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• BondRotationHelper.java

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com.actelion.research.chem.conf.BondRotationHelper 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 Thomas Sander
 */

package com.actelion.research.chem.conf;

import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.phesa.PheSAAlignment;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.IntStream;

public class BondRotationHelper {
	
	private StereoMolecule mMol;
	private int[] mRotatableBonds;
	private boolean[] mIsRotatableBond;
	private int[][] mSmallerSideAtomLists;
	private int[][] mBiggerSideAtomLists;
	private int[][] mTorsionAtoms;
	private int[][] mRearAtoms;
	private int[] mRotationCenters;
	private int[] mRotationCentersBig;
	private String[] mTorsionIDs;
	private boolean includeTerminalPolarH;
	private int[] terminalPolarHBond;
	
	public BondRotationHelper(StereoMolecule mol) {
		this(mol,false);
	}
	
	public BondRotationHelper(StereoMolecule mol, boolean includeTerminalPolarH) {
		mMol = mol;
		this.includeTerminalPolarH = includeTerminalPolarH;
		initialize();
	}
	
	public void initialize() {
		int[] disconnectedFragmentNo = new int[mMol.getAllAtoms()];
		int disconnectedFragmentCount = mMol.getFragmentNumbers(disconnectedFragmentNo, false, true);
		int disconnectedFragmentSize[] = new int[disconnectedFragmentCount];
		for (int atom=0; atom rotBonds = new ArrayList();
		IntStream.range(0, mIsRotatableBond.length).forEach(e -> {
			if(mIsRotatableBond[e])
				rotBonds.add(e);
		});
		mRotatableBonds = rotBonds.stream().mapToInt(i->i).toArray();
		mTorsionAtoms = new int[mRotatableBonds.length][];
		mRearAtoms = new int[mRotatableBonds.length][];
		mSmallerSideAtomLists = new int[mRotatableBonds.length][];
		mBiggerSideAtomLists = new int[mRotatableBonds.length][];
		mRotationCenters = new int[mRotatableBonds.length];
		mRotationCentersBig = new int[mRotatableBonds.length];
		mTorsionIDs = new String[mRotatableBonds.length];
		
		for(int i=0;i terminalHBonds = new ArrayList<>();
		for(int b=0;b0) {
					isRotatableBond[b]=true;
					terminalHBonds.add(b);
					continue;
				}
			}
			if(mMol.getAtomicNo(a2)==7 || mMol.getAtomicNo(a2)==8) {
				if(mMol.getNonHydrogenNeighbourCount(a2)==1 && mMol.getAllHydrogens(a2)>0) {
					isRotatableBond[b]=true;
					terminalHBonds.add(b);
				}
			}
		}
		return terminalHBonds.stream().mapToInt(Integer::intValue).toArray();
	}
	
	//populates smallerSideAtomList array and returns the rotation center
	private void findSmallerSideAtomList(int disconnectedFragmentSize, int[] disconnectedFragmentNo, int bondIndex) {
		boolean[] isMember = new boolean[mMol.getAllAtoms()];
		int memberCount = mMol.getSubstituent(mRearAtoms[bondIndex][0], mTorsionAtoms[bondIndex][1], isMember, null, null);
		
		int alkyneAtoms = 0;	// if we have an extended linear sp-atom strain
		if (mRearAtoms[bondIndex][0] != mTorsionAtoms[bondIndex][2])
			alkyneAtoms = mMol.getPathLength(mRearAtoms[bondIndex][0], mTorsionAtoms[bondIndex][2]);

		boolean invert = false;
		if (memberCount > disconnectedFragmentSize-alkyneAtoms-memberCount) {
			memberCount = disconnectedFragmentSize-alkyneAtoms-memberCount;
			invert = true;
			}

		// if invert, then flag all linear alkyne atoms to be avoided
		if (invert && alkyneAtoms != 0) {
			int spAtom = mRearAtoms[bondIndex][0];
			int backAtom = mTorsionAtoms[bondIndex][1];
        	while (mMol.getAtomPi(spAtom) == 2
           		&& mMol.getConnAtoms(spAtom) == 2
           		&& mMol.getAtomicNo(spAtom) < 10) {
        		isMember[spAtom] = true;
           		for (int j=0; j<2; j++) {
           			int connAtom = mMol.getConnAtom(spAtom, j);
           			if (connAtom != backAtom) {
           				backAtom = spAtom;
           				spAtom = connAtom;
           				break;
           				}
           			}
           		}
			}

		int memberNo = 0;
		int fragmentNo = disconnectedFragmentNo[mTorsionAtoms[bondIndex][1]];
		int [] smallerSideAtomList = new int[memberCount];
		for (int atom=0; atom bigSideAtoms = new HashSet();
		Set smallSideAtoms = new HashSet();
		for(int a : smallerSideAtomList)
			smallSideAtoms.add(a);
		for(int a=0;a