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