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 com.actelion.research.chem.forcefield.mmff.Csv;
  import com.actelion.research.chem.forcefield.mmff.Tables;
  
  /**
   * Atom table, corresponds to the MMFFPROP.PAR parameters table provided
   * in the MMFF literature. This table specifies the chemical, topological
   * and geometrical properties associated with each of the MMFF atom types.
   */
  public final class Atom implements com.actelion.research.chem.forcefield.mmff.Searchable {
      private final int[][] table;
  
      public Atom(Tables t, String csvpath) {
          table = Csv.readIntsFile(csvpath);
      }
  
      @Override
      public int get(int row, int col) {
          return table[row][col];
      }
  
      @Override
      public int length() {
          return table.length;
      }
  
      /**
       * Returns the ASPEC type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The ASPEC value for the atom.
       */
      public int aspec(int type) {
          return table[index(type)][1];
      }
  
      /**
       * Returns the CRD type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The CRD value for the atom.
       */
      public int crd(int type) {
          return table[index(type)][2];
      }
  
      /**
       * Returns the VAL type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The VAL type for the atom.
       */
      public int val(int type) {
          return table[index(type)][3];
      }
  
      /**
       * Returns the PILP type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The PILP type for the atom.
       */
      public int pilp(int type) {
          return table[index(type)][4];
      }
  
      /**
       * Returns the MLTB type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The MLTB type for the atom.
       */
      public int mltb(int type) {
          return table[index(type)][5];
      }
  
      /**
       * Returns the Arom bool of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The Arom bool for the atom.
       */
      public boolean arom(int type) {
          return table[index(type)][6] > 0;
      }
  
      /**
       * Returns the linear bool of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The Linear bool for the atom.
       */
      public boolean linear(int type) {
          int idx = index(type);
          return idx >= 0 ? table[idx][7] > 0 : false;
      }
  
      /**
       * Returns the SBMB type of an atom given its MMFF type.
       *  @param type The MMFF atom type of the atom.
       *  @return The SBMB boolean for the atom.
       */
      public boolean sbmb(int type) {
          return table[index(type)][8] > 0;
      }
  
      /**
       * Returns the index of a given atom type in the 'atprop' table.
       *  @param type The atom type.
       *  @return An index in the atprop table, or -1 if no index was found.
       */
      private int index(int type) {
          return com.actelion.research.chem.forcefield.mmff.Search.binary(0, type, this);
      }
  }
  