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)
options:
-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
EStateFingerprinter
--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
HybridizationFingerprinter
--KlekotaRoth Make 4860-bit Klekota-Roth fingerprint, using
KlekotaRothFingerprinter
--Pubchem Make 881-bit PubChem fingerprint, using
PubchemFingerprinter
--Substructure Make 307-bit substructure fingerprint, using
SubstructureFingerprinter
--ShortestPath Make fingerprints based on the shortest path between
atoms, ring systems, and more, using
ShortestPathFingerprinter
--ECFP0 Make ECFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP0)
--ECFP2 Make ECFP2-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP2)
--ECFP4 Make ECFP4-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP4)
--ECFP6 Make ECFP6-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP6)
--FCFP0 Make FCFP0-like circular feature fingerprints, using
CircularFingerprinter(CLASS_FCFP0)
--FCFP2 Make FCFP2-like circular feature fingerprints, using
CircularFingerprinter(CLASS_FCFP2)
--FCFP4 Make FCFP4-like circular feature fingerprints, using
CircularFingerprinter(CLASS_FCFP4)
--FCFP6 Make FCFP6-like circular feature fingerprints, using
CircularFingerprinter(CLASS_FCFP6)
--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
(default=0)
--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?
(default=ignore)
--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
https://pypi.org/project/zstandard/ . To get the Java jar file, see
https://github.com/luben/zstd-jni 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