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Jmol: an open-source Java viewer for chemical structures in 3D
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/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2017-04-12 23:13:56 -0500 (Wed, 12 Apr 2017) $
 * $Revision: 21516 $
 *
 * Copyright (C) 2005  The Jmol Development Team
 *
 * Contact: [email protected]
 *
 *  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.smiles;

import java.util.Hashtable;

import java.util.Map;

import javajs.util.AU;
import javajs.util.Lst;
import javajs.util.P3;
import javajs.util.SB;
import javajs.util.T3;

import org.jmol.java.BS;
import org.jmol.util.BSUtil;
import org.jmol.util.Edge;
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.util.Node;
import org.jmol.viewer.JC;

/**
 * A class to build and carry out a SMILES or SMARTS match
 * @author Bob Hanson [email protected]
 */
public class SmilesSearch extends JmolMolecule {

  public SmilesSearch() {
    top = this;
    v = new VTemp();
  }

  /* ============================================================= */
  /*                             Setup                             */
  /* ============================================================= */

  boolean isSmarts;

  SmilesSearch top;
  
  String pattern;
  SmilesAtom[] patternAtoms = new SmilesAtom[16];
  Node[] targetAtoms;
  int targetAtomCount;
  private BS bsSelected;

  VTemp v; // temporary vector set
  
  boolean aromaticOpen; // will also be openSMARTS if isSmarts is TRUE
  boolean aromaticStrict;
  boolean aromaticPlanar;
  boolean aromaticDouble;
  boolean noAromatic;
  boolean ignoreAtomClass;
  boolean ignoreStereochemistry;
  boolean invertStereochemistry;
  boolean exitFirstMatch;  
  boolean groupByModel; // or byMolecule (default)
  boolean setAtropicity;

  /**
   * Set in set() to indicate to SmilesMatcher that 
   * the string already has aromatic atoms indicated and so
   * no aromaticity model should be applied.
   */
  
  boolean patternAromatic; 
  boolean haveTopo;  
  boolean isTopology;
  boolean patternBioSequence;
  SmilesSearch[] subSearches;
  boolean haveSelected;
  boolean haveBondStereochemistry;
  SmilesStereo stereo;
  boolean needRingData;
  boolean needAromatic = true; // we just have to always consider aromatic, except in the case of bioSequences.
  boolean needRingMemberships;

  int nDouble;
  int ringDataMax = Integer.MIN_VALUE;
  SB ringSets;
  int ringCount;


  Lst measures = new  Lst();
  
  int flags;
  BS bsAromatic = new BS();
  BS bsAromatic5 = new BS();
  BS bsAromatic6 = new BS();
  String atropKeys;
  
  SmilesAtom lastChainAtom;

  boolean asVector;
  boolean getMaps;
  boolean isNormalized;
  boolean haveComponents;
  
  void setTop(SmilesSearch parent) {
    while (parent.top != parent)
      parent = parent.top;
    this.top = parent;
  }

  //  private data 
  
  private boolean isSilent;
  private boolean isRingCheck;
  private int selectedAtomCount;
  private BS[] ringData;
  private int[] ringCounts;
  private int[] ringConnections;
  private BS bsFound = new BS(); 
  private Map htNested;
  private int nNested;
  private SmilesBond nestedBond;

  private Lst