SYMBOL INDEX (1707 symbols across 266 files)

FILE: .flexci/gen_config.py
  function test_config (line 11) | def test_config(python, chainer, target, chainerx):
  function main (line 40) | def main():
  function dump_pbtxt (line 58) | def dump_pbtxt(key, value, level=0):

FILE: chainer_chemistry/dataset/converters/cgcnn_converter.py
  function cgcnn_converter (line 9) | def cgcnn_converter(batch, device=None, padding=None):

FILE: chainer_chemistry/dataset/converters/concat_mols.py
  function concat_mols (line 5) | def concat_mols(batch, device=None, padding=0):

FILE: chainer_chemistry/dataset/converters/megnet_converter.py
  function megnet_converter (line 6) | def megnet_converter(batch, device=None, padding=0):

FILE: chainer_chemistry/dataset/graph_dataset/base_graph_data.py
  class BaseGraphData (line 6) | class BaseGraphData(object):
    method __init__ (line 9) | def __init__(self, *args, **kwargs):
    method to_device (line 13) | def to_device(self, device):
  class PaddingGraphData (line 35) | class PaddingGraphData(BaseGraphData):
    method __init__ (line 44) | def __init__(self, x=None, adj=None, super_node=None, pos=None, y=None,
  class SparseGraphData (line 55) | class SparseGraphData(BaseGraphData):
    method __init__ (line 65) | def __init__(self, x=None, edge_index=None, edge_attr=None,

FILE: chainer_chemistry/dataset/graph_dataset/base_graph_dataset.py
  class BaseGraphDataset (line 11) | class BaseGraphDataset(object):
    method __init__ (line 17) | def __init__(self, data_list, *args, **kwargs):
    method register_feature (line 20) | def register_feature(self, key, batch_method, skip_if_none=True):
    method update_feature (line 34) | def update_feature(self, key, batch_method):
    method __len__ (line 45) | def __len__(self):
    method __getitem__ (line 48) | def __getitem__(self, item):
    method converter (line 51) | def converter(self, batch, device=None):
  class PaddingGraphDataset (line 70) | class PaddingGraphDataset(BaseGraphDataset):
    method __init__ (line 74) | def __init__(self, data_list):
  class SparseGraphDataset (line 84) | class SparseGraphDataset(BaseGraphDataset):
    method __init__ (line 88) | def __init__(self, data_list):
    method converter (line 98) | def converter(self, batch, device=None):
    method converter_with_padding (line 123) | def converter_with_padding(self, batch, device=None):

FILE: chainer_chemistry/dataset/graph_dataset/feature_converters.py
  function batch_with_padding (line 6) | def batch_with_padding(name, batch, device=None, pad=0):
  function batch_without_padding (line 23) | def batch_without_padding(name, batch, device=None):
  function concat_with_padding (line 39) | def concat_with_padding(name, batch, device=None, pad=0):
  function concat (line 56) | def concat(name, batch, device=None, axis=0):
  function shift_concat (line 73) | def shift_concat(name, batch, device=None, shift_attr='x', shift_axis=1):
  function shift_concat_with_padding (line 96) | def shift_concat_with_padding(name, batch, device=None, shift_attr='x',

FILE: chainer_chemistry/dataset/indexer.py
  class ExtractBySliceNotSupportedError (line 5) | class ExtractBySliceNotSupportedError(Exception):
  class BaseIndexer (line 9) | class BaseIndexer(object):
    method __getitem__ (line 12) | def __getitem__(self, item):
  class BaseFeatureIndexer (line 16) | class BaseFeatureIndexer(BaseIndexer):
    method __init__ (line 32) | def __init__(self, dataset):
    method features_length (line 36) | def features_length(self):
    method dataset_length (line 45) | def dataset_length(self):
    method shape (line 49) | def shape(self):
    method extract_feature_by_slice (line 52) | def extract_feature_by_slice(self, slice_index, j):
    method extract_feature (line 69) | def extract_feature(self, i, j):
    method create_feature_index_list (line 81) | def create_feature_index_list(self, feature_index):
    method preprocess (line 102) | def preprocess(self, item):
    method postprocess (line 105) | def postprocess(self, item):
    method __getitem__ (line 108) | def __getitem__(self, item):
    method check_type_feature_index (line 139) | def check_type_feature_index(self, j):
    method _extract_feature (line 144) | def _extract_feature(self, data_index, j):

FILE: chainer_chemistry/dataset/indexers/numpy_tuple_dataset_feature_indexer.py
  class NumpyTupleDatasetFeatureIndexer (line 4) | class NumpyTupleDatasetFeatureIndexer(BaseFeatureIndexer):
    method __init__ (line 12) | def __init__(self, dataset):
    method features_length (line 16) | def features_length(self):
    method extract_feature_by_slice (line 19) | def extract_feature_by_slice(self, slice_index, j):
    method extract_feature (line 22) | def extract_feature(self, i, j):

FILE: chainer_chemistry/dataset/networkx_preprocessors/base_networkx.py
  class BaseNetworkxPreprocessor (line 10) | class BaseNetworkxPreprocessor(object):
    method __init__ (line 13) | def __init__(self, *args, **kwargs):
    method get_x (line 16) | def get_x(self, graph):
    method get_y (line 27) | def get_y(self, graph):
  class BasePaddingNetworkxPreprocessor (line 37) | class BasePaddingNetworkxPreprocessor(BaseNetworkxPreprocessor):
    method __init__ (line 42) | def __init__(self, use_coo=False, *args, **kwargs):
    method construct_data (line 45) | def construct_data(self, graph):
    method create_dataset (line 91) | def create_dataset(self, graph_list):
  class BaseSparseNetworkxPreprocessor (line 108) | class BaseSparseNetworkxPreprocessor(BaseNetworkxPreprocessor):
    method construct_data (line 113) | def construct_data(self, graph):
    method add_self_loop (line 137) | def add_self_loop(self, graph):
    method create_dataset (line 142) | def create_dataset(self, graph_list):

FILE: chainer_chemistry/dataset/networkx_preprocessors/reddit_coo.py
  function get_reddit_coo_data (line 11) | def get_reddit_coo_data(dirpath):

FILE: chainer_chemistry/dataset/parsers/base_parser.py
  class BaseParser (line 1) | class BaseParser(object):
    method __init__ (line 2) | def __init__(self):
  class BaseFileParser (line 6) | class BaseFileParser(BaseParser):
    method __init__ (line 9) | def __init__(self, preprocessor):
    method parse (line 13) | def parse(self, filepath):

FILE: chainer_chemistry/dataset/parsers/csv_file_parser.py
  class CSVFileParser (line 6) | class CSVFileParser(DataFrameParser):
    method __init__ (line 22) | def __init__(self, preprocessor,
    method parse (line 32) | def parse(self, filepath, return_smiles=False, target_index=None,
    method extract_total_num (line 62) | def extract_total_num(self, filepath):

FILE: chainer_chemistry/dataset/parsers/data_frame_parser.py
  class DataFrameParser (line 14) | class DataFrameParser(BaseFileParser):
    method __init__ (line 30) | def __init__(self, preprocessor,
    method parse (line 44) | def parse(self, df, return_smiles=False, target_index=None,
    method extract_total_num (line 184) | def extract_total_num(self, df):

FILE: chainer_chemistry/dataset/parsers/sdf_file_parser.py
  class SDFFileParser (line 12) | class SDFFileParser(BaseFileParser):
    method __init__ (line 23) | def __init__(self, preprocessor, labels=None, postprocess_label=None,
    method parse (line 31) | def parse(self, filepath, return_smiles=False, target_index=None,
    method extract_total_num (line 171) | def extract_total_num(self, filepath):

FILE: chainer_chemistry/dataset/parsers/smiles_parser.py
  class SmilesParser (line 6) | class SmilesParser(DataFrameParser):
    method __init__ (line 18) | def __init__(self, preprocessor,
    method parse (line 26) | def parse(self, smiles_list, return_smiles=False, target_index=None,
    method extract_total_num (line 56) | def extract_total_num(self, smiles_list):

FILE: chainer_chemistry/dataset/preprocessors/atomic_number_preprocessor.py
  class AtomicNumberPreprocessor (line 8) | class AtomicNumberPreprocessor(MolPreprocessor):
    method __init__ (line 24) | def __init__(self, max_atoms=-1, out_size=-1):
    method get_input_features (line 32) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/base_preprocessor.py
  class BasePreprocessor (line 6) | class BasePreprocessor(object):
    method __init__ (line 9) | def __init__(self):
    method process (line 12) | def process(self, filepath):

FILE: chainer_chemistry/dataset/preprocessors/cgcnn_preprocessor.py
  function get_atom_init_json_filepath (line 18) | def get_atom_init_json_filepath(download_if_not_exist=True):
  class CGCNNPreprocessor (line 40) | class CGCNNPreprocessor(MolPreprocessor):
    method __init__ (line 47) | def __init__(self, max_num_nbr=12, max_radius=8, expand_dim=40):
    method get_input_features (line 58) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/common.py
  class MolFeatureExtractionError (line 9) | class MolFeatureExtractionError(Exception):
  function type_check_num_atoms (line 14) | def type_check_num_atoms(mol, num_max_atoms=-1):
  function construct_atomic_number_array (line 35) | def construct_atomic_number_array(mol, out_size=-1):
  function construct_adj_matrix (line 70) | def construct_adj_matrix(mol, out_size=-1, self_connection=True):
  function construct_discrete_edge_matrix (line 121) | def construct_discrete_edge_matrix(mol, out_size=-1,
  function mol_basic_info_feature (line 180) | def mol_basic_info_feature(mol, atom_array, adj):
  function mol_atom_type_feature (line 191) | def mol_atom_type_feature(mol, atom_array, adj):
  function mol_atom_freq_feature (line 196) | def mol_atom_freq_feature(mol, atom_array, adj):
  function mol_bond_type_feature (line 201) | def mol_bond_type_feature(mol, atom_array, adj):
  function mol_bond_freq_feature (line 208) | def mol_bond_freq_feature(mol, atom_array, adj):
  function construct_supernode_feature (line 219) | def construct_supernode_feature(mol, atom_array, adj, feature_functions=...

FILE: chainer_chemistry/dataset/preprocessors/ecfp_preprocessor.py
  class ECFPPreprocessor (line 10) | class ECFPPreprocessor(MolPreprocessor):
    method __init__ (line 12) | def __init__(self, radius=2):
    method get_input_features (line 16) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/ggnn_preprocessor.py
  class GGNNPreprocessor (line 11) | class GGNNPreprocessor(MolPreprocessor):
    method __init__ (line 29) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 39) | def get_input_features(self, mol):
  class GGNNSparsePreprocessor (line 55) | class GGNNSparsePreprocessor(GGNNPreprocessor):
    method __init__ (line 58) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method construct_sparse_data (line 64) | def construct_sparse_data(self, x, adj, y):
    method create_dataset (line 92) | def create_dataset(self, *args, **kwargs):

FILE: chainer_chemistry/dataset/preprocessors/gin_preprocessor.py
  class GINPreprocessor (line 11) | class GINPreprocessor(MolPreprocessor):
    method __init__ (line 16) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False):
    method get_input_features (line 38) | def get_input_features(self, mol):
  class GINSparsePreprocessor (line 53) | class GINSparsePreprocessor(MolPreprocessor):
    method __init__ (line 56) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False):
    method get_input_features (line 64) | def get_input_features(self, mol):
    method construct_sparse_data (line 70) | def construct_sparse_data(self, x, adj, y):
    method create_dataset (line 94) | def create_dataset(self, *args, **kwargs):

FILE: chainer_chemistry/dataset/preprocessors/gnnfilm_preprocessor.py
  class GNNFiLMPreprocessor (line 7) | class GNNFiLMPreprocessor(MolPreprocessor):
    method __init__ (line 25) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 35) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/gwm_preprocessor.py
  class NFPGWMPreprocessor (line 8) | class NFPGWMPreprocessor(NFPPreprocessor):
    method get_input_features (line 9) | def get_input_features(self, mol):
  class GGNNGWMPreprocessor (line 17) | class GGNNGWMPreprocessor(GGNNPreprocessor):
    method get_input_features (line 18) | def get_input_features(self, mol):
  class GINGWMPreprocessor (line 26) | class GINGWMPreprocessor(GINPreprocessor):
    method get_input_features (line 27) | def get_input_features(self, mol):
  class RSGCNGWMPreprocessor (line 35) | class RSGCNGWMPreprocessor(RSGCNPreprocessor):
    method get_input_features (line 36) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/megnet_preprocessor.py
  class ChemicalFeaturesFactory (line 20) | class ChemicalFeaturesFactory(object):
    method get_instance (line 24) | def get_instance(self):
  function construct_atom_type_vec (line 33) | def construct_atom_type_vec(mol, num_max_atoms, atom_list=None,
  function construct_atom_chirality_vec (line 58) | def construct_atom_chirality_vec(mol, num_max_atoms):
  function construct_atom_ring_vec (line 72) | def construct_atom_ring_vec(mol, num_max_atoms):
  function construct_hybridization_vec (line 85) | def construct_hybridization_vec(mol, num_max_atoms):
  function construct_hydrogen_bonding (line 102) | def construct_hydrogen_bonding(mol, num_max_atoms):
  function construct_aromaticity_vec (line 117) | def construct_aromaticity_vec(mol, num_max_atoms):
  function construct_atom_feature (line 126) | def construct_atom_feature(mol, use_all_feature, atom_list=None,
  function construct_bond_vec (line 176) | def construct_bond_vec(mol, i, j):
  function get_is_in_ring (line 194) | def get_is_in_ring(mol):
  function construct_ring_feature_vec (line 217) | def construct_ring_feature_vec(is_in_ring, i, j):
  function construct_expanded_distance_vec (line 225) | def construct_expanded_distance_vec(distance_matrix_3d, converter, i, j):
  function construct_pair_feature (line 233) | def construct_pair_feature(mol, use_all_feature):
  function construct_global_state_feature (line 299) | def construct_global_state_feature(mol):
  class MEGNetPreprocessor (line 315) | class MEGNetPreprocessor(MolPreprocessor):
    method __init__ (line 339) | def __init__(self, max_atoms=-1, add_Hs=True,
    method get_input_features (line 356) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/mol_preprocessor.py
  class MolPreprocessor (line 7) | class MolPreprocessor(BasePreprocessor):
    method __init__ (line 15) | def __init__(self, add_Hs=False, kekulize=False):
    method prepare_smiles_and_mol (line 20) | def prepare_smiles_and_mol(self, mol):
    method get_label (line 43) | def get_label(self, mol, label_names=None):
    method get_input_features (line 85) | def get_input_features(self, mol):
    method create_dataset (line 96) | def create_dataset(self, *args, **kwargs):
    method process (line 99) | def process(self, filepath):

FILE: chainer_chemistry/dataset/preprocessors/nfp_preprocessor.py
  class NFPPreprocessor (line 9) | class NFPPreprocessor(MolPreprocessor):
    method __init__ (line 27) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 37) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/relgat_preprocessor.py
  class RelGATPreprocessor (line 8) | class RelGATPreprocessor(MolPreprocessor):
    method __init__ (line 24) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False):
    method get_input_features (line 32) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/relgcn_preprocessor.py
  class RelGCNPreprocessor (line 4) | class RelGCNPreprocessor(GGNNPreprocessor):
    method __init__ (line 22) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 28) | def get_input_features(self, mol):
  class RelGCNSparsePreprocessor (line 40) | class RelGCNSparsePreprocessor(GGNNSparsePreprocessor):

FILE: chainer_chemistry/dataset/preprocessors/rsgcn_preprocessor.py
  class RSGCNPreprocessor (line 10) | class RSGCNPreprocessor(MolPreprocessor):
    method __init__ (line 28) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 38) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/schnet_preprocessor.py
  function construct_distance_matrix (line 16) | def construct_distance_matrix(mol, out_size=-1, contain_Hs=False):
  class SchNetPreprocessor (line 68) | class SchNetPreprocessor(MolPreprocessor):
    method __init__ (line 86) | def __init__(self, max_atoms=-1, out_size=-1, add_Hs=False,
    method get_input_features (line 96) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/weavenet_preprocessor.py
  function construct_atom_type_vec (line 24) | def construct_atom_type_vec(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_ATOMS,
  function construct_formal_charge_vec (line 49) | def construct_formal_charge_vec(mol,
  function construct_hybridization_vec (line 59) | def construct_hybridization_vec(mol,
  function construct_partial_charge_vec (line 80) | def construct_partial_charge_vec(
  function construct_atom_ring_vec (line 91) | def construct_atom_ring_vec(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_ATO...
  function construct_hydrogen_bonding (line 105) | def construct_hydrogen_bonding(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_...
  function construct_num_hydrogens_vec (line 120) | def construct_num_hydrogens_vec(mol,
  function construct_aromaticity_vec (line 139) | def construct_aromaticity_vec(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_A...
  function construct_atom_feature (line 148) | def construct_atom_feature(mol, add_Hs,
  function construct_bond_vec (line 202) | def construct_bond_vec(mol, i, j):
  function construct_distance_vec (line 220) | def construct_distance_vec(distance_matrix, i, j):
  function construct_ring_feature_vec (line 227) | def construct_ring_feature_vec(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_...
  function construct_pair_feature (line 243) | def construct_pair_feature(mol, num_max_atoms=WEAVE_DEFAULT_NUM_MAX_ATOMS):
  class WeaveNetPreprocessor (line 272) | class WeaveNetPreprocessor(MolPreprocessor):
    method __init__ (line 298) | def __init__(self, max_atoms=WEAVE_DEFAULT_NUM_MAX_ATOMS, add_Hs=True,
    method get_input_features (line 315) | def get_input_features(self, mol):

FILE: chainer_chemistry/dataset/preprocessors/wle.py
  function apply_wle_for_datasets (line 10) | def apply_wle_for_datasets(datasets, cutoff=0, k=1):
  function apply_cwle_for_datasets (line 42) | def apply_cwle_for_datasets(datasets, k=1):
  function _findmaxidx (line 81) | def _findmaxidx(datasets, idx):
  function findmaxidx (line 99) | def findmaxidx(datasets, target='atom_label'):

FILE: chainer_chemistry/dataset/preprocessors/wle_atom_array_update.py
  function update_atom_arrays (line 8) | def update_atom_arrays(atom_arrays, adj_arrays, cutoff, with_focus_atom=...
  function shrink_expanded_labels (line 20) | def shrink_expanded_labels(expanded_atom_lists,
  function list_all_expanded_labels (line 73) | def list_all_expanded_labels(atom_arrays, adj_arrays, with_focus_atom=Tr...

FILE: chainer_chemistry/dataset/preprocessors/wle_io.py
  function create_datasets (line 10) | def create_datasets(atom_arrays, adj_arrays, teach_signals, wle_arrays=N...
  function load_dataset_elements (line 57) | def load_dataset_elements(datasets):

FILE: chainer_chemistry/dataset/preprocessors/wle_util.py
  function _index (line 7) | def _index(atom, values):
  function to_index (line 15) | def to_index(mols, values):
  function compress_relation_axis (line 21) | def compress_relation_axis(adj_array):
  function _to_string (line 33) | def _to_string(atom_label, neighbor_labels, with_focus_atom):
  function get_neighbor_representation (line 42) | def get_neighbor_representation(idx, atom_array, neighbors, with_focus_a...
  function get_focus_node_label (line 53) | def get_focus_node_label(expanded_label):

FILE: chainer_chemistry/dataset/splitters/base_splitter.py
  function converter_default (line 4) | def converter_default(dataset, indices):
  function converter_numpy_tuple_dataset (line 8) | def converter_numpy_tuple_dataset(dataset, indices):
  class BaseSplitter (line 17) | class BaseSplitter(object):
    method k_fold_split (line 18) | def k_fold_split(self, dataset, k):
    method _split (line 21) | def _split(self, dataset, **kwargs):
    method train_valid_test_split (line 24) | def train_valid_test_split(self, dataset, frac_train=0.8, frac_valid=0.1,
    method train_valid_split (line 43) | def train_valid_split(self, dataset, frac_train=0.9, frac_valid=0.1,

FILE: chainer_chemistry/dataset/splitters/deepchem_scaffold_splitter.py
  function generate_scaffold (line 10) | def generate_scaffold(smiles, include_chirality=False):
  class DeepChemScaffoldSplitter (line 18) | class DeepChemScaffoldSplitter(BaseSplitter):
    method _split (line 23) | def _split(self, dataset, frac_train=0.8, frac_valid=0.1, frac_test=0.1,
    method train_valid_test_split (line 67) | def train_valid_test_split(self, dataset, smiles_list, frac_train=0.8,
    method train_valid_split (line 103) | def train_valid_split(self, dataset, smiles_list, frac_train=0.9,

FILE: chainer_chemistry/dataset/splitters/random_splitter.py
  class RandomSplitter (line 6) | class RandomSplitter(BaseSplitter):
    method _split (line 8) | def _split(self, dataset, frac_train=0.8, frac_valid=0.1, frac_test=0.1,
    method train_valid_test_split (line 24) | def train_valid_test_split(self, dataset, frac_train=0.8, frac_valid=0.1,
    method train_valid_split (line 73) | def train_valid_split(self, dataset, frac_train=0.9, frac_valid=0.1,

FILE: chainer_chemistry/dataset/splitters/scaffold_splitter.py
  function generate_scaffold (line 10) | def generate_scaffold(smiles, include_chirality=False):
  class ScaffoldSplitter (line 18) | class ScaffoldSplitter(BaseSplitter):
    method _split (line 23) | def _split(self, dataset, frac_train=0.8, frac_valid=0.1, frac_test=0.1,
    method train_valid_test_split (line 62) | def train_valid_test_split(self, dataset, smiles_list, frac_train=0.8,
    method train_valid_split (line 98) | def train_valid_split(self, dataset, smiles_list, frac_train=0.9,

FILE: chainer_chemistry/dataset/splitters/stratified_splitter.py
  function _approximate_mode (line 8) | def _approximate_mode(class_counts, n_draws):
  class StratifiedSplitter (line 23) | class StratifiedSplitter(BaseSplitter):
    method _split (line 26) | def _split(self, dataset, frac_train=0.8, frac_valid=0.1, frac_test=0.1,
    method train_valid_test_split (line 109) | def train_valid_test_split(self, dataset, labels=None, label_axis=-1,
    method train_valid_split (line 164) | def train_valid_split(self, dataset, labels=None, label_axis=-1,

FILE: chainer_chemistry/dataset/splitters/time_splitter.py
  class TimeSplitter (line 6) | class TimeSplitter(BaseSplitter):
    method _split (line 9) | def _split(self, dataset, frac_train=0.8, frac_valid=0.1, frac_test=0.1,
    method train_valid_test_split (line 29) | def train_valid_test_split(self, dataset, time_list=None, frac_train=0.8,
    method train_valid_split (line 73) | def train_valid_split(self, dataset, time_list=None, frac_train=0.9,

FILE: chainer_chemistry/dataset/utils.py
  class GaussianDistance (line 4) | class GaussianDistance(object):
    method __init__ (line 13) | def __init__(self, centers=None, width=0.5):
    method expand (line 20) | def expand(self, d):
    method expand_from_distances (line 33) | def expand_from_distances(self, distances):

FILE: chainer_chemistry/datasets/citation_network/citation.py
  function citation_to_networkx (line 8) | def citation_to_networkx(dirpath, name):

FILE: chainer_chemistry/datasets/citation_network/citeseer.py
  function get_citeseer_label_names (line 17) | def get_citeseer_label_names():
  function get_citeseer_dirpath (line 23) | def get_citeseer_dirpath(download_if_not_exist=True):
  function get_citeseer_filepath (line 45) | def get_citeseer_filepath(download_if_not_exist=True):
  function _get_citeseer_filepath (line 70) | def _get_citeseer_filepath():
  function download_and_extract_citeseer (line 85) | def download_and_extract_citeseer(save_dirpath):

FILE: chainer_chemistry/datasets/citation_network/cora.py
  function get_cora_label_names (line 21) | def get_cora_label_names():
  function get_cora_dirpath (line 27) | def get_cora_dirpath(download_if_not_exist=True):
  function get_cora_filepath (line 49) | def get_cora_filepath(download_if_not_exist=True):
  function _get_cora_filepath (line 75) | def _get_cora_filepath():
  function download_and_extract_cora (line 91) | def download_and_extract_cora(save_dirpath):

FILE: chainer_chemistry/datasets/molnet/molnet.py
  function get_molnet_dataset (line 25) | def get_molnet_dataset(dataset_name, preprocessor=None, labels=None,
  function get_molnet_dataframe (line 166) | def get_molnet_dataframe(dataset_name, pdbbind_subset=None):
  function get_molnet_filepath (line 205) | def get_molnet_filepath(dataset_name, filetype='onefile',
  function _get_molnet_filepath (line 244) | def _get_molnet_filepath(file_name):
  function download_dataset (line 260) | def download_dataset(dataset_url, save_filepath):
  function get_pdbbind_smiles (line 279) | def get_pdbbind_smiles(pdbbind_subset, preprocessor=None, labels=None,
  function get_pdbbind_grid (line 385) | def get_pdbbind_grid(pdbbind_subset, split=None, frac_train=.8, frac_val...
  function get_grid_featurized_pdbbind_dataset (line 434) | def get_grid_featurized_pdbbind_dataset(subset):
  function get_grid_featurized_pdbbind_dirpath (line 451) | def get_grid_featurized_pdbbind_dirpath(subset, download_if_not_exist=Tr...
  function get_grid_featurized_pdbbind_filepath (line 482) | def get_grid_featurized_pdbbind_filepath(subset):

FILE: chainer_chemistry/datasets/molnet/molnet_config.py
  function mae (line 16) | def mae(x, t):
  function mse (line 20) | def mse(x, t):
  function rmse (line 24) | def rmse(x, t):
  function r2_score (line 28) | def r2_score(x, t):

FILE: chainer_chemistry/datasets/molnet/pdbbind_time.py
  function get_pdbbind_time (line 10) | def get_pdbbind_time():
  function get_pdbbind_time_filepath (line 24) | def get_pdbbind_time_filepath(download_if_not_exist=True):
  function _get_pdbbind_time_filepath (line 50) | def _get_pdbbind_time_filepath(file_name):
  function download_pdbbind_time (line 66) | def download_pdbbind_time(url, save_filepath):

FILE: chainer_chemistry/datasets/numpy_tuple_dataset.py
  class NumpyTupleDataset (line 10) | class NumpyTupleDataset(object):
    method __init__ (line 25) | def __init__(self, *datasets):
    method __getitem__ (line 37) | def __getitem__(self, index):
    method __len__ (line 46) | def __len__(self):
    method get_datasets (line 49) | def get_datasets(self):
    method converter (line 53) | def converter(self):
    method features (line 57) | def features(self):
    method save (line 78) | def save(cls, filepath, numpy_tuple_dataset):
    method load (line 94) | def load(cls, filepath, allow_pickle=True):

FILE: chainer_chemistry/datasets/qm9.py
  function get_qm9_label_names (line 26) | def get_qm9_label_names():
  function get_qm9 (line 31) | def get_qm9(preprocessor=None, labels=None, return_smiles=False,
  function get_qm9_filepath (line 71) | def get_qm9_filepath(download_if_not_exist=True):
  function _get_qm9_filepath (line 94) | def _get_qm9_filepath():
  function download_and_extract_qm9 (line 107) | def download_and_extract_qm9(save_filepath):

FILE: chainer_chemistry/datasets/reddit/reddit.py
  function reddit_to_networkx (line 18) | def reddit_to_networkx(dirpath):
  function get_reddit_dirpath (line 35) | def get_reddit_dirpath(download_if_not_exist=True):
  function get_reddit_filepath (line 57) | def get_reddit_filepath(download_if_not_exist=True):
  function _get_reddit_filepath (line 82) | def _get_reddit_filepath():
  function download_and_extract_reddit (line 98) | def download_and_extract_reddit(save_dirpath):

FILE: chainer_chemistry/datasets/tox21.py
  function get_tox21_label_names (line 38) | def get_tox21_label_names():
  function get_tox21 (line 43) | def get_tox21(preprocessor=None, labels=None, return_smiles=False,
  function _get_tox21_filepath (line 109) | def _get_tox21_filepath(dataset_type):
  function get_tox21_filepath (line 136) | def get_tox21_filepath(dataset_type, download_if_not_exist=True):
  function _download_and_extract_tox21 (line 165) | def _download_and_extract_tox21(config_name, save_filepath):
  function download_and_extract_tox21 (line 183) | def download_and_extract_tox21():

FILE: chainer_chemistry/datasets/zinc.py
  function get_zinc250k_label_names (line 20) | def get_zinc250k_label_names():
  function get_zinc250k (line 25) | def get_zinc250k(preprocessor=None, labels=None, return_smiles=False,
  function get_zinc250k_filepath (line 65) | def get_zinc250k_filepath(download_if_not_exist=True):
  function _get_zinc250k_filepath (line 89) | def _get_zinc250k_filepath():
  function _remove_new_line (line 102) | def _remove_new_line(s):
  function download_and_extract_zinc250k (line 106) | def download_and_extract_zinc250k(save_filepath):

FILE: chainer_chemistry/functions/activation/megnet_softplus.py
  function megnet_softplus (line 4) | def megnet_softplus(x):

FILE: chainer_chemistry/functions/activation/shifted_softplus.py
  function shifted_softplus (line 5) | def shifted_softplus(x, beta=1, shift=0.5, threshold=20):

FILE: chainer_chemistry/functions/activation/softmax.py
  function softmax (line 4) | def softmax(x, axis=1, mask=None, mask_value=1e10):

FILE: chainer_chemistry/functions/evaluation/r2_score.py
  class R2Score (line 6) | class R2Score(function.Function):
    method __init__ (line 8) | def __init__(self, sample_weight, multioutput, ignore_nan=False):
    method check_type_forward (line 17) | def check_type_forward(self, in_types):
    method forward (line 30) | def forward(self, inputs):
  function r2_score (line 52) | def r2_score(pred, true, sample_weight=None, multioutput='uniform_average',

FILE: chainer_chemistry/functions/loss/mean_absolute_error.py
  class MeanAbsoluteError (line 9) | class MeanAbsoluteError(function_node.FunctionNode):
    method __init__ (line 13) | def __init__(self, ignore_nan=False):
    method check_type_forward (line 17) | def check_type_forward(self, in_types):
    method forward_cpu (line 25) | def forward_cpu(self, inputs):
    method forward_gpu (line 34) | def forward_gpu(self, inputs):
    method backward (line 42) | def backward(self, indexes, gy):
  function mean_absolute_error (line 54) | def mean_absolute_error(x0, x1, ignore_nan=False):

FILE: chainer_chemistry/functions/loss/mean_squared_error.py
  class MeanSquaredError (line 9) | class MeanSquaredError(function_node.FunctionNode):
    method __init__ (line 13) | def __init__(self, ignore_nan=False):
    method check_type_forward (line 17) | def check_type_forward(self, in_types):
    method forward_cpu (line 25) | def forward_cpu(self, inputs):
    method forward_gpu (line 33) | def forward_gpu(self, inputs):
    method backward (line 42) | def backward(self, indexes, gy):
  function mean_squared_error (line 59) | def mean_squared_error(x0, x1, ignore_nan=False):

FILE: chainer_chemistry/functions/math/matmul.py
  function matmul (line 10) | def matmul(a, b, transa=False, transb=False):

FILE: chainer_chemistry/iterators/balanced_serial_iterator.py
  class BalancedSerialIterator (line 11) | class BalancedSerialIterator(iterator.Iterator):
    method __init__ (line 35) | def __init__(self, dataset, batch_size, labels, repeat=True, shuffle=T...
    method __next__ (line 77) | def __next__(self):
    method epoch_detail (line 111) | def epoch_detail(self):
    method previous_epoch_detail (line 115) | def previous_epoch_detail(self):
    method serialize (line 122) | def serialize(self, serializer):
    method _update_order (line 136) | def _update_order(self):
    method reset (line 155) | def reset(self):
    method show_label_stats (line 164) | def show_label_stats(self):

FILE: chainer_chemistry/iterators/index_iterator.py
  class IndexIterator (line 6) | class IndexIterator(iterator.Iterator):
    method __init__ (line 20) | def __init__(self, index_list, shuffle=True, num=0):
    method update_current_index_list (line 31) | def update_current_index_list(self):
    method __next__ (line 37) | def __next__(self):
    method get_next_indices (line 40) | def get_next_indices(self, num):
    method serialize (line 80) | def serialize(self, serializer):

FILE: chainer_chemistry/link_hooks/variable_monitor_link_hook.py
  function _default_extract_pre (line 8) | def _default_extract_pre(hook, args):
  function _default_extract_post (line 20) | def _default_extract_post(hook, args):
  class VariableMonitorLinkHook (line 32) | class VariableMonitorLinkHook(chainer.LinkHook):
    method __init__ (line 87) | def __init__(self, target_link, name='VariableMonitorLinkHook',
    method add_process (line 119) | def add_process(self, key, fn):
    method delete_process (line 134) | def delete_process(self, key):
    method get_variable (line 149) | def get_variable(self):
    method forward_preprocess (line 156) | def forward_preprocess(self, args):
    method forward_postprocess (line 163) | def forward_postprocess(self, args):

FILE: chainer_chemistry/links/array/shape_transformer_to_2d.py
  class ShapeTransformerTo2D (line 5) | class ShapeTransformerTo2D(chainer.Link):
    method __init__ (line 19) | def __init__(self, axis=1):
    method transform (line 25) | def transform(self, x):
    method inverse_transform (line 39) | def inverse_transform(self, x):

FILE: chainer_chemistry/links/connection/embed_atom_id.py
  class EmbedAtomID (line 5) | class EmbedAtomID(chainer.links.EmbedID):
    method __init__ (line 20) | def __init__(self, out_size, in_size=MAX_ATOMIC_NUM, initialW=None,
    method __call__ (line 26) | def __call__(self, x):

FILE: chainer_chemistry/links/connection/graph_linear.py
  class GraphLinear (line 4) | class GraphLinear(chainer.links.Linear):
    method __call__ (line 14) | def __call__(self, x):

FILE: chainer_chemistry/links/connection/graph_mlp.py
  class GraphMLP (line 9) | class GraphMLP(chainer.Chain):
    method __init__ (line 21) | def __init__(self, channels, in_channels=None, activation=relu):
    method __call__ (line 34) | def __call__(self, x):

FILE: chainer_chemistry/links/normalization/graph_batch_normalization.py
  class GraphBatchNormalization (line 4) | class GraphBatchNormalization(chainer.links.BatchNormalization):
    method __call__ (line 10) | def __call__(self, x):

FILE: chainer_chemistry/links/readout/cgcnn_readout.py
  class CGCNNReadout (line 5) | class CGCNNReadout(chainer.Chain):
    method __init__ (line 12) | def __init__(self, out_dim=128):
    method __call__ (line 17) | def __call__(self, atom_feat, atom_idx):

FILE: chainer_chemistry/links/readout/general_readout.py
  class GeneralReadout (line 5) | class GeneralReadout(chainer.Link):
    method __init__ (line 19) | def __init__(self, mode='sum', activation=None, **kwargs):
    method __call__ (line 24) | def __call__(self, h, axis=1, **kwargs):
  class ScatterGeneralReadout (line 43) | class ScatterGeneralReadout(chainer.Link):
    method __init__ (line 53) | def __init__(self, mode='sum', activation=None, **kwargs):
    method __call__ (line 58) | def __call__(self, h, batch, **kwargs):

FILE: chainer_chemistry/links/readout/ggnn_readout.py
  class GGNNReadout (line 7) | class GGNNReadout(chainer.Chain):
    method __init__ (line 24) | def __init__(self, out_dim, in_channels=None, nobias=False,
    method __call__ (line 37) | def __call__(self, h, h0=None, is_real_node=None):

FILE: chainer_chemistry/links/readout/megnet_readout.py
  class MEGNetReadout (line 9) | class MEGNetReadout(chainer.Chain):
    method __init__ (line 24) | def __init__(self, out_dim=32, in_channels=32, n_layers=1,
    method __call__ (line 42) | def __call__(self, atoms_feat, pair_feat, global_feat):

FILE: chainer_chemistry/links/readout/mpnn_readout.py
  class MPNNReadout (line 8) | class MPNNReadout(chainer.Chain):
    method __init__ (line 19) | def __init__(self, out_dim, in_channels, n_layers=1, processing_steps=3):
    method __call__ (line 34) | def __call__(self, h, **kwargs):

FILE: chainer_chemistry/links/readout/nfp_readout.py
  class NFPReadout (line 7) | class NFPReadout(chainer.Chain):
    method __init__ (line 17) | def __init__(self, out_dim, in_channels):
    method __call__ (line 24) | def __call__(self, h, is_real_node=None, **kwargs):

FILE: chainer_chemistry/links/readout/scatter_ggnn_readout.py
  class ScatterGGNNReadout (line 7) | class ScatterGGNNReadout(chainer.Chain):
    method __init__ (line 26) | def __init__(self, out_dim, in_channels=None, nobias=False,
    method __call__ (line 45) | def __call__(self, h, batch, h0=None, is_real_node=None):

FILE: chainer_chemistry/links/readout/schnet_readout.py
  class SchNetReadout (line 8) | class SchNetReadout(chainer.Chain):
    method __init__ (line 17) | def __init__(self, out_dim=1, in_channels=None,
    method __call__ (line 26) | def __call__(self, h, **kwargs):

FILE: chainer_chemistry/links/readout/set2set.py
  class Set2Set (line 10) | class Set2Set(chainer.Chain):
    method __init__ (line 26) | def __init__(self, in_channels, n_layers=1):
    method __call__ (line 41) | def __call__(self, h):
    method reset_state (line 64) | def reset_state(self):

FILE: chainer_chemistry/links/scaler/base.py
  function to_array (line 4) | def to_array(x):
  class BaseScaler (line 11) | class BaseScaler(chainer.Link):
    method fit (line 17) | def fit(self, x, **kwargs):
    method transform (line 24) | def transform(self, x, **kwargs):
    method inverse_transform (line 31) | def inverse_transform(self, x, **kwargs):
    method fit_transform (line 38) | def fit_transform(self, x, **kwargs):
    method forward (line 42) | def forward(self, x, **kwargs):

FILE: chainer_chemistry/links/scaler/flow_scaler.py
  function _sigmoid_derivative (line 8) | def _sigmoid_derivative(x):
  function format_x (line 13) | def format_x(x):
  class FlowScaler (line 26) | class FlowScaler(BaseScaler):
    method __init__ (line 41) | def __init__(self, hidden_num=20):
    method _initialize_params (line 58) | def _initialize_params(self, in_size):
    method W1 (line 65) | def W1(self):
    method W2 (line 69) | def W2(self):
    method _forward (line 72) | def _forward(self, x):
    method _derivative (line 81) | def _derivative(self, x):
    method _loss (line 91) | def _loss(self, x):
    method fit (line 110) | def fit(self, x, batch_size=100, iteration=3000):
    method transform (line 163) | def transform(self, x, batch_size=100):

FILE: chainer_chemistry/links/scaler/max_abs_scaler.py
  function format_x (line 11) | def format_x(x):
  class MaxAbsScaler (line 20) | class MaxAbsScaler(BaseScaler):
    method __init__ (line 22) | def __init__(self):
    method fit (line 29) | def fit(self, x, indices=None, axis=1):
    method _compute_max_abs_all (line 67) | def _compute_max_abs_all(self, input_dim):
    method transform (line 78) | def transform(self, x, axis=1):
    method inverse_transform (line 93) | def inverse_transform(self, x, axis=1):

FILE: chainer_chemistry/links/scaler/min_max_scaler.py
  function format_x (line 11) | def format_x(x):
  class MinMaxScaler (line 20) | class MinMaxScaler(BaseScaler):
    method __init__ (line 22) | def __init__(self):
    method fit (line 31) | def fit(self, x, indices=None, axis=1):
    method _compute_min_diff_all (line 70) | def _compute_min_diff_all(self, input_dim):
    method transform (line 85) | def transform(self, x, axis=1):
    method inverse_transform (line 100) | def inverse_transform(self, x, axis=1):

FILE: chainer_chemistry/links/scaler/standard_scaler.py
  function format_x (line 11) | def format_x(x):
  class StandardScaler (line 20) | class StandardScaler(BaseScaler):
    method __init__ (line 22) | def __init__(self):
    method fit (line 31) | def fit(self, x, indices=None, axis=1):
    method _compute_mean_std_all (line 76) | def _compute_mean_std_all(self, input_dim):
    method transform (line 89) | def transform(self, x, axis=1):
    method inverse_transform (line 103) | def inverse_transform(self, x, axis=1):

FILE: chainer_chemistry/links/update/cgcnn_update.py
  class CGCNNUpdate (line 5) | class CGCNNUpdate(chainer.Chain):
    method __init__ (line 13) | def __init__(self, n_site_features=64):
    method __call__ (line 20) | def __call__(self, site_feat, nbr_feat, nbr_feat_idx):

FILE: chainer_chemistry/links/update/ggnn_update.py
  class GGNNUpdate (line 10) | class GGNNUpdate(chainer.Chain):
    method __init__ (line 21) | def __init__(self, in_channels=None, hidden_channels=16,
    method __call__ (line 39) | def __call__(self, h, adj, **kwargs):
    method reset_state (line 76) | def reset_state(self):

FILE: chainer_chemistry/links/update/gin_update.py
  class GINUpdate (line 8) | class GINUpdate(chainer.Chain):
    method __init__ (line 32) | def __init__(self, in_channels=None, hidden_channels=16, out_channels=...
    method __call__ (line 45) | def __call__(self, h, adj, **kwargs):
  class GINSparseUpdate (line 92) | class GINSparseUpdate(chainer.Chain):
    method __init__ (line 95) | def __init__(self, in_channels=None, hidden_channels=16, out_channels=...
    method __call__ (line 110) | def __call__(self, h, edge_index):

FILE: chainer_chemistry/links/update/gnn_film_update.py
  class GNNFiLMUpdate (line 8) | class GNNFiLMUpdate(chainer.Chain):
    method __init__ (line 17) | def __init__(self, hidden_channels=16, n_edge_types=5,
    method forward (line 31) | def forward(self, h, adj):

FILE: chainer_chemistry/links/update/megnet_update.py
  class DenseLayer (line 8) | class DenseLayer(chainer.Chain):
    method __init__ (line 9) | def __init__(self, hidden_dim=[64, 32], activation=megnet_softplus):
    method __call__ (line 18) | def __call__(self, v):
  class UpdateLayer (line 24) | class UpdateLayer(chainer.Chain):
    method __init__ (line 25) | def __init__(self, hidden_dim=[64, 64, 32], activation=megnet_softplus):
    method __call__ (line 34) | def __call__(self, v):
  function get_mean_feat (line 43) | def get_mean_feat(feat, idx, out_shape, xp):
  class MEGNetUpdate (line 56) | class MEGNetUpdate(chainer.Chain):
    method __init__ (line 73) | def __init__(self, dim_for_dense=[64, 32], dim_for_update=[64, 64, 32],
    method __call__ (line 95) | def __call__(self, atoms_feat, pair_feat, global_feat,

FILE: chainer_chemistry/links/update/mpnn_update.py
  class MPNNUpdate (line 8) | class MPNNUpdate(chainer.Chain):
    method __init__ (line 24) | def __init__(self, in_channels=None, hidden_channels=16, out_channels=...
    method __call__ (line 40) | def __call__(self, h, adj, **kwargs):
    method reset_state (line 50) | def reset_state(self):
  class EdgeNet (line 54) | class EdgeNet(chainer.Chain):
    method __init__ (line 66) | def __init__(self, out_channels, nn=None):
    method __call__ (line 79) | def __call__(self, h, adj):

FILE: chainer_chemistry/links/update/nfp_update.py
  class NFPUpdate (line 9) | class NFPUpdate(chainer.Chain):
    method __init__ (line 18) | def __init__(self, in_channels, out_channels, max_degree=6,
    method __call__ (line 30) | def __call__(self, h, adj, deg_conds):

FILE: chainer_chemistry/links/update/relgat_update.py
  class RelGATUpdate (line 7) | class RelGATUpdate(chainer.Chain):
    method __init__ (line 24) | def __init__(self, in_channels, out_channels, n_heads=3, n_edge_types=4,
    method __call__ (line 42) | def __call__(self, h, adj, **kwargs):

FILE: chainer_chemistry/links/update/relgcn_update.py
  class RelGCNUpdate (line 7) | class RelGCNUpdate(chainer.Chain):
    method __init__ (line 16) | def __init__(self, in_channels, out_channels, n_edge_types=4,
    method __call__ (line 27) | def __call__(self, h, adj, **kwargs):
  class RelGCNSparseUpdate (line 57) | class RelGCNSparseUpdate(chainer.Chain):
    method __init__ (line 60) | def __init__(self, in_channels, out_channels, n_edge_types):
    method __call__ (line 69) | def __call__(self, h, edge_index, edge_attr):

FILE: chainer_chemistry/links/update/rsgcn_update.py
  class RSGCNUpdate (line 7) | class RSGCNUpdate(chainer.Chain):
    method __init__ (line 15) | def __init__(self, in_channels, out_channels, **kwargs):
    method __call__ (line 23) | def __call__(self, h, adj, **kwargs):

FILE: chainer_chemistry/links/update/schnet_update.py
  class CFConv (line 18) | class CFConv(chainer.Chain):
    method __init__ (line 29) | def __init__(self, num_rbf=300, radius_resolution=0.1, gamma=10.0,
    method __call__ (line 40) | def __call__(self, h, dist):
  class SchNetUpdate (line 71) | class SchNetUpdate(chainer.Chain):
    method __init__ (line 84) | def __init__(self, hidden_channels=64, num_rbf=300,
    method __call__ (line 95) | def __call__(self, h, adj, **kwargs):

FILE: chainer_chemistry/models/cgcnn.py
  class CGCNN (line 8) | class CGCNN(chainer.Chain):
    method __init__ (line 22) | def __init__(self, out_dim=128, n_update_layers=3, n_atom_features=64):
    method __call__ (line 31) | def __call__(self, atom_feat, nbr_feat, atom_idx, feat_idx):

FILE: chainer_chemistry/models/cwle/cwle_graph_conv_model.py
  function to_array (line 17) | def to_array(x):
  class CWLEGraphConvModel (line 24) | class CWLEGraphConvModel(chainer.Chain):
    method __init__ (line 56) | def __init__(self, hidden_channels, out_dim, update_layer, readout_layer,
    method __call__ (line 164) | def __call__(self, atom_array, adj, wle_array=None, is_real_node=None):
    method reset_state (line 219) | def reset_state(self):
    method preprocess_addtional_kwargs (line 224) | def preprocess_addtional_kwargs(self, *args, **kwargs):

FILE: chainer_chemistry/models/cwle/cwle_net.py
  class GGNN_CWLE (line 18) | class GGNN_CWLE(CWLEGraphConvModel):
    method __init__ (line 19) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class RelGCN_CWLE (line 35) | class RelGCN_CWLE(CWLEGraphConvModel):
    method __init__ (line 36) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class RelGAT_CWLE (line 52) | class RelGAT_CWLE(CWLEGraphConvModel):
    method __init__ (line 53) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class GIN_CWLE (line 69) | class GIN_CWLE(CWLEGraphConvModel):
    method __init__ (line 70) | def __init__(self, out_dim, hidden_channels=16,
  class NFP_CWLE (line 88) | class NFP_CWLE(CWLEGraphConvModel):
    method __init__ (line 89) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method preprocess_addtional_kwargs (line 104) | def preprocess_addtional_kwargs(self, *args, **kwargs):
  class RSGCN_CWLE (line 123) | class RSGCN_CWLE(CWLEGraphConvModel):
    method __init__ (line 124) | def __init__(self, out_dim, hidden_channels=32, n_update_layers=4,

FILE: chainer_chemistry/models/ggnn.py
  class GGNN (line 11) | class GGNN(chainer.Chain):
    method __init__ (line 31) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method __call__ (line 58) | def __call__(self, atom_array, adj, is_real_node=None):
    method reset_state (line 95) | def reset_state(self):
  class SparseGGNN (line 99) | class SparseGGNN(GGNN):
    method __init__ (line 106) | def __init__(self, *args, **kwargs):
    method __call__ (line 109) | def __call__(self, atom_array, data, row, col, edge_type,

FILE: chainer_chemistry/models/gin.py
  class GIN (line 11) | class GIN(chainer.Chain):
    method __init__ (line 33) | def __init__(self, out_dim, node_embedding=False, hidden_channels=16,
    method __call__ (line 77) | def __call__(self, atom_array, adj, is_real_node=None):
  class GINSparse (line 122) | class GINSparse(chainer.Chain):
    method __init__ (line 125) | def __init__(self, out_dim, node_embedding=False, hidden_channels=16,
    method __call__ (line 168) | def __call__(self, sparse_batch, is_real_node=None):

FILE: chainer_chemistry/models/gnn_film.py
  class GNNFiLM (line 11) | class GNNFiLM(chainer.Chain):
    method __init__ (line 34) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method __call__ (line 65) | def __call__(self, atom_array, adj, is_real_node=None):
    method reset_state (line 103) | def reset_state(self):

FILE: chainer_chemistry/models/gwle/gwle_graph_conv_model.py
  function to_array (line 17) | def to_array(x):
  class GWLEGraphConvModel (line 24) | class GWLEGraphConvModel(chainer.Chain):
    method __init__ (line 56) | def __init__(self, hidden_channels, out_dim, update_layer, readout_layer,
    method __call__ (line 166) | def __call__(self, atom_array, adj, wle_array=None, is_real_node=None):
    method reset_state (line 224) | def reset_state(self):
    method preprocess_addtional_kwargs (line 229) | def preprocess_addtional_kwargs(self, *args, **kwargs):

FILE: chainer_chemistry/models/gwle/gwle_net.py
  class GGNN_GWLE (line 18) | class GGNN_GWLE(GWLEGraphConvModel):
    method __init__ (line 19) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class RelGCN_GWLE (line 35) | class RelGCN_GWLE(GWLEGraphConvModel):
    method __init__ (line 36) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class RelGAT_GWLE (line 52) | class RelGAT_GWLE(GWLEGraphConvModel):
    method __init__ (line 53) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class GIN_GWLE (line 69) | class GIN_GWLE(GWLEGraphConvModel):
    method __init__ (line 70) | def __init__(self, out_dim, hidden_channels=16,
  class NFP_GWLE (line 88) | class NFP_GWLE(GWLEGraphConvModel):
    method __init__ (line 89) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method preprocess_addtional_kwargs (line 104) | def preprocess_addtional_kwargs(self, *args, **kwargs):
  class RSGCN_GWLE (line 123) | class RSGCN_GWLE(GWLEGraphConvModel):
    method __init__ (line 124) | def __init__(self, out_dim, hidden_channels=32, n_update_layers=4,

FILE: chainer_chemistry/models/gwm/gwm.py
  class WarpGateUnit (line 8) | class WarpGateUnit(chainer.Chain):
    method __init__ (line 24) | def __init__(self, output_type='graph', hidden_dim=16,
    method __call__ (line 45) | def __call__(self, h, g):
  class SuperNodeTransmitterUnit (line 57) | class SuperNodeTransmitterUnit(chainer.Chain):
    method __init__ (line 68) | def __init__(self, hidden_dim_super=16, hidden_dim=16, dropout_ratio=-1):
    method __call__ (line 77) | def __call__(self, g, n_nodes):
  class GraphTransmitterUnit (line 100) | class GraphTransmitterUnit(chainer.Chain):
    method __init__ (line 112) | def __init__(self, hidden_dim_super=16, hidden_dim=16, n_heads=8,
    method __call__ (line 126) | def __call__(self, h, g, step=0):
  class GWM (line 185) | class GWM(chainer.Chain):
    method __init__ (line 206) | def __init__(self, hidden_dim=16, hidden_dim_super=16, n_layers=4,
    method __call__ (line 259) | def __call__(self, h, h_new, g, step=0):
    method reset_state (line 300) | def reset_state(self):

FILE: chainer_chemistry/models/gwm/gwm_graph_conv_model.py
  function to_array (line 14) | def to_array(x):
  class GWMGraphConvModel (line 21) | class GWMGraphConvModel(chainer.Chain):
    method __init__ (line 52) | def __init__(self, hidden_channels, out_dim, update_layer, readout_layer,
    method __call__ (line 165) | def __call__(self, atom_array, adj, super_node=None, is_real_node=None):
    method reset_state (line 221) | def reset_state(self):
    method preprocess_addtional_kwargs (line 228) | def preprocess_addtional_kwargs(self, *args, **kwargs):

FILE: chainer_chemistry/models/gwm/gwm_net.py
  class GGNN_GWM (line 11) | class GGNN_GWM(GWMGraphConvModel):
    method __init__ (line 12) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
  class GIN_GWM (line 27) | class GIN_GWM(GWMGraphConvModel):
    method __init__ (line 28) | def __init__(self, out_dim, hidden_channels=16,
  class NFP_GWM (line 46) | class NFP_GWM(GWMGraphConvModel):
    method __init__ (line 47) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method preprocess_addtional_kwargs (line 62) | def preprocess_addtional_kwargs(self, *args, **kwargs):
  class RSGCN_GWM (line 81) | class RSGCN_GWM(GWMGraphConvModel):
    method __init__ (line 82) | def __init__(self, out_dim, hidden_channels=32, n_update_layers=4,

FILE: chainer_chemistry/models/megnet.py
  function reshaped_feat (line 10) | def reshaped_feat(feat, idx):
  class MEGNet (line 23) | class MEGNet(chainer.Chain):
    method __init__ (line 40) | def __init__(self, out_dim=32, n_update_layers=3, dropout_ratio=-1,
    method __call__ (line 60) | def __call__(self, atoms_feat, pair_feat, global_feat, *args):

FILE: chainer_chemistry/models/mlp.py
  class MLP (line 6) | class MLP(chainer.Chain):
    method __init__ (line 18) | def __init__(self, out_dim, hidden_dim=16, n_layers=2, activation=relu):
    method __call__ (line 29) | def __call__(self, x):

FILE: chainer_chemistry/models/mpnn.py
  class MPNN (line 15) | class MPNN(chainer.Chain):
    method __init__ (line 36) | def __init__(
    method __call__ (line 99) | def __call__(self, atom_array, adj):
    method reset_state (line 141) | def reset_state(self):

FILE: chainer_chemistry/models/nfp.py
  class NFP (line 10) | class NFP(chainer.Chain):
    method __init__ (line 28) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method __call__ (line 50) | def __call__(self, atom_array, adj, is_real_node=None):

FILE: chainer_chemistry/models/prediction/base.py
  function _to_tuple (line 13) | def _to_tuple(x):
  function _extract_numpy (line 19) | def _extract_numpy(x):
  class BaseForwardModel (line 25) | class BaseForwardModel(link.Chain):
    method __init__ (line 32) | def __init__(self):
    method initialize (line 37) | def initialize(self, device=-1):
    method update_device (line 51) | def update_device(self, device=-1):
    method _forward (line 62) | def _forward(self, data, fn, batchsize=16,
    method save_pickle (line 126) | def save_pickle(self, filepath, protocol=None):
    method load_pickle (line 181) | def load_pickle(filepath, device=-1):

FILE: chainer_chemistry/models/prediction/classifier.py
  function _argmax (line 14) | def _argmax(*args):
  class Classifier (line 19) | class Classifier(BaseForwardModel):
    method __init__ (line 79) | def __init__(self, predictor,
    method _convert_to_scalar (line 116) | def _convert_to_scalar(self, value):
    method __call__ (line 129) | def __call__(self, *args, **kwargs):
    method predict_proba (line 186) | def predict_proba(
    method predict (line 220) | def predict(
    method compute_accuracy (line 252) | def compute_accuracy(self):
    method compute_accuracy (line 258) | def compute_accuracy(self, value):
    method accuracy (line 264) | def accuracy(self):
    method accuracy (line 270) | def accuracy(self, value):
    method accfun (line 276) | def accfun(self):
    method accfun (line 282) | def accfun(self, value):

FILE: chainer_chemistry/models/prediction/graph_conv_predictor.py
  class GraphConvPredictor (line 7) | class GraphConvPredictor(chainer.Chain):
    method __init__ (line 10) | def __init__(
    method __call__ (line 44) | def __call__(self, *args, **kwargs):
    method predict (line 52) | def predict(self, atoms, adjs):

FILE: chainer_chemistry/models/prediction/node_classifier.py
  class NodeClassifier (line 5) | class NodeClassifier(Classifier):
    method __call__ (line 8) | def __call__(self, data, train_mask, valid_mask, *args, **kwargs):

FILE: chainer_chemistry/models/prediction/regressor.py
  class Regressor (line 12) | class Regressor(BaseForwardModel):
    method __init__ (line 42) | def __init__(self, predictor,
    method _convert_to_scalar (line 72) | def _convert_to_scalar(self, value):
    method __call__ (line 85) | def __call__(self, *args, **kwargs):
    method predict (line 152) | def predict(

FILE: chainer_chemistry/models/prediction/set_up_predictor.py
  function set_up_predictor (line 45) | def set_up_predictor(

FILE: chainer_chemistry/models/relgat.py
  class RelGAT (line 11) | class RelGAT(chainer.Chain):
    method __init__ (line 44) | def __init__(self, out_dim, hidden_channels=16, n_update_layers=4,
    method __call__ (line 90) | def __call__(self, atom_array, adj):

FILE: chainer_chemistry/models/relgcn.py
  function rescale_adj (line 12) | def rescale_adj(adj):
  class RelGCN (line 35) | class RelGCN(chainer.Chain):
    method __init__ (line 56) | def __init__(self, out_dim=64, hidden_channels=None, n_update_layers=N...
    method __call__ (line 87) | def __call__(self, x, adj):
  class RelGCNSparse (line 109) | class RelGCNSparse(chainer.Chain):
    method __init__ (line 130) | def __init__(self, out_dim=64, hidden_channels=None, n_update_layers=N...
    method __call__ (line 161) | def __call__(self, sparse_batch):

FILE: chainer_chemistry/models/rsgcn.py
  class RSGCN (line 10) | class RSGCN(chainer.Chain):
    method __init__ (line 40) | def __init__(self, out_dim, hidden_channels=32, n_update_layers=4,
    method __call__ (line 70) | def __call__(self, atom_array, adj, **kwargs):

FILE: chainer_chemistry/models/schnet.py
  class SchNet (line 10) | class SchNet(chainer.Chain):
    method __init__ (line 34) | def __init__(self, out_dim=1, hidden_channels=64, n_update_layers=3,
    method __call__ (line 55) | def __call__(self, atom_features, dist_features):

FILE: chainer_chemistry/models/weavenet.py
  class LinearLayer (line 14) | class LinearLayer(chainer.Chain):
    method __init__ (line 16) | def __init__(self, n_channel, n_layer):
    method forward (line 24) | def forward(self, x):
  class AtomToPair (line 34) | class AtomToPair(chainer.Chain):
    method __init__ (line 35) | def __init__(self, n_channel, n_layer, n_atom):
    method forward (line 44) | def forward(self, x):
  class PairToAtom (line 78) | class PairToAtom(chainer.Chain):
    method __init__ (line 79) | def __init__(self, n_channel, n_layer, n_atom, mode='sum'):
    method forward (line 90) | def forward(self, x):
  class WeaveModule (line 103) | class WeaveModule(chainer.Chain):
    method __init__ (line 105) | def __init__(self, n_atom, output_channel, n_sub_layer,
    method forward (line 120) | def forward(self, atom_x, pair_x, atom_only=False):
  class WeaveNet (line 137) | class WeaveNet(chainer.Chain):
    method __init__ (line 151) | def __init__(self, weave_channels=None, hidden_dim=16,
    method __call__ (line 168) | def __call__(self, atom_x, pair_x, train=True):

FILE: chainer_chemistry/saliency/calculator/base_calculator.py
  function _to_tuple (line 20) | def _to_tuple(x):
  function _to_variable (line 26) | def _to_variable(x):
  function _extract_numpy (line 32) | def _extract_numpy(x):
  function _concat (line 38) | def _concat(batch_list):
  function add_linkhook (line 49) | def add_linkhook(linkhook, prefix='', logger=None):
  function delete_linkhook (line 62) | def delete_linkhook(linkhook, prefix='', logger=None):
  class BaseCalculator (line 73) | class BaseCalculator(object):
    method __init__ (line 104) | def __init__(self, model, target_extractor=None, output_extractor=None,
    method compute (line 115) | def compute(self, data, M=1, batchsize=16,
    method aggregate (line 157) | def aggregate(self, saliency_arrays, method='raw', ch_axis=None):
    method _compute_core (line 188) | def _compute_core(self, *inputs):
    method get_target_var (line 195) | def get_target_var(self, inputs):
    method get_output_var (line 211) | def get_output_var(self, outputs):
    method _forward (line 223) | def _forward(self, data, batchsize=16,

FILE: chainer_chemistry/saliency/calculator/calculator_utils.py
  class GaussianNoiseSampler (line 4) | class GaussianNoiseSampler(object):
    method __init__ (line 7) | def __init__(self, mode='relative', scale=0.15):
    method sample (line 11) | def sample(self, target_array):

FILE: chainer_chemistry/saliency/calculator/gradient_calculator.py
  class GradientCalculator (line 6) | class GradientCalculator(BaseCalculator):
    method __init__ (line 37) | def __init__(self, model, target_extractor=None, output_extractor=None,
    method _compute_core (line 45) | def _compute_core(self, *inputs):

FILE: chainer_chemistry/saliency/calculator/integrated_gradients_calculator.py
  class IntegratedGradientsCalculator (line 6) | class IntegratedGradientsCalculator(GradientCalculator):
    method __init__ (line 32) | def __init__(self, model, target_extractor=None, output_extractor=None,
    method _compute_core (line 42) | def _compute_core(self, *inputs):

FILE: chainer_chemistry/saliency/calculator/occlusion_calculator.py
  function _to_tuple (line 10) | def _to_tuple(x):
  class OcclusionCalculator (line 20) | class OcclusionCalculator(BaseCalculator):
    method __init__ (line 48) | def __init__(self, model, target_extractor=None, output_extractor=None,
    method _compute_core (line 63) | def _compute_core(self, *inputs):

FILE: chainer_chemistry/saliency/visualizer/base_visualizer.py
  class BaseVisualizer (line 1) | class BaseVisualizer(object):
    method visualize (line 5) | def visualize(self, *args, **kwargs):

FILE: chainer_chemistry/saliency/visualizer/image_visualizer.py
  class ImageVisualizer (line 13) | class ImageVisualizer(BaseVisualizer):
    method __init__ (line 21) | def __init__(self, logger=None):
    method visualize (line 24) | def visualize(self, saliency, image=None, save_filepath=None,

FILE: chainer_chemistry/saliency/visualizer/mol_visualizer.py
  function _convert_to_2d (line 14) | def _convert_to_2d(axes, nrows, ncols):
  function is_visible (line 27) | def is_visible(begin, end):
  class MolVisualizer (line 36) | class MolVisualizer(BaseVisualizer):
    method __init__ (line 44) | def __init__(self, logger=None):
    method visualize (line 47) | def visualize(self, saliency, mol, save_filepath=None,
  class SmilesVisualizer (line 151) | class SmilesVisualizer(MolVisualizer):
    method visualize (line 153) | def visualize(self, saliency, smiles, save_filepath=None,

FILE: chainer_chemistry/saliency/visualizer/table_visualizer.py
  class TableVisualizer (line 8) | class TableVisualizer(BaseVisualizer):
    method visualize (line 12) | def visualize(self, saliency, feature_names=None, save_filepath=None,

FILE: chainer_chemistry/saliency/visualizer/visualizer_utils.py
  function red_blue_cmap (line 7) | def red_blue_cmap(x):
  function min_max_scaler (line 26) | def min_max_scaler(saliency, logger=None):
  function abs_max_scaler (line 48) | def abs_max_scaler(saliency, logger=None):
  function normalize_scaler (line 68) | def normalize_scaler(saliency, axis=None, logger=None):

FILE: chainer_chemistry/training/extensions/auto_print_report.py
  function create_header_and_templates (line 10) | def create_header_and_templates(entries):
  function filter_and_sort_entries (line 22) | def filter_and_sort_entries(all_entries, unit='epoch'):
  class AutoPrintReport (line 43) | class AutoPrintReport(extension.Extension):
    method __init__ (line 59) | def __init__(self, log_report='LogReport', out=sys.stdout):
    method get_log_report (line 71) | def get_log_report(self, trainer):
    method __call__ (line 82) | def __call__(self, trainer):
    method serialize (line 125) | def serialize(self, serializer):
    method _print (line 130) | def _print(self, observation):

FILE: chainer_chemistry/training/extensions/batch_evaluator.py
  function _get_1d_numpy_array (line 13) | def _get_1d_numpy_array(v):
  class BatchEvaluator (line 28) | class BatchEvaluator(Evaluator):
    method __init__ (line 30) | def __init__(self, iterator, target, converter=convert.concat_examples,
    method evaluate (line 48) | def evaluate(self):

FILE: chainer_chemistry/training/extensions/prc_auc_evaluator.py
  function _to_list (line 9) | def _to_list(a):
  class PRCAUCEvaluator (line 25) | class PRCAUCEvaluator(BatchEvaluator):
    method __init__ (line 72) | def __init__(self, iterator, target, converter=convert.concat_examples,
    method prc_auc_score (line 86) | def prc_auc_score(self, y_total, t_total):

FILE: chainer_chemistry/training/extensions/r2_score_evaluator.py
  class R2ScoreEvaluator (line 7) | class R2ScoreEvaluator(BatchEvaluator):
    method __init__ (line 60) | def __init__(self, iterator, target, converter=convert.concat_examples,
    method r2_score (line 78) | def r2_score(self, pred, true, sample_weight=None,

FILE: chainer_chemistry/training/extensions/roc_auc_evaluator.py
  function _to_list (line 9) | def _to_list(a):
  class ROCAUCEvaluator (line 25) | class ROCAUCEvaluator(BatchEvaluator):
    method __init__ (line 72) | def __init__(self, iterator, target, converter=convert.concat_examples,
    method roc_auc_score (line 86) | def roc_auc_score(self, y_total, t_total):

FILE: chainer_chemistry/utils/extend.py
  function _to_list (line 8) | def _to_list(a):
  function extend_node (line 16) | def extend_node(node, out_size, axis=-1, value=0):
  function extend_adj (line 38) | def extend_adj(adj, out_size, axis=None, value=0):
  function extend_arrays_to_size (line 61) | def extend_arrays_to_size(arrays, out_size, axis=-1, value=0):
  function extend_arrays_to_shape (line 94) | def extend_arrays_to_shape(arrays, out_shape, value=0):

FILE: chainer_chemistry/utils/json_utils.py
  class JSONEncoderEX (line 13) | class JSONEncoderEX(json.JSONEncoder):
    method default (line 16) | def default(self, obj):
  function save_json (line 33) | def save_json(filepath, params, ignore_error=False, indent=4, logger=None):
  function load_json (line 62) | def load_json(filepath):

FILE: chainer_chemistry/utils/permutation.py
  function permute_node (line 4) | def permute_node(node, permutation_index, axis=-1):
  function permute_adj (line 24) | def permute_adj(adj, permutation_index, axis=None):

FILE: chainer_chemistry/utils/sparse_utils.py
  function _flatten (line 12) | def _flatten(x):
  function sparse_utils_available (line 19) | def sparse_utils_available():
  function is_sparse (line 25) | def is_sparse(x):
  function convert_sparse_with_edge_type (line 32) | def convert_sparse_with_edge_type(data, row, col, num_nodes,
  function _convert_to_sparse (line 104) | def _convert_to_sparse(dense_adj):

FILE: chainer_chemistry/utils/train_utils.py
  function run_train (line 11) | def run_train(model, train, valid=None,
  function run_node_classification_train (line 88) | def run_node_classification_train(model, data,

FILE: docs/source/_autosummary_check.py
  function _is_rst_exists (line 10) | def _is_rst_exists(entity):
  function check (line 14) | def check(app, exception):
  function _list_chainer_functions (line 36) | def _list_chainer_functions():
  function _list_chainer_links (line 43) | def _list_chainer_links():
  function _list_chainer_models (line 50) | def _list_chainer_models():

FILE: docs/source/conf.py
  function setup (line 189) | def setup(app):
  function _build_finished (line 192) | def _build_finished(app, exception):

FILE: examples/molnet/predict_molnet.py
  function parse_arguments (line 30) | def parse_arguments():
  function main (line 63) | def main():

FILE: examples/molnet/summary_eval_molnet.py
  function save_evaluation_plot (line 17) | def save_evaluation_plot(x, y_mean, metric, dataset_name, filename):
  function main (line 38) | def main():

FILE: examples/molnet/train_molnet.py
  function parse_arguments (line 29) | def parse_arguments():
  function dataset_part_filename (line 71) | def dataset_part_filename(dataset_part, num_data):
  function download_entire_dataset (line 84) | def download_entire_dataset(dataset_name, num_data, labels, method, cach...
  function fit_scaler (line 116) | def fit_scaler(datasets):
  function main (line 140) | def main():

FILE: examples/molnet_wle/predict_molnet_wle.py
  function parse_arguments (line 33) | def parse_arguments():
  function main (line 69) | def main():

FILE: examples/molnet_wle/train_molnet_wle.py
  function dict_for_wles (line 33) | def dict_for_wles():
  function parse_arguments (line 65) | def parse_arguments():
  function dataset_part_filename (line 116) | def dataset_part_filename(dataset_part, num_data):
  function download_entire_dataset (line 129) | def download_entire_dataset(dataset_name, num_data, labels, method, cach...
  function fit_scaler (line 252) | def fit_scaler(datasets):
  function main (line 276) | def main():

FILE: examples/network_graph/padding_model_wrapper.py
  class PaddingModelWrapper (line 5) | class PaddingModelWrapper(chainer.Chain):
    method __init__ (line 6) | def __init__(self, predictor):
    method forward (line 11) | def forward(self, data):

FILE: examples/network_graph/train_network_graph.py
  function get_cora (line 21) | def get_cora():
  function get_citeseer (line 25) | def get_citeseer():
  function get_reddit (line 29) | def get_reddit():
  function parse_arguments (line 48) | def parse_arguments():
  function generate_random_mask (line 84) | def generate_random_mask(n, train_num, seed=777):

FILE: examples/own_dataset/plot.py
  function save_evaluation_plot (line 10) | def save_evaluation_plot(x, y, metric, filename):
  function main (line 31) | def main():

FILE: examples/own_dataset/predict_own_dataset.py
  function parse_arguments (line 26) | def parse_arguments():
  function main (line 68) | def main():

FILE: examples/own_dataset/train_own_dataset.py
  function rmse (line 23) | def rmse(x0, x1):
  function parse_arguments (line 27) | def parse_arguments():
  function main (line 71) | def main():

FILE: examples/qm9/plot.py
  function save_evaluation_plot (line 12) | def save_evaluation_plot(x, y, metric, filename):
  function main (line 34) | def main():

FILE: examples/qm9/predict_qm9.py
  function parse_arguments (line 28) | def parse_arguments():
  function main (line 66) | def main():

FILE: examples/qm9/train_qm9.py
  function rmse (line 23) | def rmse(x0, x1):
  function parse_arguments (line 27) | def parse_arguments():
  function main (line 75) | def main():

FILE: examples/tox21/data.py
  class _CacheNamePolicy (line 10) | class _CacheNamePolicy(object):
    method _get_cache_directory_path (line 16) | def _get_cache_directory_path(self, method, labels, prefix, num_data):
    method __init__ (line 25) | def __init__(self, method, labels, prefix='input', num_data=-1):
    method get_train_file_path (line 33) | def get_train_file_path(self):
    method get_val_file_path (line 36) | def get_val_file_path(self):
    method get_test_file_path (line 39) | def get_test_file_path(self):
    method create_cache_directory (line 42) | def create_cache_directory(self):
  function load_dataset (line 50) | def load_dataset(method, labels, prefix='input', num_data=-1):

FILE: examples/tox21/predict_tox21_with_classifier.py
  function main (line 28) | def main():

FILE: examples/tox21/train_tox21.py
  function main (line 33) | def main():

FILE: tests/dataset_tests/parsers_tests/test_csv_file_parser.py
  function mol_smiles (line 14) | def mol_smiles():
  function mols (line 22) | def mols(mol_smiles):
  function label_a (line 27) | def label_a():
  function csv_file (line 32) | def csv_file(tmpdir, mol_smiles, label_a):
  function csv_file_invalid (line 43) | def csv_file_invalid(tmpdir):
  function check_input_features (line 54) | def check_input_features(actual, expect):
  function check_features (line 60) | def check_features(actual, expect_input_features, expect_label):
  function test_csv_file_parser_not_return_smiles (line 69) | def test_csv_file_parser_not_return_smiles(csv_file, mols):
  function test_csv_file_parser_return_smiles (line 88) | def test_csv_file_parser_return_smiles(csv_file, mols, label_a):
  function test_csv_file_parser_target_index (line 112) | def test_csv_file_parser_target_index(csv_file_invalid, mols, label_a):
  function test_csv_file_parser_extract_total_num (line 141) | def test_csv_file_parser_extract_total_num(csv_file):
  function test_csv_parser_return_is_successful (line 148) | def test_csv_parser_return_is_successful(csv_file_invalid, mols, label_a):

FILE: tests/dataset_tests/parsers_tests/test_data_frame_parser.py
  function mol_smiles (line 12) | def mol_smiles():
  function mols (line 20) | def mols(mol_smiles):
  function label_a (line 25) | def label_a():
  function data_frame (line 30) | def data_frame(mol_smiles, label_a):
  function check_input_features (line 38) | def check_input_features(actual, expect):
  function check_features (line 44) | def check_features(actual, expect_input_features, expect_label):
  function test_data_frame_parser_not_return_smiles (line 53) | def test_data_frame_parser_not_return_smiles(data_frame, mols):
  function test_data_frame_parser_return_smiles (line 73) | def test_data_frame_parser_return_smiles(data_frame, mols, label_a):
  function test_data_frame_parser_target_index (line 97) | def test_data_frame_parser_target_index(data_frame, mols, label_a):
  function test_data_frame_parser_return_is_successful (line 126) | def test_data_frame_parser_return_is_successful(mols, label_a):
  function test_data_frame_parser_extract_total_num (line 152) | def test_data_frame_parser_extract_total_num(data_frame):

FILE: tests/dataset_tests/parsers_tests/test_sdf_file_parser.py
  function mols (line 13) | def mols():
  function sdf_file (line 21) | def sdf_file(tmpdir, mols):
  function sdf_file_long (line 31) | def sdf_file_long(tmpdir):
  function check_input_features (line 42) | def check_input_features(actual, expect):
  function test_sdf_file_parser_not_return_smiles (line 48) | def test_sdf_file_parser_not_return_smiles(sdf_file, mols):
  function test_sdf_file_parser_return_smiles (line 66) | def test_sdf_file_parser_return_smiles(sdf_file, mols):
  function test_sdf_file_parser_target_index (line 89) | def test_sdf_file_parser_target_index(sdf_file, mols):
  function test_sdf_file_parser_return_is_successful (line 117) | def test_sdf_file_parser_return_is_successful(sdf_file_long, mols):
  function test_sdf_file_parser_extract_total_num (line 138) | def test_sdf_file_parser_extract_total_num(sdf_file):

FILE: tests/dataset_tests/parsers_tests/test_smiles_parser.py
  function mol_smiles (line 11) | def mol_smiles():
  function mols (line 19) | def mols(mol_smiles):
  function check_input_features (line 23) | def check_input_features(actual, expect):
  function test_smiles_parser_not_return_smiles (line 29) | def test_smiles_parser_not_return_smiles(mol_smiles, mols):
  function test_smiles_parser_return_smiles (line 47) | def test_smiles_parser_return_smiles(mol_smiles, mols):
  function test_smiles_parser_target_index (line 71) | def test_smiles_parser_target_index(mol_smiles, mols):
  function test_smiles_parser_return_is_successful (line 100) | def test_smiles_parser_return_is_successful(mols):
  function test_smiles_parser_extract_total_num (line 122) | def test_smiles_parser_extract_total_num(mol_smiles):

FILE: tests/dataset_tests/preprocessor_tests/test_common.py
  function sample_molecule (line 11) | def sample_molecule():
  function sample_molecule_2 (line 16) | def sample_molecule_2():
  class TestGetAtomicNumbers (line 20) | class TestGetAtomicNumbers(object):
    method test_normal (line 22) | def test_normal(self, sample_molecule):
    method test_padding (line 29) | def test_padding(self, sample_molecule):
    method test_normal_truncated (line 36) | def test_normal_truncated(self, sample_molecule):
  class TestGetAdjMatrix (line 41) | class TestGetAdjMatrix(object):
    method test_normal (line 43) | def test_normal(self, sample_molecule_2):
    method test_normal_no_self_connection (line 58) | def test_normal_no_self_connection(self, sample_molecule_2):
    method test_normal_padding (line 74) | def test_normal_padding(self, sample_molecule_2):
    method test_normal_truncated (line 90) | def test_normal_truncated(self, sample_molecule_2):
  class TestConstructDiscreteEdgeMatrix (line 95) | class TestConstructDiscreteEdgeMatrix(object):
    method test_default (line 127) | def test_default(self, sample_molecule_2):
    method test_add_self_connection_channel (line 132) | def test_add_self_connection_channel(self, sample_molecule_2):
    method test_padding (line 139) | def test_padding(self, sample_molecule_2):
    method test_truncated (line 146) | def test_truncated(self, sample_molecule_2):
  function test_construct_super_node_feature_adj_ndim2 (line 151) | def test_construct_super_node_feature_adj_ndim2(sample_molecule):
  function test_construct_super_node_feature_adj_ndim3 (line 171) | def test_construct_super_node_feature_adj_ndim3(sample_molecule):

FILE: tests/dataset_tests/preprocessors_tests/test_atomic_number_preprocessor.py
  function mol (line 11) | def mol():
  function test_atomic_number_default_preprocessor (line 16) | def test_atomic_number_default_preprocessor(mol):
  function test_atomic_number_non_default_padding_preprocessor (line 23) | def test_atomic_number_non_default_padding_preprocessor(mol):
  function test_atomic_number_non_default_max_atoms_preprocessor (line 31) | def test_atomic_number_non_default_max_atoms_preprocessor(mol):
  function test_atomic_number_preprocessor (line 43) | def test_atomic_number_preprocessor(mol):
  function test_atomic_number_preprocessor_default (line 51) | def test_atomic_number_preprocessor_default():
  function test_atomic_number_preprocessor_assert_raises (line 62) | def test_atomic_number_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_cgcnn_preprocessor.py
  function test_cgcnn_preprocessor_init (line 6) | def test_cgcnn_preprocessor_init():

FILE: tests/dataset_tests/preprocessors_tests/test_gat_preprocessor.py
  function test_gat_preprocessor (line 10) | def test_gat_preprocessor():
  function test_gat_preprocessor_assert_raises (line 31) | def test_gat_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_ggnn_preprocessor.py
  function test_ggnn_preprocessor (line 8) | def test_ggnn_preprocessor():
  function test_ggnn_preprocessor_kekulize (line 79) | def test_ggnn_preprocessor_kekulize():
  function test_ggnn_preprocessor_assert_raises (line 128) | def test_ggnn_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_gwm_preprocessor.py
  function mol (line 10) | def mol():
  function test_gwm_preprocessor (line 18) | def test_gwm_preprocessor(mol, pp_type):

FILE: tests/dataset_tests/preprocessors_tests/test_mol_preprocessor.py
  function mol (line 8) | def mol():
  function pp (line 16) | def pp():
  class TestGetLabel (line 20) | class TestGetLabel(object):
    method test_default (line 22) | def test_default(self, mol, pp):
    method test_empty (line 26) | def test_empty(self, mol, pp):
    method test_one_label (line 30) | def test_one_label(self, mol, pp):
    method test_two_labels (line 34) | def test_two_labels(self, mol, pp):
    method test_non_existent_label (line 38) | def test_non_existent_label(self, mol, pp):

FILE: tests/dataset_tests/preprocessors_tests/test_nfp_preprocessor.py
  function mol (line 10) | def mol():
  function pp (line 16) | def pp():
  function test_nfp_preprocessor (line 20) | def test_nfp_preprocessor(mol, pp):
  function test_nfp_preprocessor_default (line 35) | def test_nfp_preprocessor_default():
  function test_nfp_preprocessor_assert_raises (line 51) | def test_nfp_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_relgcn_preprocessor.py
  function test_relgcn_preprocessor (line 8) | def test_relgcn_preprocessor():
  function test_relgcn_preprocessor_kekulize (line 79) | def test_relgcn_preprocessor_kekulize():
  function test_relgcn_preprocessor_assert_raises (line 128) | def test_relgcn_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_rsgcn_preprocessor.py
  function mol (line 11) | def mol():
  function test_rsgcn_default_preprocessor (line 15) | def test_rsgcn_default_preprocessor(mol):
  function test_rsgcn_non_default_padding_preprocessor (line 29) | def test_rsgcn_non_default_padding_preprocessor(mol):
  function test_rsgcn_non_default_max_atoms_preprocessor (line 44) | def test_rsgcn_non_default_max_atoms_preprocessor(mol):
  function test_rsgcn_preprocessor (line 62) | def test_rsgcn_preprocessor(mol):
  function test_rsgcn_preprocessor_default (line 76) | def test_rsgcn_preprocessor_default():
  function test_rsgcn_preprocessor_assert_raises (line 91) | def test_rsgcn_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_schnet_preprocessor.py
  function mol (line 10) | def mol():
  function pp (line 16) | def pp():
  function test_schnet_preprocessor (line 20) | def test_schnet_preprocessor(mol, pp):
  function test_schnet_preprocessor_default (line 37) | def test_schnet_preprocessor_default():
  function test_schnet_preprocessor_assert_raises (line 53) | def test_schnet_preprocessor_assert_raises():

FILE: tests/dataset_tests/preprocessors_tests/test_weavenet_preprocessor.py
  function test_weave_preprocessor (line 10) | def test_weave_preprocessor(max_atoms, use_fixed_atom_feature):

FILE: tests/dataset_tests/preprocessors_tests/test_wle.py
  function small_datasets (line 9) | def small_datasets():
  function _get_elements (line 53) | def _get_elements(datasets, idx):
  function _get_atom_arrays (line 57) | def _get_atom_arrays(datasets):
  function _get_adj_arrays (line 61) | def _get_adj_arrays(datasets):
  function _get_wle_arrays (line 65) | def _get_wle_arrays(datasets):
  function _get_teach_signals (line 69) | def _get_teach_signals(datasets, is_cwle=False):
  function _check_np_array (line 76) | def _check_np_array(actuals, expects):
  function test_wle (line 84) | def test_wle(small_datasets):
  function test_2_hop_wle (line 120) | def test_2_hop_wle(small_datasets):
  function test_cwle (line 163) | def test_cwle(small_datasets):
  function test_findmaxidx_atom_label (line 206) | def test_findmaxidx_atom_label(small_datasets):
  function cwle_datasets (line 213) | def cwle_datasets():
  function test_findmaxidx_wle (line 235) | def test_findmaxidx_wle(cwle_datasets):

FILE: tests/dataset_tests/preprocessors_tests/test_wle_atom_array_update.py
  function k3_datasets (line 11) | def k3_datasets():
  function _is_all_same (line 23) | def _is_all_same(arr):
  function _is_all_different (line 29) | def _is_all_different(arr):
  function test_update_atom_array (line 37) | def test_update_atom_array(k3_datasets, cutoff):
  function single_atom_datasets (line 57) | def single_atom_datasets():
  function test_update_atom_array_2 (line 70) | def test_update_atom_array_2(single_atom_datasets, cutoff):
  function different_sample_size_datasets (line 102) | def different_sample_size_datasets():
  function test_update_atom_array_with_diffent_sample_sizes (line 114) | def test_update_atom_array_with_diffent_sample_sizes(
  function different_graph_size_datasets (line 128) | def different_graph_size_datasets():
  function test_update_atom_array_with_different_graph_size (line 143) | def test_update_atom_array_with_different_graph_size(
  function line_graph_datasets (line 158) | def line_graph_datasets():
  function test_update_atom_array_twice (line 175) | def test_update_atom_array_twice(line_graph_datasets):
  function small_datasets (line 190) | def small_datasets():
  function test_list_all_expanded_labels_with_focus_atom (line 232) | def test_list_all_expanded_labels_with_focus_atom(small_datasets):
  function test_list_all_expanded_labels_without_focus_atom (line 257) | def test_list_all_expanded_labels_without_focus_atom(small_datasets):

FILE: tests/dataset_tests/preprocessors_tests/test_wle_util.py
  function test_to_index (line 7) | def test_to_index():
  function test_to_index_non_existence (line 20) | def test_to_index_non_existence():
  function test_compress_relation_axis_2_dim (line 28) | def test_compress_relation_axis_2_dim():
  function test_compress_relation_axis_3_dim (line 34) | def test_compress_relation_axis_3_dim():
  function test_compress_relation_axis_invalid_ndim (line 57) | def test_compress_relation_axis_invalid_ndim():
  function small_molecule (line 68) | def small_molecule():
  function test_get_neighbor_representation_with_focus_atom (line 80) | def test_get_neighbor_representation_with_focus_atom(small_molecule):
  function test_get_neighbor_representation_without_focus_atom (line 89) | def test_get_neighbor_representation_without_focus_atom(small_molecule):
  function test_get_focus_node_label (line 105) | def test_get_focus_node_label(label, expect):
  function test_get_focus_node_label_invalid (line 111) | def test_get_focus_node_label_invalid(label):

FILE: tests/dataset_tests/splitters_tests/test_deepchem_scaffold_splitter.py
  function smiles_list (line 13) | def smiles_list():
  function dataset (line 30) | def dataset(smiles_list):
  function test_generate_scaffold (line 39) | def test_generate_scaffold():
  function test_split (line 46) | def test_split(dataset):
  function test_split_fix_seed (line 64) | def test_split_fix_seed(dataset):
  function test_split_fail (line 76) | def test_split_fail(dataset):
  function test_train_valid_test_split (line 84) | def test_train_valid_test_split(dataset):
  function test_train_valid_test_split_return_dataset (line 95) | def test_train_valid_test_split_return_dataset(dataset):
  function test_train_valid_split (line 109) | def test_train_valid_split(dataset):
  function test_train_valid_split_return_dataset (line 119) | def test_train_valid_split_return_dataset(dataset):

FILE: tests/dataset_tests/splitters_tests/test_random_splitter.py
  function dataset (line 9) | def dataset():
  function ndarray_dataset (line 17) | def ndarray_dataset():
  function test_split (line 22) | def test_split(dataset):
  function test_split_fix_seed (line 40) | def test_split_fix_seed(dataset):
  function test_split_fail (line 50) | def test_split_fail(dataset):
  function test_train_valid_test_split (line 59) | def test_train_valid_test_split(dataset):
  function test_train_valid_test_split_return_dataset (line 68) | def test_train_valid_test_split_return_dataset(dataset):
  function test_train_valid_test_split_ndarray_return_dataset (line 80) | def test_train_valid_test_split_ndarray_return_dataset(ndarray_dataset):
  function test_train_valid_split (line 92) | def test_train_valid_split(dataset):
  function test_train_valid_split_return_dataset (line 100) | def test_train_valid_split_return_dataset(dataset):

FILE: tests/dataset_tests/splitters_tests/test_scaffold_splitter.py
  function smiles_list (line 13) | def smiles_list():
  function dataset (line 30) | def dataset(smiles_list):
  function test_generate_scaffold (line 39) | def test_generate_scaffold():
  function test_split (line 46) | def test_split(dataset):
  function test_split_fix_seed (line 64) | def test_split_fix_seed(dataset):
  function test_split_fail (line 76) | def test_split_fail(dataset):
  function test_train_valid_test_split (line 84) | def test_train_valid_test_split(dataset):
  function test_train_valid_test_split_return_dataset (line 95) | def test_train_valid_test_split_return_dataset(dataset):
  function test_train_valid_split (line 109) | def test_train_valid_split(dataset):
  function test_train_valid_split_return_dataset (line 119) | def test_train_valid_split_return_dataset(dataset):

FILE: tests/dataset_tests/splitters_tests/test_stratified_splitter.py
  function cls_dataset (line 9) | def cls_dataset():
  function cls_label (line 17) | def cls_label():
  function cls_ndarray_dataset (line 23) | def cls_ndarray_dataset():
  function reg_dataset (line 30) | def reg_dataset():
  function test_classification_split (line 37) | def test_classification_split(cls_dataset):
  function test_classification_split_by_labels_ndarray (line 69) | def test_classification_split_by_labels_ndarray(cls_dataset, cls_label):
  function test_classification_split_by_labels_list (line 103) | def test_classification_split_by_labels_list(cls_dataset, cls_label):
  function test_regression_split (line 138) | def test_regression_split(reg_dataset):
  function test_classification_split_fix_seed (line 170) | def test_classification_split_fix_seed(cls_dataset):
  function test_split_fail_by_frac_ratio (line 180) | def test_split_fail_by_frac_ratio(cls_dataset):
  function test_split_fail_by_invalid_task_type (line 189) | def test_split_fail_by_invalid_task_type(cls_dataset):
  function test_regression_split_fix_seed (line 199) | def test_regression_split_fix_seed(reg_dataset):
  function test_train_valid_test_classification_split (line 209) | def test_train_valid_test_classification_split(cls_dataset):
  function test_train_valid_test_classification_split_return_dataset (line 226) | def test_train_valid_test_classification_split_return_dataset(cls_dataset):
  function test_train_valid_test_classification_split_ndarray_return_dataset (line 241) | def test_train_valid_test_classification_split_ndarray_return_dataset(
  function test_train_valid_test_regression_split (line 259) | def test_train_valid_test_regression_split(reg_dataset):
  function test_train_valid_test_regression_split_return_dataset (line 276) | def test_train_valid_test_regression_split_return_dataset(reg_dataset):
  function test_train_valid_classification_split (line 291) | def test_train_valid_classification_split(cls_dataset):
  function test_train_valid_classification_split_return_dataset (line 304) | def test_train_valid_classification_split_return_dataset(cls_dataset):
  function test_train_valid_classification_split_ndarray_return_dataset (line 315) | def test_train_valid_classification_split_ndarray_return_dataset(
  function test_train_valid_test_cls_split_by_labels_return_dataset (line 329) | def test_train_valid_test_cls_split_by_labels_return_dataset(cls_dataset,
  function test_train_valid_cls_split_by_labels_return_dataset (line 346) | def test_train_valid_cls_split_by_labels_return_dataset(cls_dataset,
  function test_train_valid_regression_split (line 359) | def test_train_valid_regression_split(reg_dataset):
  function test_train_valid_regression_split_return_dataset (line 372) | def test_train_valid_regression_split_return_dataset(reg_dataset):

FILE: tests/dataset_tests/splitters_tests/test_time_splitter.py
  function time_list (line 9) | def time_list():
  function dataset (line 26) | def dataset():
  function test_split (line 33) | def test_split(dataset, time_list):
  function test_split_fail (line 57) | def test_split_fail(dataset, time_list):
  function test_train_valid_test_split (line 65) | def test_train_valid_test_split(dataset, time_list):
  function test_train_valid_test_split_return_dataset (line 78) | def test_train_valid_test_split_return_dataset(dataset, time_list):
  function test_train_valid_split (line 90) | def test_train_valid_split(dataset, time_list):
  function test_train_split_return_dataset (line 101) | def test_train_split_return_dataset(dataset, time_list):

FILE: tests/dataset_tests/test_converters.py
  function data_1d (line 9) | def data_1d():
  function data_1d_expect (line 16) | def data_1d_expect():
  function data_2d (line 23) | def data_2d():
  function data_2d_expect (line 30) | def data_2d_expect():
  function test_concat_mols_1d_cpu (line 36) | def test_concat_mols_1d_cpu(data_1d, data_1d_expect):
  function test_concat_mols_2d_cpu (line 42) | def test_concat_mols_2d_cpu(data_2d, data_2d_expect):
  function test_concat_mols_1d_gpu (line 49) | def test_concat_mols_1d_gpu(data_1d, data_1d_expect):
  function test_concat_mols_2d_gpu (line 60) | def test_concat_mols_2d_gpu(data_2d, data_2d_expect):

FILE: tests/dataset_tests/test_numpy_tuple_feature_indexer.py
  function data (line 10) | def data():
  function indexer (line 18) | def indexer(data):
  class TestNumpyTupleDatasetFeatureIndexer (line 24) | class TestNumpyTupleDatasetFeatureIndexer(object):
    method test_feature_length (line 26) | def test_feature_length(self, indexer):
    method test_extract_feature_by_slice (line 32) | def test_extract_feature_by_slice(self, indexer, data, slice_index, j):
    method test_extract_feature_by_ndarray (line 46) | def test_extract_feature_by_ndarray(self, indexer, data, ndarray_index...

FILE: tests/datasets_tests/molnet_tests/test_molnet.py
  function test_get_molnet_filepath_without_download (line 19) | def test_get_molnet_filepath_without_download():
  function test_get_molnet_filepath_with_download (line 30) | def test_get_molnet_filepath_with_download():
  function test_get_grid_featurized_pdbbind_dataset (line 40) | def test_get_grid_featurized_pdbbind_dataset():
  function test_get_molnet_bbbp_dataset (line 71) | def test_get_molnet_bbbp_dataset():
  function test_get_molnet_bbbp_dataset_change_split_ratio (line 100) | def test_get_molnet_bbbp_dataset_change_split_ratio():
  function test_get_molnet_bbbp_dataset_with_smiles (line 130) | def test_get_molnet_bbbp_dataset_with_smiles():
  function test_get_molnet_clearance_dataset (line 160) | def test_get_molnet_clearance_dataset():
  function test_get_molnet_clearance_dataset_with_return_smiles_enabled (line 187) | def test_get_molnet_clearance_dataset_with_return_smiles_enabled():
  function test_get_molnet_pdbbind_dataset (line 218) | def test_get_molnet_pdbbind_dataset():
  function test_get_molnet_pdbbind_dataset_with_pdb_id (line 252) | def test_get_molnet_pdbbind_dataset_with_pdb_id():
  function test_get_molnet_grid_featurized_pdbbind_dataset (line 287) | def test_get_molnet_grid_featurized_pdbbind_dataset():
  function test_get_molnet_qm7_dataset (line 317) | def test_get_molnet_qm7_dataset():
  function test_get_molnet_qm7_dataset_with_smiles (line 348) | def test_get_molnet_qm7_dataset_with_smiles():
  function test_get_molnet_bbbp_dataframe (line 381) | def test_get_molnet_bbbp_dataframe():
  function test_get_molnet_pdbbind_smiles_dataframe (line 387) | def test_get_molnet_pdbbind_smiles_dataframe():
  function test_get_molnet_pdbbind_grid_dataframe (line 394) | def test_get_molnet_pdbbind_grid_dataframe():

FILE: tests/datasets_tests/molnet_tests/test_pdbbind_time.py
  function test_get_pdbbind_time_filepath (line 9) | def test_get_pdbbind_time_filepath():
  function test_get_pdbbind_time (line 21) | def test_get_pdbbind_time():

FILE: tests/datasets_tests/test_numpy_tuple_dataset.py
  function data (line 12) | def data():
  function long_data (line 20) | def long_data():
  class TestNumpyTupleDataset (line 27) | class TestNumpyTupleDataset(object):
    method test_len (line 29) | def test_len(self, data):
    method test_get_item_integer_index (line 34) | def test_get_item_integer_index(self, data, index):
    method test_get_item_slice_index (line 43) | def test_get_item_slice_index(self, data, index):
    method test_get_item_ndarray_index (line 61) | def test_get_item_ndarray_index(self, long_data, index):
    method test_get_item_list_index (line 77) | def test_get_item_list_index(self, long_data, index):
    method test_invalid_datasets (line 92) | def test_invalid_datasets(self):
    method test_save_load (line 98) | def test_save_load(self, data):
    method test_get_datasets (line 110) | def test_get_datasets(self, data):

FILE: tests/datasets_tests/test_qm9.py
  function test_get_qm9_filepath_without_download (line 14) | def test_get_qm9_filepath_without_download():
  function test_get_qm9_filepath_with_download (line 25) | def test_get_qm9_filepath_with_download():
  function test_get_qm9 (line 37) | def test_get_qm9():
  function test_get_qm9_smiles (line 58) | def test_get_qm9_smiles():
  function test_get_qm9_label_names (line 95) | def test_get_qm9_label_names():

FILE: tests/datasets_tests/test_tox21.py
  function test_get_tox21_filepath_without_download (line 19) | def test_get_tox21_filepath_without_download(dataset_type):
  function test_get_tox21_filepath_with_download (line 33) | def test_get_tox21_filepath_with_download(dataset_type):
  function test_get_tox21 (line 47) | def test_get_tox21():
  function test_get_tox21_label_names (line 64) | def test_get_tox21_label_names():
  function test_get_tox21_filepath_assert_raises (line 71) | def test_get_tox21_filepath_assert_raises():

FILE: tests/datasets_tests/test_zinc.py
  function test_get_zinc_filepath_without_download (line 14) | def test_get_zinc_filepath_without_download():
  function test_get_zinc_filepath_with_download (line 25) | def test_get_zinc_filepath_with_download():
  function test_get_zinc (line 37) | def test_get_zinc():
  function test_get_zinc_smiles (line 57) | def test_get_zinc_smiles():
  function test_get_zinc_label_names (line 106) | def test_get_zinc_label_names():

FILE: tests/functions_tests/activation/test_megnet_softplus.py
  function test_forward_cpu (line 10) | def test_forward_cpu():
  function test_forward_zero_cpu (line 19) | def test_forward_zero_cpu():
  function test_forward_avoid_overflow_cpu (line 26) | def test_forward_avoid_overflow_cpu():
  function test_forward_gpu (line 34) | def test_forward_gpu():
  function test_forward_zero_gpu (line 44) | def test_forward_zero_gpu():
  function test_forward_avoid_overflow_gpu (line 52) | def test_forward_avoid_overflow_gpu():

FILE: tests/functions_tests/activation/test_shifted_softplus.py
  function test_forward_cpu (line 9) | def test_forward_cpu():
  function test_forward_zero_cpu (line 18) | def test_forward_zero_cpu():
  function test_forward_avoid_overflow_cpu (line 25) | def test_forward_avoid_overflow_cpu():
  function test_forward_gpu (line 33) | def test_forward_gpu():
  function test_forward_zero_gpu (line 43) | def test_forward_zero_gpu():
  function test_forward_avoid_overflow_gpu (line 51) | def test_forward_avoid_overflow_gpu():

FILE: tests/functions_tests/activation/test_softmax.py
  function test_forward_cpu (line 9) | def test_forward_cpu():
  function test_forward_cpu_with_mask (line 18) | def test_forward_cpu_with_mask():
  function test_forward_gpu (line 29) | def test_forward_gpu():
  function test_forward_gpu_with_mask (line 39) | def test_forward_gpu_with_mask():

FILE: tests/functions_tests/evaluation/test_r2_score.py
  function r2_score (line 9) | def r2_score(pred, true, sample_weight=None, multioutput="uniform_average",
  function inputs (line 40) | def inputs():
  function check_forward (line 54) | def check_forward(inputs):
  function check_forward_ignore_nan (line 64) | def check_forward_ignore_nan(inputs):
  function check_forward_ignore_nan_with_nonnan_value (line 74) | def check_forward_ignore_nan_with_nonnan_value(inputs):
  function test_forward_cpu (line 84) | def test_forward_cpu(inputs):
  function test_forward_gpu (line 91) | def test_forward_gpu(inputs):

FILE: tests/functions_tests/loss/test_mean_absolute_error.py
  function inputs (line 12) | def inputs():
  function grads (line 27) | def grads():
  function check_forward (line 35) | def check_forward(inputs):
  function check_forward_ignore_nan (line 53) | def check_forward_ignore_nan(inputs):
  function check_forward_ignore_nan_with_nonnan_value (line 74) | def check_forward_ignore_nan_with_nonnan_value(inputs):
  function test_forward_cpu (line 95) | def test_forward_cpu(inputs):
  function test_forward_gpu (line 102) | def test_forward_gpu(inputs):
  function check_backward (line 108) | def check_backward(inputs):
  function check_backward_ignore_nan (line 115) | def check_backward_ignore_nan(inputs):
  function check_backward_ignore_nan_with_nonnan_value (line 125) | def check_backward_ignore_nan_with_nonnan_value(inputs):
  function test_backward_cpu (line 134) | def test_backward_cpu(inputs):
  function test_backward_gpu (line 141) | def test_backward_gpu(inputs):
  function check_double_backward (line 149) | def check_double_backward(inputs, grads):
  function check_double_backward_ignore_nan (line 159) | def check_double_backward_ignore_nan(inputs, grads):
  function check_double_backward_ignore_nan_with_nonnan_value (line 170) | def check_double_backward_ignore_nan_with_nonnan_value(inputs, grads):
  function test_double_backward_cpu (line 181) | def test_double_backward_cpu(inputs, grads):
  function test_double_backward_gpu (line 188) | def test_double_backward_gpu(inputs, grads):

FILE: tests/functions_tests/loss/test_mean_squared_error.py
  function inputs (line 12) | def inputs():
  function grads (line 24) | def grads():
  function check_forward (line 32) | def check_forward(inputs):
  function check_forward_ignore_nan (line 50) | def check_forward_ignore_nan(inputs):
  function check_forward_ignore_nan_with_nonnan_value (line 71) | def check_forward_ignore_nan_with_nonnan_value(inputs):
  function test_forward_cpu (line 92) | def test_forward_cpu(inputs):
  function test_forward_gpu (line 99) | def test_forward_gpu(inputs):
  function check_backward (line 105) | def check_backward(inputs):
  function check_backward_ignore_nan (line 112) | def check_backward_ignore_nan(inputs):
  function check_backward_ignore_nan_with_nonnan_value (line 121) | def check_backward_ignore_nan_with_nonnan_value(inputs):
  function test_backward_cpu (line 130) | def test_backward_cpu(inputs):
  function test_backward_gpu (line 137) | def test_backward_gpu(inputs):
  function check_double_backward (line 145) | def check_double_backward(inputs, grads):
  function check_double_backward_ignore_nan (line 153) | def check_double_backward_ignore_nan(inputs, grads):
  function check_double_backward_ignore_nan_with_nonnan_value (line 163) | def check_double_backward_ignore_nan_with_nonnan_value(inputs, grads):
  function test_double_backward_cpu (line 173) | def test_double_backward_cpu(inputs, grads):
  function test_double_backward_gpu (line 180) | def test_double_backward_gpu(inputs, grads):

FILE: tests/iterators_tests/test_balanced_serial_iterator.py
  class DummySerializer (line 10) | class DummySerializer(serializer.Serializer):
    method __init__ (line 12) | def __init__(self, target):
    method __getitem__ (line 16) | def __getitem__(self, key):
    method __call__ (line 21) | def __call__(self, key, value):
  class DummyDeserializer (line 26) | class DummyDeserializer(serializer.Deserializer):
    method __init__ (line 28) | def __init__(self, target):
    method __getitem__ (line 32) | def __getitem__(self, key):
    method __call__ (line 36) | def __call__(self, key, value):
  function test_balanced_serial_iterator (line 46) | def test_balanced_serial_iterator():
  function _test_balanced_serial_iterator_no_batch_balancing (line 51) | def _test_balanced_serial_iterator_no_batch_balancing():
  function _test_balanced_serial_iterator_with_batch_balancing (line 76) | def _test_balanced_serial_iterator_with_batch_balancing():
  function test_balanced_serial_iterator_serialization (line 95) | def test_balanced_serial_iterator_serialization():
  function _test_balanced_serial_iterator_serialization_no_batch_balancing (line 100) | def _test_balanced_serial_iterator_serialization_no_batch_balancing():
  function _test_balanced_serial_iterator_serialization_with_batch_balancing (line 135) | def _test_balanced_serial_iterator_serialization_with_batch_balancing():

FILE: tests/iterators_tests/test_index_iterator.py
  class DummySerializer (line 9) | class DummySerializer(serializer.Serializer):
    method __init__ (line 11) | def __init__(self, target):
    method __getitem__ (line 15) | def __getitem__(self, key):
    method __call__ (line 20) | def __call__(self, key, value):
  class DummyDeserializer (line 25) | class DummyDeserializer(serializer.Deserializer):
    method __init__ (line 27) | def __init__(self, target):
    method __getitem__ (line 31) | def __getitem__(self, key):
    method __call__ (line 35) | def __call__(self, key, value):
  function test_index_iterator (line 45) | def test_index_iterator():
  function _test_index_iterator_no_shuffle (line 50) | def _test_index_iterator_no_shuffle():
  function _test_index_iterator_with_shuffle (line 77) | def _test_index_iterator_with_shuffle():
  function test_index_iterator_serialization (line 96) | def test_index_iterator_serialization():
  function _test_index_iterator_serialization_no_shuffle (line 101) | def _test_index_iterator_serialization_no_shuffle():
  function _test_index_iterator_serialization_with_shuffle (line 123) | def _test_index_iterator_serialization_with_shuffle():

FILE: tests/link_hooks_tests/test_variable_monitor_link_hook.py
  class DummyModel (line 13) | class DummyModel(chainer.Chain):
    method __init__ (line 14) | def __init__(self):
    method forward (line 22) | def forward(self, x):
  function model (line 29) | def model():
  function test_variable_monitor_link_hook_pre (line 35) | def test_variable_monitor_link_hook_pre(model):
  function test_variable_monitor_link_hook_post (line 47) | def test_variable_monitor_link_hook_post(model):
  function test_variable_monitor_link_hook_process (line 59) | def test_variable_monitor_link_hook_process(model):
  function test_variable_monitor_link_hook_assert_raises (line 82) | def test_variable_monitor_link_hook_assert_raises(model):

FILE: tests/links_tests/array_tests/test_shape_transformer_to_2d.py
  function test_shape_transformer_2d_2d_array (line 8) | def test_shape_transformer_2d_2d_array(axis):
  function test_shape_transformer_2d_3d_array (line 22) | def test_shape_transformer_2d_3d_array(axis):
  function test_shape_transformer_2d_error (line 41) | def test_shape_transformer_2d_error():

FILE: tests/links_tests/connection_tests/test_embed_atom_id.py
  function model (line 15) | def model():
  function data (line 22) | def data():
  function check_forward (line 30) | def check_forward(model, x_data):
  function test_forward_cpu (line 41) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 47) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 53) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 60) | def test_backward_gpu(model, data):

FILE: tests/links_tests/connection_tests/test_graph_linear.py
  function model (line 15) | def model():
  function data (line 22) | def data():
  function test_forward_cpu (line 30) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 38) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 45) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 52) | def test_backward_gpu(model, data):

FILE: tests/links_tests/connection_tests/test_graph_mlp.py
  function model (line 16) | def model():
  function data (line 23) | def data():
  function test_forward_cpu (line 31) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 40) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 48) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 55) | def test_backward_gpu(model, data):

FILE: tests/links_tests/readout_tests/test_cgcnn_readout.py
  function readout (line 18) | def readout():
  function data (line 23) | def data():
  function check_forward (line 45) | def check_forward(readout, data):
  function test_forward_cpu (line 50) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 56) | def test_forward_gpu(readout, data):

FILE: tests/links_tests/readout_tests/test_general_readout.py
  function readouts (line 17) | def readouts():
  function data (line 23) | def data():
  function check_forward (line 32) | def check_forward(readout, atom_data):
  function test_forward_cpu (line 40) | def test_forward_cpu(readouts, data):
  function test_forward_gpu (line 47) | def test_forward_gpu(readouts, data):
  function test_forward_cpu_assert_raises (line 54) | def test_forward_cpu_assert_raises(data):
  function test_backward_cpu (line 61) | def test_backward_cpu(readouts, data):
  function test_backward_gpu (line 71) | def test_backward_gpu(readouts, data):
  function test_forward_cpu_graph_invariant (line 82) | def test_forward_cpu_graph_invariant(readouts, data):

FILE: tests/links_tests/readout_tests/test_ggnn_readout.py
  function readout (line 18) | def readout():
  function data (line 23) | def data():
  function check_forward (line 35) | def check_forward(readout, atom_data, atom_data0):
  function test_forward_cpu (line 40) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 46) | def test_forward_gpu(readout, data):
  function test_backward_cpu (line 52) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 59) | def test_backward_gpu(readout, data):
  function test_forward_cpu_graph_invariant (line 66) | def test_forward_cpu_graph_invariant(readout, data):

FILE: tests/links_tests/readout_tests/test_megnet_readout.py
  function readout (line 19) | def readout():
  function data (line 24) | def data():
  function check_forward (line 38) | def check_forward(readout, data):
  function test_forward_cpu (line 43) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 49) | def test_forward_gpu(readout, data):
  function test_backward_cpu (line 55) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 62) | def test_backward_gpu(readout, data):

FILE: tests/links_tests/readout_tests/test_mpnn_readout.py
  function readout (line 20) | def readout():
  function data (line 26) | def data():
  function check_forward (line 36) | def check_forward(readout, atom_data):
  function test_foward_cpu (line 42) | def test_foward_cpu(readout, data):
  function test_foward_gpu (line 49) | def test_foward_gpu(readout, data):
  function test_backward_cpu (line 56) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 64) | def test_backward_gpu(readout, data):
  function test_foward_cpu_graph_invariant (line 72) | def test_foward_cpu_graph_invariant(readout, data):

FILE: tests/links_tests/readout_tests/test_nfp_readout.py
  function readout (line 17) | def readout():
  function data (line 22) | def data():
  function check_forward (line 31) | def check_forward(readout, atom_data):
  function test_forward_cpu (line 36) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 42) | def test_forward_gpu(readout, data):
  function test_backward_cpu (line 48) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 55) | def test_backward_gpu(readout, data):
  function test_forward_cpu_graph_invariant (line 62) | def test_forward_cpu_graph_invariant(readout, data):

FILE: tests/links_tests/readout_tests/test_schnet_readout.py
  function readout (line 17) | def readout():
  function data (line 22) | def data():
  function check_forward (line 31) | def check_forward(readout, atom_data):
  function test_forward_cpu (line 36) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 42) | def test_forward_gpu(readout, data):
  function test_backward_cpu (line 48) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 55) | def test_backward_gpu(readout, data):
  function test_forward_cpu_graph_invariant (line 62) | def test_forward_cpu_graph_invariant(readout, data):

FILE: tests/links_tests/readout_tests/test_set2set.py
  function readout (line 19) | def readout():
  function data (line 25) | def data():
  function check_forward (line 36) | def check_forward(readout, atom_data):
  function test_forward_cpu (line 43) | def test_forward_cpu(readout, data):
  function test_forward_gpu (line 50) | def test_forward_gpu(readout, data):
  function check_backward (line 57) | def check_backward(readout, atom_data, y_grad):
  function test_backward_cpu (line 78) | def test_backward_cpu(readout, data):
  function test_backward_gpu (line 84) | def test_backward_gpu(readout, data):
  function test_forward_cpu_graph_invariant (line 91) | def test_forward_cpu_graph_invariant(readout, data):

FILE: tests/links_tests/scaler_tests/test_flow_scaler.py
  function test_flow_scaler_transform_uniform (line 13) | def test_flow_scaler_transform_uniform():
  function test_flow_scaler_transform_mix_gaussian (line 25) | def test_flow_scaler_transform_mix_gaussian():
  function test_flow_scaler_transform_variable (line 40) | def test_flow_scaler_transform_variable():
  function test_flow_scaler_transform_gpu (line 54) | def test_flow_scaler_transform_gpu():
  function test_flow_scaler_serialize (line 69) | def test_flow_scaler_serialize(tmpdir):
  function test_flow_scaler_pipeline (line 90) | def test_flow_scaler_pipeline():
  function test_flow_scaler_pipeline_gpu (line 103) | def test_flow_scaler_pipeline_gpu():

FILE: tests/links_tests/scaler_tests/test_max_abs_scaler.py
  function data (line 11) | def data():
  function test_max_abs_scaler_transform (line 28) | def test_max_abs_scaler_transform(data, indices):
  function test_max_abs_scaler_transform_variable (line 48) | def test_max_abs_scaler_transform_variable(data):
  function test_max_abs_scaler_transform_gpu (line 60) | def test_max_abs_scaler_transform_gpu(data):
  function test_max_abs_scaler_inverse_transform (line 73) | def test_max_abs_scaler_inverse_transform(data, indices):
  function test_max_abs_scaler_3darray (line 90) | def test_max_abs_scaler_3darray(data, axis):
  function test_max_abs_scaler_fit_transform (line 117) | def test_max_abs_scaler_fit_transform(data):
  function test_max_abs_scaler_serialize (line 131) | def test_max_abs_scaler_serialize(tmpdir, data, indices):
  function test_max_abs_scaler_assert_raises (line 147) | def test_max_abs_scaler_assert_raises():
  function test_max_abs_scaler_transform_zero_max (line 159) | def test_max_abs_scaler_transform_zero_max():

FILE: tests/links_tests/scaler_tests/test_min_max_scaler.py
  function data (line 11) | def data():
  function test_min_max_scaler_transform (line 28) | def test_min_max_scaler_transform(data, indices):
  function test_min_max_scaler_transform_variable (line 49) | def test_min_max_scaler_transform_variable(data):
  function test_min_max_scaler_transform_gpu (line 61) | def test_min_max_scaler_transform_gpu(data):
  function test_min_max_scaler_inverse_transform (line 74) | def test_min_max_scaler_inverse_transform(data, indices):
  function test_min_max_scaler_3darray (line 91) | def test_min_max_scaler_3darray(data, axis):
  function test_min_max_scaler_fit_transform (line 118) | def test_min_max_scaler_fit_transform(data):
  function test_min_max_scaler_serialize (line 132) | def test_min_max_scaler_serialize(tmpdir, data, indices):
  function test_min_max_scaler_assert_raises (line 149) | def test_min_max_scaler_assert_raises():
  function test_min_max_scaler_transform_zero_max (line 161) | def test_min_max_scaler_transform_zero_max():

FILE: tests/links_tests/scaler_tests/test_standard_scaler.py
  function data (line 12) | def data():
  function test_standard_scaler_transform (line 29) | def test_standard_scaler_transform(data, indices):
  function test_standard_scaler_transform_variable (line 45) | def test_standard_scaler_transform_variable(data):
  function test_standard_scaler_transform_gpu (line 57) | def test_standard_scaler_transform_gpu(data):
  function test_standard_scaler_inverse_transform (line 70) | def test_standard_scaler_inverse_transform(data, indices):
  function test_standard_scaler_3darray (line 87) | def test_standard_scaler_3darray(data, axis):
  function test_standard_scaler_fit_transform (line 114) | def test_standard_scaler_fit_transform(data):
  function test_standard_scaler_serialize (line 128) | def test_standard_scaler_serialize(tmpdir, data, indices):
  function test_standard_scaler_assert_raises (line 145) | def test_standard_scaler_assert_raises():
  function test_standard_scaler_transform_zero_std (line 157) | def test_standard_scaler_transform_zero_std():
  function test_standard_scaler_forward (line 167) | def test_standard_scaler_forward(data):

FILE: tests/links_tests/update_tests/test_cgcnn_update.py
  function update (line 20) | def update():
  function data (line 25) | def data():
  function check_forward (line 51) | def check_forward(update, data):
  function test_forward_cpu (line 56) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 62) | def test_forward_gpu(update, data):

FILE: tests/links_tests/update_tests/test_ggnn_update.py
  function update (line 23) | def update():
  function data (line 29) | def data():
  function convert_to_sparse (line 46) | def convert_to_sparse(dense_adj):
  function check_forward (line 53) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 60) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 74) | def test_forward_gpu(update, data):
  function check_backward (line 87) | def check_backward(update, atom_data, adj_data, y_grad):
  function test_backward_cpu (line 109) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 119) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 129) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_gin_update.py
  function update (line 23) | def update():
  function data (line 30) | def data():
  function check_forward (line 45) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 51) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 58) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 65) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 73) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 81) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_gnn_film_update.py
  function update (line 20) | def update():
  function data (line 26) | def data():
  function check_forward (line 44) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 50) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 57) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 64) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 72) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 81) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_megnet_update.py
  function update (line 22) | def update():
  function data (line 27) | def data():
  function check_forward (line 73) | def check_forward(update, data):
  function test_forward_cpu (line 81) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 89) | def test_forward_gpu(update, data):

FILE: tests/links_tests/update_tests/test_mpnn_update.py
  function message (line 21) | def message():
  function update (line 27) | def update():
  function data (line 33) | def data():
  function check_message_forward (line 51) | def check_message_forward(message, atom_data, adj_data):
  function test_message_forward_cpu (line 57) | def test_message_forward_cpu(message, data):
  function test_message_forward_gpu (line 64) | def test_message_forward_gpu(message, data):
  function test_message_backward_cpu (line 71) | def test_message_backward_cpu(message, data):
  function test_message_backward_gpu (line 80) | def test_message_backward_gpu(message, data):
  function check_forward (line 91) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 97) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 104) | def test_forward_gpu(update, data):
  function check_backward (line 111) | def check_backward(update, atom_data, adj_data, y_grad):
  function test_backward_cpu (line 132) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 139) | def test_backward_gpu(update, data):

FILE: tests/links_tests/update_tests/test_nfp_update.py
  function update (line 20) | def update():
  function data (line 25) | def data():
  function check_forward (line 43) | def check_forward(update, atom_data, adj_data, deg_conds):
  function test_forward_cpu (line 48) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 54) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 60) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 67) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 74) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_relgat_update.py
  function update (line 21) | def update():
  function data (line 28) | def data():
  function check_forward (line 43) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 48) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 54) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 60) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 71) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 78) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_relgcn_update.py
  function update (line 20) | def update():
  function data (line 26) | def data():
  function check_forward (line 41) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 46) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 52) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 58) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 65) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 72) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_rsgcn_update.py
  function update (line 20) | def update():
  function data (line 25) | def data():
  function check_forward (line 39) | def check_forward(update, atom_data, adj_data):
  function test_forward_cpu (line 44) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 50) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 56) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 63) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 70) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/links_tests/update_tests/test_schnet_update.py
  function update (line 19) | def update():
  function data (line 24) | def data():
  function check_forward (line 41) | def check_forward(update, atom_data, dist_data):
  function test_forward_cpu (line 46) | def test_forward_cpu(update, data):
  function test_forward_gpu (line 52) | def test_forward_gpu(update, data):
  function test_backward_cpu (line 58) | def test_backward_cpu(update, data):
  function test_backward_gpu (line 65) | def test_backward_gpu(update, data):
  function test_forward_cpu_graph_invariant (line 72) | def test_forward_cpu_graph_invariant(update, data):

FILE: tests/models_tests/gwm_tests/test_gwm.py
  function graph_warp_gate_unit (line 18) | def graph_warp_gate_unit():
  function super_warp_gate_unit (line 23) | def super_warp_gate_unit():
  function super_node_transmitter_unit (line 28) | def super_node_transmitter_unit():
  function graph_transmitter_unit (line 34) | def graph_transmitter_unit():
  function gwm (line 40) | def gwm():
  function data (line 49) | def data():
  function test_graph_transmitter_unit_forward (line 67) | def test_graph_transmitter_unit_forward(graph_transmitter_unit, data):
  function test_graph_transmitter_unit_backward (line 74) | def test_graph_transmitter_unit_backward(graph_transmitter_unit, data):
  function test_super_node_transmitter_unit_forward (line 83) | def test_super_node_transmitter_unit_forward(super_node_transmitter_unit,
  function test_super_node_transmitter_unit_backward (line 90) | def test_super_node_transmitter_unit_backward(super_node_transmitter_unit,
  function test_graph_warp_gate_unit_forward (line 98) | def test_graph_warp_gate_unit_forward(graph_warp_gate_unit, data):
  function test_graph_warp_gate_unit_backward (line 105) | def test_graph_warp_gate_unit_backward(graph_warp_gate_unit, data):
  function test_super_warp_gate_unit_forward (line 114) | def test_super_warp_gate_unit_forward(super_warp_gate_unit, data):
  function test_super_warp_gate_unit_backward (line 120) | def test_super_warp_gate_unit_backward(super_warp_gate_unit, data):
  function check_forward (line 128) | def check_forward(gwm, embed_atom_data, new_embed_atom_data, supernode):
  function test_forward_cpu (line 135) | def test_forward_cpu(gwm, data):
  function test_forward_gpu (line 141) | def test_forward_gpu(gwm, data):
  function check_backward (line 150) | def check_backward(gwm, embed_atom_data, new_embed_atom_data, supernode,
  function test_backward_cpu (line 161) | def test_backward_cpu(gwm, data):
  function test_backward_gpu (line 166) | def test_backward_gpu(gwm, data):
  function test_forward_cpu_graph_invariant (line 171) | def test_forward_cpu_graph_invariant(gwm, data):

FILE: tests/models_tests/gwm_tests/test_gwm_graph_conv_model.py
  function plain_context (line 43) | def plain_context(request):
  function gwm_context (line 57) | def gwm_context(request):
  function make_model (line 70) | def make_model(update, readout, ch, bn, wt):
  function make_gwm_model (line 78) | def make_gwm_model(update, readout, ch, bn, wt):
  function make_data (line 86) | def make_data(adj_type):
  function test_plain_model_forward (line 108) | def test_plain_model_forward(plain_context):
  function test_gwm_model_forward (line 120) | def test_gwm_model_forward(gwm_context):
  function test_plain_model_forward_general_readout (line 141) | def test_plain_model_forward_general_readout(
  function test_gwm_model_forward_general_readout (line 164) | def test_gwm_model_forward_general_readout(update):
  function test_model_forward_general_weight_tying (line 201) | def test_model_forward_general_weight_tying(update, readout, gwm):
  function test_model_forward_general_concat_hidden (line 235) | def test_model_forward_general_concat_hidden(update, readout, gwm):
  function test_model_forward_general_sum_hidden (line 260) | def test_model_forward_general_sum_hidden(update, readout, gwm):

FILE: tests/models_tests/prediction_tests/test_base.py
  class DummyForwardModel (line 11) | class DummyForwardModel(BaseForwardModel):
    method __init__ (line 13) | def __init__(self, device=-1, dummy_str='dummy'):
    method __call__ (line 21) | def __call__(self, x):
  function _test_save_load_pickle (line 26) | def _test_save_load_pickle(device, tmpdir):
  function test_save_load_pickle_cpu (line 49) | def test_save_load_pickle_cpu(tmpdir):
  function test_save_load_pickle_gpu (line 54) | def test_save_load_pickle_gpu(tmpdir):

FILE: tests/models_tests/prediction_tests/test_classifier.py
  class AccuracyWithIgnoreLabel (line 18) | class AccuracyWithIgnoreLabel(object):
    method __call__ (line 20) | def __call__(self, y, t):
  class DummyPredictor (line 24) | class DummyPredictor(chainer.Chain):
    method __call__ (line 25) | def __call__(self, x):
  class TestClassifier (line 33) | class TestClassifier(object):
    method setup_method (line 35) | def setup_method(self, method):
    method check_call (line 40) | def check_call(
    method test_call_cpu (line 74) | def test_call_cpu(self, metrics_fun, compute_metrics):
    method test_call_three_args_cpu (line 79) | def test_call_three_args_cpu(self, metrics_fun, compute_metrics):
    method test_call_positive_cpu (line 84) | def test_call_positive_cpu(self, metrics_fun, compute_metrics):
    method test_call_kwargs_cpu (line 89) | def test_call_kwargs_cpu(self, metrics_fun, compute_metrics):
    method test_call_no_arg_cpu (line 94) | def test_call_no_arg_cpu(self, metrics_fun, compute_metrics):
    method test_call_gpu (line 100) | def test_call_gpu(self, metrics_fun, compute_metrics):
    method test_call_three_args_gpu (line 107) | def test_call_three_args_gpu(self, metrics_fun, compute_metrics):
    method test_call_positive_gpu (line 114) | def test_call_positive_gpu(self, metrics_fun, compute_metrics):
    method test_call_kwargs_gpu (line 121) | def test_call_kwargs_gpu(self, metrics_fun, compute_metrics):
    method test_call_no_arg_gpu (line 128) | def test_call_no_arg_gpu(self, metrics_fun, compute_metrics):
    method to_gpu (line 133) | def to_gpu(self):
    method test_report_key (line 138) | def test_report_key(self, metrics_fun, compute_metrics):
  class TestInvalidArgument (line 165) | class TestInvalidArgument(object):
    method setup_class (line 168) | def setup_class(cls):
    method check_invalid_argument (line 172) | def check_invalid_argument(self):
    method test_invalid_argument_cpu (line 179) | def test_invalid_argument_cpu(self):
    method test_invalid_argument_gpu (line 183) | def test_invalid_argument_gpu(self):
  class TestInvalidLabelKey (line 188) | class TestInvalidLabelKey(object):
    method setup_class (line 191) | def setup_class(cls):
    method test_invalid_label_key_type (line 194) | def test_invalid_label_key_type(self):
    method check_invalid_key (line 198) | def check_invalid_key(self, gpu, label_key):
    method test_invalid_index_cpu (line 206) | def test_invalid_index_cpu(self):
    method test_invalid_argument_gpu (line 210) | def test_invalid_argument_gpu(self):
    method test_invalid_index_too_small_cpu (line 213) | def test_invalid_index_too_small_cpu(self):
    method test_invalid_index_too_small_gpu (line 217) | def test_invalid_index_too_small_gpu(self):
    method test_invalid_str_key_cpu (line 220) | def test_invalid_str_key_cpu(self):
    method test_invalid_str_key_gpu (line 224) | def test_invalid_str_key_gpu(self):
  class TestClassifierPrediction (line 228) | class TestClassifierPrediction(object):
    method setup_class (line 231) | def setup_class(cls):
    method test_predict_cpu (line 237) | def test_predict_cpu(self):
    method test_predict_gpu (line 245) | def test_predict_gpu(self):
    method check_predict_proba (line 250) | def check_predict_proba(self, device):
    method test_predict_proba_cpu (line 261) | def test_predict_proba_cpu(self):
    method test_predict_proba_gpu (line 265) | def test_predict_proba_gpu(self):

FILE: tests/models_tests/prediction_tests/test_graph_conv_predictor.py
  function model (line 24) | def model():
  function data (line 33) | def data():
  function check_forward (line 45) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 51) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 57) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 64) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 72) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 80) | def test_forward_cpu_graph_invariant(model, data):

FILE: tests/models_tests/prediction_tests/test_regressor.py
  class DummyPredictor (line 13) | class DummyPredictor(chainer.Chain):
    method __call__ (line 14) | def __call__(self, x):
  class TestRegressor (line 22) | class TestRegressor(object):
    method setup_method (line 24) | def setup_method(self, method):
    method check_call (line 29) | def check_call(
    method test_call_cpu (line 63) | def test_call_cpu(self, metrics_fun, compute_metrics):
    method test_call_three_args_cpu (line 68) | def test_call_three_args_cpu(self, metrics_fun, compute_metrics):
    method test_call_positive_cpu (line 73) | def test_call_positive_cpu(self, metrics_fun, compute_metrics):
    method test_call_kwargs_cpu (line 78) | def test_call_kwargs_cpu(self, metrics_fun, compute_metrics):
    method test_call_no_arg_cpu (line 83) | def test_call_no_arg_cpu(self, metrics_fun, compute_metrics):
    method test_call_gpu (line 89) | def test_call_gpu(self, metrics_fun, compute_metrics):
    method test_call_three_args_gpu (line 96) | def test_call_three_args_gpu(self, metrics_fun, compute_metrics):
    method test_call_positive_gpu (line 103) | def test_call_positive_gpu(self, metrics_fun, compute_metrics):
    method test_call_kwargs_gpu (line 110) | def test_call_kwargs_gpu(self, metrics_fun, compute_metrics):
    method test_call_no_arg_gpu (line 117) | def test_call_no_arg_gpu(self, metrics_fun, compute_metrics):
    method to_gpu (line 122) | def to_gpu(self):
    method test_report_key (line 127) | def test_report_key(self, metrics_fun, compute_metrics):
  class TestInvalidArgument (line 154) | class TestInvalidArgument(object):
    method setup_class (line 157) | def setup_class(cls):
    method check_invalid_argument (line 161) | def check_invalid_argument(self):
    method test_invalid_argument_cpu (line 168) | def test_invalid_argument_cpu(self):
    method test_invalid_argument_gpu (line 172) | def test_invalid_argument_gpu(self):
  class TestInvalidLabelKey (line 177) | class TestInvalidLabelKey(object):
    method setup_class (line 180) | def setup_class(cls):
    method test_invalid_label_key_type (line 183) | def test_invalid_label_key_type(self):
    method check_invalid_key (line 187) | def check_invalid_key(self, gpu, label_key):
    method test_invalid_index_cpu (line 195) | def test_invalid_index_cpu(self):
    method test_invalid_argument_gpu (line 199) | def test_invalid_argument_gpu(self):
    method test_invalid_index_too_small_cpu (line 202) | def test_invalid_index_too_small_cpu(self):
    method test_invalid_index_too_small_gpu (line 206) | def test_invalid_index_too_small_gpu(self):
    method test_invalid_str_key_cpu (line 209) | def test_invalid_str_key_cpu(self):
    method test_invalid_str_key_gpu (line 213) | def test_invalid_str_key_gpu(self):
  class TestRegressorPrediction (line 217) | class TestRegressorPrediction(object):
    method setup_class (line 220) | def setup_class(cls):
    method test_predict_cpu (line 226) | def test_predict_cpu(self):
    method test_predict_gpu (line 234) | def test_predict_gpu(self):

FILE: tests/models_tests/prediction_tests/test_set_up_predictor.py
  function models_dict (line 44) | def models_dict():
  function test_setup_predictor (line 81) | def test_setup_predictor(models_dict):
  function test_call_invalid_model (line 93) | def test_call_invalid_model():
  function test_set_up_predictor_with_conv_kwargs (line 103) | def test_set_up_predictor_with_conv_kwargs():

FILE: tests/models_tests/test_cgcnn.py
  function model (line 19) | def model():
  function data (line 24) | def data():
  function check_forward (line 54) | def check_forward(model, data):
  function test_forward_cpu (line 59) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 65) | def test_forward_gpu(model, data):

FILE: tests/models_tests/test_ggnn.py
  function model (line 22) | def model():
  function sparse_model (line 28) | def sparse_model():
  function data (line 34) | def data():
  function check_forward (line 47) | def check_forward(model, *args):
  function test_forward_cpu (line 54) | def test_forward_cpu(model, sparse_model, data):
  function test_forward_gpu (line 66) | def test_forward_gpu(model, sparse_model, data):
  function test_backward_cpu (line 75) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 84) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 91) | def test_forward_cpu_graph_invariant(model, data):
  function test_forward_cpu_input_size_invariant (line 103) | def test_forward_cpu_input_size_invariant(model, data):

FILE: tests/models_tests/test_gin.py
  function model (line 20) | def model():
  function data (line 26) | def data():
  function check_forward (line 37) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 43) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 50) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 57) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 65) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 73) | def test_forward_cpu_graph_invariant(model, data):

FILE: tests/models_tests/test_gnn_film.py
  function model (line 21) | def model():
  function data (line 27) | def data():
  function check_forward (line 39) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 45) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 52) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 59) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 67) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 75) | def test_forward_cpu_graph_invariant(model, data):

FILE: tests/models_tests/test_megnet.py
  function model (line 23) | def model():
  function data (line 28) | def data():
  function check_forward (line 69) | def check_forward(model, data):
  function test_forward_cpu (line 74) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 82) | def test_forward_gpu(model, data):

FILE: tests/models_tests/test_mlp.py
  function model (line 14) | def model():
  function data (line 19) | def data():
  function check_forward (line 27) | def check_forward(model, data):
  function test_forward_cpu (line 32) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 37) | def test_forward_gpu(model, data):
  function test_mlp_assert_raises (line 42) | def test_mlp_assert_raises():
  function test_backward_cpu (line 47) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 53) | def test_backward_gpu(model, data):

FILE: tests/models_tests/test_mpnn.py
  function model (line 22) | def model(request):
  function data (line 33) | def data():
  function check_forward (line 47) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 53) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 60) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 67) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 75) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 83) | def test_forward_cpu_graph_invariant(model, data):
  function test_invalid_message_funcion (line 100) | def test_invalid_message_funcion():
  function test_invalid_readout_funcion (line 106) | def test_invalid_readout_funcion():

FILE: tests/models_tests/test_nfp.py
  function model (line 18) | def model():
  function data (line 23) | def data():
  function check_forward (line 36) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 41) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 47) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 54) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 62) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 69) | def test_forward_cpu_graph_invariant(model, data):
  function test_forward_cpu_input_size_invariant (line 81) | def test_forward_cpu_input_size_invariant(model, data):

FILE: tests/models_tests/test_relgat.py
  function model (line 18) | def model(request):
  function data (line 23) | def data():
  function check_forward (line 36) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 41) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 47) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 54) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 64) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 73) | def test_forward_cpu_graph_invariant(model, data):

FILE: tests/models_tests/test_relgcn.py
  function model (line 19) | def model():
  function data (line 24) | def data():
  function check_forward (line 35) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 40) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 46) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 52) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 59) | def test_backward_gpu(model, data):
  function test_forward_cpu_invariant (line 66) | def test_forward_cpu_invariant(model, data):
  function test_rescale_adj (line 78) | def test_rescale_adj(data):

FILE: tests/models_tests/test_rsgcn.py
  function model (line 21) | def model():
  function model_no_dropout (line 26) | def model_no_dropout():
  function model_with_nfp (line 33) | def model_with_nfp():
  function model_with_nfp_no_dropout (line 39) | def model_with_nfp_no_dropout():
  function data (line 46) | def data():
  function check_forward (line 61) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 66) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 72) | def test_forward_gpu(model, data):
  function test_forward_cpu_with_nfp (line 78) | def test_forward_cpu_with_nfp(model_with_nfp, data):
  function test_backward_cpu (line 83) | def test_backward_cpu(model_no_dropout, data):
  function test_backward_gpu (line 99) | def test_backward_gpu(model_no_dropout, data):
  function test_backward_cpu_with_nfp (line 115) | def test_backward_cpu_with_nfp(model_with_nfp_no_dropout, data):
  function test_forward_cpu_graph_invariant (line 127) | def test_forward_cpu_graph_invariant(model, data):
  function test_forward_cpu_input_size_invariant (line 143) | def test_forward_cpu_input_size_invariant(model, data):

FILE: tests/models_tests/test_schnet.py
  function model (line 17) | def model():
  function data (line 22) | def data():
  function check_forward (line 38) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 43) | def test_forward_cpu(model, data):
  function test_forward_gpu (line 49) | def test_forward_gpu(model, data):
  function test_backward_cpu (line 55) | def test_backward_cpu(model, data):
  function test_backward_gpu (line 62) | def test_backward_gpu(model, data):
  function test_forward_cpu_graph_invariant (line 69) | def test_forward_cpu_graph_invariant(model, data):

FILE: tests/models_tests/test_weavenet.py
  function model (line 20) | def model():
  function model_processed (line 25) | def model_processed():
  function data (line 31) | def data():
  function check_forward (line 54) | def check_forward(model, atom_data, adj_data):
  function test_forward_cpu (line 60) | def test_forward_cpu(model, model_processed, data):
  function test_forward_gpu (line 67) | def test_forward_gpu(model, model_processed, data):
  function test_backward_cpu (line 76) | def test_backward_cpu(model, model_processed, data):
  function test_backward_gpu (line 86) | def test_backward_gpu(model, model_processed, data):
  function _test_forward_cpu_graph_invariant (line 98) | def _test_forward_cpu_graph_invariant(
  function test_forward_cpu_graph_invariant_embed (line 118) | def test_forward_cpu_graph_invariant_embed(model, data):
  function test_forward_cpu_graph_invariant_processed (line 124) | def test_forward_cpu_graph_invariant_processed(model_processed, data):

FILE: tests/saliency_tests/calculator_tests/test_base_calculator.py
  class DummyCalculator (line 13) | class DummyCalculator(BaseCalculator):
    method _compute_core (line 16) | def _compute_core(self, *inputs):
  class DummyModel (line 21) | class DummyModel(chainer.Chain):
    method __init__ (line 22) | def __init__(self):
    method forward (line 30) | def forward(self, x):
  function model (line 37) | def model():
  function test_base_calculator_compute (line 43) | def test_base_calculator_compute(model):
  function test_base_calculator_compute_noise_sampler (line 54) | def test_base_calculator_compute_noise_sampler(model):
  function test_base_calculator_compute_target_extractor (line 67) | def test_base_calculator_compute_target_extractor(model):
  function test_base_calculator_aggregate (line 79) | def test_base_calculator_aggregate():

FILE: tests/saliency_tests/calculator_tests/test_calculator_utils.py
  function test_gaussian_noise_sampler (line 8) | def test_gaussian_noise_sampler(mode):
  function test_gaussian_noise_sampler_assert_raises (line 16) | def test_gaussian_noise_sampler_assert_raises():

FILE: tests/saliency_tests/calculator_tests/test_gradient_calculator.py
  class DummyModel (line 13) | class DummyModel(chainer.Chain):
    method __init__ (line 14) | def __init__(self):
    method forward (line 21) | def forward(self, x):
  function test_gradient_calculator (line 27) | def test_gradient_calculator():
  function test_gradient_calculator_multiple_output (line 38) | def test_gradient_calculator_multiple_output():
  function test_gradient_calculator_multiply_target (line 51) | def test_gradient_calculator_multiply_target():
  function test_gradient_calculator_target_extractor (line 62) | def test_gradient_calculator_target_extractor():

FILE: tests/saliency_tests/calculator_tests/test_integrated_gradient_calculator.py
  class DummyModel (line 13) | class DummyModel(chainer.Chain):
    method __init__ (line 14) | def __init__(self):
    method forward (line 21) | def forward(self, x):
  function test_integrated_gradient_calculator (line 27) | def test_integrated_gradient_calculator():
  function test_integrated_gradient_calculator_target_extractor (line 38) | def test_integrated_gradient_calculator_target_extractor():

FILE: tests/saliency_tests/calculator_tests/test_occlusion_calculator.py
  class DummyModel (line 13) | class DummyModel(chainer.Chain):
    method __init__ (line 14) | def __init__(self):
    method forward (line 21) | def forward(self, x):
  class DummyCNNModel (line 25) | class DummyCNNModel(chainer.Chain):
    method __init__ (line 26) | def __init__(self):
    method forward (line 33) | def forward(self, x):
  function test_occlusion_calculator (line 39) | def test_occlusion_calculator():
  function test_occlusion_calculator_cnn (line 50) | def test_occlusion_calculator_cnn():
  function test_occlusion_calculator_target_extractor (line 62) | def test_occlusion_calculator_target_extractor():

FILE: tests/saliency_tests/visualizer_tests/test_image_visualizer.py
  function test_image_visualizer (line 18) | def test_image_visualizer(tmpdir):
  function test_table_visualizer_assert_raises (line 39) | def test_table_visualizer_assert_raises():

FILE: tests/saliency_tests/visualizer_tests/test_mol_visualizer.py
  function test_mol_visualizer (line 11) | def test_mol_visualizer(tmpdir):
  function test_smiles_visualizer (line 30) | def test_smiles_visualizer(tmpdir):
  function test_mol_visualizer_assert_raises (line 57) | def test_mol_visualizer_assert_raises(tmpdir):

FILE: tests/saliency_tests/visualizer_tests/test_table_visualizer.py
  function test_table_visualizer (line 17) | def test_table_visualizer(tmpdir):
  function test_table_visualizer_assert_raises (line 34) | def test_table_visualizer_assert_raises():

FILE: tests/saliency_tests/visualizer_tests/test_visualizer_utils.py
  function test_abs_max_scaler (line 10) | def test_abs_max_scaler():
  function test_min_max_scaler (line 23) | def test_min_max_scaler():
  function test_normalize_scaler (line 36) | def test_normalize_scaler():
  function test_red_blue_cmap (line 49) | def test_red_blue_cmap():

FILE: tests/test_init.py
  function test_version (line 7) | def test_version():

FILE: tests/training_tests/extensions_tests/test_auto_print_report.py
  class TestAutoPrintReport (line 11) | class TestAutoPrintReport(object):
    method _setup (line 12) | def _setup(self, stream=None, delete_flush=False):
    method test_stream_with_flush_is_flushed (line 30) | def test_stream_with_flush_is_flushed(self):
    method test_stream_without_flush_raises_no_exception (line 37) | def test_stream_without_flush_raises_no_exception(self):
    method test_real_stream_raises_no_exception (line 42) | def test_real_stream_raises_no_exception(self):

FILE: tests/training_tests/extensions_tests/test_prc_auc_evaluator.py
  function data0 (line 18) | def data0():
  function data1 (line 26) | def data1():
  function data2 (line 35) | def data2():
  class DummyPredictor (line 43) | class DummyPredictor(chainer.Chain):
    method __call__ (line 45) | def __call__(self, y):
  function test_prc_auc_evaluator (line 50) | def test_prc_auc_evaluator(data0, data1):
  function _test_prc_auc_evaluator_default_args (line 55) | def _test_prc_auc_evaluator_default_args(data0):
  function _test_prc_auc_evaluator_with_labels (line 78) | def _test_prc_auc_evaluator_with_labels(data1):
  function test_prc_auc_evaluator_raise_value_error (line 104) | def test_prc_auc_evaluator_raise_value_error(data2):
  function _test_prc_auc_evaluator_raise_error (line 112) | def _test_prc_auc_evaluator_raise_error(data, raise_value_error=True):

FILE: tests/training_tests/extensions_tests/test_r2_score_evaluator.py
  function inputs (line 13) | def inputs():
  function r2_score (line 27) | def r2_score(pred, true, sample_weight=None, multioutput="uniform_average",
  class DummyPredictor (line 57) | class DummyPredictor(chainer.Chain):
    method __call__ (line 59) | def __call__(self, y):
  function test_r2_score_evaluator (line 64) | def test_r2_score_evaluator(inputs):
  function test_r2_score_evaluator_gpu (line 72) | def test_r2_score_evaluator_gpu(inputs):
  function _test_r2_score_evaluator (line 83) | def _test_r2_score_evaluator(inputs):
  function _test_r2_score_evaluator_ignore_nan (line 103) | def _test_r2_score_evaluator_ignore_nan(inputs):
  function _test_r2_score_evaluator_ignore_nan_with_nonnan_value (line 124) | def _test_r2_score_evaluator_ignore_nan_with_nonnan_value(inputs):
  function _test_r2_score_evaluator_raw_values (line 145) | def _test_r2_score_evaluator_raw_values(inputs):

FILE: tests/training_tests/extensions_tests/test_roc_auc_evaluator.py
  function data0 (line 17) | def data0():
  function data1 (line 25) | def data1():
  function data2 (line 34) | def data2():
  class DummyPredictor (line 42) | class DummyPredictor(chainer.Chain):
    method __call__ (line 44) | def __call__(self, y):
  function test_roc_auc_evaluator (line 49) | def test_roc_auc_evaluator(data0, data1):
  function _test_roc_auc_evaluator_default_args (line 54) | def _test_roc_auc_evaluator_default_args(data0):
  function _test_roc_auc_evaluator_with_labels (line 79) | def _test_roc_auc_evaluator_with_labels(data1):
  function test_roc_auc_evaluator_raise_value_error (line 107) | def test_roc_auc_evaluator_raise_value_error(data2):
  function _test_roc_auc_evaluator_raise_error (line 115) | def _test_roc_auc_evaluator_raise_error(data, raise_value_error=True):

FILE: tests/utils_tests/test_extend.py
  function test_extend_node_2d (line 20) | def test_extend_node_2d(x):
  function test_extend_node_3d (line 33) | def test_extend_node_3d(x, axis):
  function test_extend_node_assert_raises (line 48) | def test_extend_node_assert_raises():
  function test_extend_adj (line 54) | def test_extend_adj(adj):
  function test_extend_adj_assert_raises (line 63) | def test_extend_adj_assert_raises():

FILE: tests/utils_tests/test_json_utils.py
  function test_save_json (line 32) | def test_save_json(tmpdir):
  function test_save_json_ignore_error (line 38) | def test_save_json_ignore_error(tmpdir):
  function test_load_json (line 49) | def test_load_json(tmpdir):

FILE: tests/utils_tests/test_permutation.py
  function test_permute_node_2d (line 17) | def test_permute_node_2d(x):
  function test_permute_node_3d (line 32) | def test_permute_node_3d(x, axis):
  function test_permute_adj (line 51) | def test_permute_adj(adj):
  function test_permute_adj_axis12 (line 62) | def test_permute_adj_axis12():
  function test_permute_adj_error (line 75) | def test_permute_adj_error():

FILE: tests/utils_tests/test_sparse_utils.py
  function naive_convert (line 12) | def naive_convert(data, row, col, edge_type, num_edge_type):
  function test_convert_sparse_with_edge_type (line 47) | def test_convert_sparse_with_edge_type(in_shape, num_edge_type):

FILE: tests/utils_tests/test_train_utils.py
  function model (line 22) | def model():
  function train_data (line 27) | def train_data():
  function valid_data (line 36) | def valid_data():
  function test_run_train_cpu (line 44) | def test_run_train_cpu(model, train_data, valid_data):
  function test_run_train_cpu_iterator (line 48) | def test_run_train_cpu_iterator(model, train_data, valid_data):
  function test_run_train_invalid (line 56) | def test_run_train_invalid(model, train_data):
  function test_run_train_gpu (line 62) | def test_run_train_gpu(model, train_data, valid_data):
  function test_run_train_chainerx_native (line 71) | def test_run_train_chainerx_native(model, train_data, valid_data):
  function test_run_train_chainerx_cuda0 (line 81) | def test_run_train_chainerx_cuda0(model, train_data, valid_data):