1. DataBase

class pharmaforge.database.DataBase[source]

Bases: object

A class to represent a pymongo database of molecules

Methods

`add_data`(filepath)	Add data to the database
`find_all_unique`([aslist])	Find all unique keys in the entire database
`find_empty_molecules`()	Find all empty molecules in the database
`find_molecule`(mol_key[, verbose])	Find a molecule in the database
`find_shared_molecules`(db_key1, db_key2)	Find all shared molecules between two databases
`find_unique`(db_key)	Find all unique keys in an individual database
`obtain_feature`(feature_key[, db_key])	Obtain a feature from the database

add_data(filepath)[source]

Add data to the database

Parameters:: filepath (str or Path) – The name or path to the data file to add. The file must be in hdf5 format.
Return type:: None

:raises ValueError : If the file type is not hdf5: :raises FileNotFoundError : If the file is not found, or the path does not exist:

find_all_unique(aslist=False)[source]

Find all unique keys in the entire database

Parameters:: aslist (bool) – Whether to return the unique keys as a list or a dictionary
Returns:: unique – A dictionary of all unique keys in the database
Return type:: dictionary of lists

find_empty_molecules()[source]

Find all empty molecules in the database

Returns:: empty – A dictionary of all empty molecules in the database
Return type:: dictionary of lists

find_molecule(mol_key, verbose=True)[source]

Find a molecule in the database

Parameters:: mol_key (str) – The key of the molecule to search
Returns:: mol – The molecule data
Return type:: dict

find_shared_molecules(db_key1, db_key2)[source]

Find all shared molecules between two databases

Parameters:

db_key1 (str) – The key of the first database to search
db_key2 (strAdding SMILES codes to HDF5 Files) – The key of the second database to search

Returns:

shared – A list of all shared molecules between the two databases

Return type:

list

find_unique(db_key)[source]

Find all unique keys in an individual database

Parameters:: db_key (str) – The key of the database to search
Returns:: unique – A list of all unique keys in the database
Return type:: list

obtain_feature(feature_key, db_key=None)[source]

Obtain a feature from the database

Parameters:

feature_key (str) – The key of the feature to obtain
db_key (str) – The key of the database to search

Returns:

feature – A list of the feature values

Return type:

list

class pharmaforge.database.Loader(client_addr='mongodb://localhost:27017/', database_name=None, collection_name=None)[source]

Bases: object

A class ot access the database, once it has been put into the mongoDB

Parameters:

client_addr (str, optional) – The address of the client to open. Default is ‘mongodb://localhost:27017/’
database_name (str, optional) – The name of the database to open. Default is None
collection_name (str, optional) – The name of the collection to open. Default is None

client

The MongoDB client

Type:: pymongo.MongoClient

db

The database object

Type:: pymongo.database.Database

collection

The collection object

Type:: pymongo.collection.Collection

Methods

`list_collection_entry`([entry])	List all the data in the selected entry of the collection
`list_collections`([verbose])	List all collections in the selected database
`list_db_names`()	List all database names in the client
`select_collection`(collection_name)	Select a collection from the database
`select_db`(db_name[, verbose])	Select a database from the client

list_collection_entry(entry=None)[source]

List all the data in the selected entry of the collection

Parameters:: entry (str) – The name of the entry to list. If None, all entries will be listed
Return type:: None

list_collections(verbose=True)[source]

List all collections in the selected database

Parameters:: verbose (bool) – Whether to print the collection names or not
Returns:: collection_names – A list of all collection names in the database
Return type:: list

list_db_names()[source]

List all database names in the client

Parameters:: None
Returns:: db_names – A list of all database names in the client
Return type:: list

select_collection(collection_name)[source]

Select a collection from the database

Parameters:: collection_name (str) – The name of the collection to select
Return type:: None

select_db(db_name, verbose=True)[source]

Select a database from the client

Parameters:: db_name (str) – The name of the database to select
Return type:: None