matchStuntDouble("*", names[0]); |
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} |
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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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matchRigidAtoms("*", names[0], names[1], bs); |
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matchStuntDouble(names[0], names[1]); |
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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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break; |
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} |
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|
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return matched; |
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} |
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|
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void NameFinder::matchMolecule(const std::string& molName, BitSet& 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, BitSet& 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::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& 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*> rbNodes = getMatchedChildren(*i, rbName); |
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std::vector<TreeNode*>::iterator j; |
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for (j = rbNodes.begin(); j != rbNodes.end(); ++j) { |
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std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
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std::vector<TreeNode*>::iterator k; |
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for(k = rbAtomNodes.begin(); k != rbAtomNodes.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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|
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|
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std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) { |
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std::vector<TreeNode*> matchedNodes; |
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std::map<std::string, TreeNode*>::iterator i; |
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for (i = node->children.begin(); i != node->children.end(); ++i) { |
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if (isMatched( i->first, name)) { |
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matchedNodes.push_back(i->second); |
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} |
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} |
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|
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return matchedNodes; |
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} |
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|
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bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
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return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); |
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} |
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|
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} |