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com.actelion.research.chem.descriptor.flexophore.PPNodeViz Maven / Gradle / Ivy

/*
 * Copyright (c) 1997 - 2022
 * Idorsia Pharmaceuticals Ltd.
 * Hegenheimermattweg 91
 * 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 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.chem.Coordinates;
import com.actelion.research.util.ArrayUtils;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;

/**
 * Pharmacophore node with information about corresponding atoms in the molecule used for construction.
 */
public class PPNodeViz extends PPNode implements Serializable {
	
	
	private static final long serialVersionUID = 22022013;

	private static final double LIM_EQUAL_COORD=0.00001;
	
	private static final float SIMILARITY_NODES=-1;
	
	// Indices of mapping original atoms in molecule.
	// Only together with MolDistHistViz and visualization of the structure and the descriptor.
	private HashSet hsIndexOriginalAtoms;
	
	private Coordinates coordinates;
	
	private float similarityMappingNodes;

	// Just an index used for the mapping of two nodes in two different MolDistHistViz objects.
	private int mappingIndex;
	
	// Index to track the fate of the nodes.
	private byte index;
	
	// Corresponding count for the isosphere in jmol.  
	private int indexSphereViz;
	
	private boolean marked;

	public PPNodeViz(){
		super(new PPNode()); 
		init();
	}

	public PPNodeViz(PPNodeViz node){
		copy(node);
	}

	
	public PPNodeViz(PPNode node){
		super(node);
		init();
	}
	
	private void init(){
		
		coordinates = new Coordinates();
		
		hsIndexOriginalAtoms = new HashSet();
		
		mappingIndex = INFO_DEFAULT;
		
		index = INFO_DEFAULT;

		similarityMappingNodes = SIMILARITY_NODES;


	}
	
	public int getIndex() {
		return index;
	}

	public void setIndex(int id) {
		index = (byte)id;
	}

	/**
	 * Only atoms are added that are not yet in the list,
	 * check PPAtom.equals for comparison.
	 * @param node
	 */
	public void addAtoms(PPNodeViz node){
		super.addAtoms(node);
		hsIndexOriginalAtoms.addAll(node.hsIndexOriginalAtoms);
	}
	
	public void addIndexOriginalAtom(int index){
		if(hsIndexOriginalAtoms==null)
			hsIndexOriginalAtoms = new HashSet();
		
		hsIndexOriginalAtoms.add(index);
	}
	
	/**
	 * Copy of node into this
	 * @param node
	 */
	public void copy(PPNodeViz node){
		super.copy(node);
		
		coordinates = new Coordinates(node.coordinates);
		
		mappingIndex = node.mappingIndex;

		hsIndexOriginalAtoms = new HashSet();
		
		hsIndexOriginalAtoms.addAll(node.hsIndexOriginalAtoms);
		
		index = node.index;
		
		indexSphereViz = node.indexSphereViz;
		
		similarityMappingNodes = node.similarityMappingNodes;
		
		marked = node.marked;

		heteroAtom = node.heteroAtom;

	}
	
	/**
	 * @return the marked
	 */
	public boolean isMarked() {
		return marked;
	}
	/**
	 * @param marked the marked to set
	 */
	public void setMarked(boolean marked) {
		this.marked = marked;
	}
	
	public PPNodeViz getCopy(){
		return new PPNodeViz(this);
	}
	
	public List getListIndexOriginalAtoms() {
		return new ArrayList(hsIndexOriginalAtoms);
	}
	
	public int [] getArrayIndexOriginalAtoms() {
		return ArrayUtils.toIntArray(hsIndexOriginalAtoms);
	}

	public HashSet getIndexOriginalAtoms() {
		return hsIndexOriginalAtoms;
	}

	public int getMappingIndex() {
		return mappingIndex;
	}
	
	public void setMappingIndex(int info) {
		this.mappingIndex = info;
	}
	
	public void clearInfo() {
		mappingIndex = INFO_DEFAULT ;
	}

	public boolean hasSamePosition(PPNodeViz node){
		return equal(coordinates, node.coordinates);
	}
	


	/**
	 * 26.03.2007 MvK 
	 * Own equal function for coordinates. In Joels fct seems to be an 
	 * error with rounding in insignificant digits.
	 * @param c1
	 * @param c2
	 * @return
	 */
	private boolean equal(Coordinates c1, Coordinates c2){
		boolean bEq = true;
		
		if(Math.abs(c1.x-c2.x)>LIM_EQUAL_COORD)
			bEq = false;
		else if(Math.abs(c1.y-c2.y)>LIM_EQUAL_COORD)
			bEq = false;
		else if(Math.abs(c1.z-c2.z)>LIM_EQUAL_COORD)
			bEq = false;
		
		return bEq;
	}
	
	public void resetInfoColor(){
		mappingIndex = INFO_DEFAULT;
	}

	
	public Coordinates getCoordinates() {
		return coordinates;
	}

	public void setCoordinates(double x, double y, double z) {
		coordinates.x = x;
		coordinates.y = y;
		coordinates.z = z;
	}

	public void setCoordinates(Coordinates c) {
		coordinates.x = c.x;
		coordinates.y = c.y;
		coordinates.z = c.z;
	}

	public void setCoordinatesNull() {
		coordinates=null;
	}
	public double getX(){
		return coordinates.x;
	}
	public double getY(){
		return coordinates.y;
	}
	public double getZ(){
		return coordinates.z;
	}
	public void setX(double x){
		coordinates.x = x;
	}
	public void setY(double y){
		coordinates.y = y;
	}
	public void setZ(double z){
		coordinates.z = z;
	}
	public int getIndexSphereVisualization() {
		return indexSphereViz;
	}
	protected void setIndexSphereVisualization(int indexSphereViz) {
		this.indexSphereViz = indexSphereViz;
	}
	
	/**
	 * @return the similarityMappingNodes
	 */
	public float getSimilarityMappingNodes() {
		return similarityMappingNodes;
	}
	/**
	 * @param similarityMappingNodes the similarityMappingNodes to set
	 */
	public void setSimilarityMappingNodes(float similarityMappingNodes) {
		this.similarityMappingNodes = similarityMappingNodes;
	}

	/**
	 *
	 * @return
	 */
	public String toStringPPNodeText(){
		return super.toStringText();
	}

	public String toString(){
		StringBuilder sb = new StringBuilder();
		sb.append("(");

		if(modeFlexophore==ConstantsFlexophore.MODE_SOFT_PPPOINTS) {
			sb.append(super.toStringText());
		} else if(modeFlexophore==ConstantsFlexophore.MODE_HARD_PPPOINTS) {
			sb.append(super.toStringLongHardPPPoint());
		} else {
			throw new RuntimeException("Unknown Flexophore mode " + modeFlexophore + "!");
		}

		sb.append(", coord ");
		sb.append(coordinates.toString());
		
		sb.append(", mapping color ");
		sb.append(mappingIndex);
		
		sb.append(", index ");
		sb.append(index);
		sb.append(", indexAtom viz ");
		sb.append(indexSphereViz);
		
		sb.append(")");
		
		return sb.toString();
	}

	public String toStringShort(){
		return super.toString();
	}

}