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"
namespace oopse {

NameFinder::NameFinder(SimInfo* info) {
    loadNames();
}


void NameFinder::loadNames() {

    root_ = new NameNode;
    root_.type = rootNode;

    NameNode* newNode;            
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        newNode = new NameNode;
        newNode.type = molNode;
        newNode.name = mol->getMoleculeName();
        
        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            atomNames_.insert(atom->getType());
        }
        
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
            rbNames_.insert(rb->getType());
        }        
    }    
}

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

    bool error = true;
    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, rigidbody name
            isMolName();
            isAtomName();
            isRigidBodyName();
            break;
        case 2:
            //could be molecule.*(include atoms and rigidbodies) or rigidbody.*
            break;
        case 3:
            //must be molecule.rigidbody.*
            
            break;
        default:            
            break;           
    }

    return matched;
}

}
Revision:	283
Committed:	Thu Feb 3 23:14:05 2005 UTC (20 years, 9 months ago) by tim
File size:	3852 byte(s)
Log Message:	more work in selection library
#	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	namespace oopse {
43
44	NameFinder::NameFinder(SimInfo* info) {
45	loadNames();
46	}
47
48
49
50	void NameFinder::loadNames() {
51
52	root_ = new NameNode;
53	root_.type = rootNode;
54
55	NameNode* newNode;
56	SimInfo::MoleculeIterator mi;
57	Molecule* mol;
58	Molecule::AtomIterator ai;
59	Atom* atom;
60	Molecule::RigidBodyIterator rbIter;
61	RigidBody* rb;
62	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
63	newNode = new NameNode;
64	newNode.type = molNode;
65	newNode.name = mol->getMoleculeName();
66
67	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
68	atomNames_.insert(atom->getType());
69	}
70
71	//change the positions of atoms which belong to the rigidbodies
72	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
73	rbNames_.insert(rb->getType());
74	}
75	}
76	}
77
78	bool NameFinder::match(const std::string& name, BitSet& bs){
79
80	bool error = true;
81	StringTokenizer tokenizer(name, ".");
82
83	std::vector<std::string> names;
84	while(tokenizer.hasMoreTokens()) {
85	names.push_back(tokenizer.nextToken());
86	}
87
88	int size = names.size();
89	switch(size) {
90	case 1 :
91	//could be molecule name, atom name, rigidbody name
92	isMolName();
93	isAtomName();
94	isRigidBodyName();
95	break;
96	case 2:
97	//could be molecule.(include atoms and rigidbodies) or rigidbody.
98	break;
99	case 3:
100	//must be molecule.rigidbody.*
101
102	break;
103	default:
104	break;
105	}
106
107	return matched;
108	}
109
110	}