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• Fragmenter3D.java

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com.actelion.research.chem.shredder.Fragmenter3D Maven / Gradle / Ivy

package com.actelion.research.chem.shredder;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.TorsionDB;
import com.actelion.research.chem.conf.TorsionDescriptor;
import com.actelion.research.chem.conf.TorsionDescriptorHelper;
import com.actelion.research.util.IntArrayComparator;

import java.util.ArrayList;
import java.util.TreeSet;

public class Fragmenter3D {
	private int mMinAtoms,mMaxAtoms,mMaxBonds,mMinExits,mMaxExits;
	private ArrayList mFragmentList;

	/**
	 * 
	 * @param minAtoms
	 * @param maxAtoms
	 * @param maxBonds
	 * @param minExits
	 * @param maxExits
	 */
	public Fragmenter3D(int minAtoms, int maxAtoms, int maxBonds, int minExits, int maxExits) {
		mMinAtoms = minAtoms;
		mMaxAtoms = maxAtoms;
		mMaxBonds = maxBonds;
		mMinExits = minExits;
		mMaxExits = maxExits;
		mFragmentList = new ArrayList<>();
		}

	/**
	 * Applying the constraints passed to the Fragmenter3D constructor, this method shredders
	 * the given 3D-molecule and returns all generated 3D-fragments as an ArrayList.
	 * The list is re-used by subsequent calls to this nethod. Thus, process/consume the
	 * fragment list before calling this method again.
	 * @param mol
	 * @return Fragment3D list of passed molecule
	 */
	public ArrayList getFragments(StereoMolecule mol) {
		mFragmentList.clear();

		mol.stripSmallFragments();
		mol.removeExplicitHydrogens(false, true);

		boolean[] isRotatableBond = new boolean[mol.getAllBonds()];
		int count = TorsionDB.findRotatableBonds(mol, true, isRotatableBond);

		int[] fragmentNo = new int[mol.getAllAtoms()];
		int fragmentCount = mol.getFragmentNumbers(fragmentNo, isRotatableBond, true);

		int[] atomCount = new int[fragmentCount];
		for (int atom=0; atom baseFragmentCombinationSet = new TreeSet<>(new IntArrayComparator());
		boolean[] isMemberFragment = new boolean[fragmentCount];
		for (int i=0; i baseFragmentCombinationSet, Fragment3DData[] fragmentData) {
		if (usedBaseFragmentCount - mMaxBonds > 1 || atomCount > mMaxAtoms)
			return;

		int[] baseFragmentList = new int[usedBaseFragmentCount];
		int index = 0;
		for (int i=0; i= mMinAtoms)
			addFragment(mol, fragmentNo, isMemberFragment);

		for (int neighbour:fragmentData[previousBaseFragment].neighbourFragment) {
			if (!isMemberFragment[neighbour]) {
				isMemberFragment[neighbour] = true;

				addNewFragments(mol, fragmentNo, isMemberFragment, neighbour,
						usedBaseFragmentCount+1, atomCount+fragmentData[neighbour].atomCount, baseFragmentCombinationSet, fragmentData);

				isMemberFragment[neighbour] = false;
				}
			}
		}

	private void addFragment(StereoMolecule mol, int[] fragmentNo, boolean[] isMemberFragment) {
		int atomCount = 0;
		int extendedAtomCount = 0;

		// mark all atoms with specified fragmentNo and two layers around it
		boolean[] includeAtom = new boolean[mol.getAllAtoms()];
		boolean[] isExitAtom = new boolean[mol.getAllAtoms()];
		for (int atom=0; atom mMaxExits)
			return;

		int bondCount = 0;
		for (int bond=0; bond