Docjar: joelib/JOE.java

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Source code: joelib/JOE.java

1   ///////////////////////////////////////////////////////////////////////////////
2   //  Filename: $RCSfile: JOE.java,v $
3   //  Purpose:  File converting.
4   //  Language: Java
5   //  Compiler: JDK 1.4
6   //  Authors:  Joerg K. Wegner
7   //  Version:  $Revision: 1.10 $
8   //            $Date: 2003/08/22 15:56:15 $
9   //            $Author: wegner $
10  //
11  //  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
12  //
13  //  This program is free software; you can redistribute it and/or modify
14  //  it under the terms of the GNU General Public License as published by
15  //  the Free Software Foundation version 2 of the License.
16  //
17  //  This program is distributed in the hope that it will be useful,
18  //  but WITHOUT ANY WARRANTY; without even the implied warranty of
19  //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20  //  GNU General Public License for more details.
21  ///////////////////////////////////////////////////////////////////////////////
22  package joelib;
23  
24  
25  /*==========================================================================*
26   * IMPORTS
27   *==========================================================================     */
28  import joelib.test.Convert;
29  
30  
31  /*==========================================================================*
32   * CLASS DECLARATION
33   *==========================================================================*/
34  
35  /**
36   * Class for converting molecules and calculating descriptors.
37   *
38   * <p>
39   * <blockquote><pre>
40   * Usage:
41   * java -cp . joelib.JOE [options] &lt;input file> [&lt;output file>]
42   *
43   * Options:
44   * [-i&lt;inputFormat>]       - Format of the input file
45   * [-o&lt;outputFormat>]      - Format of the output file
46   * [-h]                    - Remove hydrogens from molecule
47   * [+h]                    - Add hydrogens to molecule
48   * [+p]                    - Add only polar hydrogens (+h implicit)
49   * [-e]                    - Converts only non-empty molecules
50   * [-d]                    - Remove all descriptors from the molecule
51   * [+d]                    - Add all available descriptors to the molecule
52   * [+v]                    - Switch verbosity ON
53   * [+snd]                  - Show all available native value descriptors
54   * [+sad]                  - Show all available atom property descriptors
55   * [+sall]                 - Show all available descriptors
56   * [+x&lt;descriptor name>]   - Converts only molecules where &lt;descriptor name> exists
57   * [-r&lt;skip  desc. rule>]  - Skips molecules, if rule fits
58   * [+r&lt;conv. desc. rule>]  - Converts only molecules where rule fits
59   * [+f&lt;lineStructure>]     - Required if you use FLAT output format which other input format
60   * [+s&lt;lineStructure>]     - Can be used for an alternate SMILES entry line structure
61   * [-m&lt;SMARTS rule>]       - Skips molecules, if SMARTS rule fits
62   * [+m&lt;SMARTS rule>]       - Converts only molecules where SMARTS rule fits
63   * [-um&lt;SMARTS rule>]      - Skips molecules, if SMARTS rule fits
64   * [+um&lt;SMARTS rule>]      - Converts only molecules where SMARTS rule fits
65  * [-?][--help]            - Shows this message
66   *
67   *If no output file is defined, all molecules will be written to stdout.
68   *
69   *Filter rules have the form:
70   *&lt;native value descriptor>&lt;relation>&lt;value>
71   *where &lt;relation> is &lt;, &lt;=, ==, >, >= or !=
72   *Example:
73   *"+rNumber_of_halogen_atoms==2"
74   *
75   *SMARTS filter rules have the form:
76   *&lt;SMARTS pattern>&lt;relation>&lt;value>
77   *where &lt;relation> is &lt;, &lt;=, ==, >, >= or !=
78   *Example:
79   *"+umaNC=O==1"
80   *Converts all molecules, where the molecule contains ONE NC=O group connected to an aromatic atom (aNC=O).
81   * </pre></blockquote>
82   *
83   * @author     wegnerj
84   * @license GPL
85   * @cvsversion    $Revision: 1.10 $, $Date: 2003/08/22 15:56:15 $
86   * @see joelib.test.Convert
87   * @see joelib.process.filter.NativeValueFilter
88   * @cite smarts
89   */
90  public class JOE
91  {
92      //~ Methods ////////////////////////////////////////////////////////////////
93  
94      /*-------------------------------------------------------------------------*
95       * main
96       *-------------------------------------------------------------------------*/
97  
98      /**
99       *  The main program for the TestSmarts class
100      *
101      * @param  args  The command line arguments
102      */
103     public static void main(String[] args)
104     {
105         Convert convert = new Convert();
106 
107         int status = convert.parseCommandLine(args);
108 
109         if (status == Convert.CONTINUE)
110         {
111             convert.convert();
112         }
113         else if (status == Convert.STOP_USAGE)
114         {
115             convert.usage();
116             System.exit(1);
117         }
118         else if (status == Convert.STOP)
119         {
120             System.exit(0);
121         }
122     }
123 }
124 ///////////////////////////////////////////////////////////////////////////////
125 //  END OF FILE.
126 ///////////////////////////////////////////////////////////////////////////////