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root/OpenMD/trunk/src/selection/NameFinder.cpp

Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 452 by tim, Tue Apr 5 23:09:48 2005 UTC vs.
Revision 1962 by gezelter, Wed Jan 15 22:26:18 2014 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 234107 (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 oopse {
47	>	namespace OpenMD {
48
49	<	TreeNode::~TreeNode(){
49	>	TreeNode::~TreeNode(){
50		std::map<std::string, TreeNode*>::iterator i;
51		for ( i = children.begin(); i != children.end(); ++i) {
52	<	i->second->~TreeNode();
52	>	i->second->~TreeNode();
53		}
54		children.clear();
55	<	}
55	>	}
56
57	<
58	<	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
59	<	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
57	>	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	>	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
59	>	nObjects_.push_back(info_->getNGlobalBonds());
60	>	nObjects_.push_back(info_->getNGlobalBends());
61	>	nObjects_.push_back(info_->getNGlobalTorsions());
62	>	nObjects_.push_back(info_->getNGlobalInversions());
63		loadNames();
64	<	}
64	>	}
65
66	<
63	<	NameFinder::~NameFinder(){
66	>	NameFinder::~NameFinder(){
67		delete root_;
68	<	}
68	>	}
69
70	<	void NameFinder::loadNames() {
68	<
69	<	std::map<std::string, TreeNode*>::iterator foundIter;
70	>	void NameFinder::loadNames() {
71		SimInfo::MoleculeIterator mi;
71	–	Molecule* mol;
72		Molecule::AtomIterator ai;
73	–	Atom* atom;
73		Molecule::RigidBodyIterator rbIter;
74	+	Molecule::BondIterator bondIter;
75	+	Molecule::BendIterator bendIter;
76	+	Molecule::TorsionIterator torsionIter;
77	+	Molecule::InversionIterator inversionIter;
78	+
79	+	Molecule* mol;
80	+	Atom* atom;
81		RigidBody* rb;
82	+	Bond* bond;
83	+	Bend* bend;
84	+	Torsion* torsion;
85	+	Inversion* inversion;
86
87		root_ = new TreeNode;
88	<	root_->bs.resize(nStuntDouble_);
88	>	root_->bs.resize(nObjects_);
89		root_->bs.setAll(); //
90
91	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
91	>	for (mol = info_->beginMolecule(mi); mol != NULL;
92	>	mol = info_->nextMolecule(mi)) {
93
94	<	std::string molName = mol->getMoleculeName();
95	<	TreeNode* currentMolNode = createNode(root_, molName);
94	>	std::string molName = mol->getMoleculeName();
95	>	TreeNode* molNode = createNode(root_, molName);
96
97	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
98	<	std::string atomName = atom->getType();
99	<	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
97	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
98	>	std::string atomName = atom->getType();
99	>	TreeNode* atomNode = createNode(molNode, atomName);
100
101	<	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
102	<	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
103	<	}
101	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
102	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
103	>	}
104
105	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
106	<	std::string rbName = rb->getType();
107	<	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
105	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
106	>	rb = mol->nextRigidBody(rbIter)) {
107	>	std::string rbName = rb->getType();
108	>	TreeNode* rbNode = createNode(molNode, rbName);
109
110	<	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
111	<	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
110	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
111	>	rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
112
113	<	//create nodes for atoms belong to this rigidbody
114	<	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115	<	std::string rbAtomName = atom->getType();
116	<	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
113	>	// COMMENTED OUT because rigid bodies are IntegrableObjects
114	>	// (e.g. they are independently mobile, so selecting their
115	>	// member atoms will give some odd results if we are computing
116	>	// degrees of freedom elsewhere.
117
118	<	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
119	<	}
118	>	// //create nodes for atoms belong to this rigidbody
119	>	// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
120	>	//   std::string rbAtomName = atom->getType();
121	>	//   TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
122
123	+	//   rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
124	+	// }
125	+	}
126	+
127	+	for (bond = mol->beginBond(bondIter); bond != NULL;
128	+	bond = mol->nextBond(bondIter)) {
129	+
130	+	std::string bondName = bond->getName();
131	+	TreeNode* bondNode = createNode(molNode, bondName);
132	+
133	+	molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
134	+	bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
135	+
136	+	std::vector<Atom*> atoms = bond->getAtoms();
137	+	std::vector<Atom*>::iterator ai;
138	+
139	+	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
140	+	std::string atomName = (*ai)->getType();
141	+	TreeNode* atomNode = createNode(bondNode, atomName);
142	+	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
143		}
144	+	}
145	+	for (bend = mol->beginBend(bendIter); bend != NULL;
146	+	bend = mol->nextBend(bendIter)) {
147	+
148	+	std::string bendName = bend->getName();
149	+	TreeNode* bendNode = createNode(molNode, bendName);
150	+
151	+	molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
152	+	bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
153	+
154	+	std::vector<Atom*> atoms = bend->getAtoms();
155	+	std::vector<Atom*>::iterator ai;
156
157	<	}
157	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
158	>	std::string atomName = (*ai)->getType();
159	>	TreeNode* atomNode = createNode(bendNode, atomName);
160	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
161	>	}
162
163	<	}
163	>	}
164	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
165	>	torsion = mol->nextTorsion(torsionIter)) {
166
167	<	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
167	>	std::string torsionName = torsion->getName();
168	>	TreeNode* torsionNode = createNode(molNode, torsionName);
169	>
170	>	molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
171	>	torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
172	>
173	>	std::vector<Atom*> atoms = torsion->getAtoms();
174	>	std::vector<Atom*>::iterator ai;
175	>
176	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
177	>	std::string atomName = (*ai)->getType();
178	>	TreeNode* atomNode = createNode(torsionNode, atomName);
179	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
180	>	}
181	>
182	>	}
183	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
184	>	inversion = mol->nextInversion(inversionIter)) {
185	>
186	>	std::string inversionName = inversion->getName();
187	>	TreeNode* inversionNode = createNode(molNode, inversionName);
188	>
189	>	molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
190	>	inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
191	>	std::vector<Atom*> atoms = inversion->getAtoms();
192	>	std::vector<Atom*>::iterator ai;
193	>
194	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
195	>	std::string atomName = (*ai)->getType();
196	>	TreeNode* atomNode = createNode(inversionNode, atomName);
197	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
198	>	}
199	>	}
200	>	}
201	>	}
202	>
203	>	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
204		TreeNode* node;
205		std::map<std::string, TreeNode*>::iterator foundIter;
206		foundIter = parent->children.find(name);
207		if ( foundIter  == parent->children.end()) {
208	<	node = new TreeNode;
209	<	node->name = name;
210	<	node->bs.resize(nStuntDouble_);
211	<	parent->children.insert(std::make_pair(name, node));
208	>	node = new TreeNode;
209	>	node->name = name;
210	>	node->bs.resize(nObjects_);
211	>	parent->children.insert(std::make_pair(name, node));
212		}else {
213	<	node = foundIter->second;
213	>	node = foundIter->second;
214		}
215		return node;
216	<	}
216	>	}
217
218	<	BitSet NameFinder::match(const std::string& name){
219	<	BitSet bs(nStuntDouble_);
218	>	SelectionSet NameFinder::match(const std::string& name){
219	>	SelectionSet bs(nObjects_);
220
221		StringTokenizer tokenizer(name, ".");
222
223		std::vector<std::string> names;
224		while(tokenizer.hasMoreTokens()) {
225	<	names.push_back(tokenizer.nextToken());
225	>	names.push_back(tokenizer.nextToken());
226		}
227
228		int size = names.size();
141	–	switch(size) {
142	–	case 1 :
143	–	//could be molecule name, atom name and rigidbody name
144	–	matchMolecule(names[0], bs);
145	–	matchStuntDouble("*", names[0], bs);
146	–
147	–	break;
148	–	case 2:
149	–	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
229
230	<	if (!isInteger(names[1])){
231	<	matchRigidAtoms("*", names[0], names[1], bs);
232	<	matchStuntDouble(names[0], names[1], bs);
233	<	} else {
234	<	int internalIndex = lexi_cast<int>(names[1]);
235	<	if (internalIndex < 0) {
236	<	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
237	<	} else {
238	<	matchInternalIndex(names[0], internalIndex, bs);
239	<	}
240	<	}
241	<
242	<	break;
243	<	case 3:
244	<	//must be molecule.rigidbody.*
245	<	matchRigidAtoms(names[0], names[1], names[2], bs);
246	<	break;
247	<	default:
248	<	std::cerr << "invalid name: " << name << std::endl;
249	<	break;
230	>	switch(size) {
231	>	case 1 :
232	>	//could be molecule name, atom name and rigidbody name
233	>	matchMolecule(names[0], bs);
234	>	matchStuntDouble("*", names[0], bs);
235	>	matchBond("*", names[0], bs);
236	>	matchBend("*", names[0], bs);
237	>	matchTorsion("*", names[0], bs);
238	>	matchInversion("*", names[0], bs);
239	>
240	>	break;
241	>	case 2:
242	>	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
243	>
244	>	if (!isInteger(names[1])){
245	>	matchRigidAtoms("*", names[0], names[1], bs);
246	>	matchStuntDouble(names[0], names[1], bs);
247	>	} else {
248	>	int internalIndex = lexi_cast<int>(names[1]);
249	>	if (internalIndex < 0) {
250	>	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
251	>	} else {
252	>	matchInternalIndex(names[0], internalIndex, bs);
253	>	}
254	>	}
255	>
256	>	break;
257	>	case 3:
258	>	//must be molecule.rigidbody.*
259	>	matchRigidAtoms(names[0], names[1], names[2], bs);
260	>	break;
261	>	default:
262	>	std::cerr << "invalid name: " << name << std::endl;
263	>	break;
264		}
265
266		return bs;
267	<	}
267	>	}
268
269	<	void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
269	>	void NameFinder::matchMolecule(const std::string& molName, SelectionSet& bs) {
270		std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
271		std::vector<TreeNode*>::iterator i;
272		for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
273	<	bs |= (*i)->bs;
273	>	bs |= (*i)->bs;
274		}
275	<	}
275	>	}
276
277	<	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
277	>	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
278		std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
279		std::vector<TreeNode*>::iterator i;
280		for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
281	<	std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);
282	<	std::vector<TreeNode*>::iterator j;
283	<	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
284	<	bs |= (*j)->bs;
285	<	}
281	>	std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);
282	>	std::vector<TreeNode*>::iterator j;
283	>	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
284	>	bs |= (*j)->bs;
285	>	}
286		}
287
288	<	}
288	>	}
289
290	<	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
290	>	void NameFinder::matchBond(const std::string& molName,
291	>	const std::string& bondName, SelectionSet& bs){
292		std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
293		std::vector<TreeNode*>::iterator i;
294		for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
295	<	std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);
296	<	std::vector<TreeNode*>::iterator j;
297	<	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
298	<	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
299	<	std::vector<TreeNode*>::iterator k;
300	<	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
301	<	bs |= (*k)->bs;
302	<	}
303	<	}
295	>	std::vector<TreeNode*> bondNodes = getMatchedChildren(*i, bondName);
296	>	std::vector<TreeNode*>::iterator j;
297	>	for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
298	>	bs |= (*j)->bs;
299	>	std::vector<TreeNode*> bondAtomNodes = getAllChildren(*j);
300	>	std::vector<TreeNode*>::iterator k;
301	>	for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
302	>	bs |= (*k)->bs;
303	>	}
304	>	}
305		}
306	+	}
307
308	<	}
308	>	void NameFinder::matchBend(const std::string& molName, const std::string& bendName,  SelectionSet& bs){
309	>	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
310	>	std::vector<TreeNode*>::iterator i;
311	>	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
312	>	std::vector<TreeNode*> bendNodes = getMatchedChildren(*i, bendName);
313	>	std::vector<TreeNode*>::iterator j;
314	>	for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
315	>	std::vector<TreeNode*> bendAtomNodes = getAllChildren(*j);
316	>	std::vector<TreeNode*>::iterator k;
317	>	for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
318	>	bs |= (*k)->bs;
319	>	}
320	>	}
321	>	}
322	>	}
323	>	void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
324	>	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
325	>	std::vector<TreeNode*>::iterator i;
326	>	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
327	>	std::vector<TreeNode*> torsionNodes = getMatchedChildren(*i, torsionName);
328	>	std::vector<TreeNode*>::iterator j;
329	>	for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
330	>	std::vector<TreeNode*> torsionAtomNodes = getAllChildren(*j);
331	>	std::vector<TreeNode*>::iterator k;
332	>	for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
333	>	bs |= (*k)->bs;
334	>	}
335	>	}
336	>	}
337	>	}
338	>	void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
339	>	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
340	>	std::vector<TreeNode*>::iterator i;
341	>	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
342	>	std::vector<TreeNode*> inversionNodes = getMatchedChildren(*i, inversionName);
343	>	std::vector<TreeNode*>::iterator j;
344	>	for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
345	>	std::vector<TreeNode*> inversionAtomNodes = getAllChildren(*j);
346	>	std::vector<TreeNode*>::iterator k;
347	>	for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
348	>	bs |= (*k)->bs;
349	>	}
350	>	}
351	>	}
352	>	}
353
354	+	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
355	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
356	+	std::vector<TreeNode*>::iterator i;
357	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
358	+	std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);
359	+	std::vector<TreeNode*>::iterator j;
360	+	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
361	+	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
362	+	std::vector<TreeNode*>::iterator k;
363	+	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
364	+	bs |= (*k)->bs;
365	+	}
366	+	}
367	+	}
368
369	<	std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
369	>	}
370	>
371	>	std::vector<TreeNode*> NameFinder::getAllChildren(TreeNode* node)  {
372	>	std::vector<TreeNode*> childNodes;
373	>	std::map<std::string, TreeNode*>::iterator i;
374	>	for (i = node->children.begin(); i != node->children.end(); ++i) {
375	>	childNodes.push_back(i->second);
376	>	}
377	>	return childNodes;
378	>	}
379	>
380	>	std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
381		std::vector<TreeNode*> matchedNodes;
382		std::map<std::string, TreeNode*>::iterator i;
383		for (i = node->children.begin(); i != node->children.end(); ++i) {
384	<	if (isMatched( i->first, name)) {
385	<	matchedNodes.push_back(i->second);
386	<	}
384	>	if (isMatched( i->first, name)) {
385	>	matchedNodes.push_back(i->second);
386	>	}
387		}
388
389		return matchedNodes;
390	<	}
390	>	}
391
392	<	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
393	<	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
394	<	}
392	>	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
393	>	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
394	>	}
395
396
397	<	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){
397	>	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){
398
234	–	std::map<std::string, TreeNode*>::iterator foundIter;
399		SimInfo::MoleculeIterator mi;
400		Molecule* mol;
401
402	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
402	>	for (mol = info_->beginMolecule(mi); mol != NULL;
403	>	mol = info_->nextMolecule(mi)) {
404
405	<	if (isMatched(mol->getMoleculeName(), name) ) {
406	<	int natoms = mol->getNAtoms();
407	<	int nrigidbodies = mol->getNRigidBodies();
408	<	if (internalIndex >= natoms + nrigidbodies) {
409	<	continue;
410	<	} else if (internalIndex < natoms) {
411	<	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
412	<	continue;
413	<	} else if ( internalIndex < natoms + nrigidbodies) {
414	<	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
415	<	}
416	<	}
252	<
253	<	}
254	<
255	<	}
256	<
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	<	}
405	>	if (isMatched(mol->getMoleculeName(), name) ) {
406	>	int natoms = mol->getNAtoms();
407	>	int nrigidbodies = mol->getNRigidBodies();
408	>	if (internalIndex >= natoms + nrigidbodies) {
409	>	continue;
410	>	} else if (internalIndex < natoms) {
411	>	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
412	>	continue;
413	>	} else if ( internalIndex < natoms + nrigidbodies) {
414	>	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
415	>	}
416	>	}
417		}
418	+	}
419
420	+	bool NameFinder::isInteger(const std::string &str) {
421	+	for(unsigned int i = 0; i < str.size(); ++i){
422	+	if (!std::isdigit(str[i])) {
423	+	return false;
424	+	}
425	+	}
426		return true;
427	<	}
266	<
427	>	}
428		}

Comparing trunk/src/selection/NameFinder.cpp (property svn:keywords):
Revision 452 by tim, Tue Apr 5 23:09:48 2005 UTC vs.
Revision 1962 by gezelter, Wed Jan 15 22:26:18 2014 UTC

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