dmlc--dgl
Mufei Li
147 行
4.2 KiB
ReStructuredText
147 行
4.2 KiB
ReStructuredText
.. _apiutilsmols:
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Utils for Molecules
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===================
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Utilities in DGL-LifeSci for working with molecules.
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RDKit Utils
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-----------
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RDKit utils for loading molecules and accessing their information.
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.get_mol_3d_coordinates
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dgllife.utils.load_molecule
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dgllife.utils.multiprocess_load_molecules
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Graph Construction
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------------------
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The modeling of graph neural networks starts with constructing appropriate graph topologies. We provide
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three common graph constructions:
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* ``bigraph``: Bi-directed graphs corresponding exactly to molecular graphs
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* ``complete_graph``: Graphs with all pairs of atoms connected
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* ``nearest_neighbor_graph``: Graphs where each atom is connected to its closest (k) atoms based on molecule coordinates
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.mol_to_graph
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dgllife.utils.smiles_to_bigraph
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dgllife.utils.mol_to_bigraph
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dgllife.utils.smiles_to_complete_graph
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dgllife.utils.mol_to_complete_graph
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dgllife.utils.k_nearest_neighbors
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dgllife.utils.mol_to_nearest_neighbor_graph
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dgllife.utils.smiles_to_nearest_neighbor_graph
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Featurization for Molecules
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---------------------------
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To apply graph neural networks, we need to prepare node and edge features for molecules. Intuitively,
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they can be developed based on various descriptors (features) of atoms/bonds/molecules. Particularly, we can
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work with numerical descriptors directly or use ``one_hot_encoding`` for categorical descriptors. When using
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multiple descriptors together, we can simply concatenate them with ``ConcatFeaturizer``.
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General Utils
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```````````
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.one_hot_encoding
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dgllife.utils.ConcatFeaturizer
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Featurization for Nodes
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```````````````````````
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We consider the following atom descriptors:
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* type/atomic number
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* degree (excluding neighboring hydrogen atoms)
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* total degree (including neighboring hydrogen atoms)
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* explicit valence
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* implicit valence
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* hybridization
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* total number of neighboring hydrogen atoms
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* formal charge
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* number of radical electrons
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* aromatic atom
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* ring membership
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* chirality
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* mass
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We can employ their numerical values directly or with one-hot encoding.
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.atom_type_one_hot
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dgllife.utils.atomic_number_one_hot
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dgllife.utils.atomic_number
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dgllife.utils.atom_degree_one_hot
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dgllife.utils.atom_degree
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dgllife.utils.atom_total_degree_one_hot
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dgllife.utils.atom_total_degree
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dgllife.utils.atom_explicit_valence_one_hot
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dgllife.utils.atom_explicit_valence
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dgllife.utils.atom_implicit_valence_one_hot
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dgllife.utils.atom_implicit_valence
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dgllife.utils.atom_hybridization_one_hot
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dgllife.utils.atom_total_num_H_one_hot
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dgllife.utils.atom_total_num_H
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dgllife.utils.atom_formal_charge_one_hot
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dgllife.utils.atom_formal_charge
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dgllife.utils.atom_num_radical_electrons_one_hot
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dgllife.utils.atom_num_radical_electrons
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dgllife.utils.atom_is_aromatic_one_hot
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dgllife.utils.atom_is_aromatic
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dgllife.utils.atom_is_in_ring_one_hot
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dgllife.utils.atom_is_in_ring
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dgllife.utils.atom_chiral_tag_one_hot
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dgllife.utils.atom_mass
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For using featurization methods like above in creating node features:
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.BaseAtomFeaturizer
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dgllife.utils.BaseAtomFeaturizer.feat_size
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dgllife.utils.CanonicalAtomFeaturizer
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dgllife.utils.CanonicalAtomFeaturizer.feat_size
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Featurization for Edges
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```````````````````````
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We consider the following bond descriptors:
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* type
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* conjugated bond
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* ring membership
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* stereo configuration
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.bond_type_one_hot
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dgllife.utils.bond_is_conjugated_one_hot
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dgllife.utils.bond_is_conjugated
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dgllife.utils.bond_is_in_ring_one_hot
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dgllife.utils.bond_is_in_ring
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dgllife.utils.bond_stereo_one_hot
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For using featurization methods like above in creating edge features:
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.. autosummary::
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:toctree: ../generated/
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dgllife.utils.BaseBondFeaturizer
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dgllife.utils.BaseBondFeaturizer.feat_size
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dgllife.utils.CanonicalBondFeaturizer
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dgllife.utils.CanonicalBondFeaturizer.feat_size
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