com.actelion.research.chem.conf.BondRotationHelper Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
There is a newer version: 2024.12.1
package com.actelion.research.chem.conf;

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

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

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;

	
	
	public BondRotationHelper(StereoMolecule mol) {
		mMol = mol;
		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 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