chemfp.cdk_types module¶

This module should not be imported directly.

It contains internal implementation details of CDK fingerprint generation.

This module is included in the documentation because parts of this module are returned to the user, and are part of the public API.

class chemfp.cdk_types.CDKBaseFingerprintType(fingerprint_kwargs)¶

Bases: chemfp.types.ThreadsafeFingerprinterMixin, chemfp.types.FingerprintType

fingerprinter_can_fail = True¶: a CDK fingerprinter can raise an exception if the molecule isn’t correctly prepared

from_inchi(content: Union[str, bytes], *, delimiter: Optional[Literal[to_eol, space, tab, comma, whitespace, native, , ], None] = 'to-eol', errors: str = 'strict')¶

Generate a fingerprint from an InChI string and its id

This is equivalent to calling:

mol = fptype.toolkit.from_inchi(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:	delimiter (One of None, 'to_eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: "to-eol")) – The separator between the SMILES and the id errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:	a fingerprint byte string

from_inchistring(content: Union[str, bytes], *, delimiter: Optional[Literal[to_eol, space, tab, comma, whitespace, native, , ], None] = 'to-eol', errors: str = 'strict')¶

Generate a fingerprint from an InChI string

This is equivalent to calling:

mol = fptype.toolkit.from_inchistring(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:	delimiter (One of None, 'to_eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: "to-eol")) – The separator between the SMILES and the id errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:	a fingerprint byte string

from_molfile(content: Union[str, bytes], *, AddStereo0d: bool = True, AddStereoElements: bool = True, InterpretHydrogenIsotopes: bool = True, ForceReadAs3DCoordinates: bool = False, mode: Literal[RELAXED, STRICT] = 'RELAXED', implementation: Optional[Literal[cdk, chemfp], None] = 'cdk', errors: str = 'strict')¶

Generate a fingerprint from a molfile record

This is equivalent to calling:

mol = fptype.toolkit.from_molfile(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:

AddStereo0d (Boolean (default: True)) – if true, create stereo from parity value when no coordinates
AddStereoElements (Boolean (default: True)) – if true, detect and create IStereoElements
InterpretHydrogenIsotopes (Boolean (default: True)) – if true, interpret D and T as hydrogen isotopes
ForceReadAs3DCoordinates (Boolean (default: False)) – if true, always interpret coordinates as 3D
mode ('RELAXED' will attempt to recover, 'STRICT' will not) – strictness mode when parsing a record
implementation (either 'cdk' or 'chemfp') – use CDK or chemfp to identify records
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a fingerprint byte string

from_sdf(content: Union[str, bytes], *, AddStereo0d: bool = True, AddStereoElements: bool = True, InterpretHydrogenIsotopes: bool = True, ForceReadAs3DCoordinates: bool = False, mode: Literal[RELAXED, STRICT] = 'RELAXED', implementation: Optional[Literal[cdk, chemfp], None] = 'cdk', errors: str = 'strict')¶

Generate a fingerprint from an SDF record

This is equivalent to calling:

mol = fptype.toolkit.from_sdf(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:

AddStereo0d (Boolean (default: True)) – if true, create stereo from parity value when no coordinates
AddStereoElements (Boolean (default: True)) – if true, detect and create IStereoElements
InterpretHydrogenIsotopes (Boolean (default: True)) – if true, interpret D and T as hydrogen isotopes
ForceReadAs3DCoordinates (Boolean (default: False)) – if true, always interpret coordinates as 3D
mode ('RELAXED' will attempt to recover, 'STRICT' will not) – strictness mode when parsing a record
implementation (either 'cdk' or 'chemfp') – use CDK or chemfp to identify records
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a fingerprint byte string

from_smi(content: Union[str, bytes], *, has_header: bool = False, delimiter: Optional[Literal[to_eol, space, tab, comma, whitespace, native, , ], None] = 'to-eol', implementation: Optional[Literal[cdk, chemfp], None] = 'cdk', kekulise: bool = True, cxsmiles: bool = True, errors: str = 'strict')¶

Generate a fingerprint from a SMILES string and its id

This is equivalent to calling:

mol = fptype.toolkit.from_smi(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:

has_header (Boolean (default: False)) – If true, treat the first line of the SMILES file as a header
delimiter (One of None, 'to_eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: "to-eol")) – The separator between the SMILES and the id
implementation (either 'cdk' or 'chemfp') – use CDK or chemfp to identify records
kekulise (Boolean (default: True)) – if true, ensure a valid Kekule intepretation exists
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string (only works with ‘chemfp’ implementation)
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a fingerprint byte string

from_smiles(content: Union[str, bytes], *, kekulise: bool = True, cxsmiles: bool = True, errors: str = 'strict')¶

Generate a fingerprint from a SMILES string

This is equivalent to calling:

mol = fptype.toolkit.from_smistring(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:	kekulise (Boolean (default: True)) – if true, ensure a valid Kekule intepretation exists cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:	a fingerprint byte string

from_smistring(content: Union[str, bytes], *, kekulise: bool = True, cxsmiles: bool = True, errors: str = 'strict')¶

Generate a fingerprint from a SMILES string

This is equivalent to calling:

mol = fptype.toolkit.from_smistring(content, ..., errors=errors)
fp = fptype.from_mol(mol) if (mol is not None) else None

Parameters:	kekulise (Boolean (default: True)) – if true, ensure a valid Kekule intepretation exists cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:	a fingerprint byte string

module = <module 'chemfp.cdk_toolkit>'¶

software = ...¶: a description of the CDK and chemfp versions

class chemfp.cdk_types.CDKDaylightFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s Daylight-like fingerprint, version 2.0

The CDK-Daylight/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
searchDepth - maximum path length (default: 7)
pathLimit - maximum number of paths (default: 42000)
hashPseudoAtoms - include pseudo-atoms in the hash calculation (default: 0)

name = 'CDK-Daylight/2.0'¶

class chemfp.cdk_types.CDKGraphOnlyFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s GraphOnly fingerprint, version 2.0

The CDK-GraphOnly/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
searchDepth - maximum path length (default: 7)
pathLimit - maximum number of paths (default: 42000)
hashPseudoAtoms - include pseudo-atoms in the hash calculation (default: 0)

name = 'CDK-GraphOnly/2.0'¶

class chemfp.cdk_types.CDKMACCSFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s implementation of the 166 MACCS keys, version 2.0

The CDK-MACCS/2.0 fingerprints have no parameters.

name = 'CDK-MACCS/2.0'¶

num_bits = 166¶

class chemfp.cdk_types.CDKEStateFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s implementation of the EState fingerprint, version 2.0

The CDK-EState/2.0 fingerprints have no parameters.

name = 'CDK-EState/2.0'¶

num_bits = 79¶

class chemfp.cdk_types.CDKExtendedFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s Extended fingerprint, version 2.0

The CDK-Extended/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
searchDepth - maximum path length (default: 7)
pathLimit - maximum number of paths (default: 42000)
hashPseudoAtoms - include pseudo-atoms in the hash calculation (default: 0)

name = 'CDK-Extended/2.0'¶

class chemfp.cdk_types.CDKHybridizationFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s Hybridization fingerprint, version 2.0

The CDK-Hybridization/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
searchDepth - maximum path length (default: 7)
pathLimit - maximum number of paths (default: 42000)
hashPseudoAtoms - include pseudo-atoms in the hash calculation (default: 0)

name = 'CDK-Hybridization/2.0'¶

class chemfp.cdk_types.CDKKlekotaRothFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s implementation of the Klekota-Roth fingerprints

The CDK-KlekotaRoth/2.0 fingerprints have no parameters.

name = 'CDK-KlekotaRoth/2.0'¶

num_bits = 4860¶

class chemfp.cdk_types.CDKPubchemFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s implementation of the Klekota-Roth fingerprints

The CDK-Pubchem/2.0 fingerprints have no parameters.

name = 'CDK-Pubchem/2.0'¶

num_bits = 881¶

class chemfp.cdk_types.CDKSubstructureFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s Substructure fingerprints

The CDK-Substructure/2.0 fingerprints have no parameters.

name = 'CDK-Substructure/2.0'¶

num_bits = 307¶

class chemfp.cdk_types.CDKShortestPathFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s ShortestPath fingerprint, version 2.0

The CDK-ShortestPath/2.0 FingerprintType parameter is:

size - the number of bits in the fingerprint (default: 1024)

This is generated by CDK versions older than 2.7.

fingerprinter_can_fail = True¶

name = 'CDK-ShortestPath/2.0'¶

class chemfp.cdk_types.CDKShortestPathFingerprintType_v27(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s ShortestPath fingerprint, version 2.7

The CDK-ShortestPath/2.7 FingerprintType parameter is:

size - the number of bits in the fingerprint (default: 1024)

This version is new in CDK 2.7, where the internal PRNG was changed from a Mersenne Twister to XorShift, resulting in a different bit pattern.

fingerprinter_can_fail = True¶

name = 'CDK-ShortestPath/2.7'¶

class chemfp.cdk_types.CDKECFP0FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the ECFP0 fingerprint, version 2.0

The CDK-ECFP0/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-ECFP0/2.0'¶

class chemfp.cdk_types.CDKECFP2FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the ECFP2 fingerprint, version 2.0

The CDK-ECFP2/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-ECFP2/2.0'¶

class chemfp.cdk_types.CDKECFP4FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the ECFP4 fingerprint, version 2.0

The CDK-ECFP4/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-ECFP4/2.0'¶

class chemfp.cdk_types.CDKECFP6FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the ECFP6 fingerprint, version 2.0

The CDK-ECFP6/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-ECFP6/2.0'¶

class chemfp.cdk_types.CDKFCFP0FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the FCFP0 fingerprint, version 2.0

The CDK-FCFP0/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-FCFP0/2.0'¶

class chemfp.cdk_types.CDKFCFP2FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the FCFP2 fingerprint, version 2.0

The CDK-FCFP2/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-FCFP2/2.0'¶

class chemfp.cdk_types.CDKFCFP4FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the FCFP4 fingerprint, version 2.0

The CDK-FCFP4/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-FCFP4/2.0'¶

class chemfp.cdk_types.CDKFCFP6FingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.cdk_types.VariableSizeFingerprint

CDK’s implementation of the FCFP6 fingerprint, version 2.0

The CDK-FCFP6/2.0 FingerprintType parameters are:

size - the number of bits in the fingerprint (default: 1024)
perceiveStereochemistry - if True, re-perceive stereochemistry from 2D/3D coordinates

name = 'CDK-FCFP6/2.0'¶

class chemfp.cdk_types.CDKAtomPairs2DFingerprintType_v20(fingerprint_kwargs)¶

Bases: chemfp.types.NoFingerprintParametersMixin, chemfp.cdk_types.FixedSizeFingerprint

CDK’s implementation of the atom pairs fingerprint from Yap Chun Wei’s PaDEL.

The CDK-AtomPairs2D/2.0 FingerprintType takes no parameters.

name = 'CDK-AtomPairs2D/2.0'¶

num_bits = 780¶