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package com.actelion.research.chem.conf;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94;
import org.openmolecules.chem.conf.gen.ConformerGenerator;

import java.util.HashMap;
import java.util.Map;

public class ConformerSetGenerator {
	
	private int mMaxNrConfs;
	private int mStrategy;
	private boolean mUseFF;
	private ConformerGenerator mConfGen;
	private static  long DEFAULT_SEED = 12345L;
	
	public ConformerSetGenerator(int maxNrConfs, int strategy, boolean useFF, long seed) {
		mMaxNrConfs = maxNrConfs;
		mStrategy = strategy;
		mUseFF = useFF;
		mConfGen = new ConformerGenerator(seed, useFF);
	}
	
	/**
	 * STRATEGY_LIKELY_RANDOM was evaluated to be the best strategy for reproducing bioactive
	 * conformers (J.W. 05/19)
	 * 
	 */
	
	public ConformerSetGenerator() {
		this(200,ConformerGenerator.STRATEGY_LIKELY_RANDOM,false,DEFAULT_SEED);
		
	}
	
	public ConformerSetGenerator(boolean useFF) {
		this(200,ConformerGenerator.STRATEGY_LIKELY_RANDOM,useFF,DEFAULT_SEED);
		
	}
	
	public ConformerSetGenerator(boolean useFF, long seed) {
		this(200,ConformerGenerator.STRATEGY_LIKELY_RANDOM,useFF,seed);
		
	}
	
	public ConformerSet generateConformerSet(StereoMolecule mol) {   
		StereoMolecule m = new StereoMolecule(mol);
		m.ensureHelperArrays(Molecule.cHelperCIP);
		m.stripSmallFragments();
		ConformerGenerator.addHydrogenAtoms(m);
		Canonizer can = new Canonizer(m);
		m = can.getCanMolecule(true);
		m.ensureHelperArrays(Molecule.cHelperCIP);
		if(mUseFF) {
			ForceFieldMMFF94.initialize(ForceFieldMMFF94.MMFF94SPLUS);
		}
		Map ffOptions = new HashMap();
		ConformerSet confSet = new ConformerSet();
		mConfGen.initializeConformers(m,mStrategy,100000,false);
		boolean nextConf = true;
		int i=0;
		while(i