Loading deepchem/feat/base_classes.py +6 −6 Original line number Diff line number Diff line Loading @@ -214,8 +214,8 @@ class MolecularFeaturizer(Featurizer): Child classes need to implement the _featurize method for calculating features for a single molecule. Notes ----- Note ---- The subclasses of this class require RDKit to be installed. """ Loading Loading @@ -294,8 +294,8 @@ class MaterialStructureFeaturizer(Featurizer): classes need to implement the _featurize method for calculating features for a single crystal structure. Notes ----- Note ---- Some subclasses of this class will require pymatgen and matminer to be installed. """ Loading Loading @@ -360,8 +360,8 @@ class MaterialCompositionFeaturizer(Featurizer): classes need to implement the _featurize method for calculating features for a single crystal composition. Notes ----- Note ---- Some subclasses of this class will require pymatgen and matminer to be installed. """ Loading deepchem/feat/material_featurizers/elemnet_featurizer.py +2 −2 Original line number Diff line number Diff line Loading @@ -36,8 +36,8 @@ class ElemNetFeaturizer(MaterialCompositionFeaturizer): >>> featurizer = ElemNetFeaturizer() >>> features = featurizer.featurize([comp]) Notes ----- Note ---- This class requires Pymatgen to be installed. """ Loading deepchem/feat/molecule_featurizers/maccs_keys_fingerprint.py +2 −2 Original line number Diff line number Diff line Loading @@ -16,8 +16,8 @@ class MACCSKeysFingerprint(MolecularFeaturizer): Journal of chemical information and computer sciences 42.6 (2002): 1273-1280. .. [2] https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MACCSkeys.py Notes ----- Note ---- This class requires RDKit to be installed. """ Loading deepchem/feat/molecule_featurizers/pubchem_fingerprint.py +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ class PubChemFingerprint(MolecularFeaturizer): ---------- .. [1] ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf Notes Note ----- This class requires RDKit and PubChemPy to be installed. PubChemPy use REST API to get the fingerprint, so you need the internet access. Loading docs/source/api_reference/featurizers.rst +47 −5 Original line number Diff line number Diff line Loading @@ -34,12 +34,12 @@ These featurizers work with datasets of molecules. Graph Convolution Featurizers ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ MolGraphConvFeaturizer ********************** We are simplifying our graph convolution models by a joint data representation (:code:`GraphData`) in a future version of DeepChem, so we provide several featurizers. .. autoclass:: deepchem.feat.MolGraphConvFeaturizer :members: :inherited-members: :code:`ConvMolFeaturizer` and :code:`WeaveFeaturizer` are used with graph convolution models which inherited :code:`KerasModel`. On the other hand, :code:`MolGraphConvFeaturizer` is used with graph convolution models which inherited :code;`TorchModel`. ConvMolFeaturizer ***************** Loading @@ -55,6 +55,13 @@ WeaveFeaturizer :members: :inherited-members: MolGraphConvFeaturizer ********************** .. autoclass:: deepchem.feat.MolGraphConvFeaturizer :members: :inherited-members: Utilities ********* Loading Loading @@ -366,3 +373,38 @@ UserDefinedFeaturizer .. autoclass:: deepchem.feat.UserDefinedFeaturizer :members: :inherited-members: Base Featurizers (for develop) ------------------------------ Featurizer ^^^^^^^^^^ The :code:`dc.feat.Featurizer` class is the abstract parent class for all featurizers. .. autoclass:: deepchem.feat.Featurizer :members: MolecularFeaturizer ^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MolecularFeaturizer :members: MaterialCompositionFeaturizer ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MaterialCompositionFeaturizer :members: MaterialStructureFeaturizer ^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MaterialStructureFeaturizer :members: ComplexFeaturizer ^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.ComplexFeaturizer :members: Loading
deepchem/feat/base_classes.py +6 −6 Original line number Diff line number Diff line Loading @@ -214,8 +214,8 @@ class MolecularFeaturizer(Featurizer): Child classes need to implement the _featurize method for calculating features for a single molecule. Notes ----- Note ---- The subclasses of this class require RDKit to be installed. """ Loading Loading @@ -294,8 +294,8 @@ class MaterialStructureFeaturizer(Featurizer): classes need to implement the _featurize method for calculating features for a single crystal structure. Notes ----- Note ---- Some subclasses of this class will require pymatgen and matminer to be installed. """ Loading Loading @@ -360,8 +360,8 @@ class MaterialCompositionFeaturizer(Featurizer): classes need to implement the _featurize method for calculating features for a single crystal composition. Notes ----- Note ---- Some subclasses of this class will require pymatgen and matminer to be installed. """ Loading
deepchem/feat/material_featurizers/elemnet_featurizer.py +2 −2 Original line number Diff line number Diff line Loading @@ -36,8 +36,8 @@ class ElemNetFeaturizer(MaterialCompositionFeaturizer): >>> featurizer = ElemNetFeaturizer() >>> features = featurizer.featurize([comp]) Notes ----- Note ---- This class requires Pymatgen to be installed. """ Loading
deepchem/feat/molecule_featurizers/maccs_keys_fingerprint.py +2 −2 Original line number Diff line number Diff line Loading @@ -16,8 +16,8 @@ class MACCSKeysFingerprint(MolecularFeaturizer): Journal of chemical information and computer sciences 42.6 (2002): 1273-1280. .. [2] https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MACCSkeys.py Notes ----- Note ---- This class requires RDKit to be installed. """ Loading
deepchem/feat/molecule_featurizers/pubchem_fingerprint.py +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ class PubChemFingerprint(MolecularFeaturizer): ---------- .. [1] ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf Notes Note ----- This class requires RDKit and PubChemPy to be installed. PubChemPy use REST API to get the fingerprint, so you need the internet access. Loading
docs/source/api_reference/featurizers.rst +47 −5 Original line number Diff line number Diff line Loading @@ -34,12 +34,12 @@ These featurizers work with datasets of molecules. Graph Convolution Featurizers ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ MolGraphConvFeaturizer ********************** We are simplifying our graph convolution models by a joint data representation (:code:`GraphData`) in a future version of DeepChem, so we provide several featurizers. .. autoclass:: deepchem.feat.MolGraphConvFeaturizer :members: :inherited-members: :code:`ConvMolFeaturizer` and :code:`WeaveFeaturizer` are used with graph convolution models which inherited :code:`KerasModel`. On the other hand, :code:`MolGraphConvFeaturizer` is used with graph convolution models which inherited :code;`TorchModel`. ConvMolFeaturizer ***************** Loading @@ -55,6 +55,13 @@ WeaveFeaturizer :members: :inherited-members: MolGraphConvFeaturizer ********************** .. autoclass:: deepchem.feat.MolGraphConvFeaturizer :members: :inherited-members: Utilities ********* Loading Loading @@ -366,3 +373,38 @@ UserDefinedFeaturizer .. autoclass:: deepchem.feat.UserDefinedFeaturizer :members: :inherited-members: Base Featurizers (for develop) ------------------------------ Featurizer ^^^^^^^^^^ The :code:`dc.feat.Featurizer` class is the abstract parent class for all featurizers. .. autoclass:: deepchem.feat.Featurizer :members: MolecularFeaturizer ^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MolecularFeaturizer :members: MaterialCompositionFeaturizer ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MaterialCompositionFeaturizer :members: MaterialStructureFeaturizer ^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.MaterialStructureFeaturizer :members: ComplexFeaturizer ^^^^^^^^^^^^^^^^^ .. autoclass:: deepchem.feat.ComplexFeaturizer :members:
