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, 24107 (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){
    nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
    loadNames();
  }


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

  void NameFinder::loadNames() {

    std::map<std::string, TreeNode*>::iterator foundIter;
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;

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

      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
        std::string rbName = rb->getType();
        TreeNode* currentRbNode = createNode(currentMolNode, rbName);
            
        currentMolNode->bs.setBitOn(rb->getGlobalIndex());
        currentRbNode->bs.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* currentRbAtomNode = createNode(currentRbNode, rbName);;

          currentRbAtomNode->bs.setBitOn(atom->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(nStuntDouble_);
      parent->children.insert(std::make_pair(name, node));
    }else {
      node = foundIter->second;
    }
    return node;
  }

  OpenMDBitSet NameFinder::match(const std::string& name){
    OpenMDBitSet bs(nStuntDouble_);
  
    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);
            
      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, OpenMDBitSet& 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, OpenMDBitSet& 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::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& 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::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());
  }


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

    std::map<std::string, TreeNode*>::iterator foundIter;
    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.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
          continue;
        } else if ( internalIndex < natoms + nrigidbodies) {
          bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
        }
      }
        
    }    
    
  }

  bool NameFinder::isInteger(const std::string str) {
    for(int i =0; i < str.size(); ++i){
      if (!std::isdigit(str[i])) {
        return false;
      }
    }

    return true;
  }

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	9102 byte(s)
Log Message:	updated copyright notices
#	Content
1	/*
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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#include "selection/NameFinder.hpp"
43	#include "utils/wildcards.hpp"
44	#include "utils/StringTokenizer.hpp"
45	#include "primitives/Molecule.hpp"
46	#include "utils/StringUtils.hpp"
47	namespace OpenMD {
48
49	TreeNode::~TreeNode(){
50	std::map<std::string, TreeNode*>::iterator i;
51	for ( i = children.begin(); i != children.end(); ++i) {
52	i->second->~TreeNode();
53	}
54	children.clear();
55	}
56
57
58	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
59	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
60	loadNames();
61	}
62
63
64	NameFinder::~NameFinder(){
65	delete root_;
66	}
67
68	void NameFinder::loadNames() {
69
70	std::map<std::string, TreeNode*>::iterator foundIter;
71	SimInfo::MoleculeIterator mi;
72	Molecule* mol;
73	Molecule::AtomIterator ai;
74	Atom* atom;
75	Molecule::RigidBodyIterator rbIter;
76	RigidBody* rb;
77
78	root_ = new TreeNode;
79	root_->bs.resize(nStuntDouble_);
80	root_->bs.setAll(); //
81
82	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
83
84	std::string molName = mol->getMoleculeName();
85	TreeNode* currentMolNode = createNode(root_, molName);
86
87	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
88	std::string atomName = atom->getType();
89	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
90
91	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
92	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
93	}
94
95	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
96	std::string rbName = rb->getType();
97	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
98
99	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
100	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
101
102	//create nodes for atoms belong to this rigidbody
103	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
104	std::string rbAtomName = atom->getType();
105	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
106
107	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
108	}
109
110	}
111
112	}
113
114	}
115
116	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
117	TreeNode* node;
118	std::map<std::string, TreeNode*>::iterator foundIter;
119	foundIter = parent->children.find(name);
120	if ( foundIter == parent->children.end()) {
121	node = new TreeNode;
122	node->name = name;
123	node->bs.resize(nStuntDouble_);
124	parent->children.insert(std::make_pair(name, node));
125	}else {
126	node = foundIter->second;
127	}
128	return node;
129	}
130
131	OpenMDBitSet NameFinder::match(const std::string& name){
132	OpenMDBitSet bs(nStuntDouble_);
133
134	StringTokenizer tokenizer(name, ".");
135
136	std::vector<std::string> names;
137	while(tokenizer.hasMoreTokens()) {
138	names.push_back(tokenizer.nextToken());
139	}
140
141	int size = names.size();
142	switch(size) {
143	case 1 :
144	//could be molecule name, atom name and rigidbody name
145	matchMolecule(names[0], bs);
146	matchStuntDouble("*", names[0], bs);
147
148	break;
149	case 2:
150	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
151
152	if (!isInteger(names[1])){
153	matchRigidAtoms("*", names[0], names[1], bs);
154	matchStuntDouble(names[0], names[1], bs);
155	} else {
156	int internalIndex = lexi_cast<int>(names[1]);
157	if (internalIndex < 0) {
158	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
159	} else {
160	matchInternalIndex(names[0], internalIndex, bs);
161	}
162	}
163
164	break;
165	case 3:
166	//must be molecule.rigidbody.*
167	matchRigidAtoms(names[0], names[1], names[2], bs);
168	break;
169	default:
170	std::cerr << "invalid name: " << name << std::endl;
171	break;
172	}
173
174	return bs;
175	}
176
177	void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) {
178	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
179	std::vector<TreeNode*>::iterator i;
180	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
181	bs \|= (*i)->bs;
182	}
183	}
184
185	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){
186	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
187	std::vector<TreeNode*>::iterator i;
188	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
189	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
190	std::vector<TreeNode*>::iterator j;
191	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
192	bs \|= (*j)->bs;
193	}
194	}
195
196	}
197
198	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){
199	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
200	std::vector<TreeNode*>::iterator i;
201	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
202	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
203	std::vector<TreeNode*>::iterator j;
204	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
205	std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
206	std::vector<TreeNode*>::iterator k;
207	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
208	bs \|= (*k)->bs;
209	}
210	}
211	}
212
213	}
214
215
216	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
217	std::vector<TreeNode*> matchedNodes;
218	std::map<std::string, TreeNode*>::iterator i;
219	for (i = node->children.begin(); i != node->children.end(); ++i) {
220	if (isMatched( i->first, name)) {
221	matchedNodes.push_back(i->second);
222	}
223	}
224
225	return matchedNodes;
226	}
227
228	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
229	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
230	}
231
232
233	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){
234
235	std::map<std::string, TreeNode*>::iterator foundIter;
236	SimInfo::MoleculeIterator mi;
237	Molecule* mol;
238
239	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
240
241	if (isMatched(mol->getMoleculeName(), name) ) {
242	int natoms = mol->getNAtoms();
243	int nrigidbodies = mol->getNRigidBodies();
244	if (internalIndex >= natoms + nrigidbodies) {
245	continue;
246	} else if (internalIndex < natoms) {
247	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
248	continue;
249	} else if ( internalIndex < natoms + nrigidbodies) {
250	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
251	}
252	}
253
254	}
255
256	}
257
258	bool NameFinder::isInteger(const std::string str) {
259	for(int i =0; i < str.size(); ++i){
260	if (!std::isdigit(str[i])) {
261	return false;
262	}
263	}
264
265	return true;
266	}
267
268	}