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Chapter 10. Example applications

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.


Last changes: 08.12.2010, 16:50 CET (UTC/GMT +1 hour) wegner.
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