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 |
} |