aminoacids.java

化学图形处理软件

/* $Revision: 8130 $ $Author: egonw $ $Date: 2007-03-16 15:15:22 +0100 (Fri, 16 Mar 2007) $
 * 
 * Copyright (C) 2005-2007  Martin Eklund <[e-mail]>
 * 
 * Contact: [e-mail]
 * 
 * This program 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 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.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 */
package org.openscience.cdk.templates;

import java.util.Enumeration;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;

import org.openscience.cdk.AminoAcid;
import org.openscience.cdk.dict.DictRef;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AminoAcidManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Tool that provides templates for the (natural) amino acids.
 *
 * @author      Martin Eklund <[e-mail]>
 * @cdk.module  pdb
 * @cdk.keyword templates
 * @cdk.keyword amino acids, stuctures
 * @cdk.created 2005-02-08
 */
public class AminoAcids {

	private static final LoggingTool logger = new LoggingTool(AminoAcids.class);
	
    /**
     * Creates matrix with info about the bonds in the amino acids.
     * 0 = bond id, 1 = atom1 in bond, 2 = atom2 in bond, 3 = bond order.
     * @return info
     */
    public static int[][] aaBondInfo()	{

    	if (aminoAcids == null) {
            createAAs();
        }
        
        int[][] info = new int[153][4];
        
        int counter = 0;
        int total = 0;
        for (int aa=0; aa<aminoAcids.length; aa++) {
        	AminoAcid acid = aminoAcids[aa];

        	logger.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount());
        	total += acid.getBondCount();
        	logger.debug("total #bonds: ", total);

            Iterator bonds = acid.bonds();
            while (bonds.hasNext()) {
                IBond bond = (IBond) bonds.next();
        		info[counter][0] = counter;
        		info[counter][1] = acid.getAtomNumber(bond.getAtom(0));
        		info[counter][2] = acid.getAtomNumber(bond.getAtom(1));
        		info[counter][3] = (int)bond.getOrder();
        		counter++;
        	}
        }
        
        if (counter>153) {
        	logger.error("Error while creating AA info! Bond count is too large: ", counter);
        	return null;
        }
        
        return info;
    }
    
    private static AminoAcid[] aminoAcids = null;
    
    public final static String RESIDUE_NAME = "residueName";
    public final static String RESIDUE_NAME_SHORT = "residueNameShort";
    public final static String NO_ATOMS = "noOfAtoms";
    public final static String NO_BONDS = "noOfBonds";
    public final static String ID = "id";
    
    /**
     * Creates amino acid AminoAcid objects.
     * 
     * @return aminoAcids, a HashMap containing the amino acids as AminoAcids.
     */
    public static AminoAcid[] createAAs() {
    	if (aminoAcids != null) {
            return aminoAcids;
        }
    	
        // Create set of AtomContainers
        aminoAcids = new AminoAcid[20];

        IChemFile list = new org.openscience.cdk.ChemFile();
        CMLReader reader = new CMLReader(
        	AminoAcids.class.getClassLoader().getResourceAsStream(
        			"data/templates/list_aminoacids.cml"
        	)
        );
        try {
        	list = (IChemFile)reader.read(list);
        	List containersList = ChemFileManipulator.getAllAtomContainers(list);
        	Iterator iterator = containersList.iterator();
        	int counter = 0;
        	while(iterator.hasNext())
        	{
        		IAtomContainer ac = (IAtomContainer)iterator.next();
        		logger.debug("Adding AA: ", ac);
        		// convert into an AminoAcid
        		AminoAcid aminoAcid = new AminoAcid();
        		java.util.Iterator atoms = ac.atoms();
        		Enumeration props = ac.getProperties().keys();
        		while (props.hasMoreElements()) {
        			Object next = props.nextElement();
        			logger.debug("Prop class: " + next.getClass().getName());
        			logger.debug("Prop: " + next.toString());
        			if (next instanceof DictRef) {
        				DictRef dictRef = (DictRef)next;
        				// logger.debug("DictRef type: " + dictRef.getType());
        				if (dictRef.getType().equals("pdb:residueName")) {
        					aminoAcid.setProperty(RESIDUE_NAME, ac.getProperty(dictRef).toString().toUpperCase());
        					aminoAcid.setMonomerName(ac.getProperty(dictRef).toString());
        				} else if (dictRef.getType().equals("pdb:oneLetterCode")) {
        					aminoAcid.setProperty(RESIDUE_NAME_SHORT, ac.getProperty(dictRef));
        				} else if (dictRef.getType().equals("pdb:id")) {
        					aminoAcid.setProperty(ID, ac.getProperty(dictRef));
        					logger.debug("Set AA ID to: ", ac.getProperty(dictRef));
        				} else {
        					logger.error("Cannot deal with dictRef!");
        				}
        			}
        		}
        		while (atoms.hasNext()) {
        			org.openscience.cdk.interfaces.IAtom atom = (IAtom)atoms.next();
        			String dictRef = (String)atom.getProperty("org.openscience.cdk.dict");
        			if (dictRef != null && dictRef.equals("pdb:nTerminus")) {
        				aminoAcid.addNTerminus(atom);
        			} else if (dictRef != null && dictRef.equals("pdb:cTerminus")) {
        				aminoAcid.addCTerminus(atom);
        			} else {
        				aminoAcid.addAtom(atom);
        			}
        		}
//        		org.openscience.cdk.interfaces.IBond[] bonds = ac.getBonds();
                Iterator bonds = ac.bonds();
                while (bonds.hasNext()) {
                    IBond bond = (IBond) bonds.next();
        			aminoAcid.addBond(bond);
        		}
        		AminoAcidManipulator.removeAcidicOxygen(aminoAcid);
                aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.getAtomCount());
                aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount());
                if (counter < aminoAcids.length) {
                	aminoAcids[counter] = aminoAcid;
                } else {
                	logger.error("Could not store AminoAcid! Array too short!");
                }
                counter++;
        	}
        } catch (Exception exception) {
        	logger.error("Failed reading file: ", exception.getMessage());
        	logger.debug(exception);
        }
        
        return aminoAcids;
    }

    /**
     * Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D,
     * N, E, Q, R, K, H, F, Y, W and P.
     */
    public static HashMap getHashMapBySingleCharCode() {
        AminoAcid[] monomers = createAAs();
        HashMap map = new HashMap();
        for (int i=0; i<monomers.length; i++) {
            map.put(monomers[i].getProperty(RESIDUE_NAME_SHORT), monomers[i]);
        }
        return map;
    }
    
    /**
     * Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER,
     * THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
     */
    public static HashMap getHashMapByThreeLetterCode() {
        AminoAcid[] monomers = createAAs();
        HashMap map = new HashMap();
        for (int i=0; i<monomers.length; i++) {
            map.put(monomers[i].getProperty(RESIDUE_NAME), monomers[i]);
        }
        return map;
    }
    
    /**
     * Returns the one letter code of an amino acid given a three letter code.
     * For example, it will return "V" when "Val" was passed.
     */
    public static String convertThreeLetterCodeToOneLetterCode(String threeLetterCode) {
        AminoAcid[] monomers = createAAs();
        for (int i=0; i<monomers.length; i++) {
        	if (monomers[i].getProperty(RESIDUE_NAME).equals(threeLetterCode)) {
        		return (String)monomers[i].getProperty(RESIDUE_NAME_SHORT);
        	}
        }
        return null;
    }

    /**
     * Returns the three letter code of an amino acid given a one letter code.
     * For example, it will return "Val" when "V" was passed.
     */
    public static String convertOneLetterCodeToThreeLetterCode(String oneLetterCode) {
        AminoAcid[] monomers = createAAs();
        for (int i=0; i<monomers.length; i++) {
        	if (monomers[i].getProperty(RESIDUE_NAME_SHORT).equals(oneLetterCode)) {
        		return (String)monomers[i].getProperty(RESIDUE_NAME);
        	}
        }
        return null;
    }

}