JOE

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joelib
Class JOE

java.lang.Object
  joelib.JOE

public class JOE
extends java.lang.Object

Class for converting molecules and calculating descriptors.

 Usage:
 java -cp . joelib.JOE [options] <input file> [<output file>]

 Options:
 [-i<inputFormat>]       - Format of the input file
 [-o<outputFormat>]      - Format of the output file
 [-h]                    - Remove hydrogens from molecule
 [+h]                    - Add hydrogens to molecule
 [+p]                    - Add only polar hydrogens (+h implicit)
 [-e]                    - Converts only non-empty molecules
 [-d]                    - Remove all descriptors from the molecule
 [+d]                    - Add all available descriptors to the molecule
 [+v]                    - Switch verbosity ON
 [+snd]                  - Show all available native value descriptors
 [+sad]                  - Show all available atom property descriptors
 [+sall]                 - Show all available descriptors
 [+x<descriptor name>]   - Converts only molecules where <descriptor name> exists
 [-r<skip  desc. rule>]  - Skips molecules, if rule fits
 [+r<conv. desc. rule>]  - Converts only molecules where rule fits
 [+f<lineStructure>]     - Required if you use FLAT output format which other input format
 [+s<lineStructure>]     - Can be used for an alternate SMILES entry line structure
 [-m<SMARTS rule>]       - Skips molecules, if SMARTS rule fits
 [+m<SMARTS rule>]       - Converts only molecules where SMARTS rule fits
 [-um<SMARTS rule>]      - Skips molecules, if SMARTS rule fits
 [+um<SMARTS rule>]      - Converts only molecules where SMARTS rule fits
 [-?][--help]            - Shows this message

If no output file is defined, all molecules will be written to stdout.

Filter rules have the form:
<native value descriptor><relation><value>
where <relation> is <, <=, ==, >, >= or !=
Example:
"+rNumber_of_halogen_atoms==2"

SMARTS filter rules have the form:
<SMARTS pattern><relation><value>
where <relation> is <, <=, ==, >, >= or !=
Example:
"+umaNC=O==1"
Converts all molecules, where the molecule contains ONE NC=O group connected to an aromatic atom (aNC=O).

Constructor Summary

JOE()

Method Summary

static void main(java.lang.String[] args)
The main program for the TestSmarts class

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JOE

public JOE()

Method Detail

main

public static void main(java.lang.String[] args)

The main program for the TestSmarts class