Chapter 10. Example applications

Table of Contents
Convert
ConvertSkip
Comparison
Descriptor calculation
EuklidianComparison
Statistic
Point Group Symmetry

Convert

Example application for file conversion, descriptor calculation and process filters (here only for converting molecules).

Options

sh convert.sh [-? | --help] [-h] [+h] [+p] [-e] [-d] [+d] [+v] [+snd] [+sad] [+sall] [-salt] [-iinputFormat] [-ooutputFormat] [+xdescriptorName] [-rskipDescRule] [+rdescRule] [+slineStructure] inputFile [outputFile]

[-? | --help]

Shows the help screen including all available input/output formats and all native value descriptors.

[-h]

Removes all hydrogens from the molecule.

[-h]

Adds hydrogens to molecule.

[+p]

Adds only polar hydrogens to molecule.

[-e]

Converts only non-empty molecules.

[-d]

Removes all descriptors from molecule.

[+d]

Adds all available descriptors to molecule, which can be calculated by using JOELib.

[+v]

Switches verbosity mode ON.

[+sall]

Shows all available descriptors, which can be calculated by using JOELib.

[+snd]

Shows all available native value descriptors, which can be calculated by using JOELib.

[+sad]

Shows all available atom property descriptors, which can be calculated by using JOELib.

[-salt]

Strip salts and gets only largest contigous fragment.

[-iinputFormat]

Format of the input file.

[-ooutputFormat]

Format of the output file.

[+xdescriptorName]

Converts only molecules, where this descriptor exist. This command line parameter can occur multiple times.

[-rskipDescRule]

Skips all molecules, where this descriptor rule fits. This command line parameter can occur multiple times.

[+rdescRule]

Converts only molecules, where this descriptor rule fits. This command line parameter can occur multiple times.

[+slineStructure]

Can be used for an alternate SMILES entry line structure.

inputFile

The input file. The input format will be estimated by using the file extension.

[outputFile]

The output file. The output format will be estimated by using the file extension.

Examples

Example 10-1. Show help screen for Convert

java -cp joelib.jar joelib.test.Convert --help
shows the help screen

Example 10-2. Print molecules to standard output

java -cp joelib.jar joelib.test.Convert joelib/test/test.mol
Prints the molecule file to the screen.