pygtop.interactions (Interactions)

pygtop.interactions.get_all_interactions()[source]

Returns a list of all interactions in the Guide to PHARMACOLOGY database. This can take a few seconds.

Returns:list of Interaction objects
class pygtop.interactions.Interaction(json_data)[source]

A Guide to PHARMACOLOGY interaction object.

Parameters:json_data – A dictionary obtained from the web services.
interaction_id()[source]

Returns the interaction’s GtoP ID.

Return type:int
ligand_id()[source]

Returns the GtoP ID of the associated ligand.

Return type:int
ligand()[source]

Returns the Ligand object for this interaction.

Return type:Ligand
target_id()[source]

Returns the GtoP ID of the associated target.

Return type:int
target()[source]

Returns the Target object for this interaction.

Return type:Target
gtop_pdbs(*args, as_molecupy=False, **kwargs)

Returns a list of PDBs which the Guide to PHARMACOLOGY says contain this interaction.

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 for PDBs containing this interaction 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 containing this interaction using all means available - annotated and external.

Parameters:as_molecupy (bool) –

Returns the PDBs as molecuPy PDB objects.
Returns:list of str PDB codes
species()[source]

Returns the species in which the interaction takes place.

Return type:str
primary_target()[source]

Returns True if the the interaction represents a ligand interacting with its primary target.

Return type:bool
endogenous()[source]

Returns True if the the interaction is an endogenous interaction.

Return type:bool
interaction_type()[source]

Returns the type of interaction.

Return type:str
action()[source]

Returns the action of the interaction.

Return type:str
affinity_low()[source]

Returns the lowest reported affinity for this interaction.

Return type:float
affinity_high()[source]

Returns the highest reported affinity for this interaction.

Return type:float
affinity_type()[source]

Returns the units of the interaction.

Return type:str