/*
* 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;
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* 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.
*
*/


package com.actelion.research.chem;


public class CanonizerUtil
{
	public enum IDCODE_TYPE
	{
		NORMAL, NOSTEREO, BACKBONE, TAUTOMER, NOSTEREO_TAUTOMER
	}

	/**
	 * Generates an IDCODE for a defined and simplified state of a given molecule.
	 * Optionally the simplification and idcode generation are done for the largest
	 * unconnected fragment rather than considering all molecule fragments.
	 * Allowed simplification types are:<br>
	 * - NORMAL (with complete stereo information)<br>
	 * - NOSTEREO (without stereo information)<br>
	 * - TAUTOMER (generic tautomer: tautomer regions marked as [cBondQFSingle | cBondQFDouble] plus atom label encoding count of pi electrons, deuterium and tritium)<br>
	 * - NOSTEREO_TAUTOMER (combines NOSTEREO and TAUTOMER)<br>
	 * - BACKBONE (without stereo information; all bonds are changed to single bonds)<br>
	 *
	 * @param mol	source molecule to generate the IDCODE
	 * @param type type of IDCODE requested
	 * @param largestFragmentOnly
	 * @return
	 */
	public static String getIDCode(StereoMolecule mol, IDCODE_TYPE type, boolean largestFragmentOnly)
	{
		switch (type) {
			case NORMAL:
				return getIDCode(mol, largestFragmentOnly);
			case NOSTEREO:
				return getIDCodeNoStereo(mol, largestFragmentOnly);
			case BACKBONE:
				return getIDCodeBackBone(mol, largestFragmentOnly);
			case TAUTOMER:
				return getIDCodeTautomer(mol, largestFragmentOnly);
			case NOSTEREO_TAUTOMER:
				return getIDCodeNoStereoTautomer(mol, largestFragmentOnly);
			default:
				break;
		}
		return null;
	}

	public static long getHash(StereoMolecule m, IDCODE_TYPE type, boolean largestFragmentOnly)
	{
		String code = getIDCode(m, type, largestFragmentOnly);
		return code != null ? StrongHasher.hash(code) : 0;
	}

	public static long getNoStereoHash(StereoMolecule m, boolean largestFragmentOnly)
	{
		String code = getIDCodeNoStereo(m, largestFragmentOnly);
		return code != null ? StrongHasher.hash(code) : 0;
	}

	public static long getTautomerHash(StereoMolecule m, boolean largestFragmentOnly)
	{
		String code = getIDCodeTautomer(m, largestFragmentOnly);
		return code != null ? StrongHasher.hash(code) : 0;
	}

	public static long getNoStereoTautomerHash(StereoMolecule m, boolean largestFragmentOnly)
	{
		String code = getIDCodeNoStereoTautomer(m, largestFragmentOnly);
		return code != null ? StrongHasher.hash(code) : 0;
	}

	public static long getBackboneHash(StereoMolecule m, boolean largestFragmentOnly)
	{
		String code = getIDCodeBackBone(m, largestFragmentOnly);
		return code != null ? StrongHasher.hash(code) : 0;
	}

	private static String getIDCode(StereoMolecule mol, boolean largestFragmentOnly)
	{
		try {
			if (!largestFragmentOnly)
				return new Canonizer(mol).getIDCode();

			mol = mol.getCompactCopy();
			mol.stripSmallFragments(true);
			MoleculeNeutralizer.neutralizeChargedMolecule(mol);
			return new Canonizer(mol).getIDCode();
		} catch (Throwable e) {
			System.err.println("WARN: getIDCode() " + e);
			return null;
		}
	}

	private static String getIDCodeNoStereo(StereoMolecule mol, boolean largestFragmentOnly)
	{
		try {
			mol = mol.getCompactCopy();
			if (largestFragmentOnly) {
				mol.stripSmallFragments(true);
				MoleculeNeutralizer.neutralizeChargedMolecule(mol);
			}

			mol.stripStereoInformation();
			return new SimpleCanonizer(mol).getIDCode();
		} catch (Throwable e) {
			System.err.println("WARN: getIDCodeNoStereo() " + e);
			return null;
		}
	}

	private static String getIDCodeTautomer(StereoMolecule mol, boolean largestFragmentOnly)
	{
		try {
			if (largestFragmentOnly) {
				mol = mol.getCompactCopy();
				mol.stripSmallFragments(true);
				MoleculeNeutralizer.neutralizeChargedMolecule(mol);
			}

			StereoMolecule genericTautomer = new TautomerHelper(mol).createGenericTautomer();
			return new Canonizer(genericTautomer, Canonizer.ENCODE_ATOM_CUSTOM_LABELS).getIDCode();
		} catch (Throwable e) {
			System.err.println("WARN: getIDCodeTautomer() " + e);
			return null;
		}
	}

	private static String getIDCodeNoStereoTautomer(StereoMolecule mol, boolean largestFragmentOnly)
	{
		try {
			mol = mol.getCompactCopy();
			if (largestFragmentOnly) {
				mol.stripSmallFragments(true);
				MoleculeNeutralizer.neutralizeChargedMolecule(mol);
			}

			mol.stripStereoInformation();
			StereoMolecule genericTautomer = new TautomerHelper(mol).createGenericTautomer();
			return new Canonizer(genericTautomer, Canonizer.ENCODE_ATOM_CUSTOM_LABELS).getIDCode();
		} catch (Throwable e) {
			System.err.println("WARN: getIDCodeNoStereoTautomer() " + e);
			return null;
		}
	}

	private static String getIDCodeBackBone(StereoMolecule mol, boolean largestFragmentOnly)
	{
		try {
			mol = mol.getCompactCopy();
			if (largestFragmentOnly) {
				mol.stripSmallFragments(true);
				MoleculeNeutralizer.neutralizeChargedMolecule(mol);
			}

			mol.stripStereoInformation();

			int b = mol.getAllBonds();
			for (int i = 0; i < b; i++)
				mol.setBondType(i, Molecule.cBondTypeSingle);

			return new SimpleCanonizer(mol).getIDCode();
		} catch (Throwable e) {
			System.err.println("WARN: getIDCodeBackBone() " + e);
			return null;
		}
	}

	/**
	 * 64 bit hash, derived from numerical recipes
	 * Will move this class later to dd_core.
	 */
	public static class StrongHasher
	{
		private static final long[] byteTable;
		private static final long HSTART = 0xBB40E64DA205B064L;
		private static final long HMULT = 7664345821815920749L;

		static {
			byteTable = new long[256];
			long h = 0x544B2FBACAAF1684L;
			for (int i = 0; i < 256; i++) {
				for (int j = 0; j < 31; j++) {
					h = (h >>> 7) ^ h;
					h = (h << 11) ^ h;
					h = (h >>> 10) ^ h;
				}
				byteTable[i] = h;
			}
		}

		public static long hash(String cs) {
			if (cs == null) return 1L;
			long h = HSTART;
			final long hmult = HMULT;
			final long[] ht = byteTable;
			for (int i = cs.length()-1; i >= 0; i--) {
				char ch = cs.charAt(i);
				h = (h * hmult) ^ ht[ch & 0xff];
				h = (h * hmult) ^ ht[(ch >>> 8) & 0xff];
			}
			return h;
		}

	}
}
