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com.actelion.research.chem.io.pdb.parser.Residue Maven / Gradle / Ivy

/*
 * Copyright (c) 1997 - 2016
 * Actelion Pharmaceuticals Ltd.
 * Gewerbestrasse 16
 * CH-4123 Allschwil, Switzerland
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the the copyright holder nor the
 *    names of its contributors may be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * @author Modest v. Korff
 */

package com.actelion.research.chem.io.pdb.parser;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.Molecule3D;
import com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer;
import com.actelion.research.chem.io.pdb.converter.BondsCalculator;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * ModelGroupAtoms
 * handles a group of atoms, e.g. a Ligand Molecule or an AminoAcid residue
 *
 * Created by korffmo1 on 11.04.18.
 */
public class Residue {
	public static double BOND_CUTOFF_SQ = 3.24;
    private List records;
    private boolean isTerminal;
    private Molecule3D mol;

    public Residue(List records) {
        this.records = records;
        this.isTerminal = isTerminal();
        mol = constructFragment();
    }
        

	public boolean isTerminal() {
		isTerminal = false;
		for(AtomRecord record : records) {
			if(record.isTerminalC())
				isTerminal = true;
		}
		return isTerminal;
	}
    

    
    private Molecule3D constructFragment() {
    	boolean isAA = false;
    	if(AminoAcidsLabeledContainer.INSTANCE.get(getResname())!=null)
    		isAA = true;
    	Molecule3D fragment;
    	if(isAA) 
    		fragment = constructFragmentFromIDCode(getResname());
    	else 
    		fragment = constructFragmentFromGeometry(getResname());
    	fragment.ensureHelperArrays(Molecule.cHelperNeighbours);
    	return fragment;
    }
    
    private Molecule3D constructFragmentFromIDCode(String resname) {
		Molecule3D fragment;
		Map recordMap = new HashMap();
		for(AtomRecord record : records) {
			String atomName = record.getAtomName();
			recordMap.put(atomName,record);
		}
		fragment = AminoAcidsLabeledContainer.INSTANCE.get(resname).createResidue(recordMap);
		if(fragment==null) {
			fragment = constructFragmentFromGeometry(resname);
		}
		return fragment;
    }
    
	private Molecule3D constructFragmentFromGeometry(String resname) {
		Molecule3D fragment = new Molecule3D();
		for(AtomRecord record : records) {
			int atomicNo = record.getAtomicNo();
			int atom = fragment.addAtom(atomicNo);
			fragment.setAtomName(atom, record.getAtomName());
			fragment.setAtomAmino(atom, record.getResName());
			fragment.setAtomSequence(atom,record.getSerialId());
			fragment.setResSequence(atom, record.getResNum());
			fragment.setAtomAmino(atom, record.getResName());
			fragment.setAtomChainId(atom, record.getChainID());
			fragment.setAtomX(atom,record.getX());
			fragment.setAtomY(atom,record.getY());
			fragment.setAtomZ(atom,record.getZ());
		}

		fragment.ensureHelperArrays(Molecule.cHelperCIP);
		try {
			BondsCalculator.createBonds(fragment, true,null);
			BondsCalculator.calculateBondOrders(fragment,true);
		} catch (Exception e) {
			// TODO Auto-generated catch block
			System.err.println();
		}

		return fragment;
	}
	
	public int getResnum() {
		return records.get(0).getResNum();
	}
	
	public Molecule3D getMolecule() {
		return mol;
	}
	
	public String getResname() {
		return records.get(0).getResName();
	}
	
	public String getChainID() {
		return records.get(0).getChainID();
	}
	
	public String getInsertionCode() {
		return records.get(0).getInsertionCode();
	}
	
	
	/*
	 * check if two residues are connected by a peptide bond, this is the residue with the (supposedly) terminal nitrogen,
	 * resC should contain the terminal carbon
	 */
	public boolean areBonded(Residue resN) { 
		AtomRecord recordC = null; 
		AtomRecord recordN = null;
		boolean areBonded = false;
		for(AtomRecord rec : this.records) {
			if (rec.getAtomName().equals("C")) {
				recordN = rec;
				break;
			}
		}
		
		for(AtomRecord rec : resN.records) {
			if (rec.getAtomName().equals("N")) {
				recordC = rec;
				break;
			}
		}
		if(recordN!=null && recordC!=null) {
			double dx = recordN.getX()-recordC.getX();
			double dy = recordN.getY()-recordC.getY();
			double dz = recordN.getZ()-recordC.getZ();
			double distSq = dx*dx + dy*dy + dz*dz;
			if(distSq