Descriptor calculation

Example application for calculating descriptors: basic ones, atom property based transformations and user defined substructure counts.

Options

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.