cdk2fps command-line options

The following comes from cdk2fps --help:

usage: cdk2fps [-h]
               [--type TYPE_STRING | --using FILENAME | --Daylight |
                  --GraphOnly | --MACCS | --EState | --Extended |
                  --Hybridization | --KlekotaRoth | --Pubchem |
                  --Substructure | --ShortestPath | --ECFP0 | --ECFP2 |
                  --ECFP4 | --ECFP6 |   --FCFP0 | --FCFP2 | --FCFP4 |
                  --FCFP6 | --AtomPairs2D]
               [--substruct] [--rdmaccs] [--rdmaccs/1] [--size INT]
               [--searchDepth INT] [--pathLimit INT] [--hashPseudoAtoms 0|1]
               [--perceiveStereochemistry 0|1] [--id-tag NAME] [--in FORMAT]
               [-o FILENAME] [--out FORMAT] [--errors {strict,report,ignore}]
               [--progress | --no-progress] [--help-formats] [-R NAME=VALUE]
               [--delimiter {tab,whitespace,to-eol,space}] [--has-header]
               [--version] [--license-check]
               [filenames ...]

Generate FPS or FPB fingerprints from a structure file using CDK via JPype

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

  -h, --help            show this help message and exit
  --type TYPE_STRING    Specify a chemfp type string
  --using FILENAME      Get the fingerprint type from the metadata of a
                        fingerprint file
  --Daylight            Make Daylight-like fingerprints using
                        cdk.fingerprinter.Fingerprinter (default)
  --GraphOnly           Make Daylight-like fingerprints (ignoring bond types)
                        using GraphOnlyFingerprinter
  --MACCS               Make 166-bit MACCS keys using MACCSFingerprinter
  --EState              Make 79-bit EState fingerprints using
  --Extended            Make Daylight-like fingerprints extended with ring
                        feature bits, using ExtendedFingerprinter
  --Hybridization       Make Daylight-like fingerprints based on SP2
                        hybridization instead of aromaticity, using
  --KlekotaRoth         Make 4860-bit Klekota-Roth fingerprint, using
  --Pubchem             Make 881-bit PubChem fingerprint, using
  --Substructure        Make 307-bit substructure fingerprint, using
  --ShortestPath        Make fingerprints based on the shortest path between
                        atoms, ring systems, and more, using
  --ECFP0               Make ECFP0-like circular fingerprints, using
  --ECFP2               Make ECFP2-like circular fingerprints, using
  --ECFP4               Make ECFP4-like circular fingerprints, using
  --ECFP6               Make ECFP6-like circular fingerprints, using
  --FCFP0               Make FCFP0-like circular feature fingerprints, using
  --FCFP2               Make FCFP2-like circular feature fingerprints, using
  --FCFP4               Make FCFP4-like circular feature fingerprints, using
  --FCFP6               Make FCFP6-like circular feature fingerprints, using
  --AtomPairs2D         Make 780-bit atom-pair fingerprints adapted from Yap
                        Chun Wei's PaDEL, using AtomPairs2DFingerprinter
  --size INT            fingerprint size (default=1024)
  --searchDepth INT     search depth (default=7)
  --pathLimit INT       path limit (default=42000)
  --hashPseudoAtoms 0|1
                        include pseudo-atoms in path enumeration (default=0)
  --perceiveStereochemistry 0|1
                        re-perceive stereochemistry from 2D/3D coordinates
  --id-tag NAME         tag name containing the record id (SD files only)
  --in FORMAT           input structure format (default autodetects from the
                        filename extension)
  -o FILENAME, --output FILENAME
                        save the fingerprints to FILENAME (default=stdout)
  --out FORMAT          output structure format (default guesses from output
                        filename, or is 'fps')
  --errors {strict,report,ignore}
                        how should structure parse errors be handled?
  --progress, --no-progress
                        Show a progress bar (default: show unless the output
                        is a terminal)
  --help-formats        list the available formats and reader arguments
  -R NAME=VALUE         specify a reader argument
  --delimiter {tab,whitespace,to-eol,space}
                        delimiter style for SMILES and InChI files. Alias for
                        '-R delimiter=VALUE'.
  --has-header          Skip the first line of a SMILES or InChI file Alias
                        for '-R has_header=1'
  --version             show program's version number and exit
  --license-check       Check the license and report results to stdout.

By default the CDK structure reader determines the file format
and compression type based on the filename extension. Unknown
filename extensions are treated as a uncompressed SMILES files.

If the data comes from stdin, or the guess based on extension name is
wrong, then use "--in FORMAT" option to change the default input format.
For examples:

   --in smi
   --in sdf.gz

Use `-R` to specify format-specific reader arguments.

Use `--help-formats` for a list of available formats and reader arguments.

Supported cdk2fps formats

The following comes from cdk2fps --help-formats:

These are the structure file formats that chemfp and read when using
the CDK toolkit.

By default, chemfp uses the filename extension to determine the format
type. If the filename ends with ".gz" or ".zst" then it is intepreted
as a gzip or Zstandard compressed file, and the second-to-last
extension is used to determine the format type. Unknown or unsupported
extensions are interpreted as a SMILES file.

Note: Zstandard support may depend the "zstandard" Python package
and/or the "zstd-jni" Java package. To install the Python package see . To get the Java jar file, see and place it in your CLASSPATH.

You may instead specify the file format by name (see below), which is
especially important when reading from stdin, which has no associated
filename extension.

The supported filename extensions are:

   File Type    Extension(s)
   ==========   =============
     SMILES     can, ism, isosmi, smi, usm
      SDF       mdl, sd, sdf
     InChI      inchi

The format can also be specified by name using the '--in' option:

   File Type    Format name (append .gz or .zst if compressed)
   ==========   ==============================================
     SMILES     smi, can, usm
      SDF       sdf
     InChI      inchi

The input format parsers can be configured with the "-R" option. For
example, the following reader arguments tell the SMILES readers that
the fields are whitespace delimited and the first line is a header.

   -R delimiter=whitespace -R has_header=true

The SMILES format parsers use two additional reader arguments:
   * 'delimiter' specifies the delimiter type. The default is 'to-eol'.
     The other values are 'tab', 'whitespace', 'space' and 'native'.
     Use "-R delimiter=native" to match RDKit's native delimiter
     style, which is 'whitespace'.
   * 'has_header', if false will skip the first line of the SMILES
     file (because it is a header line).
   * 'kekulise': The default of '1' will Kekulize the SMILES. Use '0'
     to skip this step.
   * 'implementation': The default 'cdk' uses CDK's IteratingSMILESReader()
     to parse the SMILES file. The 'chemfp' implementation uses chemfp's
     Python-based SMILES file parser and CDK's SmilesParser() to parse
     parse each SMILES string. The chemfp implementation is slower
     but may have better error-handling and/or reporting.

The SDF format parser supports five reader arguments:
   * 'mode' can be one of 'RELAXED' or 'STRICT'. The default relaxed
     mode supports some records with recoverable errors. The strict
     mode fails to parse those records.
   * 'ForceReadAs3DCoordinates', with the default of '0' interprets
     V2000 records where all z-coordinates == 0.0 as 2D records. The
     value '1' tells CDK to interpret all records as 3D.
   * 'AddStereoElements' with the default of '1' adds 0D stereochemistry
     to V2000 records. The value of '0' skips that step.
   * 'InterpretHydrogenIsotopes with the default of '1' interprets the
     atom symbols 'D' and 'T' as [2H] and [3H], respectively. Use
     '0' to disable this interpretation.
   * 'implementation': The default 'cdk' uses CDK's SDFReaderFactory()
     to parse the SD file. The 'chemfp' implementation uses chemfp's
     SD file parser to parse records, and CDK's MDLReader(),
     MDLV2000Reader(), or MDLV3000Reader() to parse each record. The
     chemfp implementation is about 50% slower than the cdk parser but
     may have better error-handling and/or reporting.

The InChI format parser supports one reader argument:
   * 'delimiter' works the same as it does for the SMILES formats