chemprop.featurizers.molgraph ============================= .. py:module:: chemprop.featurizers.molgraph Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/chemprop/featurizers/molgraph/cache/index /autoapi/chemprop/featurizers/molgraph/mixins/index /autoapi/chemprop/featurizers/molgraph/molecule/index /autoapi/chemprop/featurizers/molgraph/reaction/index Attributes ---------- .. autoapisummary:: chemprop.featurizers.molgraph.CGRFeaturizer Classes ------- .. autoapisummary:: chemprop.featurizers.molgraph.MolGraphCache chemprop.featurizers.molgraph.MolGraphCacheFacade chemprop.featurizers.molgraph.MolGraphCacheOnTheFly chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer chemprop.featurizers.molgraph.RxnMode Package Contents ---------------- .. py:class:: MolGraphCache(inputs, V_fs, E_fs, featurizer, n_workers = 0) Bases: :py:obj:`MolGraphCacheFacade` A :class:`MolGraphCache` precomputes the corresponding :class:`~chemprop.data.molgraph.MolGraph`\s and caches them in memory. .. py:method:: __len__() .. py:method:: __getitem__(index) .. py:class:: MolGraphCacheFacade(inputs, V_fs, E_fs, featurizer) Bases: :py:obj:`collections.abc.Sequence`\ [\ :py:obj:`chemprop.data.molgraph.MolGraph`\ ], :py:obj:`Generic`\ [\ :py:obj:`chemprop.featurizers.base.S`\ ] A :class:`MolGraphCacheFacade` provided an interface for caching :class:`~chemprop.data.molgraph.MolGraph`\s. .. note:: This class only provides a facade for a cached dataset, but it *does not guarantee* whether the underlying data is truly cached. :param inputs: The inputs to be featurized. :type inputs: Iterable[S] :param V_fs: The node features for each input. :type V_fs: Iterable[np.ndarray] :param E_fs: The edge features for each input. :type E_fs: Iterable[np.ndarray] :param featurizer: The featurizer with which to generate the :class:`~chemprop.data.molgraph.MolGraph`\s. :type featurizer: Featurizer[S, MolGraph] .. py:class:: MolGraphCacheOnTheFly(inputs, V_fs, E_fs, featurizer) Bases: :py:obj:`MolGraphCacheFacade` A :class:`MolGraphCacheOnTheFly` computes the corresponding :class:`~chemprop.data.molgraph.MolGraph`\s as they are requested. .. py:method:: __len__() .. py:method:: __getitem__(index) .. py:class:: CuikmolmakerMolGraphFeaturizer Bases: :py:obj:`chemprop.featurizers.base.Featurizer`\ [\ :py:obj:`list`\ [\ :py:obj:`str`\ ]\ , :py:obj:`BatchCuikMolGraph`\ ] A :class:`CuikmolmakerMolGraphFeaturizer` featurizes a list of molecules at once instead of one molecule at a time for efficiency. :param atom_featurizer_mode: The mode of the atom featurizer (V1, V2, ORGANIC, RIGR) to use. :type atom_featurizer_mode: str, default="V2" :param extra_atom_fdim: the dimension of the additional features that will be concatenated onto the calculated features of each atom :type extra_atom_fdim: int, default=0 :param extra_bond_fdim: the dimension of the additional features that will be concatenated onto the calculated features of each bond :type extra_bond_fdim: int, default=0 :param add_h: whether to add hydrogens to the `Chem.Mol` objects created from the input SMILES strings :type add_h: bool, default=False .. py:attribute:: atom_featurizer_mode :type: Literal['V1', 'V2', 'ORGANIC', 'RIGR'] :value: 'V2' .. py:attribute:: extra_atom_fdim :type: int :value: 0 .. py:attribute:: extra_bond_fdim :type: int :value: 0 .. py:attribute:: add_h :type: bool :value: False .. py:attribute:: atom_fdim :type: int .. py:attribute:: bond_fdim :type: int .. py:method:: __post_init__() .. py:method:: __call__(smiles_list, atom_features_extra = None, bond_features_extra = None) featurize an input .. py:class:: SimpleMoleculeMolGraphFeaturizer Bases: :py:obj:`chemprop.featurizers.molgraph.mixins._MolGraphFeaturizerMixin`, :py:obj:`chemprop.featurizers.base.GraphFeaturizer`\ [\ :py:obj:`rdkit.Chem.Mol`\ ] A :class:`SimpleMoleculeMolGraphFeaturizer` is the default implementation of a :class:`MoleculeMolGraphFeaturizer` :param atom_featurizer: the featurizer with which to calculate feature representations of the atoms in a given molecule :type atom_featurizer: AtomFeaturizer, default=MultiHotAtomFeaturizer() :param bond_featurizer: the featurizer with which to calculate feature representations of the bonds in a given molecule :type bond_featurizer: BondFeaturizer, default=MultiHotBondFeaturizer() :param extra_atom_fdim: the dimension of the additional features that will be concatenated onto the calculated features of each atom :type extra_atom_fdim: int, default=0 :param extra_bond_fdim: the dimension of the additional features that will be concatenated onto the calculated features of each bond :type extra_bond_fdim: int, default=0 .. py:attribute:: extra_atom_fdim :type: int :value: 0 .. py:attribute:: extra_bond_fdim :type: int :value: 0 .. py:method:: __post_init__() .. py:method:: __call__(mol, atom_features_extra = None, bond_features_extra = None) .. py:type:: CGRFeaturizer :canonical: CondensedGraphOfReactionFeaturizer .. py:class:: CondensedGraphOfReactionFeaturizer Bases: :py:obj:`chemprop.featurizers.molgraph.mixins._MolGraphFeaturizerMixin`, :py:obj:`chemprop.featurizers.base.GraphFeaturizer`\ [\ :py:obj:`chemprop.types.Rxn`\ ] A :class:`CondensedGraphOfReactionFeaturizer` featurizes reactions using the condensed reaction graph method utilized in [1]_ **NOTE**: This class *does not* accept a :class:`AtomFeaturizer` instance. This is because it requries the :meth:`num_only()` method, which is only implemented in the concrete :class:`AtomFeaturizer` class :param atom_featurizer: the featurizer with which to calculate feature representations of the atoms in a given molecule :type atom_featurizer: AtomFeaturizer, default=AtomFeaturizer() :param bond_featurizer: the featurizer with which to calculate feature representations of the bonds in a given molecule :type bond_featurizer: BondFeaturizerBase, default=BondFeaturizer() :param mode_: the mode by which to featurize the reaction as either the string code or enum value :type mode_: Union[str, ReactionMode], default=ReactionMode.REAC_DIFF .. rubric:: References .. [1] Heid, E.; Green, W.H. "Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction." J. Chem. Inf. Model. 2022, 62, 2101-2110. https://doi.org/10.1021/acs.jcim.1c00975 .. py:attribute:: mode_ :type: dataclasses.InitVar[str | RxnMode] .. py:method:: __post_init__(mode_) .. py:property:: mode :type: RxnMode .. py:method:: __call__(rxn, atom_features_extra = None, bond_features_extra = None) Featurize the input reaction into a molecular graph :param rxn: a 2-tuple of atom-mapped rdkit molecules, where the 0th element is the reactant and the 1st element is the product :type rxn: Rxn :param atom_features_extra: *UNSUPPORTED* maintained only to maintain parity with the method signature of the `MoleculeFeaturizer` :type atom_features_extra: np.ndarray | None, default=None :param bond_features_extra: *UNSUPPORTED* maintained only to maintain parity with the method signature of the `MoleculeFeaturizer` :type bond_features_extra: np.ndarray | None, default=None :returns: the molecular graph of the reaction :rtype: MolGraph .. py:method:: map_reac_to_prod(reacs, pdts) :classmethod: Map atom indices between corresponding atoms in the reactant and product molecules :param reacs: An RDKit molecule of the reactants :type reacs: Chem.Mol :param pdts: An RDKit molecule of the products :type pdts: Chem.Mol :returns: * **ri2pi** (*dict[int, int]*) -- A dictionary of corresponding atom indices from reactant atoms to product atoms * **pdt_idxs** (*list[int]*) -- atom indices of poduct atoms * **rct_idxs** (*list[int]*) -- atom indices of reactant atoms .. py:class:: RxnMode Bases: :py:obj:`chemprop.utils.utils.EnumMapping` The mode by which a reaction should be featurized into a `MolGraph` .. py:attribute:: REAC_PROD concatenate the reactant features with the product features. .. py:attribute:: REAC_PROD_BALANCE concatenate the reactant features with the products feature and balances imbalanced reactions .. py:attribute:: REAC_DIFF concatenates the reactant features with the difference in features between reactants and products .. py:attribute:: REAC_DIFF_BALANCE concatenates the reactant features with the difference in features between reactants and product and balances imbalanced reactions .. py:attribute:: PROD_DIFF concatenates the product features with the difference in features between reactants and products .. py:attribute:: PROD_DIFF_BALANCE concatenates the product features with the difference in features between reactants and products and balances imbalanced reactions