`pygtop.ligands` (Ligands)¶

Contains ligand-specific objects and functions.

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

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

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.

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.

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.

class pygtop.ligands.Ligand(json_data)[source]¶

A Guide to PHARMACOLOGY ligand object.

Parameters:	json_data – A dictionary obtained from the web services.

ligand_id()[source]¶

Returns the ligand’s GtoP ID.

Return type:	int

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

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

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

ligand_type()[source]¶

Returns the ligand’s type.

Return type:	str

species()[source]¶

Returns the ligand’s species, where appropriate.

Return type:	str

radioactive()[source]¶

Returns True if the ligand is radioactive.

Return type:	bool

labelled()[source]¶

Returns True if the ligand is labelled.

Return type:	bool

approved()[source]¶

Returns True if the ligand is approved.

Return type:	bool

withdrawn()[source]¶

Returns True if the ligand has been withdrawn.

Return type:	bool

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

subunit_ids()[source]¶

Returns the the ligand IDs of all ligands which are subunits of this target.

Returns:	list of `int`

subunits()[source]¶

Returns a list of all ligands which are subunits of this ligand.

Returns:	list of `Ligand` objects

complex_ids()[source]¶

Returns the the ligand IDs of all ligands of which this target is a subunit.

Returns:	list of `int`

complexes()[source]¶

Returns a list of all ligands of which this ligand is a subunit.

Returns:	list of `Ligand` objects

prodrug_ids()[source]¶

Returns the the ligand IDs of all ligands which are prodrugs of this ligand.

Returns:	list of `int`

prodrugs()[source]¶

Returns a list of all ligands which are prodrugs of this ligand.

Returns:	list of `Ligand` objects

active_drug_ids()[source]¶

Returns the the ligand IDs of all ligands which are active equivalents of this ligand.

Returns:	list of `int`

active_drugs()[source]¶

Returns a list of all ligands which are active equivalents of this ligand.

Returns:	list of `Ligand` objects

iupac_name()[source]¶

Returns the ligand’s IUPAC name.

Return type:	str

smiles()[source]¶

Returns the ligand’s SMILES string.

Return type:	str

inchi()[source]¶

Returns the ligand’s InChI string.

Return type:	str

inchi_key()[source]¶

Returns the ligand’s InChI key.

Return type:	str

one_letter_sequence()[source]¶

Returns the ligand’s single letter amino acid sequence where appropriate.

Return type:	str

three_letter_sequence()[source]¶

Returns the ligand’s three letter amino acid sequence where appropriate.

Return type:	str

post_translational_modifications()[source]¶

Returns any post-translational modifications.

Return type:	str

chemical_modifications()[source]¶

Returns any chemical modifications.

Return type:	str

hydrogen_bond_acceptors()[source]¶

Returns the number of hydrogen bond accepting atoms.

Return type:	int

hydrogen_bond_donors()[source]¶

Returns the number of hydrogen bond donor atoms.

Return type:	int

rotatable_bonds()[source]¶

Returns the number of rotatable bonds in the ligand.

Return type:	int

topological_polar_surface_area()[source]¶

Returns the polar surface area of the ligand in Angstroms.

Return type:	float

molecular_weight()[source]¶

Returns the ligand’s mass in Daltons.

Return type:	float

log_p()[source]¶

Returns the logP value of the ligand.

Return type:	int

lipinski_rules_broken()[source]¶

Returns the number of Lipinski’s Rules the ligand breaks.

Return type:	int

synonyms(*args, strip_html=False, **kwargs)¶

Returns the number ligand’s synonyms

Returns:	list of `str`

general_comments()[source]¶

Returns general comments pertaining to the ligand.

Return type:	str

bioactivity_comments()[source]¶

Returns comments pertaining to bioactivity.

Return type:	str

clinical_use_comments()[source]¶

Returns comments pertaining to clinical use.

Return type:	str

mechanism_of_action_comments()[source]¶

Returns comments pertaining to mechanism.

Return type:	str

absorption_and_distribution_comments()[source]¶

Returns comments pertaining to absorption and distribution.

Return type:	str

metabolism_comments()[source]¶

Returns comments pertaining to metabolism.

Return type:	str

elimination_comments()[source]¶

Returns comments pertaining to elimination from the body.

Return type:	str

population_pharmacokinetics_comments()[source]¶

Returns comments pertaining to population pharmacokinetics.

Return type:	str

organ_function_impairments_comments()[source]¶

Returns comments pertaining to organ function impairment.

Return type:	str

mutations_and_pathophysiology_comments()[source]¶

Returns comments pertaining to mutations and pathophysiology.

Return type:	str

database_links()[source]¶

Returns a list of database links for this ligand.

Return type:	list of `DatabaseLink`

interactions()[source]¶

Returns a list of interactions for this ligand.

Return type:	list of `Interaction`

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.

targets()[source]¶

Returns a list of all targets which this ligand interacts with.

Returns:	list of `Target` objects

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

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

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

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

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

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

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

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

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`

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`

find_in_pdb_by_mass(molecupy_pdb)[source]¶

Searches for the ligand in a molecuPy PDB object by ligand mass and returns the small molecule it finds.

Parameters:	molecupy_pdb – The molecuPy PDB object.
Return type:	`SmallMolecule`

find_in_pdb_by_peptide_string(molecupy_pdb)[source]¶

Searches for the ligand in a molecuPy PDB object by peptide sequence and returns the chain it finds.

Parameters:	molecupy_pdb – The molecuPy PDB object.
Return type:	`Chain`

pygtop.ligands (Ligands)¶

`pygtop.ligands` (Ligands)¶