content: /*
  * 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.
  *
  */
  
  package com.actelion.research.chem.forcefield.mmff.table;
  
  import java.util.Arrays;
  
  import com.actelion.research.chem.forcefield.mmff.Csv;
  import com.actelion.research.chem.forcefield.mmff.MMFFMolecule;
  import com.actelion.research.chem.forcefield.mmff.Search;
  import com.actelion.research.chem.forcefield.mmff.Searchable;
  import com.actelion.research.chem.forcefield.mmff.Tables;
  
  public class OutOfPlane implements Searchable {
      private final Object[][] table;
      private final Tables t;
  
      /**
       *
       */
      public OutOfPlane(Tables t, String csvpath) {
          table = Csv.readFile(csvpath);
          this.t = t;
      }
  
      @Override
      public int get(int row, int col) {
          return ((Number) table[row][col]).intValue();
      }
  
      @Override
      public int length() {
          return table.length;
      }
  
      /**
       * Returns the Koop parameters from the OutOfPlane table.
       *  @param mol The molecule that the atoms are in.
       *  @param ac The central atom.
       *  @param a1 Atom neighbour 1.
       *  @param a2 Atom neighbour 2.
       *  @param a3 Atom neighbour 3.
       *  @return The Koop floating point value.
       */
      public double getKoop(MMFFMolecule mol, int ac, int a1, int a2,
                            int a3) {
          int act = mol.getAtomType(ac);
          int[] nbr = new int[]{
              mol.getAtomType(a1),
              mol.getAtomType(a2),
              mol.getAtomType(a3)};
  
          for (int i=0; i<4; i++) {
              int[] nbrf = new int[3];
  
              for (int n=0; n<3; n++)
                  nbrf[n] = t.def.table[nbr[n]-1][i+1];
              Arrays.sort(nbrf);
  
              int index = Search.binary(new int[]{1,0,2,3},
                  new int[]{act,nbrf[0],nbrf[1],nbrf[2]}, this);
  
              if (index >= 0)
                  return ((Number) table[index][4]).doubleValue();
          }
          return 0.0;
      }
  
      public double getKoop(int index) {
          return ((Number) table[index][4]).doubleValue();
      }
  }
  