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()) > 0 ? true : false;
  }


  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(unsigned int i = 0; i < str.size(); ++i){
      if (!std::isdigit(str[i])) {
        return false;
      }
    }
    return true;
  }
}
Revision:	1801
Committed:	Mon Oct 1 18:21:15 2012 UTC (13 years, 1 month ago) by gezelter
File size:	9125 byte(s)
Log Message:	Some parallel fixes for "select all" selection scripts. The distance finder selection, e.g. "select within(4.0, Au)", still needs work, however.
#	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	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59	loadNames();
60	}
61
62	NameFinder::~NameFinder(){
63	delete root_;
64	}
65
66	void NameFinder::loadNames() {
67
68	std::map<std::string, TreeNode*>::iterator foundIter;
69	SimInfo::MoleculeIterator mi;
70	Molecule* mol;
71	Molecule::AtomIterator ai;
72	Atom* atom;
73	Molecule::RigidBodyIterator rbIter;
74	RigidBody* rb;
75
76	root_ = new TreeNode;
77	root_->bs.resize(nStuntDouble_);
78	root_->bs.setAll(); //
79
80	for (mol = info_->beginMolecule(mi); mol != NULL;
81	mol = info_->nextMolecule(mi)) {
82
83	std::string molName = mol->getMoleculeName();
84	TreeNode* currentMolNode = createNode(root_, molName);
85
86	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
87	std::string atomName = atom->getType();
88	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
89
90	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
91	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
92	}
93
94	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95	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	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
114	TreeNode* node;
115	std::map<std::string, TreeNode*>::iterator foundIter;
116	foundIter = parent->children.find(name);
117	if ( foundIter == parent->children.end()) {
118	node = new TreeNode;
119	node->name = name;
120	node->bs.resize(nStuntDouble_);
121	parent->children.insert(std::make_pair(name, node));
122	}else {
123	node = foundIter->second;
124	}
125	return node;
126	}
127
128	OpenMDBitSet NameFinder::match(const std::string& name){
129	OpenMDBitSet bs(nStuntDouble_);
130
131	StringTokenizer tokenizer(name, ".");
132
133	std::vector<std::string> names;
134	while(tokenizer.hasMoreTokens()) {
135	names.push_back(tokenizer.nextToken());
136	}
137
138	int size = names.size();
139	switch(size) {
140	case 1 :
141	//could be molecule name, atom name and rigidbody name
142	matchMolecule(names[0], bs);
143	matchStuntDouble("*", names[0], bs);
144
145	break;
146	case 2:
147	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
148
149	if (!isInteger(names[1])){
150	matchRigidAtoms("*", names[0], names[1], bs);
151	matchStuntDouble(names[0], names[1], bs);
152	} else {
153	int internalIndex = lexi_cast<int>(names[1]);
154	if (internalIndex < 0) {
155	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
156	} else {
157	matchInternalIndex(names[0], internalIndex, bs);
158	}
159	}
160
161	break;
162	case 3:
163	//must be molecule.rigidbody.*
164	matchRigidAtoms(names[0], names[1], names[2], bs);
165	break;
166	default:
167	std::cerr << "invalid name: " << name << std::endl;
168	break;
169	}
170
171	return bs;
172	}
173
174	void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) {
175	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
176	std::vector<TreeNode*>::iterator i;
177	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
178	bs \|= (*i)->bs;
179	}
180	}
181
182	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){
183	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
184	std::vector<TreeNode*>::iterator i;
185	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
186	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
187	std::vector<TreeNode*>::iterator j;
188	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
189	bs \|= (*j)->bs;
190	}
191	}
192
193	}
194
195	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){
196	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
197	std::vector<TreeNode*>::iterator i;
198	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
199	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
200	std::vector<TreeNode*>::iterator j;
201	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
202	std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
203	std::vector<TreeNode*>::iterator k;
204	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
205	bs \|= (*k)->bs;
206	}
207	}
208	}
209
210	}
211
212
213	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
214	std::vector<TreeNode*> matchedNodes;
215	std::map<std::string, TreeNode*>::iterator i;
216	for (i = node->children.begin(); i != node->children.end(); ++i) {
217	if (isMatched( i->first, name)) {
218	matchedNodes.push_back(i->second);
219	}
220	}
221
222	return matchedNodes;
223	}
224
225	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
226	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
227	}
228
229
230	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){
231
232	std::map<std::string, TreeNode*>::iterator foundIter;
233	SimInfo::MoleculeIterator mi;
234	Molecule* mol;
235
236	for (mol = info_->beginMolecule(mi); mol != NULL;
237	mol = info_->nextMolecule(mi)) {
238
239	if (isMatched(mol->getMoleculeName(), name) ) {
240	int natoms = mol->getNAtoms();
241	int nrigidbodies = mol->getNRigidBodies();
242	if (internalIndex >= natoms + nrigidbodies) {
243	continue;
244	} else if (internalIndex < natoms) {
245	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
246	continue;
247	} else if ( internalIndex < natoms + nrigidbodies) {
248	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
249	}
250	}
251	}
252	}
253
254	bool NameFinder::isInteger(const std::string str) {
255	for(unsigned int i = 0; i < str.size(); ++i){
256	if (!std::isdigit(str[i])) {
257	return false;
258	}
259	}
260	return true;
261	}
262	}