2.1. General Database

class pharmaforge.recipes.GeneralDatabase.GeneralRecipe(database_name, client, input_dir=None, **kwargs)[source]

Bases: object

A class to represent a recipe for generating a database of molecules

Parameters:

  • database_name (str) – The name of the database to create

  • client (MongoClient) – The MongoDB client to use

  • input_dir (str) – The directory containing the HDF5 files to process

  • kwargs (dict) – Additional keyword arguments to pass to the recipe. These are one-for-one keypairs that get added to ALL the database entries.

Methods

add_field(collection, field_name, field_value)

Add a field to the recipe :param field_name: The name of the field to add :type field_name: str :param field_value: The value of the field to add :type field_value: any

add_field_from_kwargs()

Add a field to the recipe from the kwargs :param field_name: The name of the field to add :type field_name: str :param field_value: The value of the field to add :type field_value: any

clear_db()

Clear the database :param database_name: The name of the database to clear.

open_client(client)

Add the recipe to the client :param client: The MongoDB client to add the recipe to :type client: MongoClient

pprint_one_entry()

Pretty print one entry from the database :param None:

process_hdf5(input_dir)

Process the HDF5 files in the input directory :param input_dir: The directory containing the HDF5 files to process :type input_dir: str

check_collections
add_field(collection, field_name, field_value)[source]

Add a field to the recipe :param field_name: The name of the field to add :type field_name: str :param field_value: The value of the field to add :type field_value: any

Return type:

None

add_field_from_kwargs()[source]

Add a field to the recipe from the kwargs :param field_name: The name of the field to add :type field_name: str :param field_value: The value of the field to add :type field_value: any

Return type:

None

check_collections(verbose=False)[source]
clear_db()[source]

Clear the database :param database_name: The name of the database to clear. If None, the current database is cleared. :type database_name: str

Return type:

None

open_client(client)[source]

Add the recipe to the client :param client: The MongoDB client to add the recipe to :type client: MongoClient

Return type:

None

pprint_one_entry()[source]

Pretty print one entry from the database :param None:

Return type:

None

process_hdf5(input_dir)[source]

Process the HDF5 files in the input directory :param input_dir: The directory containing the HDF5 files to process :type input_dir: str

Return type:

None

Raises: