Mol2Exporter.java

/*
*   EuroCarbDB, a framework for carbohydrate bioinformatics
*
*   Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
*   indicated by the @author tags or express copyright attribution
*   statements applied by the authors.  
*
*   This copyrighted material is made available to anyone wishing to use, modify,
*   copy, or redistribute it subject to the terms and conditions of the GNU
*   Lesser General Public License, as published by the Free Software Foundation.
*   A copy of this license accompanies this distribution in the file LICENSE.txt.
*
*   This program 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.
*
*   Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$  
*/
package org.eurocarbdb.resourcesdb.io;

import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;

import org.eurocarbdb.resourcesdb.ResourcesDbException;
import org.eurocarbdb.resourcesdb.atom.*;
import org.eurocarbdb.resourcesdb.monosaccharide.Monosaccharide;
import org.eurocarbdb.resourcesdb.util.NumberUtils;

public class Mol2Exporter {
    
    private static void writeHeader(Monosaccharide ms, PrintStream printer) throws IOException {
        printer.println("# Monosaccharide " + ms.getName());
        printer.println("# generated by MonosaccharideDB");
        printer.println();
        printer.println("@<TRIPOS>MOLECULE");
        printer.println(ms.getName());
        printer.println(ms.getAtoms().size());
        printer.println("SACCHARIDE");
        printer.println("NO_CHARGES");
        printer.println();
        printer.println();
    }
    
    private static void writeAtoms(Monosaccharide ms, PrintStream printer) throws IOException {
        printer.println("@<TRIPOS>ATOM");
        int atomIndex = 0;
        for(Atom a : ms.getAtoms()) {
            a.setId(++atomIndex);
            String atomLine = a.getId() + " " + a.getName(); 
            atomLine += " " + NumberUtils.nullsaveDoubleValue(a.getX()) + " " + NumberUtils.nullsaveDoubleValue(a.getY()) + " " +NumberUtils.nullsaveDoubleValue( a.getZ());
            atomLine += " " + a.getMol2Type();
            printer.println(atomLine);
        }
    }
    
    private static void writeBonds(Monosaccharide ms, PrintStream printer) throws IOException {
        printer.println("@<TRIPOS>BOND");
        for(Atom a : ms.getAtoms()) {
            int bondIndex = 0;
            for(AtomConnection aCon : a.getConnections()) {
                String bondLine;
                int toId = aCon.getToAtom().getId();
                if(toId == a.getId()) {
                    toId = aCon.getFromAtom().getId();
                }
                if(a.getId() < toId) {
                    bondIndex ++;
                    String boStr;
                    if(aCon.getBondOrder() == 1) {
                        boStr = "1";
                    } else if(aCon.getBondOrder() == 1.5) {
                        boStr = "ar";
                    } else if(aCon.getBondOrder() == 2) {
                        boStr = "2";
                    } else if(aCon.getBondOrder() == 3) {
                        boStr = "3";
                    } else {
                        boStr = "un";
                    }
                    bondLine = bondIndex + " " + a.getId() + " " + toId + " " + boStr;
                    printer.println(bondLine);
                }
            }
        }
    }

    public static void export(Monosaccharide ms, FileOutputStream fOut) throws ResourcesDbException {
        if(fOut == null) {
            throw new ResourcesDbException("File output stream is null in mol2exporter.");
        }
        if(ms == null) {
            throw new ResourcesDbException("Monosaccharide is null in mol2exporter.");
        }
        try {
            PrintStream printer = new PrintStream(fOut);
            writeHeader(ms, printer);
            writeAtoms(ms, printer);
            writeBonds(ms, printer);
        } catch(IOException ioEx) {
            ResourcesDbException rEx = new ResourcesDbException("IO exception in mol2exporter");
            rEx.initCause(ioEx);
            throw rEx;
        }
    }
    
    public static void export(Monosaccharide ms, String fileName) throws ResourcesDbException {
        FileOutputStream fOut;
        try {
            fOut = new FileOutputStream(fileName);
        } catch(Exception ex) {
            ResourcesDbException rEx = new ResourcesDbException("Cannot initialize FileOutputStream for file name '" + fileName + "'");
            rEx.initCause(ex);
            throw rEx;
        }
        Mol2Exporter.export(ms, fOut);
        try {
            fOut.close();
        } catch(Exception ex) {
            ResourcesDbException rEx = new ResourcesDbException("Cannot close FileOutputStream for file name '" + fileName + "'");
            rEx.initCause(ex);
            throw rEx;
        }
    }
}