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.util;
  
  import java.text.SimpleDateFormat;
  
  /**
   * 
   * ConstantsDWAR
   * @author Modest von Korff
   * Jan 15, 2013 MvK Start implementation
   */
  public class ConstantsDWAR {
  
  	// This date format is recognized by the DataWarrior
  	public static final SimpleDateFormat SIMPLE_DATE_FORMAT = new SimpleDateFormat("MMM dd, yyyy");
  
  	// NumberFormat is not thread save.
  	public static final String PATTERN_NF_DWAR4 ="0.0000";
  
  	public static final String PATTERN_NF_DWAR = "0.000############";
  
  	// Program name for the class Platform
  	public static final String PLATFORM_NAME_DATAWARRIOR = "datawarrior";
  
  	public static final String PACKAGE_DATAWARRIOR_IDORSIA = "com.actelion.research.datawarrior.DataWarriorActelionLinux";
  
  
  	// Separator for values in DataWarrior file.
  	public static final String SEP_VALUE = "; ";
  	
  	// Line separator for multiple idcodes in a DataWarrior field
  	public static final String SEP_LINE = "<NL>";
  	
  
  	
  	// Constants from Molecule.cAtomLabel
  	public static final int ATOM_LABEL_R1 = 142;
  	public static final int ATOM_LABEL_R2 = 143;
  	public static final int ATOM_LABEL_R3 = 144;
  	
  	private static int indexAtomLabel = 129;
  	
  	public static final int ATOM_LABEL_R4 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R5 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R6 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R7 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R8 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R9 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R10 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R11 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R12 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R13 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R14 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R15 = indexAtomLabel++;
  	public static final int ATOM_LABEL_R16 = indexAtomLabel++;
  
  	
  	public static final int [] arrAtomLabelRGroups = {
  		ATOM_LABEL_R1, 
  		ATOM_LABEL_R2, 
  		ATOM_LABEL_R3, 
  		ATOM_LABEL_R4,
  		ATOM_LABEL_R5,
  		ATOM_LABEL_R6,
  		ATOM_LABEL_R7,
  		ATOM_LABEL_R8,
  		ATOM_LABEL_R9,
  		ATOM_LABEL_R10,
  		ATOM_LABEL_R11,
  		ATOM_LABEL_R12,
  		ATOM_LABEL_R13,
  		ATOM_LABEL_R14,
  		ATOM_LABEL_R15,
  		ATOM_LABEL_R16};
  
  	/**
  	 * Replaced by TAG_IDCODE2
  	 */
  	@Deprecated
  	public static final String TAG_IDCODE = "idcode";
  
  	// From SAR analysis
  	public static final String TAG_IDCODE_SCAFFOLD = "Scaffold";
  
  	public static final String TAG_COORDINATES_SCAFFOLD = "scaffoldAtomCoords";
  
  	public static final String TAG_IDCODE2 = "Structure";
  
  	public static final String TAG_COOR2 = "idcoordinates2D";
  
  	public static final String IDCODE_EMPTY = "dH";
  
  
  
  	/**
  	 * Can be one or multiple sets of 3D coordinates.
  	 */
  	public static final String TAG_COOR3D = "idcoordinates3D";
  
  	public static final String TAG_COOR3D_MMFF = "3D-Structure (low-energy random, mmff94s+)";
  
  	/**
  	 * Contains the idcode and the 3d coordinates.
  	 */
  	public static final String TAG_CONFORMERSET = "conformerSet";
  
  	public static final String TAG_COOR = "idcoordinates";
  
  	public static final String TAG_ID_QUERY = "Id Query";
  	
  	public static final String TAG_QUERY_IDENTIFIER = "QueryIdentifier";
  	
  	public static final String TAG_LIGAND_EFFICIENCY = "LE";
  
  	public static final String TAG_STRUCTURE_INCLUDE = "Include";
  
  	public static final String TAG_STRUCTURE_EXCLUDE = "Exclude";
  	
  	public static final String TAG_BONDS = "Bonds";
  	
  	public static final String TAG_ATOMS = "Atoms";
  
  	public static final String TAG_MW = "Total Molweight";
  
  	public static final String TAG_NAME = "Name";
  	
  	public static final String TAG_RECORD_NO = "Record No";
  	public static final String TAG_TRANSFORMATION = "Transformation";
  
  
  	@Deprecated // use TAG_CMP_ID instead!
  	public static final String TAG_ACTNO = "Idorsia No";
  
  	public static final String TAG_CMP_ID = "CompoundIdentifier";
  
  	public static final String TAG_SOURCE = "Source";
  
  	public static final String ATTR_YES = "Y";
  	public static final String ATTR_NO = "N";
  
  
  
  
  	public static final String [] TAG_NAMES = {TAG_NAME, TAG_ACTNO, TAG_RECORD_NO};
  
  	public static final String ODE_EXTENSION = ".ode";
  	public static final String ODT_EXTENSION = ".odt";
  
  	// DataWarrior file
  	public static final String DWAR_EXTENSION = ".dwar";
  	public static final String DWARE_EXTENSION = ".dware";
  
  	public static final String REGEX_FILE_EXTENSION = "(.*\\"+ODE_EXTENSION+")|(.*\\"+DWAR_EXTENSION+")|(.*\\"+DWARE_EXTENSION+")";
  
  	// DataWarrior query file
  	public static final String DWAQ_EXTENSION = ".dwaq";
  
  	public static final String SDF_EXTENSION = ".sdf";
  
  	
  	// Tags for reaction encoding
  	// see ReactionEncoder
  	// with reaction code, coordinates, mapping, drawing objects
  	public static final String TAG_REACTION_CODE = "ReactionCode";
  	public static final String TAG_REACTION_COORD = "ReactionCoordinates";
  	public static final String TAG_REACTION_MAPPING = "ReactionMapping";
  	public static final String TAG_REACTION_DRAW_OBJ = "ReactionDrawingObjects";
  	
  	public static final String CHARSET_ENCODING = "UTF8"
  			;
  	public static final int MOLECULE_START_R_GROUPS = 129;
  
  
  	
  
  }
  