Source code for stk.databases.value

Value Database

.. toctree::
    :maxdepth: 2

    Value MongoDB <stk.databases.mongo_db.value>


[docs]class ValueDatabase: """ Abstract base class for storing of molecular property values. Examples -------- *Subclass Implementation* The source of any of the subclasses, listed in :mod:`molecule_value_database <.databases.value>`, can serve as good examples. *Iterating Through Entries in the Database* The :meth:`.MoleculeDatabase.get_all` and :meth:`.ConstructedMoleculeDatabase.get_all` methods can be used to iterate through all of the database's entries, which can then be used to access values in the :class:`.ValueDatabase` .. testsetup:: iterating-through-entries-in-the-database import stk # Change the database used, so that when a developer # runs the doctests locally, their "stk" database is not # contaminated. _test_database = '_stk_doctest_database' _old_value_init = stk.ValueMongoDb stk.ValueMongoDb = lambda mongo_client, collection: ( _old_value_init( mongo_client=mongo_client, database=_test_database, collection=collection, ) ) _old_molecule_init = stk.MoleculeMongoDb stk.MoleculeMongoDb = lambda mongo_client: _old_molecule_init( mongo_client=mongo_client, database=_test_database, ) # Change the database MongoClient will connect to. import os import pymongo _mongo_client = pymongo.MongoClient _mongodb_uri = os.environ.get( 'MONGODB_URI', 'mongodb://localhost:27017/' ) pymongo.MongoClient = lambda: _mongo_client(_mongodb_uri) .. testcode:: iterating-through-entries-in-the-database import pymongo client = pymongo.MongoClient() molecule_db = stk.MoleculeMongoDb(client) value_db = stk.ValueMongoDb( mongo_client=client, collection='atom_counts', ) molecule = stk.BuildingBlock('BrBr') molecule_db.put(molecule) value_db.put(molecule, molecule.get_num_atoms()) for molecule in molecule_db.get_all(): try: value = value_db.get(molecule) print(value) except KeyError: # In case molecule is not in value_db. pass .. testoutput:: iterating-through-entries-in-the-database 2 .. testcleanup:: iterating-through-entries-in-the-database stk.ValueMongoDb = _old_value_init stk.MoleculeMongoDb = _old_molecule_init pymongo.MongoClient().drop_database(_test_database) pymongo.MongoClient = _mongo_client """
[docs] def put(self, molecule, value): """ Put a value into the database. Parameters ---------- molecule : :class:`.Molecule` The molecule which is associated with the `value`. value : :class:`object` Some value associated with `molecule`. Returns ------- None : :class:`NoneType` """ raise NotImplementedError()
[docs] def get(self, molecule): """ Get the stored value for `molecule`. Parameters ---------- molecule : :class:`.Molecule` The molecule whose value is to be retrieved from the database. Returns ------- :class:`object` The value associated with `molecule`. Raises ------ :class:`KeyError` If `molecule` is not found in the database. """ raise NotImplementedError()