Menu
▾
▴
[Cdk-commits] CVS: cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm/util BuildMolecule.java,NONE,1.1 CanonicalizationDir.java,NONE,1.1 Canonicalization.java,NONE,1.1 CDKConverter.java,NONE,1.1 Converter.java,NONE,1.1 FileMerger2.java,NONE,1.1 FileMerger.java,NONE,1.1 FileSplitter.java,NONE,1.1 Fingerprint.java,NONE,1.1 FormulaGenerator.java,NONE,1.1 JOELibConverter.java,NONE,1.1 LegacyConverter.java,NONE,1.1 MatrixBuilder.java,NONE,1.1 MergeIChIandCML.java,NONE,1.1 MoleculeProperties.java,NONE,1.1 MolUtil.java,NONE,1.1 multiExec.java,NONE,1.1 SaxonTransform.java,NONE,1.1 Scraper.java,NONE,1.1 SplitSDF.java,NONE,1.1 XUpdate.java,NONE,1.1
Update of /cvsroot/cdk/cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm/util
In directory sc8-pr-cvs1:/tmp/cvs-serv26020
Added Files:
BuildMolecule.java CanonicalizationDir.java
Canonicalization.java CDKConverter.java Converter.java
FileMerger2.java FileMerger.java FileSplitter.java
Fingerprint.java FormulaGenerator.java JOELibConverter.java
LegacyConverter.java MatrixBuilder.java MergeIChIandCML.java
MoleculeProperties.java MolUtil.java multiExec.java
SaxonTransform.java Scraper.java SplitSDF.java XUpdate.java
Log Message:
change them to cdk plugin
--- NEW FILE: BuildMolecule.java ---
package uk.ac.cam.ch.wwmm.util;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.awt.BorderLayout;
import java.util.StringTokenizer;
import javax.swing.JFrame;
import javax.xml.parsers.DocumentBuilderFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.ChemSequence;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.SetOfMolecules;
import org.openscience.cdk.renderer.MoleculeViewer2D;
import org.openscience.cdk.renderer.MoleculeViewer3D;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.libio.jmol.Convertor;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.CMLWriter;
import org.openscience.cdk.tools.SaturationChecker;
import org.openscience.jmol.PublicJmol;
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import uk.co.demon.ursus.dom.PMRDOMUtil;
/** license stuff goes here - probably Artistic -
*/
/**@author P.Murray-Rust, 2002
*/
/**Tests building of molecule from scratch (atom by atom)
*/
public class BuildMolecule {
/** constructor
*/
public BuildMolecule() {
}
/** build N=O and display
*/
public static void test1() {
// make empty Molecule and add atoms and bonds
Molecule molecule = new Molecule();
Atom atom1 = new Atom("N", new Point2d(1.0, 0.0));
Atom atom2 = new Atom("O");
atom2.setX2D(0.0);
atom2.setY2D(1.0);
Bond bond1 = new Bond(atom1, atom2, 2.0f);
molecule.addAtom(atom1);
molecule.addAtom(atom2);
molecule.addBond(bond1);
debug(molecule);
MoleculeViewer2D mv2d = new MoleculeViewer2D(molecule);
mv2d.display();
}
/** build C1=CC1(=O) and test coordinate generation
*/
public static void test2() {
// make empty Molecule and add atoms and bonds
Molecule molecule = new Molecule();
Atom c1 = new Atom("C");
Atom c2 = new Atom("C");
Atom c3 = new Atom("C");
Atom o1 = new Atom("O");
molecule.addAtom(c1);
molecule.addAtom(c2);
molecule.addAtom(c3);
molecule.addAtom(o1);
molecule.addBond(new Bond(c1, c2, 2.0f));
molecule.addBond(new Bond(c1, c3, 1.0f));
molecule.addBond(new Bond(c2, c3, 1.0f));
molecule.addBond(new Bond(o1, c3, 2.0f));
boolean generate2d = true;
// should generate coordinates
MoleculeViewer2D.display(molecule, generate2d);
Atom cl = new Atom("Cl");
molecule.addAtom(cl);
molecule.addBond(new Bond(c1, cl, 1.0f));
// alternative
StructureDiagramGenerator sdg = new StructureDiagramGenerator(molecule);
try {
sdg.generateCoordinates();
} catch (Exception sdge) {
System.out.println("StructureDiagramGenerator threw Exception: "+sdge);
}
debug(molecule);
System.out.println("Generating coordinates...");
molecule = sdg.getMolecule();
debug(molecule);
MoleculeViewer2D mv2d = new MoleculeViewer2D(molecule);
mv2d.display();
}
static void debugBond(PrintStream s, Bond b) {
s.println("Bond info======");
Atom[] atoms = b.getAtoms();
s.println("Bond 2D centre: "+b.get2DCenter());
s.println(b.getAtomAt(0).getSymbol()+"-"+b.getAtomAt(0).getSymbol());
try {
s.println("Bond length: "+b.getLength());
} catch (Throwable e) {
System.err.println("No bond length");
}
// s.println("Bond order: "+b.getOrder());
// s.println("Bond stereo: "+b.getStereo());
}
static void debug(Molecule molecule) {
System.out.println("=== molecule ===");
// Returns the number of Atoms in this Container.
int nAtoms = molecule.getAtomCount();
System.out.println("The molecule has "+nAtoms+" atoms");
java.util.Enumeration atoms = molecule.atoms();
while (atoms.hasMoreElements()) {
Atom atom = (Atom) atoms.nextElement();
System.out.println("Atom: "+atom);
}
// Returns the array of bonds of this AtomContainer.
System.out.println(" ---Bonds---");
Bond[] bonds = molecule.getBonds();
if (bonds == null || bonds.length == 0) {
System.out.println("NO BONDS");
} else {
// Returns the number of Bonds in this Container.
int nBonds = molecule.getBondCount();
System.out.println("The molecule has "+nBonds+" bonds");
for (int i = 0; i < nBonds; i++) {
Bond bond = bonds[i];
debugBond(System.out, bond);
}
}
}
static void convert(String filename) throws IOException, TestException {
}
static void testXYZ(String filename) throws IOException, TestException {
BufferedReader br = new BufferedReader(new FileReader(filename));
String na = br.readLine();
if (na == null) {
throw new TestException("Corrupt/empty XYZ file");
}
String title = br.readLine();
if (title == null) {
throw new TestException("Corrupt/empty XYZ file reading second line");
}
int natoms = 0;
try {
natoms = Integer.parseInt(na);
} catch (NumberFormatException nfe) {
throw new TestException("XYZ file must start with an integer");
}
Molecule molecule = new Molecule();
for (int i = 0; i < natoms; i++) {
String line = br.readLine();
if (line == null) {
throw new TestException("Not enough lines in XYZ file at line: "+(i+2));
}
StringTokenizer st = new StringTokenizer(line);
if (st.countTokens() != 4) {
throw new TestException("Bad format of line in XYZ file: "+line);
}
String element = st.nextToken();
String x = st.nextToken();
String y = st.nextToken();
String z = st.nextToken();
double x3, y3, z3;
try {
x3 = new Double(x).doubleValue();
y3 = new Double(y).doubleValue();
z3 = new Double(z).doubleValue();
} catch (NumberFormatException nfe1) {
throw new TestException("Bad coordinate in: "+line);
}
Atom a = new Atom(element, new Point3d(x3, y3, z3));
molecule.addAtom(a);
}
System.out.println("Read XYZ OK... natoms="+natoms);
joinTheDots(molecule);
// guessBondOrders(molecule);
// debug(molecule);
System.out.println("======================");
StructureDiagramGenerator sdg = new StructureDiagramGenerator(molecule);
try {
sdg.generateCoordinates();
molecule = sdg.getMolecule();
} catch (Exception sdge) {
System.out.println("StructureDiagramGenerator threw Exception: "+sdge);
}
// debug(molecule);
MoleculeViewer2D mv2d = new MoleculeViewer2D(molecule);
mv2d.display();
// MoleculeViewer3D mv3d = new MoleculeViewer3D(molecule);
// mv3d.display();
view3D(molecule);
}
static void testCML(String filename) throws Exception {
Document doc = null;
try {
doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new File(filename));
} catch (Exception ee) {
System.err.println("Parser error: "+ee);
return;
}
NodeList mols = doc.getElementsByTagName("molecule");
String out = "<cml>";
for (int i = 0; i < mols.getLength(); i++) {
Element mol = (Element) mols.item(i);
StringWriter sw = new StringWriter();
PMRDOMUtil.outputEventStream(mol, sw, 0, uk.co.demon.ursus.dom.PMRDOMUtil.PRETTY);
sw.close();
StringReader sr = new StringReader(sw.toString());
CMLReader cr = new CMLReader(sr);
ChemFile cf = (ChemFile) cr.read(new ChemFile());
// System.out.println("OBJ "+obj.getClass());
Molecule molecule = getMolecule(cf);
joinTheDots(molecule);
sw = new StringWriter();
CMLWriter cmlw = new CMLWriter(sw);
cmlw.write(molecule);
sw.close();
out += sw.toString();
}
out += "</cml>";
FileWriter fw = new FileWriter(filename+".1");
fw.write(out);
fw.close();
}
public static Molecule getMolecule(ChemFile chemFile) {
for (int i = 0; i < chemFile.getChemSequenceCount(); i++) {
ChemModel[] cms = chemFile.getChemSequence(i).getChemModels();
for (int j = 0; j < cms.length; j++) {
if (cms[j] == null) {
continue;
}
SetOfMolecules som = cms[j].getSetOfMolecules();
for (int k = 0; k < som.getMoleculeCount(); k++) {
Molecule mol = som.getMolecule(k);
if (mol != null) return mol;
}
}
}
return null;
}
public static void view3D(Molecule m) {
try
{
JFrame frame = new JFrame("CDK Molecule Viewer");
frame.getContentPane().setLayout(new BorderLayout());
org.openscience.jmol.PublicJmol jmol = org.openscience.jmol.PublicJmol.getJmol(frame);
jmol.showChemFrame(Convertor.convert(m));
frame.getContentPane().add(jmol, BorderLayout.CENTER);
} catch (Exception e)
{
e.printStackTrace();
}
}
public final static double TOLERANCE = 0.2;
static void joinTheDots(Molecule molecule) {
int natoms = molecule.getAtomCount();
Atom[] atoms = molecule.getAtoms();
for (int i = 1; i < natoms; i++) {
Atom ai = atoms[i];
String elemi = ai.getSymbol();
double radi = getRadius(elemi);
Point3d pi = ai.getPoint3D();
for (int j = 0; j < i; j++) {
Atom aj = atoms[j];
String elemj = aj.getSymbol();
double radj = getRadius(elemj);
Point3d pj = aj.getPoint3D();
double dist = pi.distance(pj);
if (dist < radi + radj + TOLERANCE) {
double paulingBO = getPaulingBO(dist, radi, radj);
double cdkBO = 1.0;
if (paulingBO < 1.3) {
cdkBO = 1.0;
} else if (paulingBO < 1.75) {
cdkBO = 1.5;
} else if (paulingBO < 2.5) {
cdkBO = 2.0;
} else if (paulingBO < 5) {
cdkBO = 3.0;
}
Bond b = new Bond(ai, aj, cdkBO);
molecule.addBond(b);
}
}
}
}
public static double getPaulingBO(double length, double covr0, double covr1) {
return Math.exp(2.303*(-length + covr0 + covr1)/0.7);
}
// not finished
public static void guessBondOrders(Molecule molecule) {
//SaturationChecker
boolean start = true;
int FINISHED = 0;
for (int i = 0; i < molecule.getAtomCount(); i++) {
Atom atom = molecule.getAtomAt(i);
atom.flags = new boolean[10];
atom.flags[FINISHED] = false;
if (atom.getSymbol().equals("C")) {
atom.setMaxBondOrder(3.0);
atom.setMaxBondOrderSum(4.0);
}
if (atom.getSymbol().equals("N")) {
atom.setMaxBondOrder(3.0);
atom.setMaxBondOrderSum(4.0);
}
if (atom.getSymbol().equals("O")) {
atom.setMaxBondOrder(2.0);
atom.setMaxBondOrderSum(2.0);
}
if (atom.getSymbol().equals("F")) {
atom.setMaxBondOrder(1.0);
atom.setMaxBondOrderSum(1.0);
}
if (atom.getSymbol().equals("H")) {
atom.setMaxBondOrder(1.0);
atom.setMaxBondOrderSum(1.0);
}
if (atom.getSymbol().equals("H")) {
} else {
int hc = 0;
Atom[] ligands = molecule.getConnectedAtoms(atom);
for (int j = 0; j < ligands.length; j++) {
if (ligands[j].getSymbol().equals("H")) hc++;
}
atom.setHydrogenCount(hc);
}
}
boolean change = true;
while (change) {
change = false;
for (int i = 0; i < molecule.getAtomCount(); i++) {
Atom atom = molecule.getAtomAt(i);
if (atom.flags[FINISHED]) continue;
System.out.println("AT....: "+atom.getSymbol()+
"/"+atom.getHydrogenCount()+
"/"+molecule.getBondCount(atom)+
"/"+molecule.getBondOrderSum(atom)+
"/"+atom.getMaxBondOrder()+
"/"+atom.getMaxBondOrderSum()+
"/"+molecule.getMinimumBondOrder(atom)+
"/"+molecule.getHighestCurrentBondOrder(atom)
);
}
for (int i = 0; i < molecule.getAtomCount(); i++) {
Atom atom = molecule.getAtomAt(i);
System.out.println("AT: "+atom.getSymbol()+
"/"+atom.getHydrogenCount()+
"/"+molecule.getBondCount(atom)+
"/"+molecule.getBondOrderSum(atom)+
"/"+molecule.getMinimumBondOrder(atom)+
"/"+molecule.getHighestCurrentBondOrder(atom)
);
}
}
for (int i = 0; i < molecule.getAtomCount(); i++) {
Atom atom = molecule.getAtomAt(i);
// if we don't do this we get Index OOB later
atom.flags = null;
}
}
static double getRadius(String elem) {
if (elem.equals("B")) return 0.83;
if (elem.equals("C")) return 0.77;
if (elem.equals("N")) return 0.7;
if (elem.equals("O")) return 0.65;
if (elem.equals("F")) return 0.60;
if (elem.equals("Si")) return 1.1;
if (elem.equals("P")) return 1.05;
if (elem.equals("S")) return 1.0;
if (elem.equals("Cl")) return 0.95;
if (elem.equals("H")) return 0.35;
return 1.5;
}
public static void main(String[] args) throws Exception {
if (args.length == 0) {
System.out.println("Usage: java uk.ac.cam.ch.wwmm.util.BuildMolecule -TEST [testnumber] -FILE [filename]");
}
int i = 0;
while (i < args.length) {
if (args[i].equals("-TEST")) {
i++;
if (args[i].equals("1")) {
test1();
} else if (args[i].equals("2")) {
test2();
} else {
System.out.println("Unknown test: "+args[i]);
}
i++;
} else if (args[i].equals("-FILE")) {
i++;
String file = args[i++];
int idx = file.lastIndexOf(".");
if (idx != -1) {
String suffix = file.substring(idx+1);
if (suffix.equals("xyz")) {
try {
testXYZ(file);
} catch (TestException te) {
System.err.println("Broken XYZ file: "+file+" ["+te+"]");
} catch (IOException ioe) {
System.err.println("ReadError: "+file+" ["+ioe+"]");
}
} else if (suffix.equals("xml")) {
try {
testCML(file);
} catch (TestException te) {
System.err.println("Broken CML file: "+file+" ["+te+"]");
} catch (IOException ioe) {
System.err.println("ReadError: "+file+" ["+ioe+"]");
}
} else {
System.out.println("Cannot read file type: "+file);
}
}
} else {
System.err.println("Unknown argument: "+args[i]);
}
}
}
};
class TestException extends Exception {
public TestException() {
}
public TestException(String s) {
super(s);
}
};
--- NEW FILE: CanonicalizationDir.java ---
package uk.ac.cam.ch.wwmm.util;
//import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileWriter;
import org.w3c.dom.*;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.xml.security.c14n.Canonicalizer;
public class CanonicalizationDir {
public static void main(String args[]) throws Exception {
//Parse the arguments
if (args.length == 0) {
System.out.println(
"Usage: java uk.ac.cam.ch.wwmm.util.CanonicalizationDir -inputDir inputDir -outputDir outputDir");
}
int i = 0;
String inputDir="";
String outputDir="";
while (i < args.length) {
if (false) {
} else if (args[i].equals("-inputDir")) {
i++;
inputDir = args[i++];
} else if (args[i].equals("-outputDir")) {
i++;
outputDir = args[i++];
} else {
System.err.println("Unknown argument: " + args[i]);
i++;
}
}
System.out.println(" inputDir = " + inputDir);
System.out.println(" outputDir = " + outputDir);
String inputFileName = "";
String inputFile="";
String outputFile="";
File dir = new File(inputDir);
File testDir;
if (dir.isDirectory()) {
String[] files = dir.list();
System.out.println("There are " + files.length + " files");
for (int j = 0; j < files.length; j++) {
System.out.println("j=" + j);
inputFileName = files[j];
testDir = new File(inputDir + "/" + inputFileName);
if (!testDir.isDirectory()) {
inputFile = inputDir + "/" + inputFileName;
outputFile = outputDir + "/" + inputFileName;
//Canonicalize the input file
org.apache.xml.security.Init.init();
DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
dfactory.setNamespaceAware(true);
dfactory.setValidating(true);
DocumentBuilder documentBuilder = dfactory.newDocumentBuilder();
// this is to throw away all validation warnings
documentBuilder.setErrorHandler(new org.apache.xml.security.utils.IgnoreAllErrorHandler());
Document doc = documentBuilder.parse(new File(inputFile));
// after playing around, we have our document now
Canonicalizer c14n = Canonicalizer.getInstance( "http://www.w3.org/TR/2001/REC-xml-c14n-20010315#WithComments");
byte outputBytes[] = c14n.canonicalizeSubtree(doc);
FileWriter fw = new FileWriter(new File(outputFile));
fw.write(new String(outputBytes));
fw.close();
} else {
System.out.println(" Directory: " + inputFileName);
}
}
}
}
}
--- NEW FILE: Canonicalization.java ---
package uk.ac.cam.ch.wwmm.util;
//import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileWriter;
import org.w3c.dom.*;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.xml.security.c14n.Canonicalizer;
public class Canonicalization {
public static void main(String args[]) throws Exception {
//Parse the arguments
if (args.length == 0) {
System.out.println(
"Usage: java uk.ac.cam.ch.wwmm.util.Canonicalization -inputFile inputFile -outputFile outputFile");
exit(0);
}
int i = 0;
String inputFile="";
String outputFile="";
while (i < args.length) {
if (false) {
exit(0);
} else if (args[i].equals("-inputFile")) {
i++;
inputFile = args[i++];
} else if (args[i].equals("-outputFile")) {
i++;
outputFile = args[i++];
} else {
System.err.println("Unknown argument: " + args[i]);
i++;
}
}
System.out.println(" inputFile = " + inputFile);
System.out.println(" outputFile = " + outputFile);
//Canonicalize the input file
org.apache.xml.security.Init.init();
DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
dfactory.setNamespaceAware(true);
dfactory.setValidating(true);
DocumentBuilder documentBuilder = dfactory.newDocumentBuilder();
// this is to throw away all validation warnings
documentBuilder.setErrorHandler(new org.apache.xml.security.utils.IgnoreAllErrorHandler());
// byte inputBytes[] = input.getBytes();
Document doc = documentBuilder.parse(new File(inputFile));
// after playing around, we have our document now
Canonicalizer c14n = Canonicalizer.getInstance( "http://www.w3.org/TR/2001/REC-xml-c14n-20010315#WithComments");
byte outputBytes[] = c14n.canonicalizeSubtree(doc);
// System.out.println(new String(outputBytes));
FileWriter fw = new FileWriter(new File(outputFile));
fw.write(outputBytes);
fw.close();
}
}
--- NEW FILE: CDKConverter.java ---
package uk.ac.cam.ch.wwmm.util;
import java.io.File;
import org.openscience.cdk.applications.FileConvertor;
import org.apache.log4j.Logger;
import org.apache.log4j.PropertyConfigurator;
/**
* Description of the Class This class is used to operate the cdk file
* converter. Entire directories can be processed, and various chemical file
* formats can be processed in batch. (currently mol, pdb work)
*
*@author Yong Zhang and Juergen Harter
*@created 19 February 2003
*/
public class CDKConverter {
static Logger logger = Logger.getLogger(CDKConverter.class.getName());
/**
* The main program for the CDKConverter class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*/
public static void main(String[] args) throws Exception {
PropertyConfigurator.configure("./build/log4j_CDK.properties");
File testDir;
if (args.length == 0) {
logger.info(
"Usage: java uk.ac.cam.ch.wwmm.util.CDKConverter -inputFormat inputFormat -inputDir inputDir -outputFormat outputFormat -outputDir outputDir");
}
int i = 0;
String inputFormat = "";
String inputDir = "";
String outputFormat = "";
String outputDir = "";
while (i < args.length) {
if (false) {
}
else if (args[i].equals("-inputFormat")) {
i++;
inputFormat = args[i++];
}
else if (args[i].equals("-inputDir")) {
i++;
inputDir = args[i++];
}
else if (args[i].equals("-outputFormat")) {
i++;
outputFormat = args[i++];
}
else if (args[i].equals("-outputDir")) {
i++;
outputDir = args[i++];
}
else {
System.err.println("Unknown argument: " + args[i]);
}
}
String inputFileName = "";
String outputFileName = "";
int loc = 0;
File dir = new File(inputDir);
logger.info(" inputFormat = " + inputFormat);
logger.info(" inputDir = " + inputDir);
logger.info(" outputFormat = " + outputFormat);
logger.info(" outputDir = " + outputDir);
FileConvertor fc = new FileConvertor(inputFormat, outputFormat);
if (dir.isDirectory()) {
String[] files = dir.list();
logger.info(" File numbers = " + files.length);
for (int j = 0; j < files.length; j++) {
inputFileName = files[j];
logger.info(inputFileName);
testDir = new File(inputDir + "/" + inputFileName);
if (!testDir.isDirectory()) {
loc = inputFileName.indexOf(".");
outputFileName = inputFileName.substring(0, loc) + "." +
outputFormat;
fc.convert(inputDir + "/" + inputFileName,
outputDir + "/" + outputFileName);
}
else {
logger.info(" Directory: " + inputFileName);
}
}
}
}
}
--- NEW FILE: Converter.java ---
package uk.ac.cam.ch.wwmm.util;
import java.awt.BorderLayout;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.io.Reader;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JFrame;
//import org.openscience.jmol.PublicJmol;
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.DocumentBuilderFactory;
import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.ChemSequence;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.SetOfMolecules;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.UnsupportedChemObjectException;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.CMLWriter;
//import org.openscience.cdk.libio.jmol.Convertor;
import org.openscience.cdk.io.ChemObjectWriter;
import org.openscience.cdk.io.IChIReader;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.renderer.MoleculeViewer2D;
import org.openscience.cdk.renderer.MoleculeViewer3D;
import org.openscience.cdk.tools.SaturationChecker;
import org.w3c.dom.Document;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.w3c.dom.NodeList;
import uk.co.demon.ursus.dom.PMRDOMUtil;
/**
* license stuff goes here - probably Artistic - Tests building of molecule
* from scratch (atom by atom)
*
*@author P.Murray-Rust, 2002
*@created 21 February 2003
*/
public class Converter {
/*
* --
* public static void view3D(Molecule m) {
* try
* {
* JFrame frame = new JFrame("CDK Molecule Viewer");
* frame.getContentPane().setLayout(new BorderLayout());
* org.openscience.jmol.PublicJmol jmol = org.openscience.jmol.PublicJmol.getJmol(frame);
* jmol.showChemFrame(Convertor.convert(m));
* frame.getContentPane().add(jmol, BorderLayout.CENTER);
* } catch (Exception e)
* {
* e.printStackTrace();
* }
* }
* --
*/
/** Description of the Field */
public final static double TOLERANCE = 0.2;
/** constructor */
public Converter() { }
/**
* Description of the Method
*
*@param s Description of the Parameter
*@param b Description of the Parameter
*/
static void debugBond(PrintStream s, Bond b) {
s.println("Bond info======");
Atom[] atoms = b.getAtoms();
s.println("Bond 2D centre: " + b.get2DCenter());
s.println(b.getAtomAt(0).getSymbol() + "-" + b.getAtomAt(0).getSymbol());
try {
s.println("Bond length: " + b.getLength());
}
catch (Throwable e) {
System.err.println("No bond length");
}
// s.println("Bond order: "+b.getOrder());
// s.println("Bond stereo: "+b.getStereo());
}
/**
* Description of the Method
*
*@param molecule Description of the Parameter
*/
static void debug(Molecule molecule) {
System.out.println("=== molecule ===");
// Returns the number of Atoms in this Container.
int nAtoms = molecule.getAtomCount();
System.out.println("The molecule has " + nAtoms + " atoms");
java.util.Enumeration atoms = molecule.atoms();
while (atoms.hasMoreElements()) {
Atom atom = (Atom) atoms.nextElement();
System.out.println("Atom: " + atom);
}
// Returns the array of bonds of this AtomContainer.
System.out.println(" ---Bonds---");
Bond[] bonds = molecule.getBonds();
if (bonds == null || bonds.length == 0) {
System.out.println("NO BONDS");
}
else {
// Returns the number of Bonds in this Container.
int nBonds = molecule.getBondCount();
System.out.println("The molecule has " + nBonds + " bonds");
for (int i = 0; i < nBonds; i++) {
Bond bond = bonds[i];
debugBond(System.out, bond);
}
}
}
/**
* Gets the molecule attribute of the Converter class
*
*@param chemFile Description of the Parameter
*@return The molecule value
*/
public static Molecule getMolecule(ChemFile chemFile) {
if (chemFile == null) {
return null;
}
for (int i = 0; i < chemFile.getChemSequenceCount(); i++) {
ChemModel[] cms = chemFile.getChemSequence(i).getChemModels();
for (int j = 0; j < cms.length; j++) {
if (cms[j] == null) {
continue;
}
SetOfMolecules som = cms[j].getSetOfMolecules();
for (int k = 0; k < som.getMoleculeCount(); k++) {
Molecule mol = som.getMolecule(k);
if (mol != null) {
return mol;
}
}
}
}
return null;
}
/**
* Description of the Method
*
*@param molecule Description of the Parameter
*/
static void joinTheDots(Molecule molecule) {
int natoms = molecule.getAtomCount();
Atom[] atoms = molecule.getAtoms();
for (int i = 1; i < natoms; i++) {
Atom ai = atoms[i];
String elemi = ai.getSymbol();
double radi = getRadius(elemi);
Point3d pi = ai.getPoint3D();
for (int j = 0; j < i; j++) {
Atom aj = atoms[j];
String elemj = aj.getSymbol();
double radj = getRadius(elemj);
Point3d pj = aj.getPoint3D();
double dist = pi.distance(pj);
if (dist < radi + radj + TOLERANCE) {
double paulingBO = getPaulingBO(dist, radi, radj);
double cdkBO = 1.0;
if (paulingBO < 1.3) {
cdkBO = 1.0;
}
else if (paulingBO < 1.75) {
cdkBO = 1.5;
}
else if (paulingBO < 2.5) {
cdkBO = 2.0;
}
else if (paulingBO < 5) {
cdkBO = 3.0;
}
Bond b = new Bond(ai, aj, cdkBO);
molecule.addBond(b);
}
}
}
}
/**
* Gets the paulingBO attribute of the Converter class
*
*@param length Description of the Parameter
*@param covr0 Description of the Parameter
*@param covr1 Description of the Parameter
*@return The paulingBO value
*/
public static double getPaulingBO(double length, double covr0, double covr1) {
return Math.exp(2.303 * (-length + covr0 + covr1) / 0.7);
}
/**
* Gets the radius attribute of the Converter class
*
*@param elem Description of the Parameter
*@return The radius value
*/
static double getRadius(String elem) {
if (elem.equals("B")) {
return 0.83;
}
if (elem.equals("C")) {
return 0.77;
}
if (elem.equals("N")) {
return 0.7;
}
if (elem.equals("O")) {
return 0.65;
}
if (elem.equals("F")) {
return 0.60;
}
if (elem.equals("Si")) {
return 1.1;
}
if (elem.equals("P")) {
return 1.05;
}
if (elem.equals("S")) {
return 1.0;
}
if (elem.equals("Cl")) {
return 0.95;
}
if (elem.equals("H")) {
return 0.35;
}
return 1.5;
}
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@return Description of the Return Value
*@exception IOException Description of the Exception
*@exception CDKException Description of the Exception
*/
public static Molecule[] readIChI(String filename) throws IOException, CDKException {
Document doc = null;
try {
doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new File(filename));
}
catch (Exception e) {
throw new CDKException("Cannot read XML file: " + e);
}
NodeList molList = doc.getElementsByTagName("structure");
Molecule[] mols = new Molecule[molList.getLength()];
System.out.println("Reading IChI: " + mols.length);
for (int i = 0; i < molList.getLength(); i++) {
System.out.println("IChI" + (i + 1));
try {
mols[i] = readIChI((Element) molList.item(i));
}
catch (ArrayIndexOutOfBoundsException aoobe) {
System.out.println("Array OOB: " + aoobe + " in mol: " + (i + 1));
// aoobe.printStackTrace();
}
catch (NumberFormatException nfe) {
System.out.println("NFE: " + nfe + " in mol: " + (i + 1));
}
}
return mols;
}
/**
* Description of the Method
*
*@param sdfReader Description of the Parameter
*@return Description of the Return Value
*@exception IOException Description of the Exception
*@exception CDKException Description of the Exception
*/
public static Molecule[] readSDF(Reader sdfReader) throws IOException, CDKException {
BufferedReader br = new BufferedReader(sdfReader);
String molContent = "";
Vector molVector = new Vector();
boolean mend = false;
while (true) {
String s = br.readLine();
if (s == null) {
break;
}
if (s.equals("$$$$")) {
MDLReader mr = new MDLReader(new StringReader(molContent));
ChemFile molFile = (ChemFile) mr.read((ChemObject) new ChemFile());
Molecule mol = Converter.getMolecule(molFile);
if (mol == null) {
throw new CDKException("Bad molecule: " + molContent);
}
molVector.addElement(mol);
molContent = "";
mend = false;
}
else if (s.equals("M END")) {
molContent += s + "\n";
mend = true;
}
else {
if (!mend) {
molContent += s + "\n";
}
}
}
Molecule[] mols = new Molecule[molVector.size()];
for (int i = 0; i < molVector.size(); i++) {
mols[i] = (Molecule) molVector.elementAt(i);
}
return mols;
}
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@param suffixin Description of the Parameter
*@return Description of the Return Value
*@exception IOException Description of the Exception
*@exception CDKException Description of the Exception
*/
public static Molecule[] readMolecules(String filename, String suffixin) throws IOException, CDKException {
File file = new File(filename);
FileReader fr = new FileReader(file);
if (suffixin.equals("sdf")) {
return Converter.readSDF(new FileReader(new File(filename)));
}
else if (suffixin.equals("mol")) {
MDLReader mr = new MDLReader(fr);
ChemFile cf = (ChemFile) mr.read((ChemObject) new ChemFile());
Molecule[] mols = new Molecule[1];
mols[0] = Converter.getMolecule(cf);
return mols;
}
else if (suffixin.equals("ichi")) {
Molecule[] mols = readIChI(filename);
return mols;
}
else if (suffixin.equals("xml") || suffixin.equals("cml")) {
Document doc = null;
try {
doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(file);
}
catch (Exception e) {
throw new CDKException("Cannot read XML file: " + e);
}
NodeList molList = doc.getElementsByTagName("molecule");
Molecule[] mols = new Molecule[molList.getLength()];
for (int i = 0; i < molList.getLength(); i++) {
mols[i] = readCML((Element) molList.item(i));
}
return mols;
}
else {
throw new CDKException("Cannot read format: " + suffixin);
}
}
/**
* Description of the Method
*
*@param molecule Description of the Parameter
*@return Description of the Return Value
*@exception IOException Description of the Exception
*@exception UnsupportedChemObjectException Description of the Exception
*/
public static Molecule readCML(Element molecule) throws IOException, UnsupportedChemObjectException {
StringWriter sw = new StringWriter();
PMRDOMUtil.outputEventStream(molecule, sw, PMRDOMUtil.PRETTY, 0);
sw.close();
StringReader sr = new StringReader(sw.toString());
CMLReader cr = new CMLReader(sr);
ChemFile cf = (ChemFile) cr.read((ChemObject) new ChemFile());
return Converter.getMolecule(cf);
}
/**
* Description of the Method
*
*@param molecule Description of the Parameter
*@return Description of the Return Value
*@exception IOException Description of the Exception
*@exception UnsupportedChemObjectException Description of the Exception
*/
public static Molecule readIChI(Element molecule) throws IOException, UnsupportedChemObjectException {
StringWriter sw = new StringWriter();
PMRDOMUtil.outputEventStream(molecule, sw, PMRDOMUtil.PRETTY, 0);
sw.close();
StringReader sr = new StringReader(sw.toString());
IChIReader ir = new IChIReader(sr);
ChemFile cf = (ChemFile) ir.read((ChemObject) new ChemFile());
return Converter.getMolecule(cf);
}
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@param number Description of the Parameter
*@param mol Description of the Parameter
*@param suffixout Description of the Parameter
*@exception IOException Description of the Exception
*@exception CDKException Description of the Exception
*/
public static void writeMolecule(String filename, int number, Molecule mol, String suffixout) throws IOException, CDKException {
if (filename == null || suffixout == null) {
System.out.println("Null output file");
return;
}
if (mol == null) {
System.out.println("Null molecule skipped");
return;
}
filename = filename.substring(0, filename.length() - suffixout.length() - 1) + "_" + number + "." + suffixout;
if (suffixout.equals("xml") || suffixout.equals("cml")) {
System.out.println("Writing to file: " + filename);
FileWriter fw = new FileWriter(filename);
ChemObjectWriter cow = new CMLWriter(fw);
try {
if (mol != null) {
cow.write(mol);
}
}
catch (NullPointerException npe) {
System.out.println("Null pointer : " + filename);
}
fw.close();
}
else if (suffixout.equals("mol")) {
FileWriter fw = new FileWriter(filename);
ChemObjectWriter cow = new MDLWriter(fw);
if (mol != null) {
cow.write(mol);
}
fw.close();
}
else {
throw new CDKException("Cannot write format: " + suffixout);
}
}
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@param mols Description of the Parameter
*@param suffixout Description of the Parameter
*@exception IOException Description of the Exception
*@exception CDKException Description of the Exception
*/
public static void writeMolecules(String filename, Molecule[] mols, String suffixout) throws IOException, CDKException {
if (suffixout.equals("xml") || suffixout.equals("cml")) {
FileWriter fw = new FileWriter(filename);
fw.write("<moleculeList>\n");
ChemObjectWriter cow = new CMLWriter(fw);
for (int i = 0; i < mols.length; i++) {
System.out.print(" " + i);
cow.write(mols[i]);
}
fw.write("</moleculeList>\n");
fw.close();
}
else if (suffixout.equals("sdf")) {
FileWriter fw = new FileWriter(filename);
ChemObjectWriter cow = new MDLWriter(fw);
for (int i = 0; i < mols.length; i++) {
cow.write(mols[i]);
fw.write("$$$$\n");
}
fw.close();
}
else {
throw new CDKException("Cannot write format: " + suffixout);
}
}
/**
* The main program for the Converter class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*/
public static void main(String[] args) throws Exception {
// try {
if (args.length == 0) {
System.out.println("Usage: java uk.ac.cam.ch.wwmm.util.Converter -TEST [testnumber] -FILE [filename]");
}
int i = 0;
String filein = null;
String suffixin = null;
String fileout = null;
String suffixout = null;
boolean concat = false;
while (i < args.length) {
if (false) {
}
else if (args[i].equals("-CONCAT")) {
concat = true;
}
else if (args[i].equals("-IN")) {
i++;
filein = args[i++];
int idx = filein.lastIndexOf(".");
if (idx != -1) {
suffixin = filein.substring(idx + 1);
}
}
else if (args[i].equals("-OUT")) {
i++;
fileout = args[i++];
int idx = fileout.lastIndexOf(".");
if (idx != -1) {
suffixout = fileout.substring(idx + 1);
}
}
else {
System.err.println("Unknown argument: " + args[i]);
}
}
if ("sdf".equals(suffixout)) {
concat = true;
}
if (filein != null) {
Molecule[] mols = readMolecules(filein, suffixin);
if (mols == null || mols.length == 0) {
System.err.println("NO MOLECULES READ");
}
else {
if (!concat) {
for (int j = 0; j < mols.length; j++) {
writeMolecule(fileout, j + 1, mols[j], suffixout);
}
}
else {
writeMolecules(fileout, mols, suffixout);
}
}
}
// } catch (NullPointerException npe) {
// npe.printStackTrace();
// }
}
}
--- NEW FILE: FileMerger2.java ---
package uk.ac.cam.ch.wwmm.util;
import java.io.*;
/**
* Description of the Class
*
*@author Administrator
*@created 21 February 2003
*/
public class FileMerger {
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@return Description of the Return Value
*@exception Exception Description of the Exception
*@exception IOException Description of the Exception
*/
private static String findCASNCI(String filename)
throws Exception, IOException {
BufferedReader in;
String inLine;
String casno;
String ncino;
in = new BufferedReader(new FileReader(new File(filename)));
inLine = in.readLine();
//NCI number is the first of the mol file
ncino = inLine;
//System.out.println(inLine);
//Find the CAS no.
while ((inLine != null) && (inLine.indexOf("<CAS_RN>") == -1)) {
inLine = in.readLine();
}
//Read the CAS no
casno = in.readLine();
in.close();
return "<name convention=\"NCI\">" + ncino.trim() + "</name>\n" +
"<name convention=\"CAS\">" + casno.trim() + "</name>\n";
}
/**
* The main program for the FileMerger class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*@exception IOException Description of the Exception
*/
public static void main(String[] args)
throws Exception, IOException {
// defines in, out as buffered readers
BufferedReader inMol;
BufferedReader inCML;
BufferedWriter outCML;
String inLineMol;
String inLineCML;
String casNCI;
//String[] filesMol="", filesCML="";
// if the program is used incorrectly this will inform the user on how it should be done
if (args.length == 0) {
System.out.println("Usage: FileMerger readdir1 readdir2 writefile");
System.exit(0);
}
//open the input directories
File dirMol = new File(args[0]);
String[] filesMol = dirMol.list();
// if (dirMol.isDirectory()) {
// String[] filesMol = dirMol.list();
// } else {
// System.out.println("readdir1 is not a directory!");
// System.exit(0);
//}
File dirCML = new File(args[1]);
//if (dirCML.isDirectory()) {
String[] filesCML = dirCML.list();
// } else {
// System.out.println("readdir2 is not a directory!");
// System.exit(0);
//}
//Open the write file
outCML = new BufferedWriter(new FileWriter(args[2]));
outCML.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>\n");
outCML.write("<entryList>\n");
for (int i = 0; i < filesMol.length; i++) {
//open the input file one by one in two directories
inCML = new BufferedReader(new FileReader(new File(args[1] + "/" +
filesCML[i])));
//discard the first two lines of the CML file, such as
//<?xml version="1.0"?>
//<list title="sequence">
inLineCML = inCML.readLine();
inLineCML = inCML.readLine();
inLineCML = inCML.readLine();
//Find the CAS no in the Mol file
outCML.write("<entry id=\"e" + Integer.toString(i + 1) +
"\">\n");
casNCI = findCASNCI(args[0] + "/" + filesMol[i]);
outCML.write(casNCI);
//Write to the end of the CML file, and write out to the big XML file
//Discard the lines after </molecule>, such as
//</list>
while ((inLineCML != null) &&
(inLineCML.indexOf("</molecule>") == -1)) {
outCML.write(inLineCML + "\n");
inLineCML = inCML.readLine();
}
//Write the end tag of entry
outCML.write("</molecule>\n");
outCML.write("</entry>\n");
inCML.close();
}
outCML.write("</entryList>\n");
outCML.write("</xml>");
outCML.flush();
outCML.close();
}
}
--- NEW FILE: FileMerger.java ---
package uk.ac.cam.ch.wwmm.util;
/**
* Merges seperate .cml files (was employed for NCI_diversity set) into one big
* .xml file, and while merging, it compares each existing .cml file to the
* corresponding .mol file and takes the CAS number from there, adding it to
* the .cml file at the correct position.
*
*@author Yong Zhang 2002
*@author Juergen Harter 2002 License: artistic license
*/
import java.io.*;
/**
* Description of the Class
*
*@author jharter
*@created 21 February 2003
*/
public class FileMerger {
/**
* Description of the Method
*
*@param filename Description of the Parameter
*@return Description of the Return Value
*@exception Exception Description of the Exception
*@exception IOException Description of the Exception
*/
private static String findCASNCI(String filename) throws Exception, IOException {
BufferedReader in;
String inLine;
String casno;
String ncino;
in = new BufferedReader(new FileReader(new File(filename)));
inLine = in.readLine();
//NCI number is the first of the mol file
ncino = inLine;
//System.out.println(inLine);
//Find the CAS no.
while ((inLine != null) && (inLine.indexOf("<CAS_RN>") == -1)) {
inLine = in.readLine();
}
//Read the CAS no
casno = in.readLine();
in.close();
return "<name convention=\"NCI\">" + ncino.trim() + "</name>\n" + "<name convention=\"CAS\">" + casno.trim() + "</name>\n";
}
/**
* The main program for the FileMerger class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*@exception IOException Description of the Exception
*/
public static void main(String[] args) throws Exception, IOException {
// defines in, out as buffered readers
BufferedReader inMol;
// defines in, out as buffered readers
BufferedReader inCML;
BufferedWriter outCML;
String inLineMol;
String inLineCML;
String casNCI;
//String[] filesMol="", filesCML="";
// if the program is used incorrectly this will inform the user on how it should be done
if (args.length == 0) {
System.out.println("Usage: FileMerger readdir1 readdir2 writefile");
System.exit(0);
}
//open the input directories
File dirMol = new File(args[0]);
String[] filesMol = dirMol.list();
// if (dirMol.isDirectory()) {
// String[] filesMol = dirMol.list();
// } else {
// System.out.println("readdir1 is not a directory!");
// System.exit(0);
//}
File dirCML = new File(args[1]);
//if (dirCML.isDirectory()) {
String[] filesCML = dirCML.list();
// } else {
// System.out.println("readdir2 is not a directory!");
// System.exit(0);
//}
//Open the write file
outCML = new BufferedWriter(new FileWriter(args[2]));
outCML.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>\n");
outCML.write("<entryList>\n");
for (int i = 0; i < filesMol.length; i++) {
//open the input file one by one in two directories
inCML = new BufferedReader(new FileReader(new File(args[1] + "/" + filesCML[i])));
//discard the first two lines of the CML file, such as
//<?xml version="1.0"?>
//<list title="sequence">
inLineCML = inCML.readLine();
inLineCML = inCML.readLine();
inLineCML = inCML.readLine();
//Find the CAS no in the Mol file
outCML.write("<entry id=\"e" + Integer.toString(i + 1) + "\">\n");
casNCI = findCASNCI(args[0] + "/" + filesMol[i]);
outCML.write(casNCI);
//Write to the end of the CML file, and write out to the big XML file
//Discard the lines after </molecule>, such as
//</list>
while ((inLineCML != null) && (inLineCML.indexOf("</molecule>") == -1)) {
outCML.write(inLineCML + "\n");
inLineCML = inCML.readLine();
}
//Write the end tag of entry
outCML.write("</molecule>\n");
outCML.write("</entry>\n");
inCML.close();
}
outCML.write("</entryList>\n");
outCML.write("</xml>");
outCML.flush();
outCML.close();
}
}
--- NEW FILE: FileSplitter.java ---
package uk.ac.cam.ch.wwmm.util;
/**
* Uses split to break up an input file around the regular expression which is
* user defined.
*
*@author Joe Townsend 2002
*@adapted from PerkinReader
*@author J.M.Goodman 2002 @ modified by Yong Zhang and Juergen Harter
* License: artistic license This is a test file to experiment with regular
* expressions and to practise using file reading and writing techniques
*/
/** modified to split a .bin file to read in and split mol files */
import java.io.*;
/**
* Description of the Class
*
*@author Administrator
*@created 21 February 2003
*/
public class FileSplitter {
/**
* The main program for the FileSplitter class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*@exception IOException Description of the Exception
*/
public static void main(String[] args) throws Exception, IOException {
// defines in, out and ink as buffered readers
BufferedReader in;
BufferedWriter out;
// if the program is used incorrectly this will inform the user on how it should be done
if (args.length == 0) {
System.out.println("Usage: FileSplitter readfile writedir filenameprefix");
System.exit(0);
}
//open the input file
in = new BufferedReader(new FileReader(new File(args[0])));
int i = 0;
String inLine;
inLine = in.readLine();
// performs operations until end of file is reached
while (inLine != null) {
// split input with the pattern
System.out.println(inLine);
i++;
out = new BufferedWriter(new FileWriter(args[1] + "/" + args[2] + Integer.toString(i) + ".mol"));
//inLine = in.readLine();
//System.out.println(inLine);
while ((inLine != null) && (inLine.indexOf("$$$$") == -1)) {
out.write(inLine);
out.newLine();
inLine = in.readLine();
}
inLine = in.readLine();
out.flush();
out.close();
}
in.close();
}
}
--- NEW FILE: Fingerprint.java ---
package uk.ac.cam.ch.wwmm.util;
import java.io.FileWriter;
import java.io.IOException;
import java.util.BitSet;
import javax.xml.parsers.DocumentBuilderFactory;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xmlcml.cml.CMLException;
import uk.co.demon.ursus.dom.PMRDOMUtil;
/**
* Description of the Class
*
*@author Administrator
*@created 21 February 2003
*/
public class Fingerprint {
/** Description of the Field */
protected Molecule molecule;
/** Description of the Field */
protected BitSet bs;
/** Description of the Field */
protected long uid;
/** Constructor for the Fingerprint object */
public Fingerprint() { }
/**
* Sets the molecule attribute of the Fingerprint object
*
*@param mol The new molecule value
*@exception CDKException Description of the Exception
*/
public void setMolecule(Molecule mol) throws CDKException {
this.molecule = mol;
bs = Fingerprinter.getFingerprint(mol);
}
/**
* Gets the uID attribute of the Fingerprint object
*
*@return The uID value
*/
public String getUID() {
return Integer.toHexString(bs.hashCode());
}
/**
* Gets the bitSet attribute of the Fingerprint object
*
*@return The bitSet value
*/
public BitSet getBitSet() {
return bs;
}
/**
* Description of the Method
*
*@return Description of the Return Value
*/
public String toString() {
return "bs: " + bs + "uid: " + this.getUID();
}
/**
* Description of the Method
*
*@param doc Description of the Parameter
*@return Description of the Return Value
*/
public Element createElement(Document doc) {
Element fp = doc.createElement("cdkFingerprint");
fp.setAttribute("bitset", bs.toString());
fp.setAttribute("uid", "" + this.getUID());
return fp;
}
/**
* Description of the Method
*
*@param infile Description of the Parameter
*@return Description of the Return Value
*/
public static Molecule readCDK(String infile) {
Molecule mol = null;
// code goes here
return mol;
}
/**
* A unit test for JUnit
*
*@param mol Description of the Parameter
*@param outfile Description of the Parameter
*@exception Exception Description of the Exception
*/
public static void test(Molecule mol, String outfile) throws Exception {
if (mol == null) {
throw new CMLException("Null molecule in Fingerprint test");
}
Fingerprint fp = new Fingerprint();
fp.setMolecule(mol);
if (outfile.equals("")) {
System.out.println("Fingerprint: " + fp);
}
else if (outfile.endsWith(".xml")) {
Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
Element top = doc.createElement("top");
doc.appendChild(top);
Element fpElem = fp.createElement(doc);
top.appendChild(fpElem);
FileWriter fw = new FileWriter(outfile);
PMRDOMUtil.outputEventStream(doc.getDocumentElement(), fw, PMRDOMUtil.PRETTY, 0);
fw.close();
}
}
/**
* adds FP to Document (e.g. for concatenation). If empty element, creates
* toplevel <fpList>
*
*@param doc The feature to be added to the ToDocument attribute
*/
public void addToDocument(Document doc) {
Element fp = this.createElement(doc);
Element top = doc.getDocumentElement();
if (top == null) {
top = doc.createElement("fpList");
doc.appendChild(top);
}
top.appendChild(fp);
}
/**
* Description of the Method
*
*@param cmlFile Description of the Parameter
*@return Description of the Return Value
*@exception Exception Description of the Exception
*/
public static Fingerprint[] parse(String cmlFile) throws Exception {
Molecule[] mols = MolUtil.readCMLEntries(cmlFile);
Fingerprint[] fps = new Fingerprint[mols.length];
for (int i = 0; i < mols.length; i++) {
fps[i] = new Fingerprint();
fps[i].setMolecule(mols[i]);
}
return fps;
}
/**
* The main program for the Fingerprint class
*
*@param args The command line arguments
*@exception Exception Description of the Exception
*/
public static void main(String[] args) throws Exception {
if (args.length == 0) {
System.out.println("Usage: uk.ac.cam.ch.wwmm.util.Fingerprint -IN file -OUT file");
}
String infile = "";
String outfile = "";
int i = 0;
while (i < args.length) {
if (args[i].equalsIgnoreCase("-in")) {
infile = args[++i];
i++;
}
else if (args[i].equalsIgnoreCase("-out")) {
outfile = args[++i];
i++;
}
else {
System.err.println("Bad arg: " + args[i++]);
}
}
if (!infile.equals("")) {
System.out.println("Input from: " + infile);
if (infile.endsWith(".xml") || infile.endsWith(".cml")) {
Molecule[] mols = MolUtil.readCMLEntries(infile);
System.out.println("MOLS: " + mols.length);
Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
for (i = 0; i < mols.length; i++) {
Fingerprint fp = new Fingerprint();
fp.setMolecule(mols[i]);
fp.addToDocument(doc);
}
if (!outfile.equals("")) {
FileWriter fw = new FileWriter(outfile);
PMRDOMUtil.outputEventStream(doc.getDocumentElement(), fw, PMRDOMUtil.PRETTY, 0);
fw.close();
}
}
else if (infile.endsWith(".mol")) {
Molecule mol = MolUtil.readMDL(infile);
test(mol, outfile);
}
else {
throw new Exception("Cannot read files of type: " + infile);
}
}
}
}
--- NEW FILE: FormulaGenerator.java ---
package uk.ac.cam.ch.wwmm.util;
import java.io.FileWriter;
import java.io.IOException;
import java.util.BitSet;
import javax.xml.parsers.DocumentBuilderFactory;
//import org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
//import org.openscience.cdk.fingerprint.Fingerprinter;
import org.xmlcml.cml.CMLException;
import uk.ac.cam.ch.wwmm.util.MolUtil;
import uk.co.demon.ursus.dom.PMRDOMUtil;
/**
* Generates CML2-compliant formula from a molecule (CDK or (future) JUMBO)
*
*@author YY
*@author JH
*@created 21 February 2003
*/
public class FormulaGenerator {
/** Description of the Field */
protected Molecule molecule;
/** Description of the Field */
protected String formula;
/** Description of the Field */
protected long uid;
/** Creates a new FormulaGenerator object. */
public FormulaGenerator() { }
/**
* set Molecule for FG must be called before use
*
*@param mol in CDK representation
*@throws CDKException invalid molecule
*/
public void setMolecule(Molecule mol)
throws CDKException {
if (mol == null) {
throw new CDKException("null molecule");
}
int num = 0;
int flag = 0;
int numOfAtom = mol.getAtomCount();
StringBuffer fm = new StringBuffer();
String[] elements = new String[numOfAtom];
int[] elementCount = new int[numOfAtom];
for (int i = 0; i < numOfAtom; i++) {
flag = 0;
String symbol = mol.getAtomAt(i).getSymbol();
if (num == 0) {
elements[num] = symbol;
elementCount[num]++;
num++;
}
else {
for (int j = 0; j < num; j++) {
if (elements[j].equals(symbol)) {
elementCount[j]++;
flag = 1;
}
}
if (flag == 0) {
elements[num] = symbol;
elementCount[num]++;
num++;
}
}
}
for (int i = 0; i < num; i++) {
if (i > 0) {
fm.append(" ");
}
fm.append(elements[i] + " " + elementCount[i]);
}
formula = fm.toString();
System.out.println("formula=" + formula);
}
/**
* returns string as
*
*@return "formula"+formula
*/
public String toString() {
return "formula: " + formula;
}
/**
* DOCUMENT ME!
*
*@param doc DOCUMENT ME!
*@return DOCUMENT ME!
*/
public Element createElement(Document doc) {
Element fg = doc.createElement("cdkFormulaGenerator");
fg.setAttribute("formula", formula.toString());
return fg;
}
/**
* DOCUMENT ME!
*
*@param infile DOCUMENT ME!
*@return DOCUMENT ME!
*@exception Exception Description of the Exception
*/
public static Molecule readCDK(String infile) throws Exception {
Molecule mol = null;
if (true) {
throw new Exception("readCDK not yet implemented");
}
// code goes here
return mol;
}
/**
* tests FG on a molecule and optionally outputs fomula to file
*
*@param mol
*@param outfile
*@throws Exception (CDKException, IOException,
* ParserConfigurationException...)
*/
public static void test(Molecule mol, String outfile)
throws Exception {
if (mol == null) {
throw new CMLException("Null molecule in FormulaGenerator test");
}
FormulaGenerator fg = new FormulaGenerator();
fg.setMolecule(mol);
...
[truncated message content] |