`kinoml.core.proteins`¶

MolecularComponent objects that represent protein-like entities.

Module Contents¶

kinoml.core.proteins.logger¶

class kinoml.core.proteins.Protein(pdb_id: str = '', molecule: Union[openeye.oechem.OEMol, openeye.oechem.OEGraphMol, MDAnalysis.core.universe.Universe, None] = None, toolkit: str = 'OpenEye', name: str = '', sequence: str = '', uniprot_id: str = '', ncbi_id: str = '', metadata: Union[dict, None] = None, **kwargs)¶

Bases: kinoml.core.components.BaseProtein, kinoml.core.sequences.AminoAcidSequence

Create a new Protein object. A molecular representation is accessible via the molecule attribute.

Examples

Create a protein from file with OpenEye toolkit molecular representation:

>>> protein = Protein.from_file("data/proteins/4f8o.pdb", name="4f8o")

Create a protein from file with MDAnalysis toolkit molecular representation:

>>> protein = Protein.from_file("data/proteins/4f8o.pdb", name="4f8o", toolkit="MDAnalysis")

Create a protein from an OpenEye molecule:

>>> from kinoml.modeling.OEModeling import read_molecules
>>> molecule = read_molecules("data/proteins/4f8o.pdb")[0]
>>> protein = Protein(molecule=molecule, name="4f8o")

Create a protein from PDB ID:

>>> protein = Protein.from_pdb("4f8o")

Create a protein from PDB ID with lazy instantiation:

>>> protein = Protein(pdb_id="4f8o")

Create a protein from PDB ID with lazy instantiation and get access to the complete wildtype amino acid sequence via providing a UniProt ID:

>>> protein = Protein(pdb_id="4f8o", uniprot_id="P31522")
>>> protein.sequence

property pdb_id¶: Decorate pdb_id to modify setter.

property molecule¶: Decorate molecule to modify setter and getter.

molecule()¶

Get the _molecule attribute. If the pdb_id attribute is given and _molecule is None, a new molecule representation will be created from the given pdb_id, e.g. in case of lazy instantiation. The toolkit being used depends on the toolkit attribute.

Returns: The molecular representation of the protein.
Return type: Universe or AtomGroup or oechem.OEMol or oechem.OEGraphMol or None

classmethod from_file(file_path: Union[pathlib.Path, str], name: str = '', toolkit: str = 'OpenEye')¶

Create a Protein from file.

Parameters

file_path (pathlib.Path or str) – The path to the molecular file. Supported formats depend on the toolkit being used.
name (str, default="") – The name of the protein.
toolkit (str, default="OpenEye") – The toolkit to use for molecular representation.

classmethod from_pdb(pdb_id: str, name: str = '', toolkit: str = 'OpenEye')¶

Create a Protein from file.

Parameters

pdb_id (str) – The PDB ID of the protein structure of interest.
name (str, default="") – The name of the protein.
toolkit (str, default="OpenEye") – The toolkit to use for molecular representation.

class kinoml.core.proteins.KLIFSKinase(pdb_id: str = '', molecule: Union[openeye.oechem.OEMol, openeye.oechem.OEGraphMol, MDAnalysis.core.universe.Universe, None] = None, toolkit: str = 'OpenEye', name: str = '', sequence: str = '', uniprot_id: str = '', ncbi_id: str = '', structure_klifs_id: Union[int, None] = None, kinase_klifs_id: Union[int, None] = None, kinase_klifs_sequence: str = '', structure_klifs_sequence: str = '', structure_klifs_residues: Union[pandas.DataFrame, None] = None, metadata: Union[dict, None] = None, **kwargs)¶

Bases: Protein

Create a new KLIFSKinase object. A molecular representation is accessible via the molecule attribute. Allows access to the sequence and residues of the KLIFS binding pocket.

Examples

Create a KLIFS kinase from PDB ID with lazy instantiation:

>>> kinase = KLIFSKinase(pdb_id="4yne")

Create a KLIFS kinase from PDB ID with lazy instantiation and gain access to the wildtype KLIFS pocket sequence via providing a UniProt ID:

>>> kinase = KLIFSKinase(pdb_id="4yne", uniprot_id="P04629")
>>> kinase.kinase_klifs_sequence()

Create a KLIFS kinase from PDB ID with lazy instantiation and gain access to the wildtype KLIFS pocket sequence via providing a KLIFS specifc kinase ID:

>>> kinase = KLIFSKinase(pdb_id="4yne", kinase_klifs_id=480)
>>> kinase.kinase_klifs_sequence()  # wildtype, does not need to match the given PDB structure

Create a KLIFS kinase from PDB ID with lazy instantiation and gain access to the KLIFS pocket sequence and residues of the structure via providing a KLIFS specifc structure ID:

>>> kinase = KLIFSKinase(pdb_id="4yne", structure_klifs_id=3620)
>>> kinase.kinase_klifs_sequence()  # wildtype, does not need to match the given PDB structure
>>> kinase.structure_klifs_sequence()  # specific to the structure
>>> kinase.structure_klifs_residues()  # specific to the structure

property kinase_klifs_sequence¶: Decorate kinase_klifs_sequence to modify setter and getter.

property structure_klifs_sequence¶: Decorate structure_klifs_sequence to modify setter and getter.

property structure_klifs_residues¶: Decorate structure_klifs_residues to modify setter and getter.

_query_sequence_sources()¶: Query available sources for sequence details. Add additional methods below to allow fetching from other sources.

_query_klifs()¶: Query KLIFS for the Uniprot ID, which allows fetching of the sequence.

kinase_klifs_sequence()¶

Get the _kinase_klifs_sequence attribute. Query KLIFS for the respective sequence if _kinase_klifs_sequence is an empty string.

Returns: The kinase KLIFS binding pocket sequence.
Return type: str
Raises: ValueError – To allow access to the kinase KLIFS sequence, the KLIFSKinase object needs to be initialized with one of the following attributes: kinase_klifs_sequence kinase_klifs_id structure_klifs_id uniprot_id

structure_klifs_sequence()¶

Get the _structure_klifs_sequence attribute. Query KLIFS for the respective sequence if _structure_klifs_sequence is an empty string.

Returns: The structure-specific KLIFS binding pocket sequence.
Return type: str
Raises: ValueError – To allow access to the structure KLIFS sequence, the KLIFSKinase object needs to be initialized with one of the following attributes: structure_klifs_sequence structure_klifs_id

structure_klifs_residues()¶

Get the _structure_klifs_residues attribute. Query KLIFS for the respective residues if _structure_klifs_residues is None.

Returns: The structure-specific KLIFS residues formatted like by opencadd.databases.klifs.
Return type: pd.DataFrame or None
Raises: ValueError – To allow access to structure KLIFS residues, the KLIFSKinase object needs to be initialized with one of the following attributes: structure_klifs_residues structure_klifs_id

kinoml.core.proteins¶

Module Contents¶

`kinoml.core.proteins`¶