/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2007-11-23 12:49:25 -0600 (Fri, 23 Nov 2007) $
 * $Revision: 8655 $
 *
 * Copyright (C) 2003-2005  The Jmol Development Team
 *
 * Contact: jmol-developers@lists.sf.net
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */

package org.jmol.minimize;

import javajs.util.Lst;


import javajs.util.BS;
import org.jmol.minimize.forcefield.AtomType;
import org.jmol.modelset.Atom;

public class MinAtom {

  public Atom atom;
  int index;
  public String sType;
  public double[] coord = new double[3];
  public double[] force = new double[3];
  private Lst<MinBond> bonds = new  Lst<MinBond>();
  public int nBonds;
  int[] bondedAtoms;
  public BS bsVdw = new BS();


  // UFF only
  private int hCount = -1;

  // MMFF only
  public double partialCharge;
  public AtomType ffAtomType;
  public int ffType;
  public Integer vdwKey;
  public BS bs14 = new BS();

  @Override
  public String toString() {
    return "#" + index + "@" + atom.i + " " + sType + " " + coord[0] + "," + coord[1] + "," + coord[2];
  }

  MinAtom(int index, Atom atom, double[] coord, int ac) {
    this.index = index;
    this.atom = atom;
    this.coord = coord;
    bsVdw.setBits(index + 1, ac);
    bsVdw.clear(index);
  }

  void set() {
    coord[0] = atom.x;
    coord[1] = atom.y;
    coord[2] = atom.z;
  }

  public MinBond getBondTo(int iAtom) {
    getBondedAtomIndexes();
    for (int i = 0; i < nBonds; i++)
      if (bondedAtoms[i] == iAtom)
        return bonds.get(i);
    return null;
  }

  public int[] getBondedAtomIndexes() {
    if (bondedAtoms == null) {
      bondedAtoms = new int[nBonds];
      for (int i = nBonds; --i >= 0;)
        bondedAtoms[i] = bonds.get(i).getOtherAtom(index);
    }
    return bondedAtoms;
  }

  public String getIdentity() {
    return atom.getInfo();
  }

  public void addBond(MinBond bond, int i) {
    bonds.addLast(bond);
    nBonds++;
    bsVdw.clear(i);
  }

  public int getBondIndex(int j) {
    return bonds.get(j).index;
  }

  public int getHCount() {
    if (hCount < 0)
      hCount = atom.getCovalentHydrogenCount();
    return hCount;
  }

}