pygtop.ligands
(Ligands)¶
Contains ligand-specific objects and functions.
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pygtop.ligands.
get_ligand_by_id
(ligand_id)[source]¶ Returns a Ligand object of the ligand with the given ID.
Parameters: ligand_id (int) – The GtoP ID of the Ligand desired. Return type: Ligand
Raises: NoSuchLigandError
if no such ligand exists in the database
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pygtop.ligands.
get_all_ligands
()[source]¶ Returns a list of all ligands in the Guide to PHARMACOLOGY database. This can take a few seconds.
Returns: list of Ligand
objects
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pygtop.ligands.
get_ligands_by
(criteria)[source]¶ Get all ligands which specify the criteria dictionary.
Parameters: criteria (dict) – A dictionary of field=value pairs. See the GtoP ligand web services page for key/value pairs which can be supplied. Returns: list of Ligand
objects.
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pygtop.ligands.
get_ligand_by_name
(name)[source]¶ Returns the ligand which matches the name given.
Parameters: name (str) – The name of the ligand to search for. Note that synonyms will not be searched. Return type: Ligand
Raises: NoSuchLigandError
if no such ligand exists in the database.
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pygtop.ligands.
get_ligands_by_smiles
(smiles, search_type='exact', cutoff=0.8)[source]¶ Search for ligands by SMILES string.
Parameters: - smiles (str) – The SMILES string to search with.
- search_type (str) – The type of search. Viable options are
"exact"
,"substructure"
or"similarity"
. - cutoff (float) – If performing a similarity search, this is the cutoff used for similarity. The default is 0.8 and the maximum is 1.
Returns: list of
Ligand
objects.
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class
pygtop.ligands.
Ligand
(json_data)[source]¶ A Guide to PHARMACOLOGY ligand object.
Parameters: json_data – A dictionary obtained from the web services. -
name
(*args, strip_html=False, **kwargs)¶ Returns the ligand’s name.
Parameters: strip_html (bool) – If True
, the name will have HTML entities stripped.Return type: str
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abbreviation
(*args, strip_html=False, **kwargs)¶ Returns the ligand’s abbreviated name.
Parameters: strip_html (bool) – If True
, the abbreviation will have HTML entities stripped.Return type: str
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inn
(*args, strip_html=False, **kwargs)¶ Returns the ligand’s INN name.
Parameters: strip_html (bool) – If True
, the name will have HTML entities stripped.Return type: str
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approval_source
(*args, strip_html=False, **kwargs)¶ Returns the regulatory body that approved the ligand, where appropriate.
Parameters: strip_html (bool) – If True
, the name will have HTML entities stripped.Return type: str
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subunit_ids
()[source]¶ Returns the the ligand IDs of all ligands which are subunits of this target.
Returns: list of int
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subunits
()[source]¶ Returns a list of all ligands which are subunits of this ligand.
Returns: list of Ligand
objects
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complex_ids
()[source]¶ Returns the the ligand IDs of all ligands of which this target is a subunit.
Returns: list of int
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complexes
()[source]¶ Returns a list of all ligands of which this ligand is a subunit.
Returns: list of Ligand
objects
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prodrug_ids
()[source]¶ Returns the the ligand IDs of all ligands which are prodrugs of this ligand.
Returns: list of int
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prodrugs
()[source]¶ Returns a list of all ligands which are prodrugs of this ligand.
Returns: list of Ligand
objects
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active_drug_ids
()[source]¶ Returns the the ligand IDs of all ligands which are active equivalents of this ligand.
Returns: list of int
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active_drugs
()[source]¶ Returns a list of all ligands which are active equivalents of this ligand.
Returns: list of Ligand
objects
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one_letter_sequence
()[source]¶ Returns the ligand’s single letter amino acid sequence where appropriate.
Return type: str
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three_letter_sequence
()[source]¶ Returns the ligand’s three letter amino acid sequence where appropriate.
Return type: str
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post_translational_modifications
()[source]¶ Returns any post-translational modifications.
Return type: str
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hydrogen_bond_acceptors
()[source]¶ Returns the number of hydrogen bond accepting atoms.
Return type: int
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topological_polar_surface_area
()[source]¶ Returns the polar surface area of the ligand in Angstroms.
Return type: float
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lipinski_rules_broken
()[source]¶ Returns the number of Lipinski’s Rules the ligand breaks.
Return type: int
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synonyms
(*args, strip_html=False, **kwargs)¶ Returns the number ligand’s synonyms
Returns: list of str
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absorption_and_distribution_comments
()[source]¶ Returns comments pertaining to absorption and distribution.
Return type: str
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elimination_comments
()[source]¶ Returns comments pertaining to elimination from the body.
Return type: str
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population_pharmacokinetics_comments
()[source]¶ Returns comments pertaining to population pharmacokinetics.
Return type: str
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organ_function_impairments_comments
()[source]¶ Returns comments pertaining to organ function impairment.
Return type: str
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mutations_and_pathophysiology_comments
()[source]¶ Returns comments pertaining to mutations and pathophysiology.
Return type: str
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database_links
()[source]¶ Returns a list of database links for this ligand.
Return type: list of DatabaseLink
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interactions
()[source]¶ Returns a list of interactions for this ligand.
Return type: list of Interaction
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get_interaction_by_id
(interaction_id)¶ Returns an Interaction object of a given ID belonging to the ligand.
Parameters: interaction_id (int) – The interactions’s ID. Return type: Interaction
Raises: NoSuchInteractionError
: if no such interaction exists in the database.
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targets
()[source]¶ Returns a list of all targets which this ligand interacts with.
Returns: list of Target
objects
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gtop_pdbs
(*args, as_molecupy=False, **kwargs)¶ Returns a list of PDBs which the Guide to PHARMACOLOGY says contain this ligand.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects. Returns: list of str
PDB codes
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smiles_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database with the ligand’s SMILES string.
Parameters: - search_type (str) – The type of search to run - whether exact matches only should be returned.
- as_molecupy (bool) –
Returns the PDBs as molecuPy PDB objects.
Returns: list of
str
PDB codes
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inchi_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database with the ligand’s InChI string.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns: list of str
PDB codes
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name_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database with the ligand’s name.
Parameters: - comparator (str) – The type of search to run - whether exact matches only should be returned, or substrings etc.
- as_molecupy (bool) –
Returns the PDBs as molecuPy PDB objects.
Returns: list of
str
PDB codes
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sequence_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database with the ligand’s amino acid sequence, if that ligand is a peptide.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns: list of str
PDB codes
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het_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database with the ligand’s amino acid sequence, if that ligand is a peptide.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns: list of str
PDB codes
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all_external_pdbs
(*args, as_molecupy=False, **kwargs)¶ Queries the RSCB PDB database by all parameters.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns: list of str
PDB codes
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all_pdbs
(*args, as_molecupy=False, **kwargs)¶ Get a list of PDB codes using all means available - annotated and external.
Parameters: as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns: list of str
PDB codes
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find_in_pdb_by_smiles
(molecupy_pdb)[source]¶ Searches for the ligand in a molecuPy PDB object by SMILES string and returns the small molecule it finds.
Parameters: molecupy_pdb – The molecuPy PDB object. Return type: SmallMolecule
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find_in_pdb_by_name
(molecupy_pdb)[source]¶ Searches for the ligand in a molecuPy PDB object by ligand name and returns the small molecule it finds.
Parameters: molecupy_pdb – The molecuPy PDB object. Return type: SmallMolecule
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