drugforge.data.services.postera.molecule_set.MoleculeSetAPI

class drugforge.data.services.postera.molecule_set.MoleculeSetAPI(url, api_version, api_key, timeout=500, **kwargs)[source]

Bases: _BaseWebAPI

Connection and commands for PostEra Molecule Set API

__init__(url, api_version, api_key, timeout=500, **kwargs)

Methods

`__init__`(url, api_version, api_key[, timeout])
`add_molecules`(molecule_set_id, data)	Add additional molecules to the MoleculeSet.
`add_molecules_from_df_with_manifold_validation`(...)
`create`(molecule_set_name, data[, return_full])	Create a MoleculeSet from a list of Molecules.
`create_molecule_set_from_df_with_manifold_validation`(...)
`destroy`(molecule_set_id)	Delete a MoleculeSet.
`exists`(molecule_set_name[, by])	Check if a molecule set exists in PostEra.
`from_settings`(settings)	Create an interface to PostEra Molecule Set API from a Settings object.
`get`(molecule_set_id)	Get summary data for a given MoleculeSet.
`get_id_from_name`(name)	Get the unique id of a MoleculeSet from its human-readable name.
`get_molecules`(molecule_set_id[, return_as])	Pull the full contents of a MoleculeSet as a DataFrame.
`get_molecules_from_id_or_name`([id, name, ...])	Get the molecules from a molecule set by either id or name.
`get_name_from_id`(id)	Get the human-readable name of a MoleculeSet from its unique id.
`list_available`([return_full])	List available MoleculeSets.
`token_name`()	Return the name of the API token which should be used in the header.
`update_molecules`(molecule_set_id, data[, ...])	Updates the custom data associated with the Molecules in a MoleculeSet.
`update_molecules_from_df_with_manifold_validation`(...)

Attributes

molecule_set_url

add_molecules(molecule_set_id: id, data: MoleculeList) → int[source]

Add additional molecules to the MoleculeSet.

Parameters:

molecule_set_id – The unique id of the MoleculeSet.
data – MoleculeList giving Molecules to add.

Returns:

Number of molecules not added due to exceeding the max number of
molecules allowed in a MoleculeSet.

create(molecule_set_name: str, data: MoleculeList, return_full: bool = False) → str[source]

Create a MoleculeSet from a list of Molecules.

Parameters:

set_name – The human-readable name for the set.
data – MoleculeList giving Molecules to add.
return_full – If True, return a dict containing summary data for the created MoleculeSet; if False, return only its unique id.

destroy(molecule_set_id: str) → None[source]

Delete a MoleculeSet.

Parameters:: molecule_set_id – The unique id of the MoleculeSet

exists(molecule_set_name: str, by='name') → bool[source]

Check if a molecule set exists in PostEra.

Parameters:

molecule_set_name – The name of the molecule set to check.
by – The identifier type to check by. Can be either “id” or “name”.

Returns:

Whether the molecule set exists in PostEra.

Return type:

bool

classmethod from_settings(settings)[source]

Create an interface to PostEra Molecule Set API from a Settings object.

Parameters:: settings – A PosteraSettings object
Returns:: MoleculeSetAPI interface object.
Return type:: MoleculeSetAPI

get(molecule_set_id: str) → dict[source]

Get summary data for a given MoleculeSet.

Parameters:: molecule_set_id – The unique id of the MoleculeSet
Return type:: Summary data as a dict.

get_id_from_name(name: str) → str[source]

Get the unique id of a MoleculeSet from its human-readable name.

Parameters:: name – The human-readable name of the MoleculeSet.
Returns:: The unique id of the MoleculeSet.
Return type:: str

get_molecules(molecule_set_id: str, return_as='dataframe') → DataFrame | list[source]

Pull the full contents of a MoleculeSet as a DataFrame.

Parameters:

molecule_set_id – The unique id of the MoleculeSet
return_as ({‘dataframe’, ‘list’}) – Whether to return the molecules as a DataFrame or a list.

get_molecules_from_id_or_name(id: str | None = None, name: str | None = None, return_as='dataframe') → tuple[DataFrame | list, str][source]

Get the molecules from a molecule set by either id or name.

Parameters:

id – The unique id of the MoleculeSet.
name – The human-readable name of the MoleculeSet.
return_as ({‘dataframe’, ‘list’}) – Whether to return the molecules as a DataFrame or a list.

Returns:

The molecules in the molecule set.

Return type:

Union[pd.DataFrame, list]

get_name_from_id(id: str) → str[source]

Get the human-readable name of a MoleculeSet from its unique id.

Parameters:: id – The unique id of the MoleculeSet.
Returns:: The human-readable name of the MoleculeSet.
Return type:: str

list_available(return_full: bool = False) → list[dict] | dict[source]

List available MoleculeSets.

Parameters:: return_full – If True, return a list of dicts containing summary data for each MoleculeSet; if False, return a dict with the unique id for each MoleculeSet as keys, human-readable name as values.

classmethod token_name() → str[source]: Return the name of the API token which should be used in the header.

update_molecules(molecule_set_id: str, data: MoleculeUpdateList, overwrite=False) → list[str][source]

Updates the custom data associated with the Molecules in a MoleculeSet.

Parameters:

molecule_set_id – The unique id of the MoleculeSet.
data – MoleculeUpdateList giving MoleculeUpdates with update data for existing Molecules.
overwrite – If True, then customData will be entirely replaced with new data submitted; if False, then old and new customData will be combined, overwriting keys existing in both.

Return type:

List of Molecule ids that were updated.