Revision: 5247
Author: hansonr
Date: 2006-06-28 06:22:16 -0700 (Wed, 28 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5247&view=rev
Log Message:
-----------
bob200603 mol2reader improvements
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
Modified: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
2006-06-27 14:38:48 UTC (rev 5246)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
2006-06-28 13:22:16 UTC (rev 5247)
@@ -29,7 +29,7 @@
import org.jmol.api.JmolAdapter;
/**
- * A MINIMAL reader for TRIPOS mol2 files.
+ * A minimal multi-file reader for TRIPOS SYBYL mol2 files.
*<p>
* <a href='http://www.tripos.com/data/support/mol2.pdf '>
* http://www.tripos.com/data/support/mol2.pdf
@@ -39,22 +39,90 @@
class Mol2Reader extends AtomSetCollectionReader {
String line;
+ int desiredModelNumber;
+ int modelNumber = 0;
+ int nAtoms = 0;
+ void initialize() {
+ desiredModelNumber = -1;
+ }
+ void initialize(int[] params) {
+ initialize();
+ if (params == null)
+ return;
+ desiredModelNumber = params[0];
+ }
+
AtomSetCollection readAtomSetCollection(BufferedReader reader)
throws Exception {
atomSetCollection = new AtomSetCollection("mol2");
line = reader.readLine();
- int atomCount = 0;
- int bondCount = 0;
- int resCount = 0;
+ modelNumber = 0;
while (line != null) {
- if (line.equals("global")) {
+ if (line.equals("@<TRIPOS>MOLECULE")) {
+ if (++modelNumber == desiredModelNumber || desiredModelNumber <= 0) {
+ try {
+ processMolecule(reader);
+ } catch (Exception e) {
+ System.out.println(e + " at line: " + line);
+ e.printStackTrace();
+ new NullPointerException();
+ }
+ if (desiredModelNumber > 0)
+ break;
+ continue;
+ }
+ }
+ line = reader.readLine();
+ }
+ return atomSetCollection;
+ }
+
+ void processMolecule(BufferedReader reader) throws Exception {
+ /* 4-6 lines:
+ ZINC02211856
+ 55 58 0 0 0
+ SMALL
+ USER_CHARGES
+ 2-diethylamino-1-[2-(2-naphthyl)-4-quinolyl]-ethanol
+
+ mol_name
+ num_atoms [num_bonds [num_subst [num_feat [num_sets]]]]
+ mol_type
+ charge_type
+ [status_bits
+ [mol_comment]]
+
+ */
+
+ String thisDataSetName = reader.readLine().trim();
+ line = reader.readLine() + " 0 0 0 0 0 0";
+ int atomCount = parseInt(line);
+ int bondCount = parseInt(line, ichNextParse);
+ int resCount = parseInt(line, ichNextParse);
+ reader.readLine();//mol_type
+ line = reader.readLine();//charge_type
+ boolean iHaveCharges = (line.indexOf("NO_CHARGES") != 0);
+ line = reader.readLine(); //optional SYBYL status
+ if (line != null && line.charAt(0) != '@') {
+ line = reader.readLine(); //optional comment
+ if (line != null && line.charAt(0) != '@') {
+ thisDataSetName += ": " + reader.readLine().trim();
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);
+ }
+ }
+ if (atomSetCollection.currentAtomSetIndex >= 0) {
+ atomSetCollection.newAtomSet();
+ atomSetCollection.setCollectionName("<collection of "
+ + (atomSetCollection.currentAtomSetIndex + 1) + " models>");
+ } else {
+ atomSetCollection.setCollectionName(thisDataSetName);
+ }
+ logger.log(thisDataSetName);
+ while (line != null && !line.equals("@<TRIPOS>MOLECULE")) {
+ if (line.equals("@<TRIPOS>ATOM")) {
+ readAtoms(reader, atomCount, iHaveCharges);
+ atomSetCollection.setAtomSetName(thisDataSetName);
} else if (line.equals("@<TRIPOS>BOND")) {
readBonds(reader, bondCount);
} else if (line.equals("@<TRIPOS>SUBSTRUCTURE")) {
@@ -64,49 +132,50 @@
}
line = reader.readLine();
}
- return atomSetCollection;
+ nAtoms+=atomCount;
}
- void readAtoms(BufferedReader reader, int atomCount) throws Exception {
+ void readAtoms(BufferedReader reader, int atomCount, boolean iHaveCharges)
throws Exception {
// 1 Cs 0.0000 4.1230 0.0000 Cs 1 RES1 0.0000
- // 1 2 3 4 5 6
- //012345678901234567890123456789012345678901234567890123456789012345678
+ // 1 C1 7.0053 11.3096 -1.5429 C.3 1 <0> -0.1912
+ // free format, but no blank lines
for (int i = 0; i < atomCount; ++i) {
- String line = reader.readLine();
- String elementSymbol = line.substring(43, 45);
- if (elementSymbol.charAt(1) == '.')
+ Atom atom = atomSetCollection.addNewAtom();
+ line = reader.readLine();
+ String[] tokens = getTokens(line);
+ //System.out.println(tokens.length + " -" + tokens[5] + "- " + line);
+ atom.x = parseFloat(tokens[2]);
+ atom.y = parseFloat(tokens[3]);
+ atom.z = parseFloat(tokens[4]);
+ String elementSymbol = tokens[5];
+ if (elementSymbol.length() > 1 && 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();
+ if (elementSymbol.length() > 2)
+ elementSymbol = elementSymbol.substring(0, 2);
atom.elementSymbol = elementSymbol;
- atom.formalCharge = charge;
- atom.x = x;
- atom.y = y;
- atom.z = z;
+ if (iHaveCharges)
+ atom.partialCharge = parseFloat(tokens[8]);
}
}
void readBonds(BufferedReader reader, int bondCount) throws Exception {
// 6 1 42 1
- // 1 2 3 4 5 6
- //012345678901234567890123456789012345678901234567890123456789012345678
+ // free format, but no blank lines
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);
+ String[] tokens = getTokens(line);
+ int atomIndex1 = parseInt(tokens[1]);
+ int atomIndex2 = parseInt(tokens[2]);
+ int order = parseInt(tokens[3]);
if (order == Integer.MIN_VALUE)
- order = JmolAdapter.ORDER_AROMATIC;
+ order = (tokens[3].equals("ar") ? JmolAdapter.ORDER_AROMATIC : 1);
atomSetCollection
- .addBond(new Bond(atomIndex1 - 1, atomIndex2 - 1, order));
+ .addBond(new Bond(nAtoms + atomIndex1 - 1, nAtoms + atomIndex2 - 1,
order));
}
}
void readResInfo(BufferedReader reader, int resCount) throws Exception {
+ // free format, but no blank lines
for (int i = 0; i < resCount; ++i) {
reader.readLine();
//to be determined -- not implemented
@@ -115,13 +184,13 @@
void readCrystalInfo(BufferedReader reader) throws Exception {
// 4.1230 4.1230 4.1230 90.0000 90.0000 90.0000 221 1
- line=reader.readLine();
+ line = reader.readLine();
float[] notionalUnitcell = new float[6];
- ichNextParse=0;
+ 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);
+ String spaceGroup = line.substring(ichNextParse, line.length()).trim();
+ atomSetCollection.setAtomSetSpaceGroup(spaceGroup);
}
}
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