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Functions181 in github.com/Hanjun-Dai/GLN

⨍ Functions 181◇ Types & classes 37
↓ 1 callersFunctionrdchiralRunText
Run from SMARTS string and SMILES string. This is NOT recommended for library application, since initialization is pretty slow. You should sep
gln/mods/rdchiral/main.py:79
↓ 1 callersFunctionreassign_atom_mapping
This function takes an atom-mapped reaction SMILES and reassigns the atom-mapping labels (numbers) from left to right, once that transform h
gln/mods/rdchiral/template_extractor.py:407
↓ 1 callersMethodremove_dump
(self, prefix)
gln/mods/mol_gnn/mol_utils.py:209
↓ 1 callersMethodreset
(self)
gln/mods/rdchiral/initialization.py:58
↓ 1 callersMethodrun
Args: raw_prod: the single product smiles beam_size: the size for beam search topk: top-k prediction of r
gln/test/model_inference.py:102
↓ 1 callersFunctionrxn_data_gen
(phase, model)
gln/test/main_test.py:45
↓ 1 callersMethodupdate
(self, aggr_out)
gln/mods/mol_gnn/gnn_family/s2v.py:25
FunctionInit
gln/mods/mol_gnn/mg_clib/src/mg_clib.cpp:9
MethodLoadParams
gln/mods/mol_gnn/mg_clib/include/config.h:18
FunctionPYBIND11_MODULE
gln/mods/torchext/src/extlib.cpp:111
FunctionPYBIND11_MODULE
gln/mods/torchext/src/extlib_cuda.cpp:49
MethodParseAtomFeat
gln/mods/mol_gnn/mg_clib/src/lib/mol_utils.cpp:6
MethodParseEdgeFeat
gln/mods/mol_gnn/mg_clib/src/lib/mol_utils.cpp:40
FunctionPrepareBatchFeature
gln/mods/mol_gnn/mg_clib/src/mg_clib.cpp:16
FunctionPrepareIndices
gln/mods/mol_gnn/mg_clib/src/mg_clib.cpp:53
Method__init__
Args: dropbox: the dropbox folder model_dump: the ckpt folder, which contains model dump and model args
gln/test/model_inference.py:21
Method__init__
(self, prod, center, template, label=None, neg_centers=None, neg_tpls=None, reaction=None, ne
gln/training/data_gen.py:20
Method__init__
(self, reaction_smarts)
gln/mods/rdchiral/initialization.py:19
Method__init__
(self, reactant_smiles)
gln/mods/rdchiral/initialization.py:69
Method__init__
(self, f)
gln/mods/mol_gnn/torch_util.py:16
Method__init__
(self)
gln/mods/mol_gnn/torch_util.py:26
Method__init__
(self, name, sanitized, *, mol=None, num_nodes=None, num_edges=None, atom_feats=None, bond_feats=None, edge_pa
gln/mods/mol_gnn/mol_utils.py:71
Method__init__
(self, sanitized)
gln/mods/mol_gnn/mol_utils.py:105
Method__init__
(self, feat_dim, hidden_size, num_hidden, feat_mode='dense', act_func='elu', dropout=0)
gln/mods/mol_gnn/gnn_family/morganfp.py:16
Method__init__
(self, embed_dim, dropout=None)
gln/mods/mol_gnn/gnn_family/utils.py:26
Method__init__
(self, latent_dim, output_dim, num_node_feats, num_edge_feats, max_lv=3, act_func='elu', msg_
gln/mods/mol_gnn/gnn_family/mpnn.py:15
Method__init__
(self, latent_dim)
gln/mods/mol_gnn/gnn_family/mean_field.py:17
Method__init__
(self, latent_dim)
gln/mods/mol_gnn/gnn_family/s2v.py:17
Method__init__
(self, node_state_dim, num_edge_feats, edge_hidden_sizes, aggr='add', act_func='elu')
gln/mods/mol_gnn/gnn_family/ggnn.py:16
Method__init__
(self, sys_args)
gln/mods/mol_gnn/mg_clib/mg_lib.py:12
Method__init__
(self, f)
gln/common/torch_util.py:17
Method__init__
(self)
gln/common/reactor.py:12
Method__init__
(self, args)
gln/graph_logic/logic_net.py:28
Method__init__
(self, args)
gln/graph_logic/graph_feat.py:33
Method__init__
(self, args)
gln/graph_logic/graph_feat.py:71
Method__init__
(self, args)
gln/graph_logic/soft_logic.py:69
Method__init__
(self, args)
gln/graph_logic/soft_logic.py:130
Method__init__
(self, args)
gln/graph_logic/soft_logic.py:174
Functionatoms_are_different
Compares two RDKit atoms based on basic properties
gln/mods/rdchiral/utils.py:98
Functionfind_edges
(task)
gln/data_process/find_centers.py:18
Functionfind_tpls
(cur_task)
gln/data_process/build_all_reactions.py:26
Methodforward
(ctx, logits, prefix_sum)
gln/mods/torchext/jagged_ops.py:16
Methodforward
(self, logits, prefix_sum)
gln/mods/torchext/jagged_ops.py:37
Methodforward
(self, x)
gln/mods/mol_gnn/torch_util.py:20
Methodforward
(self, x)
gln/mods/mol_gnn/torch_util.py:30
Methodforward
(self, z)
gln/mods/mol_gnn/torch_util.py:77
Methodforward
(self, graph_list)
gln/mods/mol_gnn/gnn_family/utils.py:37
Methodforward
(self, list_node_states, g_idx, num_graphs)
gln/mods/mol_gnn/gnn_family/utils.py:97
Methodforward
(self, x, edge_index)
gln/mods/mol_gnn/gnn_family/mean_field.py:21
Methodforward
(self, x, edge_index)
gln/mods/mol_gnn/gnn_family/s2v.py:21
Methodforward
(self, x, edge_index, edge_features)
gln/mods/mol_gnn/gnn_family/ggnn.py:32
Methodforward
(self, x)
gln/common/torch_util.py:21
Methodforward
(self, x)
gln/common/torch_util.py:30
Methodforward
(self, samples)
gln/graph_logic/logic_net.py:39
Methodforward
(self, template_list)
gln/graph_logic/graph_feat.py:41
Methodforward
(self, reaction_list)
gln/graph_logic/graph_feat.py:77
Methodforward
(self, list_mols, list_of_list_reactions, list_target_pos=None)
gln/graph_logic/soft_logic.py:85
Methodforward
(self, list_objs)
gln/graph_logic/soft_logic.py:117
Methodforward
(self, list_mols, list_of_list_templates, list_target_pos=None)
gln/graph_logic/soft_logic.py:152
Methodforward
(self, list_mols, list_of_list_centers, list_target_pos=None)
gln/graph_logic/soft_logic.py:196
Methodget_feat
(self, graph_list)
gln/mods/mol_gnn/gnn_family/morganfp.py:59
Methodget_feat
(self, graph_list)
gln/mods/mol_gnn/gnn_family/mpnn.py:36
Methodget_feat
(self, graph_list)
gln/mods/mol_gnn/gnn_family/mean_field.py:64
Methodget_feat
(self, graph_list)
gln/mods/mol_gnn/gnn_family/s2v.py:70
Methodget_feat
(self, graph_list)
gln/mods/mol_gnn/gnn_family/ggnn.py:92
Functionget_score
(pred, gnd, score_type)
gln/common/evaluate.py:35
Functionget_tpl
(task)
gln/data_process/build_raw_template.py:21
Methodinference
(self, list_mols, list_of_list_reactions)
gln/graph_logic/soft_logic.py:96
Methodinference
(self, list_mols, list_of_list_centers)
gln/graph_logic/soft_logic.py:207
Functionjagged_log_softmax_backward
gln/mods/torchext/src/extlib.cpp:93
Functionjagged_log_softmax_backward_cuda
gln/mods/torchext/src/extlib_cuda.cpp:29
Functionjagged_log_softmax_forward
gln/mods/torchext/src/extlib.cpp:52
Functionjagged_log_softmax_forward_cuda
gln/mods/torchext/src/extlib_cuda.cpp:13
Methodmessage
(self, x_i, x_j, edge_features)
gln/mods/mol_gnn/gnn_family/ggnn.py:37
Methodrun
(self)
setup.py:33
Functionscatter_max
(src, index, dim=-1, out=None, dim_size=None, fill_value=0)
gln/mods/mol_gnn/gnn_family/utils.py:128
Functionscatter_min
(src, index, dim=-1, out=None, dim_size=None, fill_value=0)
gln/mods/mol_gnn/gnn_family/utils.py:132
Methodupdate
(self, aggr_out)
gln/mods/mol_gnn/gnn_family/mean_field.py:25
Functionvprint
(level, txt, *args)
gln/mods/rdchiral/utils.py:4
Functionworker_process
(worker_func, worker_id, seed, data_q, *args)
gln/training/data_gen.py:124
Functionworker_softmax
(worker_id, seed, args)
gln/training/data_gen.py:60
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