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Functions429 in github.com/THUNLP-MT/MEAN

⨍ Functions 429◇ Types & classes 43

FunctionResidue_switch_numbering_scheme

data/ImmunoPDB.py:399

(self, *args, **kwargs)

evaluation/ddg/utils/misc.py:11

(self, data_list)

evaluation/ddg/utils/data.py:56

evaluation/ddg/utils/data.py:101

data/pdb_utils.py:375

Method__getattr__

evaluation/ddg/utils/misc.py:14

Method__getitem__

data/dataset.py:153

Method__getitem__

data/dataset.py:284

(self,scheme,allowed_domains, region_definition=None, warnings=False)

data/ImmunoPDB.py:106

data/ImmunoPDB.py:219

file_path: path to the dataset save_dir: directory to save the processed data num_entry_per_file: number of entries in a sing

data/dataset.py:26

(self, symbol, abrv, idx=0, side_chain_coord=None)

data/pdb_utils.py:49

data/pdb_utils.py:68

(self, _id, residues: List[Residue])

data/pdb_utils.py:245

(self, pdb_id, peptides)

data/pdb_utils.py:312

heavy_chain: the id of heavy chain light_chain: the id of light chain antigen_chains: the list of ids of antigen

data/pdb_utils.py:416

(self, message)

data/anarci/anarci.py:86

(self, args, save_dir, lr, max_epoch, metric_min_better=True, early_stop=False, patience=3, grad_clip=None, an

trainer/abs_trainer.py:17

(self, model, train_loader, valid_loader, config)

trainer/abs_trainer.py:33

(self, input_nf, output_nf, hidden_nf, n_channel, edges_in_d=0, act_fn=nn.SiLU(), dropout=0.1

models/MCAttGNN/mc_egnn.py:147

(self, in_node_nf, hidden_nf, out_node_nf, n_channel, in_edge_nf=0, act_fn=nn.SiLU(), n_layer

models/MCAttGNN/mc_egnn.py:243

models/MCAttGNN/mc_att_model.py:30

(self, embed_size, hidden_size, n_channel, n_edge_feats=0, n_layers=3, cdr_type='3', alpha=0.1, dropout=0.1, n

models/MCAttGNN/mc_att_model.py:337

(self, length_ref_key='mutation_mask', pad_values={'aa': 20, 'pos14': float('999'), 'icode': ' ', 'chain_id':

evaluation/ddg/utils/data.py:10

evaluation/ddg/models/predictor.py:13

evaluation/ddg/models/predictor.py:97

(self, num_funcs=6)

evaluation/ddg/models/common.py:27

(self, node_feat_dim, pair_feat_dim, spatial_attn_mode='CB', value_dim=16, query_key_dim=16, num_query_points=

evaluation/ddg/models/attention.py:40

(self, feat_dim)

evaluation/ddg/models/residue.py:9

data/dataset.py:237

data/dataset.py:287

data/pdb_utils.py:141

data/pdb_utils.py:304

Method__setattr__

(self, name, value)

evaluation/ddg/utils/misc.py:8

data/pdb_utils.py:63

data/pdb_utils.py:307

data/pdb_utils.py:385

data/pdb_utils.py:653

trainer/abs_trainer.py:28

Method_cmp_wrapper

data/dataset.py:267

Methodaccept_residue

(self, residue)

data/ImmunoPDB.py:346

Methodaccept_residue

(self, residue)

data/ImmunoPDB.py:353

Methodbasic_ipstream

Default constructor, creates an uninitialised stream.

evaluation/TMscore.cpp:569

Methodbasic_opstream

Default constructor, creates an uninitialised stream.

evaluation/TMscore.cpp:721

Methodbasic_pstream

Default constructor, creates an uninitialised stream.

evaluation/TMscore.cpp:861

Methodbasic_pstreambuf

evaluation/TMscore.cpp:1209

Methodbasic_rpstream

Default constructor, creates an uninitialised stream.

evaluation/TMscore.cpp:1033

Methodcollate_fn

data/dataset.py:241

Functioncontinuous_segments

data/pdb_utils.py:392

Methodcreate_buffers

evaluation/TMscore.cpp:1669

Methoddestroy_buffers

evaluation/TMscore.cpp:1700

(self, residue)

data/pdb_utils.py:214

Functiondownload_one_item

data/download.py:210

Functiondownload_one_item_local

(pdb_dir, item)

data/download.py:221

Methodempty_buffer

evaluation/TMscore.cpp:2005

evaluation/TMscore.cpp:1889

Functioneval_one

(tup, out_dir, cdr='H3')

Functionfake_log

(*args, **kwargs)

ita_train.py:122

Functionfetch_from_pdb

data/pdb_utils.py:719

Functionfetch_from_sabdab

(identifier, tries=5)

data/download.py:38

Methodfill_buffer

evaluation/TMscore.cpp:2086

evaluation/TMscore.cpp:2403

evaluation/TMscore.cpp:1515

Functionformat_aa_abrv

data/pdb_utils.py:153

h: [bs * n_node, hidden_size] edge_index: list of [n_row] and [n_col] where n_row == n_col (with no cutoff, n_row == bs * n_node * (n

models/MCAttGNN/mc_egnn.py:126

(self, h, edge_index, coord, edge_attr=None)

models/MCAttGNN/mc_egnn.py:226

(self, h, x, ctx_edges, att_edges, ctx_edge_attr=None, att_edge_attr=None, return_attention=False)

models/MCAttGNN/mc_egnn.py:287

(self, X, S, offsets)

models/MCAttGNN/mc_att_model.py:125

:param X: [n_all_node, n_channel, 3] :param S: [n_all_node] :param L: list of cdr types :param offsets: [batch_size +

models/MCAttGNN/mc_att_model.py:188

:param X: [n_all_node, n_channel, 3] :param S: [n_all_node] :param L: list of cdr types :param offsets: [batch_size +

models/MCAttGNN/mc_att_model.py:341

Args: pos14: (N, L, 14, 3). aa: (N, L). seq: (N, L). chain: (N, L). mask

evaluation/ddg/models/predictor.py:33

Args: node_feat_wt: (N, L, F). node_feat_mut: (N, L, F). mask: (N, L).

evaluation/ddg/models/predictor.py:75

(self, complex_wt, complex_mut, ddG_true=None)

evaluation/ddg/models/predictor.py:102

Args: x: (..., d).

evaluation/ddg/models/common.py:35

(self, R, t, p_CB, x, z, mask)

evaluation/ddg/models/attention.py:233

(self, R, t, p_CB, x, z, mask)

evaluation/ddg/models/attention.py:248

Args: aa: (N, L). pos14: (N, L, 14, 3). atom_mask: (N, L, 14).

evaluation/ddg/models/residue.py:20

Methodgenerate_analyze

:param X: [n_all_node, n_channel, 3] :param S: [n_all_node] :param L: list of cdr types :param offsets: [batch_size +

models/MCAttGNN/mc_att_model.py:472

Methodget_atom_names

data/pdb_utils.py:182

Methodget_backbone_coord_map

data/pdb_utils.py:174

Methodget_cb_pos

data/pdb_utils.py:275

data/pdb_utils.py:346

Methodget_optimizer

trainer/mcatt_trainer.py:11

Methodget_out_dim

evaluation/ddg/models/common.py:32

Methodget_pad_idx

data/pdb_utils.py:126

Methodget_scheduler

(self, optimizer)

trainer/mcatt_trainer.py:16

Methodidx_to_abrv

data/pdb_utils.py:123

(self, batch, device, greedy=True)

models/MCAttGNN/mc_att_model.py:444

Methodinit_rbuffers

evaluation/TMscore.cpp:1660

Functionis_hetero_residue

evaluation/ddg/utils/protein.py:72

evaluation/TMscore.cpp:1800

evaluation/TMscore.cpp:1835

Methodload_side_chain_coord

data/pdb_utils.py:93

evaluation/TMscore.cpp:6762

Methodnum_chains

data/pdb_utils.py:349

Given a sequence string, use anarci to number it using the scheme of choice. Only the first domain will be recognised and numbered For m

data/anarci/anarci.py:955

* @brief Start a process. * * Calls do_open( @a cmd , @a mode|pstdout ). * * @param cmd a string containing a shell

evaluation/TMscore.cpp:645

* @brief Start a process. * * Calls do_open( @a cmd , @a mode|pstdin ). * * @param cmd a string containing a shell c

evaluation/TMscore.cpp:803

* @brief Start a process. * * Calls do_open( @a cnd , @a mode ). * * @param cmd a string containing a shell command.

evaluation/TMscore.cpp:943

* @brief Start a process. * * Calls do_open( @a cmd , @a mode ). * * @param cmd a string containing a shell command

evaluation/TMscore.cpp:1112

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