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• MolDistHistVizEncoder.java

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com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder 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.descriptor.flexophore;

import com.actelion.research.calc.ArrayUtilsCalc;
import com.actelion.research.chem.*;
import com.actelion.research.chem.descriptor.DescriptorEncoder;

import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.StringTokenizer;

public class MolDistHistVizEncoder {
	
	public static final String SEP = "-1";
	
	
	private static MolDistHistVizEncoder INSTANCE;
	
	private MolDistHistEncoder molDistHistEncoder;

	/**
	 * 
	 */
	public MolDistHistVizEncoder() {
		molDistHistEncoder = new MolDistHistEncoder();
	}
	
	/**
	 * 
	 * @param vizinfo String with content generated by toStringVizInfoEncoded(). 
	 * @param flexophore the encoded descriptor
	 * @return
	 */
	public MolDistHistViz readEncoded(String vizinfo, String flexophore){
		
		StringTokenizer st = new StringTokenizer(vizinfo);
		
		String idcode = st.nextToken();
		String coord = st.nextToken();
				
		MolDistHist mdh = molDistHistEncoder.decode(flexophore);
		
		IDCodeParser parser = new IDCodeParser();
		
		StereoMolecule ster = parser.getCompactMolecule(idcode, coord);
		ster.ensureHelperArrays(StereoMolecule.cHelperRings);
		
		int cc=0;
		List liPPNodeViz = new ArrayList();
		
		boolean hasInevitablePPPoints = false;
		while(st.hasMoreTokens()){
			
			String sArr = st.nextToken();
			
			if(sArr.equals(SEP)){
				hasInevitablePPPoints = true;
				break;
			}
			
			int [] arrAtIndex = ArrayUtilsCalc.readIntArray(sArr);
			
			PPNodeViz node = new PPNodeViz(mdh.getNode(cc));
			
			Coordinates [] arrCoordinates = new Coordinates [arrAtIndex.length];
			for (int i = 0; i < arrAtIndex.length; i++) {
				
				double x = ster.getAtomX(arrAtIndex[i]);
				double y = ster.getAtomY(arrAtIndex[i]);
				double z = ster.getAtomZ(arrAtIndex[i]);
				arrCoordinates[i] = new Coordinates(x, y, z);
				node.addIndexOriginalAtom(arrAtIndex[i]);
			}

			Coordinates coordCenter = Coordinates.createBarycenter(arrCoordinates);
			node.setCoordinates(coordCenter.x, coordCenter.y, coordCenter.z);
			
			liPPNodeViz.add(node);
			cc++;
		}
		
		Molecule3D ff = new Molecule3D(ster);
		for (int i = 0; i < ff.getAllAtoms(); i++) {
			
			Coordinates c = new Coordinates(ster.getAtomX(i), ster.getAtomY(i), ster.getAtomZ(i));
			
			ff.setCoordinates(i, c);
		}
		
		MolDistHistViz mdhv = new MolDistHistViz(mdh.getNumPPNodes(), ff);
		for (int i = 0; i < mdh.getNumPPNodes(); i++) {
			mdhv.addNode(liPPNodeViz.get(i));
		}
		
		for (int i = 0; i < mdh.getNumPPNodes(); i++) {
			for (int j = i+1; j < mdh.getNumPPNodes(); j++) {
				mdhv.setDistHist(i, j, mdh.getDistHist(i, j));
			}
		}
		
		if(hasInevitablePPPoints) {
			
			String strInevitablePPPoints = st.nextToken();
			
			DescriptorEncoder de = new DescriptorEncoder();

			byte [] arrIndexInevitablePPPoints = de.decodeCounts(strInevitablePPPoints);
			
			for (int i = 0; i < arrIndexInevitablePPPoints.length; i++) {
				mdhv.addMandatoryPharmacophorePoint(arrIndexInevitablePPPoints[i]);
			}
			
		}
		
		mdhv.realize();
		
		return mdhv;
		
	}
	
	/**
	 * Encodes the structure information, that it can be written to an DWAR file. 
	 * The atom indices from the structure are mapped on the nodes 
	 * under consideration of the changed indices generated by the Canonizer.
	 * H atoms are not covered by the indices generated by the Canonizer. We take simply the old indices and hope the best.
	 * @return A String with: idcode coordinates [int array]n for each PPNode an int array is written, 
	 * it contains the indices of the mapping atoms in the idcode.  
	 */
	public static String toStringVizInfoEncoded(MolDistHistViz mdhv) {

		StringBuilder sb = new StringBuilder();
		
		if(mdhv.molecule3D == null)
			return null;
		
		Molecule3D molecule3D = MolDistHistViz.finalizeMolecule(mdhv.molecule3D);

		List> liliOriginalIndex = new ArrayList>();
		for(int i=0; i < mdhv.getNumPPNodes(); i++){
			PPNodeViz node = mdhv.getNode(i);
			List liOriginalIndex = node.getListIndexOriginalAtoms();
			liliOriginalIndex.add(liOriginalIndex);
		}
		
		StereoMolecule mol = new Molecule3D(molecule3D);
		
		mol.ensureHelperArrays(Molecule.cHelperRings);
		

		Canonizer can = new Canonizer(mol);
		
		String idcode = can.getIDCode();
		
		String coord = can.getEncodedCoordinates(true);
		
		int [] arrMap = can.getGraphIndexes();

		int nNonHAtoms = mol.getAtoms();
		
		for (int i = 0; i < liliOriginalIndex.size(); i++) {
			List liOriginalIndex = liliOriginalIndex.get(i);
			for (int j = 0; j < liOriginalIndex.size(); j++) {
				int ind = liOriginalIndex.get(j);
				try {
					if(ind hsIndexInevitablePPPoints = mdhv.getHashSetIndexInevitablePPPoints();
		
		if(hsIndexInevitablePPPoints.size() > 0)  {
			
			sb.append(" " + SEP + " ");
			
			DescriptorEncoder de = new DescriptorEncoder();
			
			byte [] a = new byte [hsIndexInevitablePPPoints.size()];
			
			int cc=0;
			for (int index : hsIndexInevitablePPPoints) {
				a[cc++]=(byte)index;
			}
			
			String strEncodedInevitablePPPoints = new String(de.encodeCounts(a), StandardCharsets.UTF_8);
			
			sb.append(strEncodedInevitablePPPoints);
		}
		
		return sb.toString();
	}
	
	public static MolDistHistVizEncoder getInstance(){
		
		if(INSTANCE == null){
			INSTANCE = new MolDistHistVizEncoder();
		}
		
		return INSTANCE;
	}


}