Revision: 5242
Author: hansonr
Date: 2006-06-25 19:56:05 -0700 (Sun, 25 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5242&view=rev
Log Message:
-----------
bob200603 adds very basic MOL2 (tripos SYBYL) file reader -- atoms, bonds, and
unit cell info only
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Resolver.java
Added Paths:
-----------
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
Added: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
(rev 0)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
2006-06-26 02:56:05 UTC (rev 5242)
@@ -0,0 +1,127 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-03-15 07:52:29 -0600 (Wed, 15 Mar 2006) $
+ * $Revision: 4614 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: [EMAIL PROTECTED]
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.adapter.smarter;
+
+import java.io.BufferedReader;
+
+import org.jmol.api.JmolAdapter;
+
+/**
+ * A MINIMAL reader for TRIPOS mol2 files.
+ *<p>
+ * <a href='http://www.tripos.com/data/support/mol2.pdf '>
+ * http://www.tripos.com/data/support/mol2.pdf
+ * </a>
+ *<p>
+ */
+class Mol2Reader extends AtomSetCollectionReader {
+
+ String line;
+
+ AtomSetCollection readAtomSetCollection(BufferedReader reader)
+ throws Exception {
+ atomSetCollection = new AtomSetCollection("mol2");
+ line = reader.readLine();
+ int atomCount = 0;
+ int bondCount = 0;
+ int resCount = 0;
+ while (line != null) {
+ if (line.equals("global")) {
+ line = reader.readLine();
+ atomCount = parseInt(line, 0, 6);
+ bondCount = parseInt(line, 6, 12);
+ resCount = parseInt(line, 12, 18);
+ } else if (line.equals("@<TRIPOS>ATOM")) {
+ readAtoms(reader, atomCount);
+ } else if (line.equals("@<TRIPOS>BOND")) {
+ readBonds(reader, bondCount);
+ } else if (line.equals("@<TRIPOS>SUBSTRUCTURE")) {
+ readResInfo(reader, resCount);
+ } else if (line.equals("@<TRIPOS>CRYSIN")) {
+ readCrystalInfo(reader);
+ }
+ line = reader.readLine();
+ }
+ return atomSetCollection;
+ }
+
+ void readAtoms(BufferedReader reader, int atomCount) throws Exception {
+ // 1 Cs 0.0000 4.1230 0.0000 Cs 1 RES1 0.0000
+ // 1 2 3 4 5 6
+ //012345678901234567890123456789012345678901234567890123456789012345678
+ for (int i = 0; i < atomCount; ++i) {
+ String line = reader.readLine();
+ String elementSymbol = line.substring(43, 45);
+ if (elementSymbol.charAt(1) == '.')
+ elementSymbol = elementSymbol.substring(0, 1);
+ float x = parseFloat(line, 13, 22);
+ float y = parseFloat(line, 22, 31);
+ float z = parseFloat(line, 31, 40);
+ int charge = (int) parseFloat(line, 60, 68);
+ Atom atom = atomSetCollection.addNewAtom();
+ atom.elementSymbol = elementSymbol;
+ atom.formalCharge = charge;
+ atom.x = x;
+ atom.y = y;
+ atom.z = z;
+ }
+ }
+
+ void readBonds(BufferedReader reader, int bondCount) throws Exception {
+ // 6 1 42 1
+ // 1 2 3 4 5 6
+ //012345678901234567890123456789012345678901234567890123456789012345678
+ for (int i = 0; i < bondCount; ++i) {
+ String line = reader.readLine();
+ parseInt(line);
+ int atomIndex1 = parseInt(line, ichNextParse);
+ int atomIndex2 = parseInt(line, ichNextParse);
+ int order = parseInt(line, ichNextParse);
+ if (order == Integer.MIN_VALUE)
+ order = JmolAdapter.ORDER_AROMATIC;
+ atomSetCollection
+ .addBond(new Bond(atomIndex1 - 1, atomIndex2 - 1, order));
+ }
+ }
+
+ void readResInfo(BufferedReader reader, int resCount) throws Exception {
+ for (int i = 0; i < resCount; ++i) {
+ reader.readLine();
+ //to be determined -- not implemented
+ }
+ }
+
+ void readCrystalInfo(BufferedReader reader) throws Exception {
+ // 4.1230 4.1230 4.1230 90.0000 90.0000 90.0000 221 1
+ line=reader.readLine();
+ float[] notionalUnitcell = new float[6];
+ ichNextParse=0;
+ for (int i = 0; i < 6; i++)
+ notionalUnitcell[i] = parseFloat(line, ichNextParse);
+ atomSetCollection.setNotionalUnitcell(notionalUnitcell, logger);
+ String spaceGroup = line.substring(ichNextParse,line.length()).trim();
+ atomSetCollection.setAtomSetSpaceGroup(spaceGroup);
+ }
+}
Modified: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2006-06-25 15:54:35 UTC (rev 5241)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2006-06-26 02:56:05 UTC (rev 5242)
@@ -266,11 +266,14 @@
final static String[] cubeRecords =
{"JVXL"};
+ final static String[] mol2Records =
+ {"@<TRIPOS>"};
+
final static String[][] fileStartsWithRecords =
- { nwchemRecords, cubeRecords};
+ { nwchemRecords, cubeRecords, mol2Records};
final static String[] fileStartsWithFormats =
- { "NWChem", "Cube"};
+ { "NWChem", "Cube", "Mol2"};
////////////////////////////////////////////////////////////////
// these test lines that startWith one of these strings
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