Dataset¶
Converters¶
chainer_chemistry.dataset.converters.concat_mols |
Concatenates a list of molecules into array(s). |
Indexers¶
chainer_chemistry.dataset.indexer.BaseIndexer |
Base class for Indexer |
chainer_chemistry.dataset.indexer.BaseFeatureIndexer |
Base class for FeatureIndexer |
chainer_chemistry.dataset.indexers.NumpyTupleDatasetFeatureIndexer |
FeatureIndexer for NumpyTupleDataset |
Parsers¶
chainer_chemistry.dataset.parsers.BaseParser |
|
chainer_chemistry.dataset.parsers.CSVFileParser |
csv file parser |
chainer_chemistry.dataset.parsers.SDFFileParser |
sdf file parser |
chainer_chemistry.dataset.parsers.DataFrameParser |
data frame parser |
chainer_chemistry.dataset.parsers.SmilesParser |
smiles parser |
Preprocessors¶
Base preprocessors¶
chainer_chemistry.dataset.preprocessors.BasePreprocessor |
Base class for preprocessor |
chainer_chemistry.dataset.preprocessors.MolPreprocessor |
preprocessor class specified for rdkit mol instance |
Concrete preprocessors¶
chainer_chemistry.dataset.preprocessors.AtomicNumberPreprocessor |
Atomic number Preprocessor |
chainer_chemistry.dataset.preprocessors.ECFPPreprocessor |
|
chainer_chemistry.dataset.preprocessors.GGNNPreprocessor |
GGNN Preprocessor |
chainer_chemistry.dataset.preprocessors.NFPPreprocessor |
NFP Preprocessor |
chainer_chemistry.dataset.preprocessors.SchNetPreprocessor |
SchNet Preprocessor |
chainer_chemistry.dataset.preprocessors.WeaveNetPreprocessor |
WeaveNet must have fixed-size atom list for now, zero_padding option is always set to True. |
Utilities¶
chainer_chemistry.dataset.preprocessors.MolFeatureExtractionError |
|
chainer_chemistry.dataset.preprocessors.type_check_num_atoms |
Check number of atoms in mol does not exceed num_max_atoms |
chainer_chemistry.dataset.preprocessors.construct_atomic_number_array |
Returns atomic numbers of atoms consisting a molecule. |
chainer_chemistry.dataset.preprocessors.construct_adj_matrix |
Returns the adjacent matrix of the given molecule. |
Splitters¶
chainer_chemistry.dataset.splitters.RandomSplitter |
Class for doing random data splits. |
chainer_chemistry.dataset.splitters.StratifiedSplitter |
Class for doing stratified data splits. |
chainer_chemistry.dataset.splitters.ScaffoldSplitter |
Class for doing data splits by chemical scaffold. |