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Functions1,028 in github.com/SantiagoMille/germinal

⨍ Functions 1,028◇ Types & classes 125
Method__init__
(self, config, global_config, name='triangle_attention')
colabdesign/colabdesign/af/alphafold/model/modules.py:686
Method__init__
(self, config, global_config, name='masked_msa_head')
colabdesign/colabdesign/af/alphafold/model/modules.py:750
Method__init__
(self, config, global_config, name='predicted_lddt_head')
colabdesign/colabdesign/af/alphafold/model/modules.py:788
Method__init__
(self, config, global_config, name='predicted_aligned_error_head')
colabdesign/colabdesign/af/alphafold/model/modules.py:846
Method__init__
(self, config, global_config, name='experimentally_resolved_head')
colabdesign/colabdesign/af/alphafold/model/modules.py:886
Method__init__
(self, config, global_config, name='triangle_multiplication')
colabdesign/colabdesign/af/alphafold/model/modules.py:931
Method__init__
(self, config, global_config, name='distogram_head')
colabdesign/colabdesign/af/alphafold/model/modules.py:1069
Method__init__
(self, config, global_config, num_output_channel,
colabdesign/colabdesign/af/alphafold/model/modules.py:1106
Method__init__
(self, config, global_config, is_extra_msa, name='evoformer_iteration')
colabdesign/colabdesign/af/alphafold/model/modules.py:1243
Method__init__
(self, config, global_config, name='evoformer')
colabdesign/colabdesign/af/alphafold/model/modules.py:1373
Method__init__
(self, config, global_config, name='single_template_embedding')
colabdesign/colabdesign/af/alphafold/model/modules.py:1596
Method__init__
(self, config, global_config, name='template_embedding')
colabdesign/colabdesign/af/alphafold/model/modules.py:1714
Method__init__
Initialize. Args: config: Structure Module Config global_config: Global Config of Model. dist_epsilon: Small value to avoid NaN
colabdesign/colabdesign/af/alphafold/model/folding.py:50
Method__init__
(self, config, global_config, name='fold_iteration')
colabdesign/colabdesign/af/alphafold/model/folding.py:292
Method__init__
(self, config, global_config, name='structure_module')
colabdesign/colabdesign/af/alphafold/model/folding.py:489
Method__init__
(self, config, global_config, name='rigid_sidechain')
colabdesign/colabdesign/af/alphafold/model/folding.py:903
Method__init__
(self, axis, create_scale: bool, create_offset: bool,
colabdesign/colabdesign/af/alphafold/model/common_modules.py:134
Method__init__
Initialize from quaternion and translation. Args: quaternion: Rotation represented by a quaternion, to be applied before translatio
colabdesign/colabdesign/af/alphafold/model/quat_affine.py:184
Method__init__
(self, config, global_config, name='alphafold_iteration')
colabdesign/colabdesign/af/alphafold/model/modules_multimer.py:72
Method__init__
(self, config, global_config, name='evoformer')
colabdesign/colabdesign/af/alphafold/model/modules_multimer.py:208
Method__init__
(self, config, global_config, name='template_embedding')
colabdesign/colabdesign/af/alphafold/model/modules_multimer.py:466
Method__init__
(self, config, global_config, name='single_template_embedding')
colabdesign/colabdesign/af/alphafold/model/modules_multimer.py:534
Method__init__
(self, config, global_config, name='template_embedding_iteration')
colabdesign/colabdesign/af/alphafold/model/modules_multimer.py:678
Method__init__
(self, f: WrappedFn, count: int, unroll: int, name
colabdesign/colabdesign/af/alphafold/model/layer_stack.py:170
Method__init__
(self, f: WrappedFn, count: int, unroll: int, name
colabdesign/colabdesign/af/alphafold/model/layer_stack.py:193
Method__init__
(self, config: ml_collections.ConfigDict, params: Optional[Mapping[str, Mapping[
colabdesign/colabdesign/af/alphafold/model/model.py:31
Method__init__
(self, same_dtype=True)
colabdesign/colabdesign/af/alphafold/model/geometry/struct_of_array.py:184
Method__init__
Initializes the data pipeline. Args: monomer_data_pipeline: An instance of pipeline.DataPipeline - that runs the data pipeline for
colabdesign/colabdesign/af/alphafold/data/pipeline_multimer.py:173
Method__init__
(self, rate)
colabdesign/colabdesign/mpnn/modules.py:16
Method__init__
(self, num_hidden, num_in, dropout=0.1, num_heads=None, scale=30, name=None)
colabdesign/colabdesign/mpnn/modules.py:87
Method__init__
(self, num_hidden, num_ff, name=None)
colabdesign/colabdesign/mpnn/modules.py:134
Method__init__
(self, num_embeddings, max_relative_feature=32)
colabdesign/colabdesign/mpnn/modules.py:145
Method__init__
(self, config)
colabdesign/colabdesign/mpnn/modules.py:159
Method__init__
Extract protein features
colabdesign/colabdesign/mpnn/modules.py:176
Method__init__
(self, vocab_size, embed_dim)
colabdesign/colabdesign/mpnn/modules.py:280
Method__init__
(self, num_letters, node_features, edge_features, hidden_dim, num_encoder_layers=3, num_deco
colabdesign/colabdesign/mpnn/modules.py:300
Method__init__
(self, model_name="v_48_020", backbone_noise=0.0, dropout=0.0, seed=None, verbos
colabdesign/colabdesign/mpnn/model.py:24
Method__init__
(self, pdb_dict_list, verbose=True, truncate=None, max_length=100, alphabet='ACDEFGHIKLMNPQRSTVWYX-')
colabdesign/colabdesign/mpnn/legacy/utils.py:51
Method__init__
(self, model_name="v_48_020", verbose=False)
colabdesign/colabdesign/mpnn/legacy/wrapper.py:17
Method__init__
(self, rate)
colabdesign/colabdesign/mpnn/legacy/modules.py:16
Method__init__
(self, num_hidden, num_in, dropout=0.1, num_heads=None, scale=30, name=None)
colabdesign/colabdesign/mpnn/legacy/modules.py:86
Method__init__
(self, num_hidden, num_ff, name=None)
colabdesign/colabdesign/mpnn/legacy/modules.py:132
Method__init__
(self, num_embeddings, max_relative_feature=32)
colabdesign/colabdesign/mpnn/legacy/modules.py:143
Method__init__
(self, config)
colabdesign/colabdesign/mpnn/legacy/modules.py:157
Method__init__
Extract protein features
colabdesign/colabdesign/mpnn/legacy/modules.py:182
Method__init__
(self, vocab_size, embed_dim)
colabdesign/colabdesign/mpnn/legacy/modules.py:285
Method__init__
(self, num_letters, node_features, edge_features, hidden_dim, num_encoder_layers=3, num_deco
colabdesign/colabdesign/mpnn/legacy/modules.py:305
Method__init__
(self, key=None, seed=None)
colabdesign/colabdesign/shared/utils.py:88
Method__init__
(self, key)
colabdesign/colabdesign/shared/prng.py:7
Method__init__
(self)
colabdesign/colabdesign/shared/parse_args.py:4
Method__init__
(self, dictionary)
colabdesign/colabdesign/shared/parse_args.py:53
Method__init__
( self, config, )
colabdesign/colabdesign/esm_msa/modules.py:37
Method__init__
( self, in_features: int, prepend_bos: bool, append_eos: bool, bias=True, eos_idx: Opt
colabdesign/colabdesign/esm_msa/modules.py:99
Method__init__
( self, layer: hk.Module, config, name=None, )
colabdesign/colabdesign/esm_msa/modules.py:137
Method__init__
( self, config, )
colabdesign/colabdesign/esm_msa/modules.py:172
Method__init__
(self, embed_dim)
colabdesign/colabdesign/esm_msa/modules.py:197
Method__init__
(self, config, padding_idx)
colabdesign/colabdesign/esm_msa/modules.py:211
Method__init__
(self, sequence_labels, sequence_strs)
colabdesign/colabdesign/esm_msa/data.py:17
Method__init__
( self, standard_toks: Sequence[str], prepend_toks: Sequence[str] = ("<null_0>", "<pad>", "<eos>",
colabdesign/colabdesign/esm_msa/data.py:87
Method__init__
(self, alphabet)
colabdesign/colabdesign/esm_msa/data.py:172
Method__init__
(self, config)
colabdesign/colabdesign/esm_msa/axial_attention.py:122
Method__init__
(self, alphabet, config)
colabdesign/colabdesign/esm_msa/model.py:23
Method__init__
(self, protocol="fixbb", use_templates=False, recycle_mode="last", num_recycles=0)
colabdesign/colabdesign/tr/joint_model.py:5
Method__init__
(self, protocol="fixbb", num_models=1, sample_models=True, data_dir="params/tr",
colabdesign/colabdesign/tr/model.py:19
Method__init__
(self)
colabdesign/colabdesign/tr/legacy/utils.py:263
Method__init__
(self, dictionary)
colabdesign/colabdesign/tr/legacy/utils.py:312
Method__init__
(self, axes=(1,2),trainable=True)
colabdesign/colabdesign/tr/legacy/model.py:73
Method__init__
( self, design_name: str, experiment_name: str, cdr_lengths: str, targ
germinal/utils/io.py:183
Method__init__
(self, layout: RunLayout)
germinal/utils/io.py:339
Method__len__
(self)
colabdesign/colabdesign/mpnn/legacy/utils.py:82
Method__len__
(self)
colabdesign/colabdesign/esm_msa/data.py:54
Method__len__
(self)
colabdesign/colabdesign/esm_msa/data.py:117
Method__matmul__
(self, other: Rigid3Array)
colabdesign/colabdesign/af/alphafold/model/geometry/rigid_matrix_vector.py:37
Method__matmul__
Composes two Rot3Arrays.
colabdesign/colabdesign/af/alphafold/model/geometry/rotation_matrix.py:64
Method__mul__
(self, other: Float)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:61
Method__neg__
(self)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:70
Method__pos__
(self)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:73
Method__post_init__
(self)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:48
Method__repr__
(self)
colabdesign/colabdesign/af/alphafold/model/quat_affine.py:340
Method__rmul__
(self, other: Float)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:64
Method__setstate__
(self, state)
colabdesign/colabdesign/af/alphafold/model/geometry/rigid_matrix_vector.py:102
Method__setstate__
(self, state)
colabdesign/colabdesign/af/alphafold/model/geometry/rotation_matrix.py:153
Method__setstate__
(self, state)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:122
Method__sub__
(self, other: Vec3Array)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:58
Method__truediv__
(self, other: Float)
colabdesign/colabdesign/af/alphafold/model/geometry/vector.py:67
Method_call_wrapped
(self, args, y)
colabdesign/colabdesign/af/alphafold/model/layer_stack.py:180
Method_call_wrapped
(self, x, *args)
colabdesign/colabdesign/af/alphafold/model/layer_stack.py:202
Function_concat_frames
(xall, x5, x6, x7)
colabdesign/colabdesign/af/alphafold/model/all_atom.py:506
Method_design_mcmc
MCMC with simulated annealing ---------------------------------------- steps = number for steps for the MCMC trajectory half_life = h
colabdesign/colabdesign/af/design.py:753
Function_fixbb_model
(seq, true)
colabdesign/colabdesign/tr/legacy/model.py:208
Method_flush_current_buf
()
colabdesign/colabdesign/esm_msa/data.py:67
Method_flush_current_seq
()
colabdesign/colabdesign/esm_msa/data.py:27
Method_forward
(tokens)
colabdesign/colabdesign/esm_msa/model.py:114
Method_forward_fn
(batch)
colabdesign/colabdesign/af/alphafold/model/model.py:44
Method_forward_sample
(inputs)
colabdesign/colabdesign/mpnn/modules.py:167
Method_forward_sample
(inputs)
colabdesign/colabdesign/mpnn/legacy/modules.py:166
Method_forward_score
(inputs)
colabdesign/colabdesign/mpnn/modules.py:162
Method_forward_score
(inputs)
colabdesign/colabdesign/mpnn/legacy/modules.py:160
Method_forward_tsample
(inputs)
colabdesign/colabdesign/mpnn/legacy/modules.py:172
Function_hallucination_model
(seq, bkg)
colabdesign/colabdesign/tr/legacy/model.py:214
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