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"
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)) {
        TreeNode* currentMolNode;            
        std::string molName = mol->getMoleculeName();

        foundIter = root_->children.find(molName);
        if ( foundIter  == root_->children.end()) {
            currentMolNode = new TreeNode;
            currentMolNode->name = molName;
            currentMolNode->bs.resize(nStuntDouble_);
        }else {
            currentMolNode = foundIter->second;
        }
        
        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            std::string atomName = atom->getType();
            TreeNode* currentAtomNode;
            foundIter = currentMolNode->children.find(molName);
            if (foundIter == currentMolNode->children.end()) {
                currentAtomNode = new TreeNode;
                currentAtomNode->name = atomName;
                currentAtomNode->bs.resize(nStuntDouble_);
            } else {
                currentAtomNode = foundIter->second;
            }
            currentMolNode->bs.setBitOn(atom->getGlobalIndex());
            currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
        }

        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
            std::string rbName = atom->getType();
            TreeNode* currentRbNode;
            foundIter = currentMolNode->children.find(molName);
            if (foundIter == currentMolNode->children.end()) {
                currentRbNode = new TreeNode;
                currentRbNode->name = rbName;
                currentRbNode->bs.resize(nStuntDouble_);
            } else {
                currentRbNode = foundIter->second;
            }
            
            currentMolNode->bs.setBitOn(rb->getGlobalIndex());
            currentRbNode->bs.setBitOn(rb->getGlobalIndex());

            //create nodes for atoms belong to this rigidbody
            for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) {
                std::string rbAtomName = atom->getType();
                TreeNode* currentRbAtomNode;
                foundIter = currentRbNode->children.find(molName);
                if (foundIter == currentRbNode->children.end()) {
                    currentRbAtomNode = new TreeNode;
                    currentRbAtomNode->name = rbAtomName;
                    currentRbAtomNode->bs.resize(nStuntDouble_);
                } else {
                    currentRbAtomNode = foundIter->second;
                }
                currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
            }

        }
        
    }    

}

bool NameFinder::match(const std::string& name, BitSet& bs){

    bool hasError = false;
    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
            if (names[0] == "*"){
                //if all molecules are selected, we don't need to do the matching, just set all of the bits
                bs.setAll();
            } else{
                matchMolecule(names[0], bs);
                matchStuntDouble("*", names[0], bs);
            } 
            
            break;
        case 2:
            //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
            matchRigidAtoms("*", names[0], names[1], bs);
            matchStuntDouble(names[0], names[1], bs);
            
            break;
        case 3:
            //must be molecule.rigidbody.*
            matchRigidAtoms(names[0], names[1], names[2], bs);
            break;
        default:      
            hasError = true;        
            break;           
    }

    return hasError; 
}

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());
}

}
Revision:	1971
Committed:	Fri Feb 4 05:42:49 2005 UTC (19 years, 5 months ago) by tim
File size:	9035 byte(s)
Log Message:	selection library get built
#	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	1967	namespace oopse {
46
47	tim	1968	TreeNode::~TreeNode(){
48			std::map<std::string, TreeNode*>::iterator i;
49			for ( i = children.begin(); i != children.end(); ++i) {
50			i->second->~TreeNode();
51			}
52			children.clear();
53			}
54
55
56			NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
57	tim	1971	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
58	tim	1967	loadNames();
59			}
60
61
62	tim	1968	NameFinder::~NameFinder(){
63			delete root_;
64			}
65	tim	1967
66			void NameFinder::loadNames() {
67
68	tim	1968	std::map<std::string, TreeNode*>::iterator foundIter;
69	tim	1967	SimInfo::MoleculeIterator mi;
70			Molecule* mol;
71			Molecule::AtomIterator ai;
72			Atom* atom;
73			Molecule::RigidBodyIterator rbIter;
74			RigidBody* rb;
75	tim	1968
76			root_ = new TreeNode;
77	tim	1971	root_->bs.resize(nStuntDouble_);
78	tim	1968	root_->bs.setAll(); //
79
80	tim	1967	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
81	tim	1968	TreeNode* currentMolNode;
82			std::string molName = mol->getMoleculeName();
83
84			foundIter = root_->children.find(molName);
85			if ( foundIter == root_->children.end()) {
86			currentMolNode = new TreeNode;
87			currentMolNode->name = molName;
88			currentMolNode->bs.resize(nStuntDouble_);
89			}else {
90	tim	1971	currentMolNode = foundIter->second;
91	tim	1968	}
92	tim	1967
93			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
94	tim	1968	std::string atomName = atom->getType();
95			TreeNode* currentAtomNode;
96			foundIter = currentMolNode->children.find(molName);
97			if (foundIter == currentMolNode->children.end()) {
98			currentAtomNode = new TreeNode;
99			currentAtomNode->name = atomName;
100			currentAtomNode->bs.resize(nStuntDouble_);
101			} else {
102			currentAtomNode = foundIter->second;
103			}
104			currentMolNode->bs.setBitOn(atom->getGlobalIndex());
105			currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
106	tim	1967	}
107	tim	1968
108			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
109			std::string rbName = atom->getType();
110			TreeNode* currentRbNode;
111			foundIter = currentMolNode->children.find(molName);
112			if (foundIter == currentMolNode->children.end()) {
113			currentRbNode = new TreeNode;
114			currentRbNode->name = rbName;
115			currentRbNode->bs.resize(nStuntDouble_);
116			} else {
117			currentRbNode = foundIter->second;
118			}
119
120			currentMolNode->bs.setBitOn(rb->getGlobalIndex());
121			currentRbNode->bs.setBitOn(rb->getGlobalIndex());
122
123			//create nodes for atoms belong to this rigidbody
124			for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) {
125			std::string rbAtomName = atom->getType();
126			TreeNode* currentRbAtomNode;
127			foundIter = currentRbNode->children.find(molName);
128			if (foundIter == currentRbNode->children.end()) {
129			currentRbAtomNode = new TreeNode;
130			currentRbAtomNode->name = rbAtomName;
131			currentRbAtomNode->bs.resize(nStuntDouble_);
132			} else {
133			currentRbAtomNode = foundIter->second;
134			}
135			currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
136			}
137
138			}
139	tim	1967
140			}
141	tim	1968
142	tim	1967	}
143
144			bool NameFinder::match(const std::string& name, BitSet& bs){
145
146	tim	1971	bool hasError = false;
147	tim	1967	StringTokenizer tokenizer(name, ".");
148
149			std::vector<std::string> names;
150			while(tokenizer.hasMoreTokens()) {
151			names.push_back(tokenizer.nextToken());
152			}
153
154			int size = names.size();
155			switch(size) {
156			case 1 :
157	tim	1968	//could be molecule name, atom name and rigidbody name
158			if (names[0] == "*"){
159			//if all molecules are selected, we don't need to do the matching, just set all of the bits
160			bs.setAll();
161			} else{
162	tim	1971	matchMolecule(names[0], bs);
163			matchStuntDouble("*", names[0], bs);
164	tim	1968	}
165
166	tim	1967	break;
167			case 2:
168	tim	1968	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
169			matchRigidAtoms("*", names[0], names[1], bs);
170	tim	1971	matchStuntDouble(names[0], names[1], bs);
171	tim	1968
172	tim	1967	break;
173			case 3:
174			//must be molecule.rigidbody.*
175	tim	1971	matchRigidAtoms(names[0], names[1], names[2], bs);
176	tim	1967	break;
177	tim	1971	default:
178			hasError = true;
179	tim	1967	break;
180			}
181
182	tim	1971	return hasError;
183	tim	1967	}
184
185	tim	1968	void NameFinder::matchMolecule(const std::string& molName, BitSet& 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	tim	1971	bs \|= (*i)->bs;
190	tim	1968	}
191	tim	1967	}
192	tim	1968
193			void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
194			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
195			std::vector<TreeNode*>::iterator i;
196			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
197			std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
198			std::vector<TreeNode*>::iterator j;
199			for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
200	tim	1971	bs \|= (*j)->bs;
201	tim	1968	}
202			}
203
204			}
205
206			void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
207			std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
208			std::vector<TreeNode*>::iterator i;
209			for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
210			std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
211			std::vector<TreeNode*>::iterator j;
212			for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
213			std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
214			std::vector<TreeNode*>::iterator k;
215			for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
216	tim	1971	bs \|= (*k)->bs;
217	tim	1968	}
218			}
219			}
220
221			}
222
223
224			std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
225			std::vector<TreeNode*> matchedNodes;
226			std::map<std::string, TreeNode*>::iterator i;
227			for (i = node->children.begin(); i != node->children.end(); ++i) {
228			if (isMatched( i->first, name)) {
229			matchedNodes.push_back(i->second);
230			}
231			}
232
233			return matchedNodes;
234			}
235
236			bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
237			return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
238			}
239
240			}