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package com.actelion.research.chem.phesa;

import com.actelion.research.chem.StereoMolecule;
import java.util.ArrayList;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;

/** 
 * @version: 1.0, February 2018
 * Author: J. Wahl
 * contains all information about a molecule (atoms, connectivity) and its shape including flexibilty (Molecular Volumes of a conformational ensemble)
 * the Coordinates of the hydrogens are contained and therefore any molecular conformer can be back-calculated on request
 * the heavy atom coordinates are implicitly given as the centers of the atomic gaussians 
 * 
*/
public class PheSAMolecule {
	private StereoMolecule mol;

	// As many objects as conformers.
	private ArrayList shape;

	
	
	public PheSAMolecule() {
		this.mol = new StereoMolecule();
		this.shape = new ArrayList();
	}
	
	public PheSAMolecule(StereoMolecule mol, MolecularVolume shape) {
		this.mol = mol;
		this.shape = new ArrayList();
		this.shape.add(shape);
	}
	
	public PheSAMolecule(StereoMolecule mol, ArrayList shape) {
		this.mol = mol;
		this.shape = shape;


	}

	/**
	 * Returns the corresponding conformer of a molecular volume
	 * @param molVol
	 * @return
	 */
	public StereoMolecule getConformer(MolecularVolume molVol) {
		int nrOfAtoms = mol.getAllAtoms();
		StereoMolecule conformer = new StereoMolecule(mol);
		int hydrogenCounter = 0;
		ArrayList hydrogens = molVol.getHydrogens();
		for(int i=0;i getVolumes() {
		return this.shape;
	}
	
	
	
}