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• 2024.9.3
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• HoseCodeCreator.java

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com.actelion.research.chem.contrib.HoseCodeCreator Maven / Gradle / Ivy

package com.actelion.research.chem.contrib;

import java.util.Arrays;
import java.util.Vector;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.ExtendedMolecule;
import com.actelion.research.chem.IDCodeParser;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;

public class HoseCodeCreator {

	public final static int FULL_HOSE_CODE=0;
	public final static int HOSE_CODE_CUT_C_SP3_SP3=1;
	
	final static boolean DEBUG=false;
	
	/** 
	 * This descriptor requires proper up/down bonds, because it encodes stereo parities. 
	 * If a passed molecule is generated from idcode parsing, make sure that coordinates 
	 * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with 
	 * the respective option. 
	 */ 
	public static String[][] getHoseCodes(StereoMolecule mol, int maxSphereSize, int type) {
		String[][] ids=new String[mol.getAtoms()][maxSphereSize];
		mol.ensureHelperArrays(Molecule.cHelperRings); 

		for (int rootAtom=0; rootAtom ids=new Vector();
		int min = 0; 
		int max = 0;
		boolean[] atomMask = new boolean[mol.getAtoms()];
		int[] atomList = new int[mol.getAtoms()]; 
		for (int sphere=0; sphere "+atom+" to "+connAtom);
						if (!atomMask[connAtom]) {
							switch (type) {
							case FULL_HOSE_CODE:
								atomMask[connAtom] = true; 
								atomList[newMax++] = connAtom;
								break;
							case HOSE_CODE_CUT_C_SP3_SP3:
								if ( ! (isCsp3(mol, atom) && isCsp3(mol,connAtom))) {
									if (DEBUG) System.out.println("NO SKIP");
									atomMask[connAtom] = true; 
									atomList[newMax++] = connAtom;
								} else {
									if (DEBUG) System.out.println("SKIP");
								}
								break;
							}
						} 
					} 
				} 
				min = max; 
				max = newMax; 
			} 

			mol.copyMoleculeByAtoms(fragment, atomMask, true, null); 

			// TO GET ONLY THE SKELETON
			/*
			for (int atom=0; atom=0) {
			return HoseCodeCreator.getHoseCodesForAtom(molecule, atomID, maxSphereSize, type);
		}
		return new String[0];
	}
	
	public static void main(String[] args) {
		StereoMolecule molecule= new IDCodeParser(false).getCompactMolecule("deT@@DjU_k``b`@@");
		StereoMolecule otherMolecule = new StereoMolecule(molecule.getAtoms(), molecule.getBonds()); 
		boolean[] atomMask = new boolean[molecule.getAtoms()];
		Arrays.fill(atomMask, true);
		molecule.copyMoleculeByAtoms(otherMolecule, atomMask, true, null);
		System.out.println(new Canonizer(otherMolecule, Canonizer.ENCODE_ATOM_CUSTOM_LABELS).getIDCode()); 		
		
		// String id="deT@`@f\bbbRK]@PT@@";
		String id="fi{qa@DyZkQPSI`cHhhdhdhddhekF\\\\fNXBBjfjjjaXTh@RB@QJh";
		
		String[] hoses= HoseCodeCreator.getHoseCodesFromDiaID(id, 20, FULL_HOSE_CODE);
		for (int i=0; i