1 /* $RCSfile$
2  * $Author: hansonr $
3  * $Date: 2006-07-14 15:35:47 -0500 (Fri, 14 Jul 2006) $
4  * $Revision: 5303 $
5  *
6  * Copyright (C) 2003-2005  Miguel, Jmol Development, www.jmol.org
7  *
8  * Contact: jmol-developers@lists.sf.net
9  *
10  *  This library is free software; you can redistribute it and/or
11  *  modify it under the terms of the GNU Lesser General Public
12  *  License as published by the Free Software Foundation; either
13  *  version 2.1 of the License, or (at your option) any later version.
14  *
15  *  This library is distributed in the hope that it will be useful,
16  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
18  *  Lesser General Public License for more details.
19  *
20  *  You should have received a copy of the GNU Lesser General Public
21  *  License along with this library; if not, write to the Free Software
22  *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
23  */
24 package org.jmol.adapter.readers.simple;
25 
26 import javajs.util.PT;
27 
28 import org.jmol.adapter.smarter.AtomSetCollectionReader;
29 import org.jmol.adapter.smarter.Atom;
30 
31 import org.jmol.api.JmolAdapter;
32 
33 /**
34  * Reads Ghemical (<a href="http://www.uku.fi/~thassine/ghemical/">
35  * http://www.uku.fi/~thassine/ghemical</a>)
36  * molecular mechanics (*.mm1gp) files.
37  * <code>
38  * !Header mm1gp 100
39  * !Info 1
40  * !Atoms 6
41  * 0 6
42  * 1 6
43  * 2 1
44  * 3 1
45  * 4 1
46  * 5 1
47  * !Bonds 5
48  * 1 0 D
49  * 2 0 S
50  * 3 0 S
51  * 4 1 S
52  * 5 1 S
53  * !Coord
54  * 0 0.06677 -0.00197151 4.968e-07
55  * 1 -0.0667699 0.00197154 -5.19252e-07
56  * 2 0.118917 -0.097636 2.03406e-06
57  * 3 0.124471 0.0904495 -4.84021e-07
58  * 4 -0.118917 0.0976359 -2.04017e-06
59  * 5 -0.124471 -0.0904493 5.12591e-07
60  * !Charges
61  * 0 -0.2
62  * 1 -0.2
63  * 2 0.1
64  * 3 0.1
65  * 4 0.1
66  * 5 0.1
67  * !End
68  * </code>
69  *
70  * @author Egon Willighagen <egonw@sci.kun.nl>
71  */
72 public class GhemicalMMReader extends AtomSetCollectionReader {
73 
74   @Override
checkLine()75   protected boolean checkLine() throws Exception {
76     if (line.startsWith("!Header")) {
77       processHeader();
78       return true;
79     }
80     if (line.startsWith("!Info")) {
81       processInfo();
82       return true;
83     }
84     if (line.startsWith("!Atoms")) {
85       processAtoms();
86       return true;
87     }
88     if (line.startsWith("!Bonds")) {
89       processBonds();
90       return true;
91     }
92     if (line.startsWith("!Coord")) {
93       processCoord();
94       return true;
95     }
96     if (line.startsWith("!Charges")) {
97       processCharges();
98       return true;
99     }
100     return true;
101   }
102 
processHeader()103   void processHeader() {
104   }
105 
processInfo()106   void processInfo() {
107   }
108 
processAtoms()109   void processAtoms() throws Exception {
110     int ac = parseIntAt(line, 6);
111     //Logger.debug("ac=" + ac);
112     for (int i = 0; i < ac; ++i) {
113       if (asc.ac != i)
114         throw new Exception("GhemicalMMReader error #1");
115       rd();
116       int atomIndex = parseIntStr(line);
117       if (atomIndex != i)
118         throw new Exception("bad atom index in !Atoms" +
119                             "expected: " + i + " saw:" + atomIndex);
120       int elementNumber = parseInt();
121       Atom atom = asc.addNewAtom();
122       atom.elementNumber = (short)elementNumber;
123     }
124   }
125 
processBonds()126   void processBonds() throws Exception {
127     int bondCount = parseIntAt(line, 6);
128     for (int i = 0; i < bondCount; ++i) {
129       rd();
130       int atomIndex1 = parseIntStr(line);
131       int atomIndex2 = parseInt();
132       String orderCode = parseToken();
133       int order = 0;
134       //bug found using FindBugs -- was not considering changes in bond order numbers
135       switch(orderCode.charAt(0)) {
136       case 'C': // Conjugated (aromatic)
137         order = JmolAdapter.ORDER_AROMATIC;
138         break;
139       case 'T':
140         order = JmolAdapter.ORDER_COVALENT_TRIPLE;
141         break;
142       case 'D':
143         order = JmolAdapter.ORDER_COVALENT_DOUBLE;
144         break;
145       case 'S':
146       default:
147         order = JmolAdapter.ORDER_COVALENT_SINGLE;
148       }
149       asc.addNewBondWithOrder(atomIndex1, atomIndex2, order);
150     }
151   }
152 
processCoord()153   void processCoord() throws Exception {
154     Atom[] atoms = asc.atoms;
155     int ac = asc.ac;
156     for (int i = 0; i < ac; ++i)
157       setAtomCoordScaled(atoms[i], PT.getTokens(rd()), 1, 10);
158   }
159 
processCharges()160   void processCharges() throws Exception {
161     Atom[] atoms = asc.atoms;
162     int ac = asc.ac;
163     for (int i = 0; i < ac; ++i) {
164       rd();
165       int atomIndex = parseIntStr(line);
166       if (atomIndex != i)
167         throw new Exception("bad atom index in !Charges" +
168                             "expected: " + i + " saw:" + atomIndex);
169       atoms[i].partialCharge = parseFloat();
170     }
171   }
172 }
173