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AminoAcids.java

/* $Revision: 8130 $ $Author: egonw $ $Date: 2007-03-16 15:15:22 +0100 (Fri, 16 Mar 2007) $
 * 
 * Copyright (C) 2005-2007  Martin Eklund <martin.eklund@farmbio.uu.se>
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 * 
 * 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 <martin.eklund@farmbio.uu.se>
 * @cdk.module  pdb
 * @cdk.keyword templates
 * @cdk.keyword amino acids, stuctures
 * @cdk.created 2005-02-08
 */
00048 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
     */
00057     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.
     */
00106     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.
     */
00192     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.
     */
00205     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.
     */
00218     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.
     */
00232     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;
    }

}

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