JOELib Tutorial: A Java based cheminformatics/computational chemistry package | ||
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Example application for calculating descriptors: basic ones, atom property based transformations and user defined substructure counts.
sh calculateDescriptors.sh [+jcc] [-jcc] [+ap] [-ap] [+SSKey] [-SSKey] [+binarySMARTS] [-binarySMARTS] [+countSMARTS] [-countSMARTS] [+normalize] [-normalize] [-iinputFormat] [-ooutputFormat] [-tTRUE_VALUE] inputFile outputFile
[-iinputFormat]
Format of the input file.[-ooutputFormat]
Format of the output file.[-tTRUE_VALUE]
Defines TRUE VALUE descriptor (will NOT be normalized).[+jcc]
Calculate all available native descriptors in JCompChem (default)[-jcc]
Does not calculate all available native descriptors in JCompChem[+ap]
Calculate all available atom property descriptors in JCompChem (default)[-ap]
Does not calculate all available atom property descriptors in JCompChem[+SSKey]
Calculate SSkey fingerprint (default)[-SSKey]
Does not calculate SSkey fingerprint[+binarySMARTS]
Calculate binary SMARTS (default)[-binarySMARTS]
Does not calculate binary SMARTS[+countSMARTS]
Calculate counting SMARTS[-countSMARTS]
Does not calculate counting SMARTS (default)[+normalize]
Normalize descriptor values. SMARTS and fingerprints are ignored[-normalize]
Do not normalize the descriptor values (default)Warning: If you use binary AND counting SMARTS you should NOT use your own names, or only the binary SMARTS results will be stored. That's obvious, ONE name, ONE result.