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
            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)

            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:	1987
Committed:	Mon Feb 7 22:36:32 2005 UTC (19 years, 4 months ago) by tim
File size:	9771 byte(s)
Log Message:	support select internal index selection, for example, select DMPC.3
#	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	#include "utils/StringUtils.hpp"
46	namespace oopse {
47
48	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	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59	loadNames();
60	}
61
62
63	NameFinder::~NameFinder(){
64	delete root_;
65	}
66
67	void NameFinder::loadNames() {
68
69	std::map<std::string, TreeNode*>::iterator foundIter;
70	SimInfo::MoleculeIterator mi;
71	Molecule* mol;
72	Molecule::AtomIterator ai;
73	Atom* atom;
74	Molecule::RigidBodyIterator rbIter;
75	RigidBody* rb;
76
77	root_ = new TreeNode;
78	root_->bs.resize(nStuntDouble_);
79	root_->bs.setAll(); //
80
81	for (mol = info_->beginMolecule(mi); mol != NULL; 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; rb = mol->nextRigidBody(rbIter)) {
95	std::string rbName = rb->getType();
96	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
97
98	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
99	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
100
101	//create nodes for atoms belong to this rigidbody
102	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
103	std::string rbAtomName = atom->getType();
104	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
105
106	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
107	}
108
109	}
110
111	}
112
113	}
114
115	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
130	BitSet NameFinder::match(const std::string& name){
131	BitSet bs(nStuntDouble_);
132
133	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	//could be molecule name, atom name and rigidbody name
144	if (names[0] == "*"){
145	//if all molecules are selected, we don't need to do the matching, just set all of the bits
146	bs.setAll();
147	} else{
148	matchMolecule(names[0], bs);
149	matchStuntDouble("*", names[0], bs);
150	}
151
152	break;
153	case 2:
154	//could be molecule.(include atoms and rigidbodies) or rigidbody.(atoms belong to rigidbody)
155
156	if (!isInteger(names[1])){
157	matchRigidAtoms("*", names[0], names[1], bs);
158	matchStuntDouble(names[0], names[1], bs);
159	} else {
160	int internalIndex = lexi_cast<int>(names[1]);
161	if (internalIndex < 0) {
162	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
163	} else {
164	matchInternalIndex(names[0], internalIndex, bs);
165	}
166	}
167
168	break;
169	case 3:
170	//must be molecule.rigidbody.*
171	matchRigidAtoms(names[0], names[1], names[2], bs);
172	break;
173	default:
174	std::cerr << "invalid name: " << name << std::endl;
175	break;
176	}
177
178	return bs;
179	}
180
181	void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
182	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
183	std::vector<TreeNode*>::iterator i;
184	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
185	bs \|= (*i)->bs;
186	}
187	}
188
189	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
190	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
191	std::vector<TreeNode*>::iterator i;
192	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
193	std::vector<TreeNode> sdNodes = getMatchedChildren(i, sdName);
194	std::vector<TreeNode*>::iterator j;
195	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
196	bs \|= (*j)->bs;
197	}
198	}
199
200	}
201
202	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
203	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
204	std::vector<TreeNode*>::iterator i;
205	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
206	std::vector<TreeNode> rbNodes = getMatchedChildren(i, rbName);
207	std::vector<TreeNode*>::iterator j;
208	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
209	std::vector<TreeNode> rbAtomNodes = getMatchedChildren(j, rbAtomName);
210	std::vector<TreeNode*>::iterator k;
211	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
212	bs \|= (*k)->bs;
213	}
214	}
215	}
216
217	}
218
219
220	std::vector<TreeNode> NameFinder::getMatchedChildren(TreeNode node, const std::string& name) {
221	std::vector<TreeNode*> matchedNodes;
222	std::map<std::string, TreeNode*>::iterator i;
223	for (i = node->children.begin(); i != node->children.end(); ++i) {
224	if (isMatched( i->first, name)) {
225	matchedNodes.push_back(i->second);
226	}
227	}
228
229	return matchedNodes;
230	}
231
232	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
233	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
234	}
235
236
237	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){
238
239	std::map<std::string, TreeNode*>::iterator foundIter;
240	SimInfo::MoleculeIterator mi;
241	Molecule* mol;
242
243	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
244
245	if (isMatched(mol->getMoleculeName(), name) ) {
246	int natoms = mol->getNAtoms();
247	int nrigidbodies = mol->getNRigidBodies();
248	if (internalIndex >= natoms + nrigidbodies) {
249	continue;
250	} else if (internalIndex < natoms) {
251	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
252	continue;
253	} else if ( internalIndex < natoms + nrigidbodies) {
254	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
255	}
256	}
257
258	}
259
260	}
261
262	bool NameFinder::isInteger(const std::string str) {
263	for(int i =0; i < str.size(); ++i){
264	if (!std::isdigit(str[i])) {
265	return false;
266	}
267	}
268
269	return true;
270	}
271
272	}