/* $Revision$ $Author$ $Date$
*
* 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.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.openscience.cdk.AminoAcid;
import org.openscience.cdk.ChemFile;
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.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
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.githash
* @cdk.keyword templates
* @cdk.keyword amino acids, stuctures
* @cdk.created 2005-02-08
*/
public class AminoAcids {
private static final ILoggingTool logger =
LoggingToolFactory.createLoggingTool(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<IBond> bonds = acid.bonds().iterator();
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().ordinal();
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 ChemFile();
CMLReader reader = new CMLReader(
AminoAcids.class.getClassLoader().getResourceAsStream(
"org/openscience/cdk/templates/data/list_aminoacids.cml"
)
);
try {
list = (IChemFile)reader.read(list);
List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(list);
Iterator<IAtomContainer> 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();
Iterator<IAtom> atoms = ac.atoms().iterator();
Iterator<Object> props = ac.getProperties().keySet().iterator();
while (props.hasNext()) {
Object next = props.next();
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()) {
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);
}
}
Iterator<IBond> bonds = ac.bonds().iterator();
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 Map<String,AminoAcid> 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;
}
}