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/*
 * 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;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * 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.
 *
 * @author Thomas Sander
 */

package com.actelion.research.chem.conf;

import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;

public class AtomAssembler {
	private final StereoMolecule mMol;

	public AtomAssembler(StereoMolecule mol) {
		mMol = mol;
		}

	public int addImplicitHydrogens() {
		mMol.ensureHelperArrays(Molecule.cHelperRings);
		int total = 0;

		for (int atom=0; atom Math.PI)
									dihedral -= 2*Math.PI;
								addAtomWithConstraints(mMol.getCoordinates(atomSequence[0]), mMol.getCoordinates(atomSequence[1]),
										mMol.getCoordinates(atomSequence[2]), atom, 1, angle, dihedral, length);

								if (count != 1) {
									dihedral += Math.PI*2/3;
									if (dihedral > Math.PI)
										dihedral -= 2*Math.PI;
									addAtomWithConstraints(mMol.getCoordinates(atomSequence[0]), mMol.getCoordinates(atomSequence[1]),
											mMol.getCoordinates(atomSequence[2]), atom, 1, angle, dihedral, length);
									}
								return count;
								}
							}
						}

					// no competing atoms
					// if we have a single bonded option for atomSequence[0], then take that
					for (int i=i0+1; inewAtom, angle c2->c3->newAtom and dihedral c1->c2->c3->newAtom are met.
	 * @param c1
	 * @param c2
	 * @param c3
	 * @param rootAtom
	 * @param angle
	 * @param dihedral
	 * @param bondLength
	 */
	private void addAtomWithConstraints(Coordinates c1, Coordinates c2, Coordinates c3, int rootAtom, int atomicNo, double angle, double dihedral, double bondLength) {
		double r = bondLength * Math.sin(Math.PI - angle);
		double x = -r * Math.sin(dihedral);
		double y = r * Math.cos(dihedral);
		double z = bondLength * Math.cos(Math.PI - angle);

		Coordinates axisZ = c3.subC(c2).unit();
		Coordinates axisX = c1.subC(c2).cross(axisZ).unit();    // needs to be mapped to x-axis
		Coordinates axisY = axisX.cross(axisZ).unit();			// needs to be mapped to y-axis

		double[][] m = new double[3][3];
		m[0][0] = -axisX.x;
		m[0][1] = -axisX.y;
		m[0][2] = -axisX.z;
		m[1][0] = -axisY.x;
		m[1][1] = -axisY.y;
		m[1][2] = -axisY.z;
		m[2][0] = axisZ.x;
		m[2][1] = axisZ.y;
		m[2][2] = axisZ.z;
		Coordinates p = new Coordinates(x, y, z).rotate(m).add(c3);
		int hydrogen = mMol.addAtom(atomicNo);
		mMol.addBond(rootAtom, hydrogen, Molecule.cBondTypeSingle);
		mMol.setAtomX(hydrogen, p.x);
		mMol.setAtomY(hydrogen, p.y);
		mMol.setAtomZ(hydrogen, p.z);
		}
	}