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());
    nObjects_.push_back(info_->getNGlobalMolecules());
    
    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);
      molNode->bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
        
      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());

        // COMMENTED OUT because rigid bodies are IntegrableObjects
        // (e.g. they are independently mobile, so selecting their
        // member atoms will give some odd results if we are computing
        // degrees of freedom elsewhere.

        // //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:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 3 months ago) by gezelter
File size:	16194 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	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	gezelter	2052	nObjects_.push_back(info_->getNGlobalMolecules());
64
65	tim	283	loadNames();
66	gezelter	507	}
67	tim	283
68	gezelter	507	NameFinder::~NameFinder(){
69	tim	284	delete root_;
70	gezelter	507	}
71	tim	283
72	gezelter	507	void NameFinder::loadNames() {
73	gezelter	1953	SimInfo::MoleculeIterator mi;
74			Molecule::AtomIterator ai;
75			Molecule::RigidBodyIterator rbIter;
76			Molecule::BondIterator bondIter;
77			Molecule::BendIterator bendIter;
78			Molecule::TorsionIterator torsionIter;
79			Molecule::InversionIterator inversionIter;
80	tim	283
81			Molecule* mol;
82			Atom* atom;
83			RigidBody* rb;
84	gezelter	1953	Bond* bond;
85			Bend* bend;
86			Torsion* torsion;
87			Inversion* inversion;
88	tim	284
89			root_ = new TreeNode;
90	gezelter	1953	root_->bs.resize(nObjects_);
91	tim	284	root_->bs.setAll(); //
92
93	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
94			mol = info_->nextMolecule(mi)) {
95	tim	288
96	gezelter	507	std::string molName = mol->getMoleculeName();
97	gezelter	1953	TreeNode* molNode = createNode(root_, molName);
98	gezelter	2052	molNode->bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
99	tim	283
100	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
101			std::string atomName = atom->getType();
102	gezelter	1953	TreeNode* atomNode = createNode(molNode, atomName);
103	tim	288
104	gezelter	1953	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
105			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
106	gezelter	507	}
107	tim	284
108	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
109			rb = mol->nextRigidBody(rbIter)) {
110	gezelter	507	std::string rbName = rb->getType();
111	gezelter	1953	TreeNode* rbNode = createNode(molNode, rbName);
112	tim	284
113	gezelter	1953	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
114			rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
115	tim	284
116	gezelter	1962	// COMMENTED OUT because rigid bodies are IntegrableObjects
117			// (e.g. they are independently mobile, so selecting their
118			// member atoms will give some odd results if we are computing
119			// degrees of freedom elsewhere.
120	tim	288
121	gezelter	1962	// //create nodes for atoms belong to this rigidbody
122			// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
123			// std::string rbAtomName = atom->getType();
124			// TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
125
126			// rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
127			// }
128	gezelter	507	}
129	gezelter	1953
130			for (bond = mol->beginBond(bondIter); bond != NULL;
131			bond = mol->nextBond(bondIter)) {
132
133			std::string bondName = bond->getName();
134			TreeNode* bondNode = createNode(molNode, bondName);
135
136			molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
137			bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
138
139			std::vector<Atom*> atoms = bond->getAtoms();
140			std::vector<Atom*>::iterator ai;
141
142			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
143			std::string atomName = (*ai)->getType();
144			TreeNode* atomNode = createNode(bondNode, atomName);
145			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
146			}
147			}
148			for (bend = mol->beginBend(bendIter); bend != NULL;
149			bend = mol->nextBend(bendIter)) {
150
151			std::string bendName = bend->getName();
152			TreeNode* bendNode = createNode(molNode, bendName);
153
154			molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
155			bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
156
157			std::vector<Atom*> atoms = bend->getAtoms();
158			std::vector<Atom*>::iterator ai;
159
160			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
161			std::string atomName = (*ai)->getType();
162			TreeNode* atomNode = createNode(bendNode, atomName);
163			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
164			}
165
166			}
167			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168			torsion = mol->nextTorsion(torsionIter)) {
169
170			std::string torsionName = torsion->getName();
171			TreeNode* torsionNode = createNode(molNode, torsionName);
172
173			molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
174			torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
175
176			std::vector<Atom*> atoms = torsion->getAtoms();
177			std::vector<Atom*>::iterator ai;
178
179			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
180			std::string atomName = (*ai)->getType();
181			TreeNode* atomNode = createNode(torsionNode, atomName);
182			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
183			}
184
185			}
186			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
187			inversion = mol->nextInversion(inversionIter)) {
188
189			std::string inversionName = inversion->getName();
190			TreeNode* inversionNode = createNode(molNode, inversionName);
191
192			molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
193			inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
194			std::vector<Atom*> atoms = inversion->getAtoms();
195			std::vector<Atom*>::iterator ai;
196
197			for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
198			std::string atomName = (*ai)->getType();
199			TreeNode* atomNode = createNode(inversionNode, atomName);
200			atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
201			}
202			}
203	gezelter	1801	}
204	gezelter	507	}
205	tim	283
206	gezelter	507	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
207	tim	288	TreeNode* node;
208			std::map<std::string, TreeNode*>::iterator foundIter;
209			foundIter = parent->children.find(name);
210			if ( foundIter == parent->children.end()) {
211	gezelter	507	node = new TreeNode;
212			node->name = name;
213	gezelter	1953	node->bs.resize(nObjects_);
214	gezelter	507	parent->children.insert(std::make_pair(name, node));
215	tim	288	}else {
216	gezelter	507	node = foundIter->second;
217	tim	288	}
218			return node;
219	gezelter	507	}
220	tim	283
221	gezelter	1953	SelectionSet NameFinder::match(const std::string& name){
222			SelectionSet bs(nObjects_);
223	tim	288
224	tim	283	StringTokenizer tokenizer(name, ".");
225
226			std::vector<std::string> names;
227			while(tokenizer.hasMoreTokens()) {
228	gezelter	507	names.push_back(tokenizer.nextToken());
229	tim	283	}
230
231			int size = names.size();
232	gezelter	1953
233	tim	283	switch(size) {
234	gezelter	507	case 1 :
235			//could be molecule name, atom name and rigidbody name
236			matchMolecule(names[0], bs);
237			matchStuntDouble("*", names[0], bs);
238	gezelter	1953	matchBond("*", names[0], bs);
239			matchBend("*", names[0], bs);
240			matchTorsion("*", names[0], bs);
241			matchInversion("*", names[0], bs);
242	tim	284
243	gezelter	507	break;
244			case 2:
245			//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
246	tim	303
247	gezelter	507	if (!isInteger(names[1])){
248			matchRigidAtoms("*", names[0], names[1], bs);
249			matchStuntDouble(names[0], names[1], bs);
250			} else {
251			int internalIndex = lexi_cast<int>(names[1]);
252			if (internalIndex < 0) {
253			std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
254			} else {
255			matchInternalIndex(names[0], internalIndex, bs);
256			}
257			}
258	tim	284
259	gezelter	507	break;
260			case 3:
261			//must be molecule.rigidbody.*
262			matchRigidAtoms(names[0], names[1], names[2], bs);
263			break;
264			default:
265			std::cerr << "invalid name: " << name << std::endl;
266			break;
267	tim	283	}
268
269	tim	288	return bs;
270	gezelter	507	}
271	tim	283
272	gezelter	1953	void NameFinder::matchMolecule(const std::string& molName, 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	bs \|= (*i)->bs;
277	tim	284	}
278	gezelter	507	}
279	tim	284
280	gezelter	1953	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
281	tim	284	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
282			std::vector<TreeNode*>::iterator i;
283			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
284	gezelter	507	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
285			std::vector<TreeNode*>::iterator j;
286			for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
287			bs \|= (*j)->bs;
288			}
289	tim	284	}
290
291	gezelter	507	}
292	tim	284
293	gezelter	1953	void NameFinder::matchBond(const std::string& molName,
294			const std::string& bondName, SelectionSet& bs){
295	tim	284	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
296			std::vector<TreeNode*>::iterator i;
297			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
298	gezelter	1953	std::vector<TreeNode> bondNodes = getMatchedChildren(i, bondName);
299			std::vector<TreeNode*>::iterator j;
300			for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
301			bs \|= (*j)->bs;
302			std::vector<TreeNode> bondAtomNodes = getAllChildren(j);
303			std::vector<TreeNode*>::iterator k;
304			for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
305			bs \|= (*k)->bs;
306			}
307			}
308			}
309			}
310
311			void NameFinder::matchBend(const std::string& molName, const std::string& bendName, SelectionSet& bs){
312			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
313			std::vector<TreeNode*>::iterator i;
314			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
315			std::vector<TreeNode> bendNodes = getMatchedChildren(i, bendName);
316			std::vector<TreeNode*>::iterator j;
317			for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
318			std::vector<TreeNode> bendAtomNodes = getAllChildren(j);
319			std::vector<TreeNode*>::iterator k;
320			for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
321			bs \|= (*k)->bs;
322			}
323			}
324			}
325			}
326			void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
327			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
328			std::vector<TreeNode*>::iterator i;
329			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
330			std::vector<TreeNode> torsionNodes = getMatchedChildren(i, torsionName);
331			std::vector<TreeNode*>::iterator j;
332			for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
333			std::vector<TreeNode> torsionAtomNodes = getAllChildren(j);
334			std::vector<TreeNode*>::iterator k;
335			for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
336			bs \|= (*k)->bs;
337			}
338			}
339			}
340			}
341			void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
342			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
343			std::vector<TreeNode*>::iterator i;
344			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
345			std::vector<TreeNode> inversionNodes = getMatchedChildren(i, inversionName);
346			std::vector<TreeNode*>::iterator j;
347			for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
348			std::vector<TreeNode> inversionAtomNodes = getAllChildren(j);
349			std::vector<TreeNode*>::iterator k;
350			for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
351			bs \|= (*k)->bs;
352			}
353			}
354			}
355			}
356
357			void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
358			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
359			std::vector<TreeNode*>::iterator i;
360			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
361	gezelter	507	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
362			std::vector<TreeNode*>::iterator j;
363			for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
364			std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
365			std::vector<TreeNode*>::iterator k;
366			for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
367			bs \|= (*k)->bs;
368			}
369			}
370	tim	284	}
371
372	gezelter	507	}
373	tim	284
374	gezelter	1953	std::vector<TreeNode> NameFinder::getAllChildren(TreeNode node) {
375			std::vector<TreeNode*> childNodes;
376			std::map<std::string, TreeNode*>::iterator i;
377			for (i = node->children.begin(); i != node->children.end(); ++i) {
378			childNodes.push_back(i->second);
379			}
380			return childNodes;
381			}
382	tim	284
383	gezelter	507	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
384	tim	284	std::vector<TreeNode*> matchedNodes;
385			std::map<std::string, TreeNode*>::iterator i;
386			for (i = node->children.begin(); i != node->children.end(); ++i) {
387	gezelter	507	if (isMatched( i->first, name)) {
388			matchedNodes.push_back(i->second);
389			}
390	tim	284	}
391
392			return matchedNodes;
393	gezelter	507	}
394	tim	284
395	gezelter	507	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
396	gezelter	1782	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
397	gezelter	507	}
398	tim	284
399	tim	303
400	gezelter	1953	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){
401	tim	303
402			SimInfo::MoleculeIterator mi;
403			Molecule* mol;
404
405	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
406			mol = info_->nextMolecule(mi)) {
407	tim	303
408	gezelter	507	if (isMatched(mol->getMoleculeName(), name) ) {
409			int natoms = mol->getNAtoms();
410			int nrigidbodies = mol->getNRigidBodies();
411			if (internalIndex >= natoms + nrigidbodies) {
412			continue;
413			} else if (internalIndex < natoms) {
414	gezelter	1953	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
415	gezelter	507	continue;
416			} else if ( internalIndex < natoms + nrigidbodies) {
417	gezelter	1953	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
418	gezelter	507	}
419			}
420	gezelter	1801	}
421	gezelter	507	}
422	tim	303
423	gezelter	1879	bool NameFinder::isInteger(const std::string &str) {
424	gezelter	1782	for(unsigned int i = 0; i < str.size(); ++i){
425	gezelter	507	if (!std::isdigit(str[i])) {
426			return false;
427			}
428	tim	303	}
429			return true;
430	gezelter	507	}
431	tim	303	}