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package com.actelion.research.chem.shredder;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.*;
import com.actelion.research.util.IntArrayComparator;

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

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

	/**
	 * 
	 * @param minAtoms
	 * @param maxAtoms
	 * @param maxBondFlexibilitySum
	 * @param minExits
	 * @param maxExits
	 */
	public Fragmenter3D(int minAtoms, int maxAtoms, int maxBondFlexibilitySum, int minExits, int maxExits) {
		mMinAtoms = minAtoms;
		mMaxAtoms = maxAtoms;
		mMaxBondFlexibilitySum = maxBondFlexibilitySum;
		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
	 * @param withHydrogen whether built fragments shall include hydrogen atoms
	 * @return Fragment3D list of given molecule
	 */
	public ArrayList buildFragments(StereoMolecule mol, boolean withHydrogen) {
		mFragmentList.clear();

		mol.stripSmallFragments();
		if (withHydrogen)
			new AtomAssembler(mol).addImplicitHydrogens();
		else
			mol.removeExplicitHydrogens(false, true);

		boolean[] isRotatableBond = new boolean[mol.getAllBonds()];
		TorsionDB.findRotatableBonds(mol, true, isRotatableBond);
		float[] bondFlexibility = new MolecularFlexibilityCalculator().calculateBondFlexibilities(mol, 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, BaseFragmentInfo[] baseFragmentInfo) {
		if (atomCount > mMaxAtoms)
			return;

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

		BaseFragmentInfo previousBaseFragmentInfo = baseFragmentInfo[previousBaseFragment];
		for (int i=0; i mMaxExits)
			return;

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