Convert

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

Options

java -cp joelib.jar joelib.test.Convert [-? | --help] [-h] [+h] [+p] [-e] [-d] [+d] [+v] [+snd] [+sad] [+sall] [-iinputFormat] [-ooutputFormat] [+xdescriptorName] [-rskipDescRule] [+rdescRule] 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.

[-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.

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

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

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