MCPcopy Create free account

hub / github.com/DirectMolecularConfGen/DMCG / functions

Functions95 in github.com/DirectMolecularConfGen/DMCG

⨍ Functions 95◇ Types & classes 14
↓ 49 callersFunctionprint
(*args, **kwargs)
confgen/utils/utils.py:126
↓ 10 callersMethodmove2origin
(self, pos, batch)
confgen/model/gnn.py:459
↓ 9 callersFunctionset_rdmol_positions
(rdkit_mol, pos)
confgen/utils/utils.py:37
↓ 8 callersMethod__init__
( self, input_size, output_sizes, use_layer_norm=False, activation=nn.
confgen/model/conv.py:124
↓ 7 callersMethodextend_x_edge
(self, pos, x, edge_attr, edge_index)
confgen/model/gnn.py:465
↓ 7 callersFunctionsafe_index
Return index of element e in list l. If e is not present, return the last index
confgen/molecule/features.py:41
↓ 6 callersMethodstep
(self, step)
confgen/utils/utils.py:24
↓ 5 callersFunctionevaluate
(model, device, loader, args)
evaluate.py:77
↓ 5 callersFunctionget_random_rotation_3d
(pos)
confgen/utils/utils.py:52
↓ 4 callersFunctionisomorphic_core
(mol)
confgen/molecule/gt.py:65
↓ 4 callersMethodrandom_augmentation
(self, pos, batch)
confgen/model/gnn.py:447
↓ 3 callersMethodalignment_loss
(pos_y, pos_x, batch, clamp=None)
confgen/model/gnn.py:588
↓ 3 callersMethodcompute_loss
(self, pos_list, extra_output, batch, args)
confgen/model/gnn.py:477
↓ 3 callersFunctioncompute_mmd
Params: source: (N, D) target: (M, D) Return: loss: MMD loss
confgen/utils/utils.py:237
↓ 3 callersFunctionevaluate
(model, device, loader, args)
train.py:70
↓ 3 callersFunctionevaluate_one
(model, device, loader)
evaluate.py:151
↓ 3 callersFunctionget_atom_feature_dims
()
confgen/molecule/features.py:73
↓ 3 callersFunctionget_best_rmsd
(gen_mol, ref_mol)
confgen/utils/utils.py:45
↓ 3 callersFunctionget_bond_feature_dims
()
confgen/molecule/features.py:117
↓ 3 callersFunctioninput_args
()
evaluate.py:139
↓ 3 callersMethodquaternion_to_rotation_matrix
(quaternion)
confgen/model/gnn.py:570
↓ 2 callersFunctionatom_to_feature_vector
Converts rdkit atom object to feature list of indices :param mol: rdkit atom object :return: list
confgen/molecule/features.py:51
↓ 2 callersFunctionbinarize
(x)
confgen/utils/utils.py:134
↓ 2 callersFunctionbinarize
(x)
confgen/molecule/graph.py:161
↓ 2 callersFunctionbond_to_feature_vector
Converts rdkit bond object to feature list of indices :param mol: rdkit bond object :return: list
confgen/molecule/features.py:92
↓ 2 callersFunctionextendedbond_to_feature_vector
(order=2)
confgen/molecule/features.py:106
↓ 2 callersMethodget_idx_split
(self)
confgen/e2c/dataset.py:203
↓ 2 callersFunctionone_hot_atoms
(atoms)
confgen/model/gnn.py:894
↓ 2 callersFunctionone_hot_bonds
(bonds)
confgen/model/gnn.py:904
↓ 2 callersMethodposition_Langevin_Dynamic
(self, batch, pos_init, args)
confgen/model/gnn.py:729
↓ 2 callersMethodreset_parameters
(self)
confgen/model/conv.py:159
↓ 1 callersMethodalignment
(pos_y, pos_x, batch)
confgen/model/gnn.py:696
↓ 1 callersMethodalignment_loss_iso_onegraph
(pos_y, pos_x, pos_y_mean, pos_x_mean, num_nodes, total_iso)
confgen/model/gnn.py:627
↓ 1 callersFunctionatomGetnum
(mol)
confgen/molecule/gt.py:48
↓ 1 callersMethodaux_loss
(pos_y, pos_x, batch)
confgen/model/gnn.py:532
↓ 1 callersFunctionclip_norm
(vec, limit, p=2)
confgen/utils/utils.py:259
↓ 1 callersFunctionevaluate_distance
(gen_mols, ref_mols)
confgen/utils/utils.py:138
↓ 1 callersFunctionevaluate_iso17
(model, device, loader, args)
evaluate.py:184
↓ 1 callersFunctionevaluate_score
(model, device, loader, args)
evaluate.py:252
↓ 1 callersMethodget_score
(self, batch, pos, args)
confgen/model/gnn.py:744
↓ 1 callersFunctiongraph_from_adgacency_matrix
(adjacency_matrix, atomicnums)
confgen/molecule/gt.py:8
↓ 1 callersFunctionguassian_kernel
Params: source: n * len(x) target: m * len(y) Return: sum(kernel_val): Sum of various kernel matrices
confgen/utils/utils.py:209
↓ 1 callersFunctioninit_distributed_mode
(args)
confgen/utils/utils.py:93
↓ 1 callersFunctionmain
()
train.py:99
↓ 1 callersFunctionmain
()
evaluate.py:396
↓ 1 callersFunctionmatch_graphs
(G1, G2)
confgen/molecule/gt.py:23
↓ 1 callersFunctionmol2xyz
(mol, addhs=False)
confgen/utils/psi4_utils.py:10
↓ 1 callersMethodprocess_cgcf
(self)
confgen/e2c/dataset.py:208
↓ 1 callersMethodprocess_confgf
(self)
confgen/e2c/dataset.py:270
↓ 1 callersMethodprocess_default
(self)
confgen/e2c/dataset.py:348
↓ 1 callersFunctionquaternion_to_rotation_matrix
(quaternion)
confgen/utils/utils.py:58
↓ 1 callersFunctionrdk2graph
(mol: Mol)
confgen/molecule/graph.py:77
↓ 1 callersMethodreparameterization
(self, mean, log_std)
confgen/model/gnn.py:453
↓ 1 callersMethodreset_parameter
(self)
confgen/model/conv.py:301
↓ 1 callersMethodreset_parameters
(self)
confgen/model/conv.py:207
↓ 1 callersMethodreset_parameters
(self)
confgen/model/conv.py:264
↓ 1 callersFunctionsafe_index
(l, e)
confgen/molecule/gt.py:37
↓ 1 callersFunctionsafe_index_bond
(bond)
confgen/molecule/gt.py:44
↓ 1 callersFunctionsetup_for_distributed
This function disables printing when not in master process
confgen/utils/utils.py:118
↓ 1 callersMethodstep
(self, epoch)
confgen/utils/utils.py:85
↓ 1 callersFunctiontrain
(model, device, loader, optimizer, scheduler, args)
train.py:27
↓ 1 callersFunctiontrain
(model, device, loader, optimizer, scheduler, args)
evaluate.py:29
↓ 1 callersMethodupdate_iso
(pos_y, pos_x, batch)
confgen/model/gnn.py:657
Method__cat_dim__
(self, key, value)
confgen/e2c/dataset.py:386
Method__init__
(self, warmup=4e3, tmax=1e5, eta_min=5e-4)
confgen/utils/utils.py:13
Method__init__
(self, args)
confgen/utils/utils.py:76
Method__init__
( self, mlp_hidden_size: int = 512, mlp_layers: int = 2, latent_size: int = 25
confgen/model/gnn.py:22
Method__init__
( self, edge_model, node_model, global_model, aggregate_edges_for_node
confgen/model/conv.py:12
Method__init__
(self, p=0.0, submodule=None)
confgen/model/conv.py:109
Method__init__
( self, input_size, output_sizes, use_layer_norm=False, activation=nn.
confgen/model/conv.py:171
Method__init__
(self, emb_dim)
confgen/model/conv.py:219
Method__init__
(self, emb_dim)
confgen/model/conv.py:228
Method__init__
(self, dim_in, dim_out, dim_c)
confgen/model/conv.py:237
Method__init__
(self, emb_dim, num_heads)
confgen/model/conv.py:250
Method__init__
(self, emb_dim, num_heads)
confgen/model/conv.py:289
Method__init__
( self, root="dataset", rdk2graph=rdk2graph, transform=None, pre_trans
confgen/e2c/dataset.py:23
Methoddownload
(self)
confgen/e2c/dataset.py:70
Methodforward
(self, batch, sample=False)
confgen/model/gnn.py:261
Methodforward
( self, x: Tensor, edge_index: Tensor, edge_attr: Tensor, u: Tensor,
confgen/model/conv.py:42
Methodforward
(self, x)
confgen/model/conv.py:115
Methodforward
(self, x)
confgen/model/conv.py:164
Methodforward
(self, x)
confgen/model/conv.py:212
Methodforward
(self, x)
confgen/model/conv.py:223
Methodforward
(self, x)
confgen/model/conv.py:232
Methodforward
(self, x, context)
confgen/model/conv.py:243
Methodforward
q: [N, C] k: [N, 2*c] v: [N, 2*c]
confgen/model/conv.py:269
Methodforward
(self, q, k, index, dim_size)
confgen/model/conv.py:305
Methodget_angle
(vec1, vec2)
confgen/model/gnn.py:554
Functionget_energy
(mol, addhs=False)
confgen/utils/psi4_utils.py:24
Functionget_rmsd_min
(inputargs)
evaluate.py:62
Functionnum_vertices
(G)
confgen/molecule/gt.py:19
Methodprocess
(self)
confgen/e2c/dataset.py:76
Methodprocessed_file_names
(self)
confgen/e2c/dataset.py:67
Methodraw_file_names
(self)
confgen/e2c/dataset.py:62
Functionrdk2graphedge
(mol: Mol)
confgen/molecule/graph.py:13