NAME

       rdkit2fps - rdkit2fps

DESCRIPTION

       usage: rdkit2fps [-h] [--fpSize INT] [--RDK] [--minPath INT] [--maxPath INT]

              [--nBitsPerHash  INT]  [--useHs  0|1] [--morgan] [--radius INT] [--useFeatures 0|1]
              [--useChirality 0|1] [--useBondTypes 0|1] [--torsions] [--targetSize INT] [--pairs]
              [--minLength   INT]   [--maxLength   INT]  [--maccs166]  [--substruct]  [--rdmaccs]
              [--id-tag NAME]  [--in  FORMAT]  [-o  FILENAME]  [--errors  {strict,report,ignore}]
              [filenames [filenames ...]]

       Generate FPS fingerprints from a structure file using RDKit

   positional arguments:
       filenames
              input structure files (default is stdin)

   optional arguments:
       -h, --help
              show this help message and exit

       --fpSize INT
              number of bits in the fingerprint (applies to RDK, Morgan, topological torsion, and
              atom pair fingerprints (default=2048)

       --id-tag NAME
              tag name containing the record id (SD files only)

       --in FORMAT
              input structure format (default guesses from filename)

       -o FILENAME, --output FILENAME
              save the fingerprints to FILENAME (default=stdout)

       --errors {strict,report,ignore}
              how should structure parse errors be handled?  (default=strict)

   RDKit topological fingerprints:
       --RDK  generate RDK fingerprints (default)

       --minPath INT
              minimum number of bonds to include in the subgraph (default=1)

       --maxPath INT
              maximum number of bonds to include in the subgraph (default=7)

       --nBitsPerHash INT
              number of bits to set per path (default=4)

       --useHs 0|1
              include information about the number of hydrogens on each atom (default=1)

   RDKit Morgan fingerprints:
       --morgan
              generate Morgan fingerprints

       --radius INT
              radius for the Morgan algorithm (default=2)

       --useFeatures 0|1
              use chemical-feature invariants (default=0)

       --useChirality 0|1
              include chirality information (default=0)

       --useBondTypes 0|1
              include bond type information (default=1)

   RDKit Topological Torsion fingerprints:
       --torsions
              generate Topological Torsion fingerprints

       --targetSize INT
              number of bits in the fingerprint (default=4)

   RDKit Atom Pair fingerprints:
       --pairs
              generate Atom Pair fingerprints

       --minLength INT
              minimum bond count for a pair (default=1)

       --maxLength INT
              maximum bond count for a pair (default=30)

   166 bit MACCS substructure keys:
       --maccs166
              generate MACCS fingerprints

   881 bit substructure keys:
       --substruct
              generate ChemFP substructure fingerprints

   ChemFP version of the 166 bit RDKit/MACCS keys:
       --rdmaccs
              generate 166 bit RDKit/MACCS fingerprints

       This program guesses the input structure format based on the filename  extension.  If  the
       data  comes  from  stdin,  or the extension name us unknown, then use "--in" to change the
       default input format. The supported format extensions are:

       File Type
              Valid FORMATs (use gz if compressed)

       ---------      ------------------------------------

       SMILES
              smi, ism, can, smi.gz, ism.gz, can.gz

       SDF    sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz