pygtop.targets (Targets)

Contains target-specific objects and functions.

pygtop.targets.get_target_by_id(target_id)[source]

Returns a Target object of the target with the given ID.

Parameters:target_id (int) – The GtoP ID of the Target desired.
Return type:Target
Raises:NoSuchTargetError: if no such target exists in the database
pygtop.targets.get_all_targets()[source]

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

Returns:list of Target objects
pygtop.targets.get_targets_by(criteria)[source]

Get all targets which specify the criteria dictionary.

Parameters:criteria (dict) – A dictionary of field=value pairs. See the GtoP target web services page for key/value pairs which can be supplied.
Returns:list of Target objects.
pygtop.targets.get_target_by_name(name)[source]

Returns the target which matches the name given.

Parameters:name (str) – The name of the target to search for. Note that synonyms will not be searched.
Return type:Target
Raises:NoSuchTargetError: if no such target exists in the database.
pygtop.targets.get_target_family_by_id(family_id)[source]

Returns a TargetFamily object of the family with the given ID.

Parameters:family_id (int) – The GtoP ID of the TargetFamily desired.
Return type:TargetFamily
Raises:NoSuchTargetFamilyError: if no such family exists in the database
pygtop.targets.get_all_target_families()[source]

Returns a list of all target families in the Guide to PHARMACOLOGY database.

Returns:list of TargetFamily objects
class pygtop.targets.Target(json_data)[source]

A Guide to PHARMACOLOGY target object.

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

Returns the target’s GtoP ID.

Return type:int
name(*args, strip_html=False, **kwargs)

Returns the target’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 target’s abbreviated name.

Parameters:strip_html (bool) – If True, the abbreviation will have HTML entities stripped.
Return type:str
systematic_name(*args, strip_html=False, **kwargs)

Returns the target’s systematic name.

Parameters:strip_html (bool) – If True, the name will have HTML entities stripped.
Return type:str
target_type()[source]

Returns the target’s type.

Return type:str
family_ids()[source]

Returns the the family IDs of any families this target is a member of.

Returns:list of int
families()[source]

Returns a list of all target families of which this target is a member.

Returns:list of TargetFamily objects
subunit_ids()[source]

Returns the the target IDs of all targets which are subunits of this target.

Returns:list of int
subunits()[source]

Returns a list of all targets which are subunits of this target.

Returns:list of Target objects
complex_ids()[source]

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

Returns:list of int
complexes()[source]

Returns a list of all targets of which this target is a subunit.

Returns:list of Target objects
synonyms(*args, strip_html=False, **kwargs)

Returns any synonyms for this target.

Parameters:strip_html (bool) – If True, the synonyms will have HTML entities stripped.
Returns:list of str

Returns any database links for this target.

Parameters:species (str) – If given, only links belonging to this species will be returned.
Returns:list of DatabaseLink objects.
genes(species=None)[source]

Returns any genes for this target.

Parameters:species (str) – If given, only genes belonging to this species will be returned.
Returns:list of Gene objects.
interactions(species=None)[source]

Returns any interactions for this target.

Parameters:species (str) – If given, only interactions belonging to this species will be returned.
Returns:list of Interaction objects.
get_interaction_by_id(interaction_id)

Returns an Interaction object of a given ID belonging to the target.

Parameters:interaction_id (int) – The interactions’s ID.
Return type:Interaction
Raises:NoSuchInteractionError: if no such interaction exists in the database.
ligands(species=None)[source]

Returns any ligands that this target interacts with.

Parameters:species (str) – If given, only ligands belonging to this species will be returned.
Returns:list of DatabaseLink objects.
gtop_pdbs(*args, as_molecupy=False, **kwargs)

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

Parameters:as_molecupy (bool) – Returns the PDBs as molecuPy PDB objects.
Returns:list of str PDB codes
uniprot_pdbs(*args, as_molecupy=False, **kwargs)

Queries the RSCB PDB database with the targets’s uniprot accessions.

Parameters:
  • as_molecupy (bool) –

    Returns the PDBs as molecuPy PDB objects.

  • species (str) – If given, only PDBs belonging to this species will be returned.
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.

  • species (str) – If given, only PDBs belonging to this species will be returned.
Returns:

list of str PDB codes
class pygtop.targets.TargetFamily(json_data)[source]

A Guide to PHARMACOLOGY target family object.

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

Returns the family’s GtoP ID.

Return type:int
name(*args, strip_html=False, **kwargs)

Returns the family’s name.

Parameters:strip_html (bool) – If True, the name will have HTML entities stripped.
Return type:str
target_ids()[source]

Returns the the target IDs of all targets in this family. Note that only immediate children are shown - if a family has subfamilies then it will not return any targets here - you must look in the sub-families.

Returns:list of int
targets()[source]

Returns a list of all targets in this family. Note that only immediate children are shown - if a family has subfamilies then it will not return any targets here - you must look in the sub-families.

Returns:list of Target objects
parent_family_ids()[source]

Returns the the target IDs of all target families of which this family is a member.

Returns:list of int
parent_families()[source]

Returns a list of all target families of which this family is a member.

Returns:list of TargetFamily objects
sub_family_ids()[source]

Returns the the target IDs of all arget families which are a member of this family.

Returns:list of int
sub_families()[source]

Returns a list of all target families which are a member of this family.

Returns:list of TargetFamily objects