gt4sd.properties.utils module¶

Summary¶

Functions:

`docking_import_check`	Verifies that __some__ of the required packages for docking are installed.
`get_activity_fn`	Get a function to measure activity/affinity against a protein target.
`get_descriptor`	Convert a macromolecule to a modlamp GlobalDescriptor object.
`get_sequence`	Safely returns an amino acid sequence of a macromolecule
`get_similarity_fn`	Get a similarity function for a target molecule.
`get_target_parameters`	Generates a tuple of scorers and weight list
`to_mol`	Safely convert a string or a rdkit.Chem.Mol to a rdkit.Chem.Mol.
`to_smiles`	Safely returns a SMILES string from a SMILES or a rdkit.Chem.Mol object.
`validate_api_token`	Validates whether the parameter configuration contains something that _could_ be a valid API key.
`validate_ip`	Validates whether the parameter configuration contains a correct IP address.

Reference¶

to_mol(mol)[source]¶

Safely convert a string or a rdkit.Chem.Mol to a rdkit.Chem.Mol.

Parameters: mol (Union[str, Mol]) – a string or a rdkit.Chem.Mol object.
Raises: TypeError – if wrong type is given.
Return type: Mol
Returns: a rdkit.Chem.Mol object.

to_smiles(mol)[source]¶

Safely returns a SMILES string from a SMILES or a rdkit.Chem.Mol object.

Parameters: SmallMolecule – either a SMILES or a rdkit.Chem.Mol object.
Return type: str
Returns: a SMILES string.

get_similarity_fn(target_mol, fp_key='FCFP4')[source]¶

Get a similarity function for a target molecule.

Parameters

target_mol (Union[str, Mol]) – a target molecule as SMILES or rdkit.Chem.Mol object.
fp_key (str) – The type of fingerprint to use. One of ECFP4, ECFP6, FCFP4 and AP.

Return type

Callable[[Union[str, Mol]], Union[float, int]]

Returns

a similarity function that can be called with a SmallMolecule.

get_activity_fn(target)[source]¶

Get a function to measure activity/affinity against a protein target.

Parameters: target (str) – name of the target protein.
Return type: Callable[[Union[str, Mol]], Union[float, int]]
Returns: an affinity function that can be called with a SmallMolecule.

get_sequence(protein)[source]¶

Safely returns an amino acid sequence of a macromolecule

Parameters

protein (Union[str, Mol]) – either an AA sequence or a rdkit.Chem.Mol object that can be converted to FASTA.

Raises

TypeError – if the input was none of the above types.
ValueError – if the sequence was empty or could not be parsed into FASTA.

Return type

str

Returns

an AA sequence.

get_descriptor(protein)[source]¶

Convert a macromolecule to a modlamp GlobalDescriptor object.

Parameters: protein (Union[str, Mol]) – either an AA sequence or a rdkit.Chem.Mol object that can be converted to FASTA.
Return type: GlobalDescriptor
Returns: GlobalDescriptor object.

get_target_parameters(target)[source]¶

Generates a tuple of scorers and weight list

Parameters: target (Union[str, Dict[str, Any]]) – scoring functions and parameters related to it
Return type: Tuple[List[Type[Any]], List[float]]
Returns: A tuple containing scoring functions and weight list

validate_ip(ip, message='')[source]¶

Validates whether the parameter configuration contains a correct IP address.

Parameters

ip (str) – The IP address to validate.
message (str) – Additional error message to be displayed.

Return type

None

validate_api_token(parameters, message='')[source]¶

Validates whether the parameter configuration contains something that _could_ be a valid API key.

Parameters

parameters (ApiTokenParameters) – ApiTokenParameters.
message (str) – Additional error message to be displayed.

Return type

None

docking_import_check()[source]¶

Verifies that __some__ of the required packages for docking are installed.

Raises: ModuleNotFoundError – If a necessary module was not found.
Return type: None