templateextractor.java

化学图形处理软件

		 * som.addMolecule(smileParser.parseSmiles(ringSmile)); }catch
		 * (Exception ex5){ System.out.println("Error in som.addmolecule due
		 * to:"+ex5); } }
		 */

		// writeChemModel(som,dataFile,"_TESTTESTTESTTESTTEST");
	}

	public void writeChemModel(IMoleculeSet som, String file, String endFix) {
		System.out.println("WRITE Molecules:" + som.getMoleculeCount());
		String molfile = file + endFix;
		try {
			FileOutputStream fout = new FileOutputStream(molfile);
			MDLWriter mdlw = new MDLWriter(fout);
			mdlw.write(som);
			mdlw.close();
		} catch (Exception ex2) {
			System.out.println("IOError:cannot write file due to:"
					+ ex2.toString());
		}
	}

	public void makeCanonicalSmileFromRingSystems(String dataFileIn,
			String dataFileOut) {
		System.out.println("Start make SMILES...");
		IMolecule m = null;
		IteratingMDLReader imdl = null;
		// QueryAtomContainer query=null;
		List data = new ArrayList();
		SmilesGenerator smiles = new SmilesGenerator();
		try {
			System.out.println("Start...");
			BufferedReader fin = new BufferedReader(new FileReader(dataFileIn));
			imdl = new IteratingMDLReader(fin, NoNotificationChemObjectBuilder
					.getInstance());
			// fin.close();
			System.out.println("Read File in..");
		} catch (Exception exc) {
			System.out.println("Could not read Molecules from file "
					+ dataFileIn + " due to: " + exc.getMessage());
		}
		while (imdl.hasNext()) {
			m = (IMolecule) imdl.next();
			/*
			 * try{ HueckelAromaticityDetector.detectAromaticity(m);
			 * }catch(Exception ex1){ System.out.println("Could not find
			 * aromaticity due to:"+ex1); }
			 */
			// query=QueryAtomContainerCreator.createAnyAtomContainer(m,true);
			// System.out.println("String:"+smiles.createSMILES(new
			// Molecule(m)));
			try {

				data.add((String) smiles.createSMILES(builder.newMolecule(m)));
			} catch (Exception exc1) {
				System.out.println("Could not create smile due to: "
						+ exc1.getMessage());
			}
		}
		try {
			imdl.close();
		} catch (Exception exc2) {
		}

		System.out.print("...ready\nWrite data...");
		BufferedWriter fout = null;
		try {
			fout = new BufferedWriter(new FileWriter(dataFileOut));
		} catch (Exception exc3) {
			System.out.println("Could not write smile in file " + dataFileOut
					+ " due to: " + exc3.getMessage());
		}
		for (int i = 0; i < data.size(); i++) {
			// System.out.println("write:"+(String)data.get(i));
			try {

				fout.write(((String) data.get(i)));
				fout.newLine();
			} catch (Exception exc4) {
			}
		}
		System.out.println("number of smiles:" + data.size());
		System.out.println("...ready");
		try {
			fout.close();
		} catch (Exception exc5) {
		}
	}

	public void makeFingerprintFromRingSystems(String dataFileIn,
			String dataFileOut, boolean anyAtom, boolean anyAtomAnyBond)
	throws Exception {
		System.out.println("Start make fingerprint from file:" + dataFileIn
				+ " ...");
		AllRingsFinder allRingsFinder = new AllRingsFinder();
		allRingsFinder.setTimeout(10000); // 10 seconds

		Map timings = new HashMap();
		
		Fingerprinter fingerPrinter = new Fingerprinter(Fingerprinter.defaultSize, Fingerprinter.defaultSearchDepth);
		IMolecule m = null;
		IteratingMDLReader imdl=null;
		//QueryAtomContainer query=null;
		IAtomContainer query = null;
		List data = new ArrayList();
		try {
			System.out.print("Read data file in ...");
			BufferedReader fin = new BufferedReader(new FileReader(dataFileIn));
			imdl = new IteratingMDLReader(fin, NoNotificationChemObjectBuilder
					.getInstance());
			// fin.close();
			System.out.println("ready");
		} catch (Exception exc) {
			System.out.println("Could not read Molecules from file "
					+ dataFileIn + " due to: " + exc.getMessage());
		}
		int moleculeCounter = 0;
		int fingerprintCounter = 0;
		System.out.print("Generated Fingerprints: " + fingerprintCounter + "    ");
		while (imdl.hasNext()) {
			// query=new QueryAtomContainer();
			query = builder.newAtomContainer();
			m = (IMolecule) imdl.next();
			moleculeCounter++;
			// System.out.println(m);
			if (anyAtom && !anyAtomAnyBond) {
				// System.out.println("AnyAtom + false");

				query = QueryAtomContainerCreator.createAnyAtomContainer(m,
						false);
			} 
			else {

				// try{
				// HueckelAromaticityDetector.detectAromaticity(m);
				// }catch(Exception ex1){
				// System.out.println("Could not find aromaticity due to:"+ex1);
				// }
				// query=createAnyAtomAtomContainer(m);
				// query=(AtomContainer)m.clone();
				query = createAnyAtomAnyBondAtomContainer(m);

			}
			try {
				long time = -System.currentTimeMillis();
				if (anyAtom || anyAtomAnyBond){
//					System.out.println("Make Fingerprint Query");
					data.add((BitSet)fingerPrinter.getFingerprint((IAtomContainer) query, allRingsFinder));
					fingerprintCounter=fingerprintCounter+1;
				} else {
					// System.out.println("Make Fingerprint Molecule");
					data.add((BitSet) fingerPrinter.getFingerprint(query));
					fingerprintCounter = fingerprintCounter + 1;
				}
				time += System.currentTimeMillis();
				// store the time
				String bin = Integer.toString((int)Math.floor(time/10));
				if (timings.containsKey(bin)) {
					timings.put(bin, new Integer((((Integer)timings.get(bin)).intValue()) + 1));
				} else {
					timings.put(bin, new Integer(1));
				}
			}catch(Exception exc1){
//				exc1.printStackTrace();
				System.out.println("QueryFingerprintError: from molecule:"
						+ moleculeCounter + " due to:" + exc1.getMessage());
				
				// OK, just adds a fingerprint with all ones, so that any
				// structure will match this template, and leave it up
				// to substructure match to figure things out
				BitSet allOnesFingerprint = new BitSet(fingerPrinter.getSize());
				for (int i=0; i<fingerPrinter.getSize(); i++) {
					allOnesFingerprint.set(i, true);
				}
				data.add(allOnesFingerprint);
				fingerprintCounter = fingerprintCounter + 1;
			}
			
			if (fingerprintCounter % 2 == 0)
				System.out.print("\b" + "/");
			else
				System.out.print("\b" + "\\");

			
			if (fingerprintCounter % 100 == 0)
				System.out.print("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" + "Generated Fingerprints: " + fingerprintCounter + "   ");

		}// while 
		try {
			imdl.close();
		} catch (Exception exc2) 
		{
			exc2.printStackTrace();
		}

		System.out.print("...ready with:" + moleculeCounter
				+ " molecules\nWrite data...of data vector:" + data.size()
				+ " fingerprintCounter:" + fingerprintCounter);
		BufferedWriter fout = null;
		try {
			fout = new BufferedWriter(new FileWriter(dataFileOut));
		} catch (Exception exc3) {
			System.out.println("Could not write Fingerprint in file "
					+ dataFileOut + " due to: " + exc3.getMessage());
		}
		for (int i = 0; i < data.size(); i++) {
			try {
				fout.write(((BitSet) data.get(i)).toString());
				fout.newLine();
			} catch (Exception exc4) {
			}
		}
		System.out.println("\nFingerprints:" + data.size()
				+ " are written...ready");
		System.out.println("\nComputing time statistics:\n" + timings.toString());
		try {
			fout.close();
		} catch (Exception exc5) {
		}
	}

	public IMolecule removeLoopBonds(IMolecule molecule, int position) {
		for (int i = 0; i < molecule.getBondCount(); i++) {
			IBond bond = molecule.getBond(i);
			if (bond.getAtom(0) == bond.getAtom(1)) {
				System.out.println("Loop found! Molecule:" + position);
				molecule.removeBond(bond);
			}
		}

		return molecule;
	}

	public IAtomContainer createAnyAtomAtomContainer(IAtomContainer atomContainer)
	throws Exception {
		IAtomContainer query = (IAtomContainer) atomContainer.clone();
		// System.out.println("createAnyAtomAtomContainer");
		for (int i = 0; i < query.getAtomCount(); i++) {
			// System.out.print(" "+i);
			query.getAtom(i).setSymbol("C");
		}
		return query;
	}

	public IAtomContainer createAnyAtomAnyBondAtomContainer(
			IAtomContainer atomContainer) throws Exception {
		IAtomContainer query = (IAtomContainer) atomContainer.clone();
		for (int i = 0; i < query.getBondCount(); i++) {
			query.getBond(i).setOrder(1);
			query.getBond(i).getAtom(0).setSymbol("C");
			query.getBond(i).getAtom(1).setSymbol("C");
		}
		return query;
	}

	public IAtomContainer resetFlags(IAtomContainer ac) {
		for (int f = 0; f < ac.getAtomCount(); f++) {
			ac.getAtom(f).setFlag(CDKConstants.VISITED, false);
		}
		for (int f = 0; f < ac.getElectronContainerCount(); f++) {
			ac.getElectronContainer(f).setFlag(CDKConstants.VISITED, false);
		}
		return ac;
	}

	public static void main(String[] args) {
		if (args.length < 4) {
			System.out.println(usage);

		}
		try {
			new TemplateExtractor().makeFingerprintFromRingSystems(args[0],
					args[1], new Boolean(args[2]).booleanValue(), new Boolean(
							args[3]).booleanValue());
		} catch (Exception e) {
			System.out.println(usage);
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}

}