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Functions1,071 in github.com/Wangchentong/Proteus

⨍ Functions 1,071◇ Types & classes 183
↓ 1 callersFunctionget_release_date
Returns the oldest revision date.
openfold/data/mmcif_parsing.py:314
↓ 1 callersFunctionget_release_date
Returns the oldest revision date.
data/mmcif_parsing.py:291
↓ 1 callersMethodget_sigma_idx
Convert continuous sigmas to the indices of the closest tabulated values. Args: sigma (torch.Tensor): IGSO3 std devs.
data/so3_utils.py:889
↓ 1 callersFunctionget_std_opt
(parameters, d_model, step)
ProteinMPNN/training/model_utils.py:509
↓ 1 callersFunctionget_stochastic_train_filter_prob
( chain_data_cache_entry: Any, )
openfold/data/data_modules.py:238
↓ 1 callersMethodget_templates
Computes the templates for given query sequence (more details above).
openfold/data/templates.py:996
↓ 1 callersFunctionget_violation_metrics
Computes violation and alignment metrics.
openfold/np/relax/amber_minimize.py:393
↓ 1 callersFunctionglorot_uniform_init_
(weights)
openfold/model/primitives.py:79
↓ 1 callersFunctionglorot_uniform_init_
(weights)
model/layers.py:280
↓ 1 callersFunctionglorot_uniform_init_
(weights)
model/ipa_pytorch.py:81
↓ 1 callersFunctionhe_normal_init_
(weights)
openfold/model/primitives.py:75
↓ 1 callersFunctionhe_normal_init_
(weights)
model/layers.py:276
↓ 1 callersFunctionhe_normal_init_
(weights)
model/ipa_pytorch.py:77
↓ 1 callersFunctionidentity_quats
( batch_dims: Tuple[int], dtype: Optional[torch.dtype] = None, device: Optional[torch.device] = N
openfold/utils/rigid_utils.py:139
↓ 1 callersFunctionidentity_rot_mats
( batch_dims: Tuple[int], dtype: Optional[torch.dtype] = None, device: Optional[torch.device] =
openfold/utils/rigid_utils.py:109
↓ 1 callersFunctionigso3_density_angle
(omega, t, L=500)
data/igso3.py:48
↓ 1 callersFunctionigso3_expansion
Compute the IGSO(3) angle probability distribution function for pairs of angles and std dev levels. The expansion is computed using a grid of
data/so3_utils.py:1306
↓ 1 callersMethodinit_feat
( self, contigs, ref_feats = None, hotspot = None, )
model/fold_module.py:551
↓ 1 callersMethodinit_strcture_model_from_conf
Loads in model checkpoint.
model/fold_module.py:78
↓ 1 callersFunctionintegrate_trapezoid_cumulative
Auxiliary function for numerically integrating a discretized 1D function using the trapezoid rule. This is mainly used for computing the cumu
data/so3_utils.py:1274
↓ 1 callersFunctioninvert_quat
(quat: torch.Tensor)
openfold/utils/rigid_utils.py:288
↓ 1 callersFunctionipa_point_weights_init_
(weights)
openfold/model/primitives.py:97
↓ 1 callersFunctionipa_point_weights_init_
(weights)
model/ipa_pytorch.py:33
↓ 1 callersFunctionis_fp16_enabled
()
openfold/utils/precision_utils.py:18
↓ 1 callersFunctionis_main_process
()
openfold/utils/logger.py:26
↓ 1 callersMethoditeration
(self, feats, m_1_prev, z_prev, x_prev, _recycle=True)
openfold/model/model.py:174
↓ 1 callersMethodknn_indices
(self, x, num_neighbour,num_linear, pair_mask = None)
model/ipa_pytorch.py:360
↓ 1 callersMethodlayer_with_ipa_embedding
(self, t, block_i: int, msa_feature:torch.Tensor,node_feature:torch.Tensor = None,pair_feature:torch.Tensor=No
model/msa.py:662
↓ 1 callersFunctionlddt
( all_atom_pred_pos: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_mask: torch.Tensor,
analysis/metrics.py:147
↓ 1 callersFunctionlddt_ca
( all_atom_pred_pos: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_mask: torch.Tensor,
analysis/metrics.py:125
↓ 1 callersFunctionlddt_loss
( logits: torch.Tensor, all_atom_pred_pos: torch.Tensor, all_atom_positions: torch.Tensor, all
openfold/utils/loss.py:461
↓ 1 callersFunctionlecun_normal_init_
(weights)
openfold/model/primitives.py:71
↓ 1 callersFunctionlecun_normal_init_
(weights)
model/layers.py:272
↓ 1 callersFunctionlecun_normal_init_
(weights)
model/ipa_pytorch.py:73
↓ 1 callersFunctionloadBlosum62
(path, softmax = False,double_stochastic = False, max_clip = 1000, pad_tokens = 0 )
data/discrete_diffuser.py:10
↓ 1 callersMethodload_cache
Load data from the cache file. Returns: Dictionary of loaded data tensors.
data/so3_utils.py:730
↓ 1 callersFunctionload_stereo_chemical_props
Load stereo_chemical_props.txt into a nice structure. Load literature values for bond lengths and bond angles and translate bond angles into
openfold/np/residue_constants.py:439
↓ 1 callersFunctionload_stereo_chemical_props
Load stereo_chemical_props.txt into a nice structure. Load literature values for bond lengths and bond angles and translate bond angles into the
data/residue_constants.py:392
↓ 1 callersFunctionmain
(args)
ProteinMPNN/protein_mpnn_run.py:4
↓ 1 callersFunctionmain
(args)
ProteinMPNN/training/training.py:4
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/assign_fixed_chains.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/make_bias_per_res_dict.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/make_tied_positions_dict.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/make_pos_neg_tied_positions_dict.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/make_fixed_positions_dict.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/parse_multiple_chains.py:3
↓ 1 callersFunctionmain
(args)
ProteinMPNN/helper_scripts/make_bias_AA.py:3
↓ 1 callersFunctionmake_atom14_masks
Construct denser atom positions (14 dimensions instead of 37).
openfold/data/data_transforms.py:575
↓ 1 callersFunctionmake_atom14_positions
Constructs denser atom positions (14 dimensions instead of 37).
openfold/np/relax/amber_minimize.py:198
↓ 1 callersFunctionmake_data_config
( config: ml_collections.ConfigDict, mode: str, num_res: int, )
openfold/data/feature_pipeline.py:50
↓ 1 callersMethodmake_masked_msa
Create data for BERT on raw MSA.
data/discrete_diffuser.py:127
↓ 1 callersFunctionmake_mmcif_features
( mmcif_object: mmcif_parsing.MmcifObject, chain_id: str )
openfold/data/data_pipeline.py:90
↓ 1 callersFunctionmake_msa_features
Constructs a feature dict of MSA features.
openfold/data/data_pipeline.py:183
↓ 1 callersFunctionmake_pdb_features
( protein_object: protein.Protein, description: str, confidence_threshold: float = 0.5, is_dis
openfold/data/data_pipeline.py:163
↓ 1 callersMethodmake_transform_from_reference
Returns a transformation object from reference coordinates. Note that this method does not take care of symmetries. If you
openfold/utils/rigid_utils.py:1375
↓ 1 callersFunctionmap_fn
(fun, x)
openfold/data/input_pipeline.py:200
↓ 1 callersFunctionmasked_msa_loss
Computes BERT-style masked MSA loss. Implements subsection 1.9.9. Args: logits: [*, N_seq, N_res, 23] predicted residue distribution
openfold/utils/loss.py:1485
↓ 1 callersFunctionmatrix_to_rotvec
(mat)
data/utils.py:294
↓ 1 callersFunctionmmcif_loop_to_dict
Extracts loop associated with a prefix from mmCIF data as a dictionary. Args: prefix: Prefix shared by each of the data items in the loop.
openfold/data/mmcif_parsing.py:153
↓ 1 callersFunctionmodel_init
(config)
ProteinMPNN/protein_mpnn_utils.py:21
↓ 1 callersFunctionmultidim_trace
Take the trace of a matrix with leading dimensions.
data/so3_utils.py:627
↓ 1 callersFunctionnonensembled_transform_fns
Input pipeline data transformers that are not ensembled.
openfold/data/input_pipeline.py:23
↓ 1 callersFunctionnormal_init_
(weights)
openfold/model/primitives.py:93
↓ 1 callersFunctionnormal_init_
(weights)
model/layers.py:294
↓ 1 callersFunctionnormal_init_
(weights)
model/ipa_pytorch.py:95
↓ 1 callersFunctionnormal_log_density
(x, mean, var)
data/so3_utils.py:63
↓ 1 callersFunctionnp_example_to_features
( np_example: FeatureDict, config: ml_collections.ConfigDict, mode: str, )
openfold/data/feature_pipeline.py:72
↓ 1 callersFunctionnp_to_tensor_dict
Creates dict of tensors from a dict of NumPy arrays. Args: np_example: A dict of NumPy feature arrays. features: A list of string
openfold/data/feature_pipeline.py:30
↓ 1 callersFunctionpad_feats
(raw_feats, max_len, use_torch=False,max_templates=None, max_msas=None)
data/utils.py:300
↓ 1 callersFunctionpad_rigid
(rigid: torch.tensor, max_len: int)
data/utils.py:355
↓ 1 callersFunctionpair
(channel_dim)
openfold/model/torchscript.py:104
↓ 1 callersFunctionparse_PDB_biounits
input: x = PDB filename atoms = atoms to extract (optional) output: (length, atoms, coords=(x,y,z)), sequence
ProteinMPNN/helper_scripts/parse_multiple_chains.py:37
↓ 1 callersFunctionparse_extra_res_fa_param
(param_fn)
ProteinMPNN/pyrosetta_utils.py:10
↓ 1 callersFunctionparse_fasta
Parses FASTA string and returns list of strings with amino-acid sequences. Arguments: fasta_string: The string contents of a FASTA file.
openfold/data/parsers.py:41
↓ 1 callersFunctionparse_file
(file_path, ca_only=False)
ProteinMPNN/protein_mpnn_utils.py:147
↓ 1 callersFunctionparse_pdb_lines
(lines)
data/utils.py:176
↓ 1 callersFunctionparse_pssm
(path)
ProteinMPNN/helper_scripts/other_tools/make_pssm_dict.py:13
↓ 1 callersFunctionprocess_chain
Convert a PDB chain object into a AlphaFold Protein instance. Forked from alphafold.common.protein.from_pdb_string WARNING: All non-standard
data/utils.py:791
↓ 1 callersMethodprocess_core
Assembles features for a protein in a ProteinNet .core file.
openfold/data/data_pipeline.py:651
↓ 1 callersMethodprocess_fasta
Assembles features for a single sequence in a FASTA file
openfold/data/data_pipeline.py:543
↓ 1 callersMethodprocess_mmcif
Assembles features for a specific chain in an mmCIF object. If chain_id is None, it is assumed that there is only one chain
openfold/data/data_pipeline.py:582
↓ 1 callersMethodprocess_pdb
Assembles features for a protein in a PDB file.
openfold/data/data_pipeline.py:617
↓ 1 callersMethodprocess_performance_stats
(self, deltas)
openfold/utils/logger.py:52
↓ 1 callersFunctionpseudo_beta_fn
Create pseudo beta features.
openfold/data/data_transforms.py:370
↓ 1 callersFunctionpseudo_beta_fn
Create pseudo beta features.
data/data_transforms.py:49
↓ 1 callersFunctionquat_multiply
Multiply a quaternion by another quaternion.
openfold/utils/rigid_utils.py:260
↓ 1 callersFunctionquat_multiply_by_vec
Multiply a quaternion by a pure-vector quaternion.
openfold/utils/rigid_utils.py:272
↓ 1 callersFunctionquat_to_rot
Converts a quaternion to a rotation matrix. Args: quat: [*, 4] quaternions Returns: [*, 3, 3] rotati
openfold/utils/rigid_utils.py:185
↓ 1 callersFunctionquat_to_rotvec
(quat, eps=1e-6)
data/utils.py:908
↓ 1 callersMethodrate
Implement `lrate` above
ProteinMPNN/training/utils.py:114
↓ 1 callersMethodrate
Implement `lrate` above
ProteinMPNN/training/model_utils.py:498
↓ 1 callersMethodrbf
(self, D, D_min=0.0, D_sigma=0.5)
model/ipa_pytorch.py:382
↓ 1 callersFunctionregularize
Regularize a point to be in accordance with convention. In 3D, regularize the norm of the rotation vector, to be between 0 and pi, following t
data/so3_utils.py:148
↓ 1 callersMethodrelpos
Computes relative positional encodings Implements Algorithm 4. Args: ri: "residue_index" featur
openfold/model/embedders.py:71
↓ 1 callersMethodreset_parameters
(self)
model/layers.py:83
↓ 1 callersMethodreset_parameters
(self)
model/layers.py:164
↓ 1 callersFunctionrosetta_xyz_to_numpy
(x)
ProteinMPNN/pyrosetta_utils.py:47
↓ 1 callersFunctionrot_to_quat
( rot: torch.Tensor, epsilon: float = 1e-7, )
openfold/utils/rigid_utils.py:208
↓ 1 callersFunctionrotate_half
(x)
model/utils.py:11
↓ 1 callersFunctionrotation_vector_from_matrix
Convert rotation matrix (in 3D) to rotation vector (axis-angle). # Adapted from geomstats # https://github.com/geomstats/geomstats/blob/maste
data/so3_utils.py:86
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