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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#include "selection/NameFinder.hpp"
#include "utils/wildcards.hpp"
#include "utils/StringTokenizer.hpp"
#include "primitives/Molecule.hpp"
#include "utils/StringUtils.hpp"
namespace oopse {

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;
}

BitSet NameFinder::match(const std::string& name){
    BitSet 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, BitSet& 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, BitSet& 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, BitSet& 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, BitSet& 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:	2147
Committed:	Tue Apr 5 23:09:48 2005 UTC (19 years, 3 months ago) by tim
File size:	9557 byte(s)
Log Message:	support '+' and '-' in atom type name;clean the code a little bit
#	User	Rev	Content
1	tim	1967	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include "selection/NameFinder.hpp"
42	tim	1968	#include "utils/wildcards.hpp"
43	tim	1971	#include "utils/StringTokenizer.hpp"
44			#include "primitives/Molecule.hpp"
45	tim	1987	#include "utils/StringUtils.hpp"
46	tim	1967	namespace oopse {
47
48	tim	1968	TreeNode::~TreeNode(){
49			std::map<std::string, TreeNode*>::iterator i;
50			for ( i = children.begin(); i != children.end(); ++i) {
51			i->second->~TreeNode();
52			}
53			children.clear();
54			}
55
56
57			NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	tim	1971	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59	tim	1967	loadNames();
60			}
61
62
63	tim	1968	NameFinder::~NameFinder(){
64			delete root_;
65			}
66	tim	1967
67			void NameFinder::loadNames() {
68
69	tim	1968	std::map<std::string, TreeNode*>::iterator foundIter;
70	tim	1967	SimInfo::MoleculeIterator mi;
71			Molecule* mol;
72			Molecule::AtomIterator ai;
73			Atom* atom;
74			Molecule::RigidBodyIterator rbIter;
75			RigidBody* rb;
76	tim	1968
77			root_ = new TreeNode;
78	tim	1971	root_->bs.resize(nStuntDouble_);
79	tim	1968	root_->bs.setAll(); //
80
81	tim	1967	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
82	tim	1972
83	tim	1968	std::string molName = mol->getMoleculeName();
84	tim	1972	TreeNode* currentMolNode = createNode(root_, molName);
85	tim	1967
86			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
87	tim	1968	std::string atomName = atom->getType();
88	tim	1972	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
89
90	tim	1968	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
91			currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
92	tim	1967	}
93	tim	1968
94			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
95	tim	1972	std::string rbName = rb->getType();
96			TreeNode* currentRbNode = createNode(currentMolNode, rbName);
97	tim	1968
98			currentMolNode->bs.setBitOn(rb->getGlobalIndex());
99			currentRbNode->bs.setBitOn(rb->getGlobalIndex());
100
101			//create nodes for atoms belong to this rigidbody
102	tim	1972	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
103	tim	1968	std::string rbAtomName = atom->getType();
104	tim	1972	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
105
106	tim	1968	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
107			}
108
109			}
110	tim	1967
111			}
112	tim	1968
113	tim	1967	}
114
115	tim	1972	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
116			TreeNode* node;
117			std::map<std::string, TreeNode*>::iterator foundIter;
118			foundIter = parent->children.find(name);
119			if ( foundIter == parent->children.end()) {
120			node = new TreeNode;
121			node->name = name;
122			node->bs.resize(nStuntDouble_);
123			parent->children.insert(std::make_pair(name, node));
124			}else {
125			node = foundIter->second;
126			}
127			return node;
128			}
129	tim	1967
130	tim	1972	BitSet NameFinder::match(const std::string& name){
131			BitSet bs(nStuntDouble_);
132
133	tim	1967	StringTokenizer tokenizer(name, ".");
134
135			std::vector<std::string> names;
136			while(tokenizer.hasMoreTokens()) {
137			names.push_back(tokenizer.nextToken());
138			}
139
140			int size = names.size();
141			switch(size) {
142			case 1 :
143	tim	1968	//could be molecule name, atom name and rigidbody name
144	tim	2147	matchMolecule(names[0], bs);
145			matchStuntDouble("*", names[0], bs);
146	tim	1968
147	tim	1967	break;
148			case 2:
149	tim	1968	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
150	tim	1987
151			if (!isInteger(names[1])){
152			matchRigidAtoms("*", names[0], names[1], bs);
153			matchStuntDouble(names[0], names[1], bs);
154			} else {
155			int internalIndex = lexi_cast<int>(names[1]);
156			if (internalIndex < 0) {
157			std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
158			} else {
159			matchInternalIndex(names[0], internalIndex, bs);
160			}
161			}
162	tim	1968
163	tim	1967	break;
164			case 3:
165			//must be molecule.rigidbody.*
166	tim	1971	matchRigidAtoms(names[0], names[1], names[2], bs);
167	tim	1967	break;
168	tim	1971	default:
169	tim	1972	std::cerr << "invalid name: " << name << std::endl;
170	tim	1967	break;
171			}
172
173	tim	1972	return bs;
174	tim	1967	}
175
176	tim	1968	void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
177			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
178			std::vector<TreeNode*>::iterator i;
179			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
180	tim	1971	bs \|= (*i)->bs;
181	tim	1968	}
182	tim	1967	}
183	tim	1968
184			void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
185			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
186			std::vector<TreeNode*>::iterator i;
187			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
188			std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
189			std::vector<TreeNode*>::iterator j;
190			for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
191	tim	1971	bs \|= (*j)->bs;
192	tim	1968	}
193			}
194
195			}
196
197			void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
198			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
199			std::vector<TreeNode*>::iterator i;
200			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
201			std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
202			std::vector<TreeNode*>::iterator j;
203			for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
204			std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
205			std::vector<TreeNode*>::iterator k;
206			for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
207	tim	1971	bs \|= (*k)->bs;
208	tim	1968	}
209			}
210			}
211
212			}
213
214
215			std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
216			std::vector<TreeNode*> matchedNodes;
217			std::map<std::string, TreeNode*>::iterator i;
218			for (i = node->children.begin(); i != node->children.end(); ++i) {
219			if (isMatched( i->first, name)) {
220			matchedNodes.push_back(i->second);
221			}
222			}
223
224			return matchedNodes;
225			}
226
227			bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
228			return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
229			}
230
231	tim	1987
232			void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){
233
234			std::map<std::string, TreeNode*>::iterator foundIter;
235			SimInfo::MoleculeIterator mi;
236			Molecule* mol;
237
238			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
239
240			if (isMatched(mol->getMoleculeName(), name) ) {
241			int natoms = mol->getNAtoms();
242			int nrigidbodies = mol->getNRigidBodies();
243			if (internalIndex >= natoms + nrigidbodies) {
244			continue;
245			} else if (internalIndex < natoms) {
246			bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
247			continue;
248			} else if ( internalIndex < natoms + nrigidbodies) {
249			bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
250			}
251			}
252
253			}
254
255	tim	1968	}
256	tim	1987
257			bool NameFinder::isInteger(const std::string str) {
258			for(int i =0; i < str.size(); ++i){
259			if (!std::isdigit(str[i])) {
260			return false;
261			}
262			}
263
264			return true;
265			}
266
267			}