cdk2fps command-line options¶
The following comes from cdk2fps --help:
Usage: cdk2fps [OPTIONS] [FILENAMES]...
Generate fingerprints from a structure file using CDK.
If specified, process the filenames, otherwise read from stdin.
Fingerprint types:
--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 ECFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP2)
--ECFP4 Make ECFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP4)
--ECFP6 Make ECFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_ECFP6)
--FCFP0 Make FCFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_FCFP0)
--FCFP2 Make FCFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_FCFP2)
--FCFP4 Make FCFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_FCFP4)
--FCFP6 Make FCFP0-like circular fingerprints, using
CircularFingerprinter(CLASS_FCFP6)
--AtomPairs2D Make 780-bit atom-pair fingerprints adapted from Yap
Chun Wei's PaDEL, using AtomPairs2DFingerprinter
--substruct Generate ChemFP substructure fingerprints (you
likely want to use --Pubchem instead)
--rdmaccs, --rdmaccs/2 Generate chemfp's MACCS fingerprints, version 2.
--rdmaccs/1 Generate chemfp's MACCS fingerprints, version 1.
--type TYPE_STR Specify a chemfp type string
--using FILENAME Get the fingerprint type from the metadata of a
fingerprint file
Fingerprint options:
--size INT Fingerprint size (default=1024)
[ShortestPath, Hybridization, Daylight, ECFP,
Extended, FCFP, GraphOnly]
--searchDepth INT Search depth (default=7) [GraphOnly,
Daylight, Hybridization, Extended]
--pathLimit INT Path limit (default=42000) [GraphOnly,
Daylight, Hybridization, Extended]
--hashPseudoAtoms 0|1 Include pseudo-atoms in path enumeration
(default=0) [GraphOnly, Daylight,
Hybridization, Extended]
--perceiveStereochemistry 0|1 Re-perceive stereochemistry from 2D/3D
coordinates (default=0) [FCFP, ECFP]
Options:
--id-tag TAG Get the record it from the tag TAG instead
of the first line of the record.
--in FORMAT Input structure format (default guesses from
filename)
-o, --output FILENAME Save the fingerprints to FILENAME
(default=stdout)
--out FORMAT Output structure format (default guesses
from output filename, or is 'fps')
--include-metadata / --no-metadata
With --no-metadata, do not include the
header metadata for FPS output.
--no-date Do not include the 'date' metadata in the
output header
--date STR An ISO 8601 date (like
'2022-02-07T11:10:15') to use for the 'date'
metadata in the output header
--delimiter VALUE Delimiter style for SMILES and InChI files.
Forces '-R delimiter=VALUE'.
--has-header Skip the first line of a SMILES or InChI
file. Forces '-R has_header=1'.
-R NAME=VALUE Specify a reader argument
--cxsmiles / --no-cxsmiles Use --no-cxsmiles to disable the default
support for CXSMILES extensions. Forces '-R
cxsmiles=1' or '-R cxsmiles=0'.
--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
--version Show the version and exit.
--license-check Check the license and report results to
stdout.
--help Show this message and exit.
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 fromcdk2fps --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 on 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 five 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).
* 'cxsmiles' describes how to handle CXSMILES extensions. The
default (true) will have CDK process the extension. If false
any extension will be treated as part of the identifier.
* '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