chemfp.rdkit_toolkit module¶

The chemfp toolkit API wrapper for the RDKit toolkit.

This module is also available as chemfp.rdkit

chemfp.rdkit_toolkit.name¶: The string “rdkit”.

chemfp.rdkit_toolkit.software¶: The string used in output file metadata to describe this version of RDKit. For example, “RDKit/2023.03.1”.

chemfp.rdkit_toolkit.is_available¶

True if the RDKit toolkit is available, otherwise False.

This mostly used as chemfp.rdkit.is_available as this module cannot be imported if RDKit is not available.

chemfp.rdkit_toolkit.avalon¶

The available version of the ‘RDKit-Avalon’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitAvalonFingerprintType_v1 with the full type:

RDKit-Avalon/1 fpSize=512 isQuery=0 bitFlags=15761407

chemfp.rdkit_toolkit.maccs166¶

The available version of the ‘RDKit-MACCS166’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitMACCSFingerprintType_v2 with the full type:

RDKit-MACCS166/2

chemfp.rdkit_toolkit.morgan¶: An alias for chemfp.rdkit_toolkit.morgan3.

chemfp.rdkit_toolkit.morgan1¶

The available version of the ‘RDKit-Morgan radius=1’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with the full type:

RDKit-Morgan/2 fpSize=2048 radius=1 useFeatures=0

chemfp.rdkit_toolkit.morgan2¶

The available version of the ‘RDKit-Morgan radius=2’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with the full type:

RDKit-Morgan/2 fpSize=2048 radius=2 useFeatures=0

chemfp.rdkit_toolkit.morgan3¶

The available version of the ‘RDKit-Morgan radius=3’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with the full type:

RDKit-Morgan/2 fpSize=2048 radius=3 useFeatures=0

chemfp.rdkit_toolkit.morgan4¶

The available version of the ‘RDKit-Morgan radius=4’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with the full type:

RDKit-Morgan/2 fpSize=2048 radius=4 useFeatures=0

chemfp.rdkit_toolkit.morgan_v2¶

An alias for chemfp.rdkit_toolkit.morgan3_v2, which is an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with radius=3 and the full type:

RDKit-Morgan/2 fpSize=2048 radius=3 useFeatures=0

chemfp.rdkit_toolkit.morgan1_v2¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with radius=1 and the full type:

RDKit-Morgan/2 fpSize=2048 radius=1 useFeatures=0

chemfp.rdkit_toolkit.morgan2_v2¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with radius=2 and the full type:

RDKit-Morgan/2 fpSize=2048 radius=2 useFeatures=0

chemfp.rdkit_toolkit.morgan3_v2¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with radius=3 and the full type:

RDKit-Morgan/2 fpSize=2048 radius=3 useFeatures=0

chemfp.rdkit_toolkit.morgan4_v2¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v2 with radius=4 and the full type:

RDKit-Morgan/2 fpSize=2048 radius=4 useFeatures=0

chemfp.rdkit_toolkit.morgan_v1¶

An alias for chemfp.rdkit_toolkit.morgan2_v1, which is an instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v1 with radius=2 and the full type:

RDKit-Morgan/1 radius=2 fpSize=2048 useFeatures=0 useChirality=0 useBondTypes=1

chemfp.rdkit_toolkit.morgan1_v1¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v1 with radius=1 and the full type:

RDKit-Morgan/1 radius=1 fpSize=2048 useFeatures=0 useChirality=0 useBondTypes=1

chemfp.rdkit_toolkit.morgan2_v1¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v1 with radius=2 and the full type:

RDKit-Morgan/1 radius=2 fpSize=2048 useFeatures=0 useChirality=0 useBondTypes=1

chemfp.rdkit_toolkit.morgan3_v1¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v1 with radius=3 and the full type:

RDKit-Morgan/1 radius=3 fpSize=2048 useFeatures=0 useChirality=0 useBondTypes=1

chemfp.rdkit_toolkit.morgan4_v1¶

An instance of chemfp.rdkit_types.RDKitMorganFingerprintType_v1 with radius=4 and the full type:

RDKit-Morgan/1 radius=4 fpSize=2048 useFeatures=0 useChirality=0 useBondTypes=1

chemfp.rdkit_toolkit.atom_pair¶

The most recent available version of the ‘RDKit-AtomPair’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitAtomPairFingerprint_v3 with the full type:

RDKit-AtomPair/3 fpSize=2048 minDistance=1 maxDistance=30 countSimulation=1

chemfp.rdkit_toolkit.atom_pair_v3¶

An instance of chemfp.rdkit_types.RDKitAtomPairFingerprint_v3 with the full type:

RDKit-AtomPair/3 fpSize=2048 minDistance=1 maxDistance=30 countSimulation=1

chemfp.rdkit_toolkit.atom_pair_v2¶

An instance of chemfp.rdkit_types.RDKitAtomPairFingerprint_v3 with the full type:

RDKit-AtomPair/2 fpSize=2048 minLength=1 maxLength=30

chemfp.rdkit_toolkit.pattern¶

The available version of the ‘RDKit-Pattern’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitPatternFingerprint_v4 with the full type:

RDKit-Pattern/4 fpSize=2048

chemfp.rdkit_toolkit.rdk¶

The available version of the ‘RDKit-Fingerprint’ fingerprint type (either version 2 or version 3), for example, an instance of :class: chemfp.rdkit_types.RDKitFingerprintType_v3 with the full type:

RDKit-Fingerprint/3 fpSize=2048 minPath=1 maxPath=7

chemfp.rdkit_toolkit.rdk_v2¶

An instance of chemfp.rdkit_types.RDKitFingerprintType_v2 with full type:

RDKit-Fingerprint/2 minPath=1 maxPath=7 fpSize=2048 nBitsPerHash=2 useHs=1

chemfp.rdkit_toolkit.rdk_v3¶

An instance of chemfp.rdkit_types.RDKitFingerprintType_v3 with full type:

RDKit-Fingerprint/3 fpSize=2048 minPath=1 maxPath=7

chemfp.rdkit_toolkit.secfp¶

The available version of the ‘RDKit-SECFP’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitSECFPFingerprintType_v1 with the full type:

RDKit-SECFP/1 fpSize=2048 radius=3 rings=1 isomeric=0 kekulize=0 min_radius=1

chemfp.rdkit_toolkit.torsion¶

The most recent available version of the ‘RDKit-Torsion’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitTorsionFingerprintType_v4 with the full type:

RDKit-Torsion/4 fpSize=2048 torsionAtomCount=4 countSimulation=1

chemfp.rdkit_toolkit.torsion_v4¶

The available version of the ‘RDKit-Torsion’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitTorsionFingerprintType_v3 with the full type:

RDKit-Torsion/4 fpSize=2048 torsionAtomCount=4 countSimulation=1

chemfp.rdkit_toolkit.torsion_v3¶

The available version of the ‘RDKit-Torsion’ fingerprint type, for example, an instance of chemfp.rdkit_types.RDKitTorsionFingerprintType_v3 with the full type:

RDKit-Torsion/3 fpSize=2048 targetSize=4

chemfp.rdkit_toolkit.add_tag(mol, tag, value)¶

Add an SD tag value to the RDKit molecule

Parameters:

mol (an RDKit molecule) – the molecule
tag (string) – the SD tag name
value (string) – the text for the tag

Returns:

None

chemfp.rdkit_toolkit.copy_molecule(mol)¶

Return a new RDKit molecule which is a copy of the given molecule

Parameters:: mol (an RDKit molecule) – the molecule to copy
Returns:: a new RDKit Mol instance

chemfp.rdkit_toolkit.create_bytes(mol, format, id=None, writer_args=None, errors='strict', level=None)¶

Convert an RDKit molecule into a structure record in the given format as a byte string

If id is not None then use it instead of the molecule’s own title. Warning: this may briefly modify the molecule, so may not be thread-safe.

Parameters:

mol (an RDKit molecule) – the molecule to use for the output
format (a format name string, or Format object) – the output structure format
id (a string, or None to use the molecule's own id) – an alternate record id
writer_args (a dictionary) – writer arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
level (None, a positive integer, or one of the strings 'min', 'default', or 'max') – compression level to use for compressed formats

Returns:

a byte string

chemfp.rdkit_toolkit.create_fasta(mol: Any, *, id: str | None = None, errors: str = 'strict') → str | None¶

Generate a FASTA record from an RDKit molecule

This is equivalent to calling:

create_string(mol, "fasta", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_helm(mol: Any, *, id: str | None = None, errors: str = 'strict') → str | None¶

Generate a HELM string from an RDKit molecule

This is equivalent to calling:

create_string(mol, "helm", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_inchi(mol: Any, *, id: str | None = None, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict') → str | None¶

Generate an InChI string and its id from an RDKit molecule

This is equivalent to calling:

create_string(mol, "inchi", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_inchikey(mol: Any, *, id: str | None = None, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict') → str | None¶

Generate an InChIKey string and its id from an RDKit molecule

This is equivalent to calling:

create_string(mol, "inchikey", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_inchikeystring(mol: Any, *, id: str | None = None, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, errors: str = 'strict') → str | None¶

Generate an InChIKey string from an RDKit molecule

This is equivalent to calling:

create_string(mol, "inchikeystring", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_inchistring(mol: Any, *, id: str | None = None, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, errors: str = 'strict') → str | None¶

Generate an InChI string from an RDKit molecule

This is equivalent to calling:

create_string(mol, "inchistring", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_molfile(mol: Any, *, id: str | None = None, includeStereo: bool = False, kekulize: bool = True, v3k: bool = False, errors: str = 'strict') → str | None¶

Generate a molfile from an RDKit molecule

This is equivalent to calling:

create_string(mol, "molfile", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: False)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_pdb(mol: Any, *, id: str | None = None, flavor: int | str = 0, errors: str = 'strict') → str | None¶

Generate a PDB record from an RDKit molecule

This is equivalent to calling:

create_string(mol, "pdb", id=id, writer_args={...}, errors=errors)

Available bit flag flavors are:

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
flavor (An integer or string of '|'- or ','-separated terms) – Output flavor bit flags
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_rdbinmol(mol: Any, *, id: str | None = None, errors: str = 'strict') → str | None¶

Generate an RDKit binary molecule byte string from an RDKit molecule

This is equivalent to calling:

create_string(mol, "rdbinmol", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_sdf(mol: Any, *, id: str | None = None, includeStereo: bool = False, kekulize: bool = True, v3k: bool = False, errors: str = 'strict') → str | None¶

Generate an SDF record from an RDKit molecule

This is equivalent to calling:

create_string(mol, "sdf", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: False)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_sdf3k(mol: Any, *, id: str | None = None, includeStereo: bool = False, kekulize: bool = True, v3k: bool = True, errors: str = 'strict') → str | None¶

Generate an SDF record in V3000 format from an RDKit molecule

This is equivalent to calling:

create_string(mol, "sdf3k", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: True)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_sequence(mol: Any, *, id: str | None = None, errors: str = 'strict') → str | None¶

Generate an IUPAC sequence from an RDKit molecule

This is equivalent to calling:

create_string(mol, "sequence", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_smi(mol: Any, *, id: str | None = None, isomericSmiles: bool = True, kekuleSmiles: bool = False, canonical: bool = True, allBondsExplicit: bool = False, allHsExplicit: bool = False, cxsmiles: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict') → str | None¶

Generate a SMILES string and its id from an RDKit molecule

This is equivalent to calling:

create_string(mol, "smi", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
isomericSmiles (Boolean (default: True)) – If true, generate an isomeric SMILES
kekuleSmiles (Boolean (default: False)) – If true, generate Kekule SMILES
canonical (Boolean (default: True)) – If true, generate a canonical SMILES
allBondsExplicit (Boolean (default: False)) – If true, include bond symbols even for single and aromatic bond
allHsExplicit (Boolean (default: False)) – If true, include hydrogen counts for every atom
cxsmiles (Boolean (default: False)) – If true, generate CXSmiles
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_smiles(mol: Any, *, id: str | None = None, isomericSmiles: bool = True, kekuleSmiles: bool = False, canonical: bool = True, allBondsExplicit: bool = False, allHsExplicit: bool = False, cxsmiles: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict') → str | None¶

Generate a SMILES string and its id from an RDKit molecule

This is equivalent to calling:

create_string(mol, "smi", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
isomericSmiles (Boolean (default: True)) – If true, generate an isomeric SMILES
kekuleSmiles (Boolean (default: False)) – If true, generate Kekule SMILES
canonical (Boolean (default: True)) – If true, generate a canonical SMILES
allBondsExplicit (Boolean (default: False)) – If true, include bond symbols even for single and aromatic bond
allHsExplicit (Boolean (default: False)) – If true, include hydrogen counts for every atom
cxsmiles (Boolean (default: False)) – If true, generate CXSmiles
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_smistring(mol: Any, *, id: str | None = None, isomericSmiles: bool = True, kekuleSmiles: bool = False, canonical: bool = True, allBondsExplicit: bool = False, allHsExplicit: bool = False, cxsmiles: bool = False, errors: str = 'strict') → str | None¶

Generate a SMILES string from an RDKit molecule

This is equivalent to calling:

create_string(mol, "smistring", id=id, writer_args={...}, errors=errors)

Parameters:

mol (an RDKit molecule) – a molecule object
id (None or a string (default: None)) – an alternate identifier for the output record, if relevant
isomericSmiles (Boolean (default: True)) – If true, generate an isomeric SMILES
kekuleSmiles (Boolean (default: False)) – If true, generate Kekule SMILES
canonical (Boolean (default: True)) – If true, generate a canonical SMILES
allBondsExplicit (Boolean (default: False)) – If true, include bond symbols even for single and aromatic bond
allHsExplicit (Boolean (default: False)) – If true, include hydrogen counts for every atom
cxsmiles (Boolean (default: False)) – If true, generate CXSmiles
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a string, or None if errors are ignored

chemfp.rdkit_toolkit.create_string(mol, format, id=None, writer_args=None, errors='strict')¶

Convert an RDKit molecule into a structure record in the given format as a Unicode string

If id is not None then use it instead of the molecule’s own title. Warning: this may briefly modify the molecule, so may not be thread-safe.

Parameters:

mol (an RDKit molecule) – the molecule to use for the output
format (a format name string, or Format object) – the output structure format
id (a string, or None to use the molecule's own id) – an alternate record id
writer_args (a dictionary) – writer arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors

Returns:

a Unicode string

chemfp.rdkit_toolkit.get_format(format)¶

Get the named format, or raise a ValueError

This will raise a ValueError if RDKit does not implement the format format_name or that format is not available.

Parameters:: format_name (a string) – the format name
Returns:: a list of chemfp.base_toolkit.Format objects

chemfp.rdkit_toolkit.get_formats(include_unavailable=False)¶

Get the list of structure formats that RDKit supports

If include_unavailable is True then also include RDKit formats which aren’t available to this specific version of RDKit, such as the InChI formats if your RDKit installation wasn’t compiled with InChI support.

Parameters:: include_unavailable (True or False) – include unavailable formats?
Returns:: a list of Format objects

chemfp.rdkit_toolkit.get_id(mol)¶

Get the molecule’s id from RDKit’s _Name property

Parameters:: mol (an RDKit molecule) – the molecule
Returns:: a string

chemfp.rdkit_toolkit.get_input_format(format)¶

Get the named input format, or raise a ValueError

This will raise a ValueError if RDKit does not implement the format format_name or that format is not an input format.

Parameters:: format_name (a string) – the format name
Returns:: a list of chemfp.base_toolkit.Format objects

chemfp.rdkit_toolkit.get_input_format_from_source(source=None, format=None)¶

Get the most appropriate format given the available source and format information

If format is a chemfp.base_toolkit.Format then return it. If it’s a Format-like object with “name” and “compression” attributes use it to make a real Format object with the same attributes. If it’s a string then use it to create a Format object.

If format is None, use the source to auto-detect the format. If auto-detection is not possible, assume it’s an uncompressed SMILES file.

Parameters:

source (a filename (as a string), a file object, or None to read from stdin) – the structure data source.
format (a Format(-like) object, string, or None) – format information, if known.

Returns:

a chemfp.base_toolkit.Format object

chemfp.rdkit_toolkit.get_input_formats()¶

Get the list of supported RDKit input formats

Returns:: a list of chemfp.base_toolkit.Format objects

chemfp.rdkit_toolkit.get_output_format(format)¶

Get the named format, or raise a ValueError

This will raise a ValueError if RDKit does not implement the format format_name or that format is not an output format.

Parameters:: format_name (a string) – the format name
Returns:: a list of chemfp.base_toolkit.Format objects

chemfp.rdkit_toolkit.get_output_format_from_destination(destination=None, format=None)¶

Get the most appropriate format given the available destination and format information

If format is a chemfp.base_toolkit.Format then return it. If it’s a Format-like object with “name” and “compression” attributes use it to make a real Format object with the same attributes. If it’s a string then use it to create a Format object.

If format is None, use the destination to auto-detect the format. If auto-detection is not possible, assume it’s an uncompressed SMILES file.

Parameters:

destination (a filename (as a string), a file object, or None to read from stdin) – The structure data source.
format (a Format(-like) object, string, or None) – format information, if known.

Returns:

a chemfp.base_toolkit.Format object

chemfp.rdkit_toolkit.get_output_formats()¶

Get the list of supported RDKit output formats

Returns:: a list of chemfp.base_toolkit.Format objects

chemfp.rdkit_toolkit.get_tag(mol, tag)¶

Get the named SD tag value, or None if it doesn’t exist

Parameters:

mol (an RDKit molecule) – the molecule
tag (string) – the SD tag name

Returns:

a string, or None

chemfp.rdkit_toolkit.get_tag_pairs(mol)¶

Get a list of all SD tag (name, value) pairs for the molecule

Parameters:: mol (an RDKit molecule) – the molecule
Returns:: a list of (string name, string value) pairs

chemfp.rdkit_toolkit.is_licensed()¶

Return True - RDKit is always licensed

Returns:: True

chemfp.rdkit_toolkit.make_id_and_molecule_parser(format, id_tag=None, reader_args=None, errors='strict')¶

Create a specialized function which takes a record and returns an (id, RDKit molecule) pair

The returned function is optimized for reading many records from individual strings because it only does parameter validation once. However, I haven’t really noticed much of a performance difference between this and chemfp.rdkit_toolkit.parse_id_and_molecule() so you can probably so I suggest you use that function directly instead of making a specialized function. (Let me know if making a specialized function is useful.)

See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters.

Parameters:

format (a format name string, or Format object) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors

Returns:

a function of the form parser(record string) -> (id, RDKit molecule)

chemfp.rdkit_toolkit.open_fasta_writer(destination: None | str | BinaryIO, *, errors: str = 'strict')¶

Open a FASTA file to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "fasta", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_fasta_writer_to_string(*, errors: str = 'strict')¶

Open a FASTA file to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("fasta", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:: errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:: a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_inchi_writer(destination: None | str | BinaryIO, *, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict')¶

Open an InChI file (with InChI and optional id) to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "inchi", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_inchi_writer_to_string(*, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict')¶

Open an InChI file (with InChI and optional id) to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("inchi", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:

options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_inchikey_writer(destination: None | str | BinaryIO, *, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict')¶

Open an InChIKey file (with InChIKey and optional id) to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "inchikey", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_inchikey_writer_to_string(*, options: str = '', logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, include_id: bool = True, errors: str = 'strict')¶

Open an InChIKey file (with InChIKey and optional id) to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("inchikey", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:

options (a string (default: "")) – an configuration string to pass to the InChI API
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
include_id (Boolean (default: True)) – if true, include the molecule id in the output
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_molecule_writer(destination=None, format=None, writer_args=None, errors='strict', location=None, encoding='utf8', encoding_errors='strict', level=None)¶

Return a MoleculeWriter which can write RDKit molecules to a destination.

A chemfp.base_toolkit.MoleculeWriter has the methods write_molecule, write_molecules, and write_ids_and_molecules, which are ways to write an RDKit molecule, an RDKit molecule iterator, or an (id, RDKit molecule) pair iterator to a file.

Molecules are written to destination. The output format can be a string like “sdf.gz” or “smi”, a chemfp.base_toolkit.Format, or Format-like object with “name” and “compression” attributes, or None to auto-detect based on the destination. If auto-detection is not possible, the output will be written as uncompressed SMILES.

The writer_args dictionary parameters depend on the format. These include:

SMILES
- delimiter - one of “tab”, “space”, “to-eol”, the space or tab characters, or None
- isomericSmiles - True to generate isomeric SMILES
- kekuleSmiles - True to generate SMILES in Kekule form
- canonical - True to generate a canonical SMILES
- allBondsExplicit - True to write explict ‘-’ and ‘:’ bonds, even if they can be inferred; default is False
- allHsExplicit - True to write explicit hydrogen counts; default is False
- cxsmiles - True to include CXSMILES annotations; default is False

InChI and InChIKey

SDF

The errors parameter specifies how to handle errors. “strict” raises an exception, “report” sends a message to stderr and goes to the next record, and “ignore” goes to the next record.

The location parameter takes a chemfp.io.Location instance. If None then a default Location will be created.

Parameters:

destination (a filename, file object, or None to write to stdout) – the structure destination
format (a format name string, or Format(-like) object, or None to auto-detect) – the output structure format
writer_args (a dictionary) – writer parameters passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track writer state information
level (None, a positive integer, or one of the strings 'min', 'default', or 'max') – compression level to use for compressed formats

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_molecule_writer_to_bytes(format, writer_args=None, errors='strict', location=None, level=None)¶

Return a MoleculeStringWriter which can write molecule records in the given format to a text string.

See chemfp.rdkit_toolkit.open_molecule_writer() for full parameter details.

Use the writer’s chemfp.base_toolkit.MoleculeStringWriter.getvalue() to get the output as a byte string.

Parameters:

format (a format name string, or Format(-like) object, or None to auto-detect) – the output structure format
writer_args (a dictionary) – writer arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track writer state information
level (None, a positive integer, or one of the strings 'min', 'default', or 'max') – compression level to use for compressed formats

Returns:

a chemfp.base_toolkit.MoleculeStringWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_molecule_writer_to_string(format, writer_args=None, errors='strict', location=None)¶

Return a MoleculeStringWriter which can write molecule records in the given format to a string.

See chemfp.rdkit_toolkit.open_molecule_writer() for full parameter details.

Use the writer’s chemfp.base_toolkit.MoleculeStringWriter.getvalue() to get the output as a Unicode string.

Parameters:

format (a format name string, or Format(-like) object, or None to auto-detect) – the output structure format
writer_args (a dictionary) – writer arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track writer state information

Returns:

a chemfp.base_toolkit.MoleculeStringWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_pdb_writer(destination: None | str | BinaryIO, *, flavor: int | str = 0, errors: str = 'strict')¶

Open a PDB file to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "pdb", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Available bit flag flavors are:

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
flavor (An integer or string of '|'- or ','-separated terms) – Output flavor bit flags
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_pdb_writer_to_string(*, flavor: int | str = 0, errors: str = 'strict')¶

Open a PDB file to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("pdb", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Available bit flag flavors are:

Parameters:

flavor (An integer or string of '|'- or ','-separated terms) – Output flavor bit flags
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_sdf3k_writer(destination: None | str | BinaryIO, *, includeStereo: bool = False, kekulize: bool = True, v3k: bool = True, errors: str = 'strict')¶

Open an SDF file in V3000 format to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "sdf3k", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: True)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_sdf3k_writer_to_string(*, includeStereo: bool = False, kekulize: bool = True, v3k: bool = True, errors: str = 'strict')¶

Open an SDF file in V3000 format to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("sdf3k", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:

includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: True)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_sdf_writer(destination: None | str | BinaryIO, *, includeStereo: bool = False, kekulize: bool = True, v3k: bool = False, errors: str = 'strict')¶

Open an SDF file to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "sdf", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: False)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_sdf_writer_to_string(*, includeStereo: bool = False, kekulize: bool = True, v3k: bool = False, errors: str = 'strict')¶

Open an SDF file to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("sdf", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:

includeStereo (Boolean (default: False)) – if true, include stereochemistry information in the record
kekulize (Boolean (default: True)) – if true, Kekulize the molecule before creating the record
v3k (Boolean (default: False)) – if true, always write in V3000 format
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_smi_writer(destination: None | str | BinaryIO, *, isomericSmiles: bool = True, kekuleSmiles: bool = False, canonical: bool = True, allBondsExplicit: bool = False, allHsExplicit: bool = False, cxsmiles: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Open a SMILES file to write RDKit molecules

This is mostly equivalent to calling:

open_molecule_writer(destination, "smi", writer_args={...}, errors=errors)

along with compression based on the destination filename’s extension.

Parameters:

destination (None, a filename string, or a file-like object) – where to write the molecules
isomericSmiles (Boolean (default: True)) – If true, generate an isomeric SMILES
kekuleSmiles (Boolean (default: False)) – If true, generate Kekule SMILES
canonical (Boolean (default: True)) – If true, generate a canonical SMILES
allBondsExplicit (Boolean (default: False)) – If true, include bond symbols even for single and aromatic bond
allHsExplicit (Boolean (default: False)) – If true, include hydrogen counts for every atom
cxsmiles (Boolean (default: False)) – If true, generate CXSmiles
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.open_smi_writer_to_string(*, isomericSmiles: bool = True, kekuleSmiles: bool = False, canonical: bool = True, allBondsExplicit: bool = False, allHsExplicit: bool = False, cxsmiles: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Open a SMILES file to write RDKit molecules to an in-memory string

This is equivalent to calling:

open_molecule_writer_to_string("smi", writer_args={...}, errors=errors)

Use write_molecules_to_string() to write compressed output.

Parameters:

isomericSmiles (Boolean (default: True)) – If true, generate an isomeric SMILES
kekuleSmiles (Boolean (default: False)) – If true, generate Kekule SMILES
canonical (Boolean (default: True)) – If true, generate a canonical SMILES
allBondsExplicit (Boolean (default: False)) – If true, include bond symbols even for single and aromatic bond
allHsExplicit (Boolean (default: False)) – If true, include hydrogen counts for every atom
cxsmiles (Boolean (default: False)) – If true, generate CXSmiles
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeWriter expecting RDKit molecules

chemfp.rdkit_toolkit.parse_fasta(content: str | bytes, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Parse a FASTA record using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "fasta", reader_args={...}, errors=errors)

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_helm(content: str | bytes, *, sanitize: bool = True, errors: str = 'strict')¶

Parse a HELM string using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "helm", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_id_and_molecule(content, format, id_tag=None, reader_args=None, errors='strict')¶

Parse the first structure record from content and return the (id, RDKit molecule) pair.

content is a string containing a single structure record in format format. (Additional records are ignored). See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters.

See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters. See chemfp.rdkit_toolkit.parse_molecule() if just want the RDKit molecule and not the the (id, RDKit molecule) pair.

Parameters:

content (a string) – the string containing a structure record
format (a format name string, or Format object) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors

Returns:

an (id, RDKit molecule) pair

chemfp.rdkit_toolkit.parse_inchi(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Parse an InChI string and its id using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "inchi", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_inchistring(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, errors: str = 'strict')¶

Parse an InChI string using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "inchistring", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_molecule(content, format, id_tag=None, reader_args=None, errors='strict')¶

Parse the first structure record from the content string and return an RDKit molecule.

content is a string containing a single structure record in format format. (Additional records are ignored). See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters. See chemfp.rdkit_toolkit.parse_id_and_molecule() if you want the (id, RDKit molecule) pair instead of just the molecule.

Parameters:

content (a string) – the string containing a structure record
format (a format name string, or Format object) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors

Returns:

an RDKit molecule

chemfp.rdkit_toolkit.parse_molfile(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, errors: str = 'strict')¶

Parse a molfile using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "molfile", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_pdb(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, flavor: Literal[0] = 0, proximityBonding: bool = True, errors: str = 'strict')¶

Parse a PDB record using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "pdb", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
flavor (0) – The value 0 (may change in the future)
proximityBonding (Boolean (default: True)) – If true, connect atoms based on a proximity search
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_rdbinmol(content: str | bytes, *, errors: str = 'strict')¶

Parse an RDKit binary molecule byte string using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "rdbinmol", reader_args={...}, errors=errors)

Parameters:: errors (one of "strict", "ignore", or "log") – specify how to handle errors
Returns:: an RDKit molecule object

chemfp.rdkit_toolkit.parse_sdf(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, includeTags: bool = True, errors: str = 'strict')¶

Parse an SDF record using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "sdf", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
includeTags (Boolean (default: True)) – if true, extract the struture data tag fields
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_sequence(content: str | bytes, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Parse an IUPAC sequence using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "sequence", reader_args={...}, errors=errors)

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_smi(content: str | bytes, *, sanitize: bool = True, cxsmiles: bool = True, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Parse a SMILES string and its id using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "smi", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_smiles(content: str | bytes, *, sanitize: bool = True, cxsmiles: bool = True, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Parse a SMILES string and its id using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "smi", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

an RDKit molecule object

chemfp.rdkit_toolkit.parse_smistring(content: str | bytes, *, sanitize: bool = True, cxsmiles: bool = True, errors: str = 'strict')¶

Parse a SMILES string using the RDKit toolkit

This is equivalent to calling:

parse_molecule(content, "smistring", reader_args={...}, errors=errors)

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
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:

an RDKit molecule object

chemfp.rdkit_toolkit.read_csv_ids_and_molecules(source, *, id_column=1, mol_column=2, dialect=None, has_header=True, compression='auto', format='smi', id_tag=None, reader_args=None, errors='report', csv_errors='strict', location=None, encoding='utf8', encoding_errors='strict')¶

Read ids and molecules from column(s) of a CSV file using RDKit.

Read from source, which may be a filename, a file-like object, or None (the default) to read from stdin.

Use id_column and mol_column to specify the columns containing the record identifier and molecule record. By default the identifiers come from column 1 (the first column) and the molecules from column 2 (the second column). Columns can be specified by integer position (starting with 1), or by a string matching the title from the header line. If id_column is None then the molecule id will come from parsing the molecule record.

Use dialect to specify the type of CSV file. The default of None infers the dialect from the filename extension; *.csv for comma-separated, and *.tsv for tab-separated. The dialect can be specified directly as “csv” or “tsv”, as a registered Python csv dialect at https://docs.python.org/3/library/csv.html (though “excel” is the same as “csv” and “excel-tab” is the same as “tsv”), or as a csv.Dialect or a .class:CSVDialect instance.

If has_header is True then the first line/record contains column titles, and if False then there are no column titles.

Use compression to specify how the file compression format. The default “auto” uses the filename extension. Other options are “gz” and “zst”, or the empty string “” to mean no compresssion.

Use format to specify the structure format for how to parse the molecule column. The default of ‘smi’ will parse it as a SMILES string and, if id_column=None, will also parse any identifier.

The id_tag and reader_args arguments contain additional format configuration parameters.

The errors and csv_errors describe how to handle failures in molecule parsing and CSV parsing, respectively. The default is to report molecule parse failures to stderr, and to stop parsing if a CSV row does not contain enough columns.

The location parameter takes a chemfp.io.Location instance. If None then a default Location will be created.

The encoding and encoding_errors are strings describing the input file character encoding, and how to handle decoding errors. See https://docs.python.org/3/library/codecs.html#error-handlers and https://docs.python.org/3/library/codecs.html#error-handlers for details.

Parameters:

source (a filename, file object, or None to read from stdin) – the CSV source
id_column (integer position (starting from 1), string, or None) – the column position or column title containing the identifier
mol_column (integer position (starting from 1), string) – the column position or column title containing the structure record
dialect (None, a string name, or a Dialect instance) – the CSV dialect
has_header (bool) – True if the first record contains titles, False of it does not
compression (string or None) – file compression format
format (a format name string, or Format object) – the molecule structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle molecule parse errors
csv_errors (one of "strict", "report", or "ignore") – specify how to handle CSV errors
location (a chemfp.io.Location object, or None) – object used to track parser state information
encoding (string) – the name of the file’s character encoding
encoding_errors (string) – the method used handle decoding errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating (id, RDKit molecule) pairs

chemfp.rdkit_toolkit.read_fasta_ids_and_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Read ids and molecules from a FASTA file using the RDKit toolkit

This is mostly equivalent to calling:

read_ids_and_molecules(source, "fasta", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_fasta_ids_and_molecules_from_string(content: str | bytes, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Read ids and molecules from a string containing a FASTA file using the RDKit toolkit

This is equivalent to calling:

read_ids_and_molecules_from_string(content, "fasta", reader_args={...}, errors=errors)

Use read_ids_and_molecules_from_string() if the content is compressed.

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_fasta_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Read molecules from a FASTA file using the RDKit toolkit

This is mostly equivalent to calling:

read_molecules(source, "fasta", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_fasta_molecules_from_string(content: str | bytes, *, sanitize: bool = True, flavor: Literal[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] = 0, errors: str = 'strict')¶

Read molecules from a string containing a FASTA file using the RDKit toolkit

This is equivalent to calling:

read_molecules_from_string(content, "fasta", reader_args={...}, errors=errors)

Use read_molecules_from_string() if the content is compressed.

Possible flavor values are:

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
flavor (integer from 0-9, inclusive (default: 0)) – The sequence type (amino acid, RNA, or DNA), and how to handle caps
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_ids_and_molecules(source=None, format=None, id_tag=None, reader_args=None, errors='strict', location=None, encoding='utf8', encoding_errors='strict')¶

Return an iterator that reads (id, RDKit molecule) pairs from a structure file

See chemfp.rdkit_toolkit.read_molecules() for full parameter details. The major difference is that this returns an iterator of (id, RDKit molecule) pairs instead of just the molecules.

Parameters:

source (a filename, file object, or None to read from stdin) – the structure source
format (a format name string, or Format object, or None to auto-detect) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track parser state information

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating (id, RDKit molecule) pairs

chemfp.rdkit_toolkit.read_ids_and_molecules_from_string(content, format, id_tag=None, reader_args=None, errors='strict', location=None)¶

Return an iterator that reads (id, RDKit molecule) pairs from a string containing structure records

content is a string containing 0 or more records in the format format. See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters. See chemfp.rdkit_toolkit.read_molecules_from_string() if you just want to read the RDKit molecules instead of (id, molecule) pairs.

Parameters:

content (a string) – the string containing structure records
format (a format name string, or Format object) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track parser state information

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating (id, RDKit molecule) pairs

chemfp.rdkit_toolkit.read_inchi_ids_and_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read ids and molecules from an InChI file (with InChI and optional id) using the RDKit toolkit

This is mostly equivalent to calling:

read_ids_and_molecules(source, "inchi", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_inchi_ids_and_molecules_from_string(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read ids and molecules from a string containing an InChI file (with InChI and optional id) using the RDKit toolkit

This is equivalent to calling:

read_ids_and_molecules_from_string(content, "inchi", reader_args={...}, errors=errors)

Use read_ids_and_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_inchi_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read molecules from an InChI file (with InChI and optional id) using the RDKit toolkit

This is mostly equivalent to calling:

read_molecules(source, "inchi", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_inchi_molecules_from_string(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, logLevel: int | None = None, treatWarningAsError: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read molecules from a string containing an InChI file (with InChI and optional id) using the RDKit toolkit

This is equivalent to calling:

read_molecules_from_string(content, "inchi", reader_args={...}, errors=errors)

Use read_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
logLevel (an integer, or None to disable logging completely (default: None)) – the log level for the InChI API
treatWarningAsError (Boolean (default: False)) – treat any InChI warnings as an error
delimiter (One of None, 'to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', or the space or tab characters (default: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_molecules(source=None, format=None, id_tag=None, reader_args=None, errors='strict', location=None, encoding='utf8', encoding_errors='strict')¶

Return an iterator that reads RDKit molecules from a structure file

Iterate through the format structure records in source. If format is None then auto-detect the format based on the source. For SD files, use id_tag to get the record id from the given SD tag instead of the title line. (read_molecules() will ignore the id_tag. It exists to make it easier to switch between reader functions.)

Note: the reader returns a new RDKit molecule each time.

The reader_args dictionary parameters depend on the format. These include:

SMILES
- delimiter - one of “tab”, “space”, “to-eol”, the space or tab characters, or None
- has_header - True or False
- sanitize - True or default sanitizes; False for unsanitized processing
InChI
- delimiter - one of “tab”, “space”, “to-eol”, the space or tab characters, or None
- sanitize - True or default sanitizes; False for unsanitized processing
- removeHs - True or default removes explicit hydrogens; False leaves them in the structure
- logLevel - an integer log level
- treatWarningAsError - True raises an exception on error; False or default keeps processing
SDF
- sanitize - True or default sanitizes; False for unsanitized processing
- removeHs - True or default removes explicit hydrogens; False leaves them in the structure
- strictParsing - True or default for strict parsing; False for lenient parsing

The errors parameter specifies how to handle errors. “strict” raises an exception, “report” sends a message to stderr and goes to the next record, and “ignore” goes to the next record.

The location parameter takes a chemfp.io.Location instance. If None then a default Location will be created.

See chemfp.rdkit_toolkit.read_ids_and_molecules() if you want (id, molecule) pairs instead of just the molecules.

Parameters:

source (a filename, file object, or None to read from stdin) – the structure source
format (a format name string, or Format object, or None to auto-detect) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader parameters passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track parser state information

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_molecules_from_string(content, format, id_tag=None, reader_args=None, errors='strict', location=None)¶

Return an iterator that reads RDKit molecules from a string containing structure records

content is a string containing 0 or more records in the format format. See chemfp.rdkit_toolkit.read_molecules() for details about the other parameters. See chemfp.rdkit_toolkit.read_ids_and_molecules_from_string() if you want to read (id, RDKit) pairs instead of just molecules.

Parameters:

content (a string) – the string containing structure records
format (a format name string, or Format object) – the input structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary) – reader arguments passed to the underlying toolkit
errors (one of "strict", "report", or "ignore") – specify how to handle errors
location (a chemfp.io.Location object, or None) – object used to track parser state information

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_pdb_ids_and_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, removeHs: bool = True, flavor: Literal[0] = 0, proximityBonding: bool = True, errors: str = 'strict')¶

Read ids and molecules from a PDB file using the RDKit toolkit

This is mostly equivalent to calling:

read_ids_and_molecules(source, "pdb", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
flavor (0) – The value 0 (may change in the future)
proximityBonding (Boolean (default: True)) – If true, connect atoms based on a proximity search
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_pdb_ids_and_molecules_from_string(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, flavor: Literal[0] = 0, proximityBonding: bool = True, errors: str = 'strict')¶

Read ids and molecules from a string containing a PDB file using the RDKit toolkit

This is equivalent to calling:

read_ids_and_molecules_from_string(content, "pdb", reader_args={...}, errors=errors)

Use read_ids_and_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
flavor (0) – The value 0 (may change in the future)
proximityBonding (Boolean (default: True)) – If true, connect atoms based on a proximity search
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_pdb_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, removeHs: bool = True, flavor: Literal[0] = 0, proximityBonding: bool = True, errors: str = 'strict')¶

Read molecules from a PDB file using the RDKit toolkit

This is mostly equivalent to calling:

read_molecules(source, "pdb", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
flavor (0) – The value 0 (may change in the future)
proximityBonding (Boolean (default: True)) – If true, connect atoms based on a proximity search
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_pdb_molecules_from_string(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, flavor: Literal[0] = 0, proximityBonding: bool = True, errors: str = 'strict')¶

Read molecules from a string containing a PDB file using the RDKit toolkit

This is equivalent to calling:

read_molecules_from_string(content, "pdb", reader_args={...}, errors=errors)

Use read_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
flavor (0) – The value 0 (may change in the future)
proximityBonding (Boolean (default: True)) – If true, connect atoms based on a proximity search
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_sdf_ids_and_molecules(source: None | str | BinaryIO, *, id_tag: None | str = None, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, includeTags: bool = True, errors: str = 'strict')¶

Read ids and molecules from an SDF file using the RDKit toolkit

This is mostly equivalent to calling:

read_ids_and_molecules(source, "sdf", id_tag=id_tag, reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

id_tag (a string, or None to use the title) – get the id from the named data item instead of using the record title
sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
includeTags (Boolean (default: True)) – if true, extract the struture data tag fields
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_sdf_ids_and_molecules_from_string(content: str | bytes, *, id_tag: None | str = None, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, includeTags: bool = True, errors: str = 'strict')¶

Read ids and molecules from a string containing an SDF file using the RDKit toolkit

This is equivalent to calling:

read_ids_and_molecules_from_string(content, "sdf", id_tag=id_tag, reader_args={...}, errors=errors)

Use read_ids_and_molecules_from_string() if the content is compressed.

Parameters:

id_tag (a string, or None to use the title) – get the id from the named data item instead of using the record title
sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
includeTags (Boolean (default: True)) – if true, extract the struture data tag fields
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_sdf_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, includeTags: bool = True, errors: str = 'strict')¶

Read molecules from an SDF file using the RDKit toolkit

This is mostly equivalent to calling:

read_molecules(source, "sdf", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
includeTags (Boolean (default: True)) – if true, extract the struture data tag fields
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_sdf_molecules_from_string(content: str | bytes, *, sanitize: bool = True, removeHs: bool = True, strictParsing: bool = True, includeTags: bool = True, errors: str = 'strict')¶

Read molecules from a string containing an SDF file using the RDKit toolkit

This is equivalent to calling:

read_molecules_from_string(content, "sdf", reader_args={...}, errors=errors)

Use read_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
removeHs (Boolean (default: True)) – If true, remove simple hydrogens from the molecular graph
strictParsing (Boolean (default: True)) – If true, require stricter adherence to the SDF specification
includeTags (Boolean (default: True)) – if true, extract the struture data tag fields
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_smi_ids_and_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, cxsmiles: bool = True, has_header: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read ids and molecules from a SMILES file using the RDKit toolkit

This is mostly equivalent to calling:

read_ids_and_molecules(source, "smi", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
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: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_smi_ids_and_molecules_from_string(content: str | bytes, *, sanitize: bool = True, cxsmiles: bool = True, has_header: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read ids and molecules from a string containing a SMILES file using the RDKit toolkit

This is equivalent to calling:

read_ids_and_molecules_from_string(content, "smi", reader_args={...}, errors=errors)

Use read_ids_and_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
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: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.IdAndMoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_smi_molecules(source: None | str | BinaryIO, *, sanitize: bool = True, cxsmiles: bool = True, has_header: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read molecules from a SMILES file using the RDKit toolkit

This is mostly equivalent to calling:

read_molecules(source, "smi", reader_args={...}, errors=errors)

along with decompression based on the source filename’s extension.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
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: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.read_smi_molecules_from_string(content: str | bytes, *, sanitize: bool = True, cxsmiles: bool = True, has_header: bool = False, delimiter: Literal['to-eol', 'space', 'tab', 'comma', 'whitespace', 'native', ' ', '\t'] | None = None, errors: str = 'strict')¶

Read molecules from a string containing a SMILES file using the RDKit toolkit

This is equivalent to calling:

read_molecules_from_string(content, "smi", reader_args={...}, errors=errors)

Use read_molecules_from_string() if the content is compressed.

Parameters:

sanitize (Boolean (default: True)) – If true, sanitize the molecule after parsing
cxsmiles (Boolean (default: True)) – If true, look for ChemAxon CXSMILES extensions after the SMILES string
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: None)) – The separator between the SMILES and the id
errors (one of "strict", "ignore", or "log") – specify how to handle errors

Returns:

a chemfp.base_toolkit.MoleculeReader iterating RDKit molecules

chemfp.rdkit_toolkit.set_id(mol, id)¶

Set the molecule’s id as RDKit’s _Name property

Parameters:

mol (an RDKit molecule) – the molecule
id (string) – the new id

Returns:

None

chemfp.rdkit_toolkit.suppress_log_output()¶

Return a context manager to disable RDKit logging.

One entry, disable the “rdApp.*” logs. On exit, re-enable.

Example:

with suppress_output():: … do something which may log …

The returned context manager is a re-entrant singleton object. The context manager may be entered multiple times. Logging will not be re-enabled until the matching number of exits.

Returns:: a context manager

chemfp.rdkit_toolkit.translate_record(content, in_format='smi', out_format='smi', *, id_tag=None, reader_args=None, writer_args=None, id=None, errors='strict')¶

Translate a molecule record from one format to another

Use the RDKit toolkit to parse the content as format in_format (default: “smi”) and translate it into out_format (default: “smi”). For an SDF record, use id_tag to get the record id from the given SD tag instead of the title line. Use reader_args and writer_args to configure format-specific parameters. Use id to set the id of the output record.

The errors parameter specifies how to handle errors. “strict” raises an exception, “report” sends a message to stderr and goes to the next record, and “ignore” goes to the next record.

Parameters:

content (a string) – the string containing a structure record
in_format (a format name string, or Format object) – the input structure format
out_format (a format name string, or Format object) – the output structure format
id_tag (string, or None to use the record title) – SD tag containing the record id
reader_args (a dictionary, or None) – reader arguments for the specified in_format
writer_args (a dictionary, or None) – writer arguments for the specified out_format
id (a string, or None to use the default) – the record id to use for the output record
errors (one of "strict", "report", or "ignore") – specify how to handle errors

Returns:

a string