pygtop.targets
(Targets)¶
Contains target-specific objects and functions.
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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
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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
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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.
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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.
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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
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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
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class
pygtop.targets.
Target
(json_data)[source]¶ A Guide to PHARMACOLOGY target object.
Parameters: json_data – A dictionary obtained from the web services. -
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
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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
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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
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family_ids
()[source]¶ Returns the the family IDs of any families this target is a member of.
Returns: list of int
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families
()[source]¶ Returns a list of all target families of which this target is a member.
Returns: list of TargetFamily
objects
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subunit_ids
()[source]¶ Returns the the target IDs of all targets which are subunits of this target.
Returns: list of int
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subunits
()[source]¶ Returns a list of all targets which are subunits of this target.
Returns: list of Target
objects
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complex_ids
()[source]¶ Returns the the target IDs of all targets of which this target is a subunit.
Returns: list of int
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complexes
()[source]¶ Returns a list of all targets of which this target is a subunit.
Returns: list of Target
objects
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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
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database_links
(species=None)[source]¶ 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.
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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.
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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.
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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.
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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.
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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
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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- as_molecupy (bool) –
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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.
- species (str) – If given, only PDBs belonging to this species will be returned.
Returns: list of
str
PDB codes- as_molecupy (bool) –
-
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class
pygtop.targets.
TargetFamily
(json_data)[source]¶ A Guide to PHARMACOLOGY target family object.
Parameters: json_data – A dictionary obtained from the web services. -
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
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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
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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
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parent_family_ids
()[source]¶ Returns the the target IDs of all target families of which this family is a member.
Returns: list of int
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parent_families
()[source]¶ Returns a list of all target families of which this family is a member.
Returns: list of TargetFamily
objects
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sub_family_ids
()[source]¶ Returns the the target IDs of all arget families which are a member of this family.
Returns: list of int
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sub_families
()[source]¶ Returns a list of all target families which are a member of this family.
Returns: list of TargetFamily
objects
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