src/selection/NameFinder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include "selection/NameFinder.hpp"
#include "utils/wildcards.hpp"
#include "utils/StringTokenizer.hpp"
#include "primitives/Molecule.hpp"
#include "utils/StringUtils.hpp"
namespace OpenMD {

  TreeNode::~TreeNode(){
    std::map<std::string, TreeNode*>::iterator i;
    for ( i = children.begin(); i != children.end(); ++i) {
      i->second->~TreeNode();
    }
    children.clear();
  }

  NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
    nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
    nObjects_.push_back(info_->getNGlobalBonds());
    nObjects_.push_back(info_->getNGlobalBends());
    nObjects_.push_back(info_->getNGlobalTorsions());
    nObjects_.push_back(info_->getNGlobalInversions());
    loadNames();
  }

  NameFinder::~NameFinder(){
    delete root_;
  }

  void NameFinder::loadNames() {
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;

    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;    

    root_ = new TreeNode;
    root_->bs.resize(nObjects_);
    root_->bs.setAll(); //
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
           
      std::string molName = mol->getMoleculeName();
      TreeNode* molNode = createNode(root_, molName);
        
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        std::string atomName = atom->getType();
        TreeNode* atomNode = createNode(molNode, atomName);
            
        molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
        atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
      }

      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        std::string rbName = rb->getType();
        TreeNode* rbNode = createNode(molNode, rbName);
            
        molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
        rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());

        //create nodes for atoms belong to this rigidbody
        for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
          std::string rbAtomName = atom->getType();
          TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);

          rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
        }
      }

      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {

        std::string bondName = bond->getName();
        TreeNode* bondNode = createNode(molNode, bondName);

        molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
        bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());

        std::vector<Atom*> atoms = bond->getAtoms();
        std::vector<Atom*>::iterator ai;
        
        for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
          std::string atomName = (*ai)->getType();
          TreeNode* atomNode = createNode(bondNode, atomName);
          atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
        }
      }
      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {

        std::string bendName = bend->getName();
        TreeNode* bendNode = createNode(molNode, bendName);

        molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
        bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());

        std::vector<Atom*> atoms = bend->getAtoms();
        std::vector<Atom*>::iterator ai;
        
        for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
          std::string atomName = (*ai)->getType();
          TreeNode* atomNode = createNode(bendNode, atomName);
          atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
        }

      }
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {

        std::string torsionName = torsion->getName();
        TreeNode* torsionNode = createNode(molNode, torsionName);

        molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
        torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());

        std::vector<Atom*> atoms = torsion->getAtoms();
        std::vector<Atom*>::iterator ai;
        
        for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
          std::string atomName = (*ai)->getType();
          TreeNode* atomNode = createNode(torsionNode, atomName);
          atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
        }

      }
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {

        std::string inversionName = inversion->getName();
        TreeNode* inversionNode = createNode(molNode, inversionName);

        molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
        inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
        std::vector<Atom*> atoms = inversion->getAtoms();
        std::vector<Atom*>::iterator ai;
        
        for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
          std::string atomName = (*ai)->getType();
          TreeNode* atomNode = createNode(inversionNode, atomName);
          atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
        }
      }
    }
  }

  TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
    TreeNode* node;    
    std::map<std::string, TreeNode*>::iterator foundIter;
    foundIter = parent->children.find(name);
    if ( foundIter  == parent->children.end()) {
      node = new TreeNode;
      node->name = name;
      node->bs.resize(nObjects_);
      parent->children.insert(std::make_pair(name, node));
    }else {
      node = foundIter->second;
    }
    return node;
  }

  SelectionSet NameFinder::match(const std::string& name){
    SelectionSet bs(nObjects_);
  
    StringTokenizer tokenizer(name, ".");

    std::vector<std::string> names;
    while(tokenizer.hasMoreTokens()) {
      names.push_back(tokenizer.nextToken());
    }

    int size = names.size();

    switch(size) {
    case 1 :
      //could be molecule name, atom name and rigidbody name
      matchMolecule(names[0], bs);
      matchStuntDouble("*", names[0], bs);
      matchBond("*", names[0], bs);
      matchBend("*", names[0], bs);
      matchTorsion("*", names[0], bs);
      matchInversion("*", names[0], bs);
            
      break;
    case 2:
      //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)

      if (!isInteger(names[1])){
        matchRigidAtoms("*", names[0], names[1], bs);
        matchStuntDouble(names[0], names[1], bs);
      } else {
        int internalIndex = lexi_cast<int>(names[1]);
        if (internalIndex < 0) {
          std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;           
        } else {
          matchInternalIndex(names[0], internalIndex, bs);
        }
      }
            
      break;
    case 3:
      //must be molecule.rigidbody.*
      matchRigidAtoms(names[0], names[1], names[2], bs);
      break;
    default:      
      std::cerr << "invalid name: " << name << std::endl;
      break;           
    }

    return bs; 
  }

  void NameFinder::matchMolecule(const std::string& molName, SelectionSet& bs) {
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      bs |= (*i)->bs;
    }    
  }

  void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);   
      std::vector<TreeNode*>::iterator j;
      for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
        bs |= (*j)->bs;
      }
    }

  }

  void NameFinder::matchBond(const std::string& molName, 
                             const std::string& bondName, SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> bondNodes = getMatchedChildren(*i, bondName);   
      std::vector<TreeNode*>::iterator j;
      for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
        bs |= (*j)->bs;
        std::vector<TreeNode*> bondAtomNodes = getAllChildren(*j);
        std::vector<TreeNode*>::iterator k;
        for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
          bs |= (*k)->bs;
        }
      }
    }
  }

  void NameFinder::matchBend(const std::string& molName, const std::string& bendName,  SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> bendNodes = getMatchedChildren(*i, bendName);   
      std::vector<TreeNode*>::iterator j;
      for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
        std::vector<TreeNode*> bendAtomNodes = getAllChildren(*j);
        std::vector<TreeNode*>::iterator k;
        for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
          bs |= (*k)->bs;
        }
      }
    }
  }
  void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> torsionNodes = getMatchedChildren(*i, torsionName);   
      std::vector<TreeNode*>::iterator j;
      for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
        std::vector<TreeNode*> torsionAtomNodes = getAllChildren(*j);
        std::vector<TreeNode*>::iterator k;
        for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
          bs |= (*k)->bs;
        }
      }
    }
  }
  void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> inversionNodes = getMatchedChildren(*i, inversionName);   
      std::vector<TreeNode*>::iterator j;
      for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
        std::vector<TreeNode*> inversionAtomNodes = getAllChildren(*j);
        std::vector<TreeNode*>::iterator k;
        for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
          bs |= (*k)->bs;
        }
      }
    }
  }

  void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
    std::vector<TreeNode*>::iterator i;
    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
      std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);   
      std::vector<TreeNode*>::iterator j;
      for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
        std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
        std::vector<TreeNode*>::iterator k;
        for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
          bs |= (*k)->bs;
        }
      }
    }

  }

  std::vector<TreeNode*> NameFinder::getAllChildren(TreeNode* node)  {
    std::vector<TreeNode*> childNodes;
    std::map<std::string, TreeNode*>::iterator i;
    for (i = node->children.begin(); i != node->children.end(); ++i) {
      childNodes.push_back(i->second);
    }
    return childNodes;
  }

  std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
    std::vector<TreeNode*> matchedNodes;
    std::map<std::string, TreeNode*>::iterator i;
    for (i = node->children.begin(); i != node->children.end(); ++i) {
      if (isMatched( i->first, name)) {
        matchedNodes.push_back(i->second);
      }
    }

    return matchedNodes;
  }

  bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
    return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
  }


  void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){

    SimInfo::MoleculeIterator mi;
    Molecule* mol;

    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
           
      if (isMatched(mol->getMoleculeName(), name) ) {
        int natoms = mol->getNAtoms();
        int nrigidbodies = mol->getNRigidBodies();
        if (internalIndex >= natoms + nrigidbodies) {
          continue;
        } else if (internalIndex < natoms) {
          bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
          continue;
        } else if ( internalIndex < natoms + nrigidbodies) {
          bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
        }
      }
    }
  }

  bool NameFinder::isInteger(const std::string &str) {
    for(unsigned int i = 0; i < str.size(); ++i){
      if (!std::isdigit(str[i])) {
        return false;
      }
    }
    return true;
  }
}
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 10 months ago) by gezelter
File size:	15798 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	User	Rev	Content
1	tim	283	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	283	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	283	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	283	*/
42			#include "selection/NameFinder.hpp"
43	tim	284	#include "utils/wildcards.hpp"
44	tim	287	#include "utils/StringTokenizer.hpp"
45			#include "primitives/Molecule.hpp"
46	tim	303	#include "utils/StringUtils.hpp"
47	gezelter	1390	namespace OpenMD {
48	tim	283
49	gezelter	507	TreeNode::~TreeNode(){
50	tim	284	std::map<std::string, TreeNode*>::iterator i;
51			for ( i = children.begin(); i != children.end(); ++i) {
52	gezelter	507	i->second->~TreeNode();
53	tim	284	}
54			children.clear();
55	gezelter	507	}
56	tim	284
57	gezelter	507	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	gezelter	1953	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
59			nObjects_.push_back(info_->getNGlobalBonds());
60			nObjects_.push_back(info_->getNGlobalBends());
61			nObjects_.push_back(info_->getNGlobalTorsions());
62			nObjects_.push_back(info_->getNGlobalInversions());
63	tim	283	loadNames();
64	gezelter	507	}
65	tim	283
66	gezelter	507	NameFinder::~NameFinder(){
67	tim	284	delete root_;
68	gezelter	507	}
69	tim	283
70	gezelter	507	void NameFinder::loadNames() {
71	gezelter	1953	SimInfo::MoleculeIterator mi;
72			Molecule::AtomIterator ai;
73			Molecule::RigidBodyIterator rbIter;
74			Molecule::BondIterator bondIter;
75			Molecule::BendIterator bendIter;
76			Molecule::TorsionIterator torsionIter;
77			Molecule::InversionIterator inversionIter;
78	tim	283
79			Molecule* mol;
80			Atom* atom;
81			RigidBody* rb;
82	gezelter	1953	Bond* bond;
83			Bend* bend;
84			Torsion* torsion;
85			Inversion* inversion;
86	tim	284
87			root_ = new TreeNode;
88	gezelter	1953	root_->bs.resize(nObjects_);
89	tim	284	root_->bs.setAll(); //
90
91	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
92			mol = info_->nextMolecule(mi)) {
93	tim	288
94	gezelter	507	std::string molName = mol->getMoleculeName();
95	gezelter	1953	TreeNode* molNode = createNode(root_, molName);
96	tim	283
97	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
98			std::string atomName = atom->getType();
99	gezelter	1953	TreeNode* atomNode = createNode(molNode, atomName);
100	tim	288
101	gezelter	1953	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
102			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
103	gezelter	507	}
104	tim	284
105	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
106			rb = mol->nextRigidBody(rbIter)) {
107	gezelter	507	std::string rbName = rb->getType();
108	gezelter	1953	TreeNode* rbNode = createNode(molNode, rbName);
109	tim	284
110	gezelter	1953	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
111			rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
112	tim	284
113	gezelter	507	//create nodes for atoms belong to this rigidbody
114			for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115			std::string rbAtomName = atom->getType();
116	gezelter	1953	TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
117	tim	288
118	gezelter	1953	rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
119	gezelter	507	}
120			}
121	gezelter	1953
122			for (bond = mol->beginBond(bondIter); bond != NULL;
123			bond = mol->nextBond(bondIter)) {
124
125			std::string bondName = bond->getName();
126			TreeNode* bondNode = createNode(molNode, bondName);
127
128			molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
129			bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
130
131			std::vector<Atom*> atoms = bond->getAtoms();
132			std::vector<Atom*>::iterator ai;
133
134			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
135			std::string atomName = (*ai)->getType();
136			TreeNode* atomNode = createNode(bondNode, atomName);
137			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
138			}
139			}
140			for (bend = mol->beginBend(bendIter); bend != NULL;
141			bend = mol->nextBend(bendIter)) {
142
143			std::string bendName = bend->getName();
144			TreeNode* bendNode = createNode(molNode, bendName);
145
146			molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
147			bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
148
149			std::vector<Atom*> atoms = bend->getAtoms();
150			std::vector<Atom*>::iterator ai;
151
152			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
153			std::string atomName = (*ai)->getType();
154			TreeNode* atomNode = createNode(bendNode, atomName);
155			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
156			}
157
158			}
159			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
160			torsion = mol->nextTorsion(torsionIter)) {
161
162			std::string torsionName = torsion->getName();
163			TreeNode* torsionNode = createNode(molNode, torsionName);
164
165			molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
166			torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
167
168			std::vector<Atom*> atoms = torsion->getAtoms();
169			std::vector<Atom*>::iterator ai;
170
171			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
172			std::string atomName = (*ai)->getType();
173			TreeNode* atomNode = createNode(torsionNode, atomName);
174			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
175			}
176
177			}
178			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
179			inversion = mol->nextInversion(inversionIter)) {
180
181			std::string inversionName = inversion->getName();
182			TreeNode* inversionNode = createNode(molNode, inversionName);
183
184			molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
185			inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
186			std::vector<Atom*> atoms = inversion->getAtoms();
187			std::vector<Atom*>::iterator ai;
188
189			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
190			std::string atomName = (*ai)->getType();
191			TreeNode* atomNode = createNode(inversionNode, atomName);
192			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
193			}
194			}
195	gezelter	1801	}
196	gezelter	507	}
197	tim	283
198	gezelter	507	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
199	tim	288	TreeNode* node;
200			std::map<std::string, TreeNode*>::iterator foundIter;
201			foundIter = parent->children.find(name);
202			if ( foundIter == parent->children.end()) {
203	gezelter	507	node = new TreeNode;
204			node->name = name;
205	gezelter	1953	node->bs.resize(nObjects_);
206	gezelter	507	parent->children.insert(std::make_pair(name, node));
207	tim	288	}else {
208	gezelter	507	node = foundIter->second;
209	tim	288	}
210			return node;
211	gezelter	507	}
212	tim	283
213	gezelter	1953	SelectionSet NameFinder::match(const std::string& name){
214			SelectionSet bs(nObjects_);
215	tim	288
216	tim	283	StringTokenizer tokenizer(name, ".");
217
218			std::vector<std::string> names;
219			while(tokenizer.hasMoreTokens()) {
220	gezelter	507	names.push_back(tokenizer.nextToken());
221	tim	283	}
222
223			int size = names.size();
224	gezelter	1953
225	tim	283	switch(size) {
226	gezelter	507	case 1 :
227			//could be molecule name, atom name and rigidbody name
228			matchMolecule(names[0], bs);
229			matchStuntDouble("*", names[0], bs);
230	gezelter	1953	matchBond("*", names[0], bs);
231			matchBend("*", names[0], bs);
232			matchTorsion("*", names[0], bs);
233			matchInversion("*", names[0], bs);
234	tim	284
235	gezelter	507	break;
236			case 2:
237			//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
238	tim	303
239	gezelter	507	if (!isInteger(names[1])){
240			matchRigidAtoms("*", names[0], names[1], bs);
241			matchStuntDouble(names[0], names[1], bs);
242			} else {
243			int internalIndex = lexi_cast<int>(names[1]);
244			if (internalIndex < 0) {
245			std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
246			} else {
247			matchInternalIndex(names[0], internalIndex, bs);
248			}
249			}
250	tim	284
251	gezelter	507	break;
252			case 3:
253			//must be molecule.rigidbody.*
254			matchRigidAtoms(names[0], names[1], names[2], bs);
255			break;
256			default:
257			std::cerr << "invalid name: " << name << std::endl;
258			break;
259	tim	283	}
260
261	tim	288	return bs;
262	gezelter	507	}
263	tim	283
264	gezelter	1953	void NameFinder::matchMolecule(const std::string& molName, SelectionSet& bs) {
265	tim	284	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
266			std::vector<TreeNode*>::iterator i;
267			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
268	gezelter	507	bs \|= (*i)->bs;
269	tim	284	}
270	gezelter	507	}
271	tim	284
272	gezelter	1953	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
273	tim	284	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
274			std::vector<TreeNode*>::iterator i;
275			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
276	gezelter	507	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
277			std::vector<TreeNode*>::iterator j;
278			for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
279			bs \|= (*j)->bs;
280			}
281	tim	284	}
282
283	gezelter	507	}
284	tim	284
285	gezelter	1953	void NameFinder::matchBond(const std::string& molName,
286			const std::string& bondName, SelectionSet& bs){
287	tim	284	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
288			std::vector<TreeNode*>::iterator i;
289			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
290	gezelter	1953	std::vector<TreeNode> bondNodes = getMatchedChildren(i, bondName);
291			std::vector<TreeNode*>::iterator j;
292			for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
293			bs \|= (*j)->bs;
294			std::vector<TreeNode> bondAtomNodes = getAllChildren(j);
295			std::vector<TreeNode*>::iterator k;
296			for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
297			bs \|= (*k)->bs;
298			}
299			}
300			}
301			}
302
303			void NameFinder::matchBend(const std::string& molName, const std::string& bendName, SelectionSet& bs){
304			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
305			std::vector<TreeNode*>::iterator i;
306			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
307			std::vector<TreeNode> bendNodes = getMatchedChildren(i, bendName);
308			std::vector<TreeNode*>::iterator j;
309			for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
310			std::vector<TreeNode> bendAtomNodes = getAllChildren(j);
311			std::vector<TreeNode*>::iterator k;
312			for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
313			bs \|= (*k)->bs;
314			}
315			}
316			}
317			}
318			void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
319			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
320			std::vector<TreeNode*>::iterator i;
321			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
322			std::vector<TreeNode> torsionNodes = getMatchedChildren(i, torsionName);
323			std::vector<TreeNode*>::iterator j;
324			for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
325			std::vector<TreeNode> torsionAtomNodes = getAllChildren(j);
326			std::vector<TreeNode*>::iterator k;
327			for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
328			bs \|= (*k)->bs;
329			}
330			}
331			}
332			}
333			void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
334			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
335			std::vector<TreeNode*>::iterator i;
336			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
337			std::vector<TreeNode> inversionNodes = getMatchedChildren(i, inversionName);
338			std::vector<TreeNode*>::iterator j;
339			for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
340			std::vector<TreeNode> inversionAtomNodes = getAllChildren(j);
341			std::vector<TreeNode*>::iterator k;
342			for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
343			bs \|= (*k)->bs;
344			}
345			}
346			}
347			}
348
349			void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
350			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
351			std::vector<TreeNode*>::iterator i;
352			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
353	gezelter	507	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
354			std::vector<TreeNode*>::iterator j;
355			for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
356			std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
357			std::vector<TreeNode*>::iterator k;
358			for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
359			bs \|= (*k)->bs;
360			}
361			}
362	tim	284	}
363
364	gezelter	507	}
365	tim	284
366	gezelter	1953	std::vector<TreeNode> NameFinder::getAllChildren(TreeNode node) {
367			std::vector<TreeNode*> childNodes;
368			std::map<std::string, TreeNode*>::iterator i;
369			for (i = node->children.begin(); i != node->children.end(); ++i) {
370			childNodes.push_back(i->second);
371			}
372			return childNodes;
373			}
374	tim	284
375	gezelter	507	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
376	tim	284	std::vector<TreeNode*> matchedNodes;
377			std::map<std::string, TreeNode*>::iterator i;
378			for (i = node->children.begin(); i != node->children.end(); ++i) {
379	gezelter	507	if (isMatched( i->first, name)) {
380			matchedNodes.push_back(i->second);
381			}
382	tim	284	}
383
384			return matchedNodes;
385	gezelter	507	}
386	tim	284
387	gezelter	507	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
388	gezelter	1782	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
389	gezelter	507	}
390	tim	284
391	tim	303
392	gezelter	1953	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){
393	tim	303
394			SimInfo::MoleculeIterator mi;
395			Molecule* mol;
396
397	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
398			mol = info_->nextMolecule(mi)) {
399	tim	303
400	gezelter	507	if (isMatched(mol->getMoleculeName(), name) ) {
401			int natoms = mol->getNAtoms();
402			int nrigidbodies = mol->getNRigidBodies();
403			if (internalIndex >= natoms + nrigidbodies) {
404			continue;
405			} else if (internalIndex < natoms) {
406	gezelter	1953	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
407	gezelter	507	continue;
408			} else if ( internalIndex < natoms + nrigidbodies) {
409	gezelter	1953	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
410	gezelter	507	}
411			}
412	gezelter	1801	}
413	gezelter	507	}
414	tim	303
415	gezelter	1879	bool NameFinder::isInteger(const std::string &str) {
416	gezelter	1782	for(unsigned int i = 0; i < str.size(); ++i){
417	gezelter	507	if (!std::isdigit(str[i])) {
418			return false;
419			}
420	tim	303	}
421			return true;
422	gezelter	507	}
423	tim	303	}