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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
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* 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.
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*    this list of conditions and the following disclaimer in the documentation
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*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
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package com.actelion.research.chem;

public class TautomerHelper {
	private StereoMolecule mMol;
	private int[] mChainAtom;
	private int[] mChainBond;
	private boolean[] mChainNeedsDoubleBond;
	private boolean[] mChainNeedsDonorAtom;
	private boolean[] mIsTautomerBond;
	private int[] mRegionPiCount;
	private int[] mRegionDCount;
	private int[] mRegionTCount;

	public TautomerHelper(StereoMolecule mol) {
		mMol = mol;
		mMol.ensureHelperArrays(Molecule.cHelperParities);
		mChainAtom = new int[mMol.getAtoms()];
		mChainBond = new int[mMol.getAtoms()];
		mChainNeedsDoubleBond = new boolean[mMol.getAtoms()];
		mChainNeedsDonorAtom = new boolean[mMol.getAtoms()];
		mIsTautomerBond = new boolean[mMol.getBonds()];
		}

	/**
	 * Identifies connected tautomeric regions and assign region numbers to all atoms.
	 * Atoms sharing the same region share the same number.

	 * 0: not member of a tautomer region; 1 and above: region number
	 * @param atomRegionNo int[mol.getAtoms()] filled with 0
	 * @param keepStereoCenters
	 * @return region count
	 */
	public int getAtomRegionNumbers(int[] atomRegionNo, boolean keepStereoCenters) {
		if (!findTautomericBonds(keepStereoCenters))
			return 0;

		int regionCount = assignRegionNumbers(atomRegionNo);
		return regionCount;
		}

	/**
	 * If no tautomers can be formed then the original molecule is returned.
	 * Otherwise the original molecule is copied and normalized to create a
	 * generic tautomer structure without touching the original molecule.
	 * Different tautomers of the same molecule should always result in the same
	 * generic tautomer structure. A generic tautomer contains one or more regions
	 * indicated by bond query features cBondQFSingle & cBondQFDouble. Bond types
	 * of all bonds of any tautomer region are cBondTypeSingle.
	 * The highest ranking atom in every region carries a label defining the number
	 * of double bonds and D and T atoms. The returned molecule has the fragment bit set.
	 * Canonicalizing the returned molecule with Canonizer mode ENCODE_ATOM_CUSTOM_LABELS
	 * produces the same idcode from any tautomer.
	 * If keepStereoCenters is true, then stereo centers with parity 1 or 2, if they are
	 * absolute or if they are part of an AND/OR group with more than one member,
	 * are considered stable (non racemising) and, thus, their proton is not considered
	 * being able to take part in a tautomeric transition.
	 * @param keepStereoCenters if true, then defined (non-racemising) stereo centers cannot be part of tautomeric regions
	 * @return generic tautomer with normalized tautomer regions and custom label to encode pi,D,T counts
	 */
	public StereoMolecule createGenericTautomer(boolean keepStereoCenters) {
		if (!findTautomericBonds(keepStereoCenters))
			return mMol;

		StereoMolecule genericTautomer = mMol.getCompactCopy();
		genericTautomer.setFragment(true);
		for (int bond=0; bond= 0) {
			int currentAtom = mChainAtom[current];

			if (forward)
				connIndex[current] = mMol.getConnAtoms(currentAtom);
			connIndex[current]--;

			int desiredBondOrder = mChainNeedsDoubleBond[current] ? 2 : 1;
			while (connIndex[current] >= 0) {
				connAtom = mMol.getConnAtom(currentAtom, connIndex[current]);
				connBond = mMol.getConnBond(currentAtom, connIndex[current]);
				if (!isProtectedAtom[connAtom]
				 && !isChainAtom[connAtom]) {	// don't allow ring closures
					if ((mMol.isDelocalizedBond(connBond) || mMol.getBondOrder(connBond) == desiredBondOrder)
					 && (mMol.getAtomPi(connAtom) != 0
					  || (mChainNeedsDonorAtom[current]) && isValidDonorAtom(connAtom))) {
						// this is a continuation of the delocalized chain or may be an endo-donor as O=C-CHR-C=C
						break;
						}
					}
				connIndex[current]--;
				}
	
			if (connIndex[current] == -1) {
				if (forward && (!mChainNeedsDonorAtom[0] || !mChainNeedsDonorAtom[current])) {
					for (int i=current; i>highestValid; i--) {
						mIsTautomerBond[mChainBond[i]] = true;

						// find and flag exo-donor atoms as CH in NH-C(-CHR2)=C
						if (!mChainNeedsDonorAtom[0] && mChainNeedsDoubleBond[i]) {
							for (int j=0; j current)
					highestValid = current;
				continue;
				}		

			current++;
			forward = true;
			mChainAtom[current] = connAtom;
			mChainBond[current] = connBond;
			mChainNeedsDoubleBond[current] = !mChainNeedsDoubleBond[current-1] && (mMol.getAtomPi(connAtom) != 0);
			mChainNeedsDonorAtom[current] = mChainNeedsDonorAtom[current-1] && (mMol.getAtomPi(connAtom) != 0);
			isChainAtom[connAtom] = true;
			}

		return tautomerBondsFound;
		}

	private boolean[] locateProtectedAtoms(boolean keepStereoCenters) {
		boolean[] isProtectedAtom = new boolean[mMol.getAtoms()];

		for (int atom=0; atom 3)
				isProtectedAtom[atom] = true;

		// protect stereo centers with defined parity
		if (keepStereoCenters)
			for (int atom=0; atom 2)
						oddAndEvenSubstituentMask |= ((i & 1) != 0) ? 1 : 2;

					for (int j=0; j