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)) {
           
        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
            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:      
            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());
}

}
Revision:	288
Committed:	Fri Feb 4 22:39:26 2005 UTC (20 years, 8 months ago) by tim
File size:	8229 byte(s)
Log Message:	half of the selection utility is working need to debug within keyword and atomproperty keyword
#	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. 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	#include "utils/wildcards.hpp"
43	#include "utils/StringTokenizer.hpp"
44	#include "primitives/Molecule.hpp"
45	namespace oopse {
46
47	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	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
58	loadNames();
59	}
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; mol = info_->nextMolecule(mi)) {
81
82	std::string molName = mol->getMoleculeName();
83	TreeNode* currentMolNode = createNode(root_, molName);
84
85	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86	std::string atomName = atom->getType();
87	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
88
89	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
90	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
91	}
92
93	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
94	std::string rbName = rb->getType();
95	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
96
97	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
98	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
99
100	//create nodes for atoms belong to this rigidbody
101	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
102	std::string rbAtomName = atom->getType();
103	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
104
105	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
106	}
107
108	}
109
110	}
111
112	}
113
114	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
115	TreeNode* node;
116	std::map<std::string, TreeNode*>::iterator foundIter;
117	foundIter = parent->children.find(name);
118	if ( foundIter == parent->children.end()) {
119	node = new TreeNode;
120	node->name = name;
121	node->bs.resize(nStuntDouble_);
122	parent->children.insert(std::make_pair(name, node));
123	}else {
124	node = foundIter->second;
125	}
126	return node;
127	}
128
129	BitSet NameFinder::match(const std::string& name){
130	BitSet bs(nStuntDouble_);
131
132	StringTokenizer tokenizer(name, ".");
133
134	std::vector<std::string> names;
135	while(tokenizer.hasMoreTokens()) {
136	names.push_back(tokenizer.nextToken());
137	}
138
139	int size = names.size();
140	switch(size) {
141	case 1 :
142	//could be molecule name, atom name and rigidbody name
143	if (names[0] == "*"){
144	//if all molecules are selected, we don't need to do the matching, just set all of the bits
145	bs.setAll();
146	} else{
147	matchMolecule(names[0], bs);
148	matchStuntDouble("*", names[0], bs);
149	}
150
151	break;
152	case 2:
153	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
154	matchRigidAtoms("*", names[0], names[1], bs);
155	matchStuntDouble(names[0], names[1], bs);
156
157	break;
158	case 3:
159	//must be molecule.rigidbody.*
160	matchRigidAtoms(names[0], names[1], names[2], bs);
161	break;
162	default:
163	std::cerr << "invalid name: " << name << std::endl;
164	break;
165	}
166
167	return bs;
168	}
169
170	void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
171	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
172	std::vector<TreeNode*>::iterator i;
173	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
174	bs \|= (*i)->bs;
175	}
176	}
177
178	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
179	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
180	std::vector<TreeNode*>::iterator i;
181	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
182	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
183	std::vector<TreeNode*>::iterator j;
184	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
185	bs \|= (*j)->bs;
186	}
187	}
188
189	}
190
191	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
192	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
193	std::vector<TreeNode*>::iterator i;
194	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
195	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
196	std::vector<TreeNode*>::iterator j;
197	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
198	std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
199	std::vector<TreeNode*>::iterator k;
200	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
201	bs \|= (*k)->bs;
202	}
203	}
204	}
205
206	}
207
208
209	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
210	std::vector<TreeNode*> matchedNodes;
211	std::map<std::string, TreeNode*>::iterator i;
212	for (i = node->children.begin(); i != node->children.end(); ++i) {
213	if (isMatched( i->first, name)) {
214	matchedNodes.push_back(i->second);
215	}
216	}
217
218	return matchedNodes;
219	}
220
221	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
222	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
223	}
224
225	}