Functions — github.com/Wangchentong/Proteus

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Functions1,071 in github.com/Wangchentong/Proteus

⨍ Functions 1,071◇ Types & classes 183

↓ 2 callersFunctionmpnn

(batch, model, ca_only,temperature,chain_id_dict=None)

ProteinMPNN/protein_mpnn_pyrosetta.py:28

↓ 2 callersFunctionparse_chain_feats

(chain_feats, scale_factor=1.)

data/utils.py:700

↓ 2 callersFunctionparse_pdb

(pdb_path, fixed_chain_list = [], ca_only=False)

ProteinMPNN/protein_mpnn_utils.py:192

↓ 2 callersFunctionplot_trans

(frame)

analysis/plotting.py:294

↓ 2 callersFunctionplt_3d

(x, ax, color=None, s=20, mode='scatter', ax_lim=None)

analysis/plotting.py:249

↓ 2 callersMethodprocess_features

( self, raw_features: FeatureDict, mode: str = "train", )

openfold/data/feature_pipeline.py:106

↓ 2 callersFunctionpseudo_beta_fn

(aatype, all_atom_positions, all_atom_masks)

openfold/utils/feats.py:34

↓ 2 callersFunctionreduce_edge_list

(l)

openfold/utils/tensor_utils.py:160

↓ 2 callersMethodreroll

(self)

openfold/data/data_modules.py:342

↓ 2 callersFunctionrotmat_to_skew_matrix

Generates skew matrix for corresponding rotation matrix. Args: mat (torch.Tensor): Batch of rotation matrices. Returns:

data/so3_utils.py:583

↓ 2 callersFunctionrotvec_to_matrix

(rotvec)

data/utils.py:291

↓ 2 callersMethodsample

Generates rotation vector(s) from IGSO(3). Args: t: continuous time in [0, 1]. n_sample: number of samples to generat

data/so3_diffuser.py:233

↓ 2 callersMethodscale_translation

Scales the translation by a constant factor. Args: trans_scale_factor: The constant fact

openfold/utils/rigid_utils.py:1351

↓ 2 callersFunctionscore

score uses the quotient rule to compute the scaling factor for the score of the IGSO(3) density. This function is used within the Diffuser cl

data/so3_diffuser.py:71

↓ 2 callersMethodscore_scaling

(self, t)

data/se3_diffuser.py:155

↓ 2 callersFunctionskew_matrix_exponential_map

Compute the matrix exponential of a rotation vector in skew matrix representation. Maps the rotation from the lie group to the rotation matri

data/so3_utils.py:260

↓ 2 callersMethodsort_actions

(actions)

openfold/utils/argparse.py:10

↓ 2 callersMethodstate_dict

(self)

openfold/utils/exponential_moving_average.py:64

↓ 2 callersMethodstate_dict

(self)

model/utils.py:161

↓ 2 callersMethodstate_dict

(self, destination=None, prefix='', keep_vars=False)

model/strcture2seq.py:34

↓ 2 callersMethodstep

Update parameters and rate

ProteinMPNN/training/utils.py:105

↓ 2 callersFunctionto_date

(s: str)

openfold/data/tools/utils.py:45

↓ 2 callersMethodtorch_score

Computes the score of IGSO(3) density as a rotation vector. Same as score function but uses pytorch and performs a look-up. Args:

data/so3_diffuser.py:274

↓ 2 callersFunctiontorsion_angles_to_frames

( r: Rigid, alpha: torch.Tensor, aatype: torch.Tensor, rrgdf: torch.Tensor, )

openfold/utils/feats.py:165

↓ 2 callersFunctiontrunc_normal_init_

(weights, scale=1.0, fan="fan_in")

openfold/model/primitives.py:57

↓ 2 callersFunctiontrunc_normal_init_

(weights, scale=1.0, fan="fan_in")

model/layers.py:258

↓ 2 callersFunctiontrunc_normal_init_

(weights, scale=1.0, fan="fan_in")

model/ipa_pytorch.py:59

↓ 2 callersFunctionupper

()

openfold/utils/tensor_utils.py:198

↓ 1 callersFunctionEvoformerBlockParams

(b, is_extra_msa=False)

openfold/utils/import_weights.py:272

↓ 1 callersFunctionN_to_AA

(x)

ProteinMPNN/pyrosetta_utils.py:41

↓ 1 callersFunctionN_to_AA

(x)

ProteinMPNN/protein_mpnn_utils.py:86

↓ 1 callersFunctionN_to_AA

(x)

ProteinMPNN/helper_scripts/parse_multiple_chains.py:30

↓ 1 callersFunctionOmega

(R, eps=1e-4)

data/so3_utils.py:46

↓ 1 callersMethod__init__

(self, optimizer, last_epoch: int = -1, verbose: bool = False, base_lr: float

openfold/utils/lr_schedulers.py:86

↓ 1 callersMethod__init__

(self, dim: int, *_, **__)

model/utils.py:71

↓ 1 callersMethod__init__

Args: c_z: Input channel dimension no_bins: Number of distogram bins

model/heads.py:7

↓ 1 callersMethod__mul__

Pointwise left multiplication of the rotation with a tensor. Can be used to e.g. mask the Rotation. Args:

openfold/utils/rigid_utils.py:407

↓ 1 callersMethod__mul__

Pointwise left multiplication of the transformation with a tensor. Can be used to e.g. mask the Rigid. Args:

openfold/utils/rigid_utils.py:969

↓ 1 callersMethod_add_batch_properties

(self, batch)

openfold/data/data_modules.py:421

↓ 1 callersFunction_assess_hhsearch_hit

Determines if template is valid (without parsing the template mmcif file). Args: hit: HhrHit for the template. hit_pdb_code: The

openfold/data/templates.py:187

↓ 1 callersFunction_attention_chunked_trainable

( query, key, value, biases, chunk_size, chunk_dim, checkpoint, )

openfold/model/primitives.py:260

↓ 1 callersMethod_batch_ot

(self, trans_0, trans_1, res_mask)

data/interpolant.py:60

↓ 1 callersFunction_build_query_to_hit_index_mapping

Gets mapping from indices in original query sequence to indices in the hit. hit_query_sequence and hit_sequence are two aligned sequences contain

openfold/data/templates.py:681

↓ 1 callersFunction_calculate_expected_aligned_error

( alignment_confidence_breaks: torch.Tensor, aligned_distance_error_probs: torch.Tensor, )

openfold/utils/loss.py:570

↓ 1 callersFunction_calculate_fan

(linear_weight_shape, fan="fan_in")

openfold/model/primitives.py:42

↓ 1 callersFunction_calculate_fan

(linear_weight_shape, fan="fan_in")

model/layers.py:244

↓ 1 callersFunction_calculate_fan

(linear_weight_shape, fan="fan_in")

model/ipa_pytorch.py:45

↓ 1 callersFunction_check_atom_mask_is_ideal

Sanity-check the atom mask is ideal, up to a possible OXT.

openfold/np/relax/amber_minimize.py:159

↓ 1 callersFunction_check_cleaned_atoms

Checks that no atom positions have been altered by cleaning.

openfold/np/relax/amber_minimize.py:125

↓ 1 callersFunction_check_residue_distances

Checks if the distance between unmasked neighbor residues is ok.

openfold/data/templates.py:478

↓ 1 callersFunction_check_residues_are_well_defined

Checks that all residues contain non-empty atom sets.

openfold/np/relax/amber_minimize.py:149

↓ 1 callersMethod_chunk

(self, x: torch.Tensor, biases: List[torch.Tensor], chunk_size: int, )

openfold/model/triangular_attention.py:61

↓ 1 callersMethod_chunk

(self, m: torch.Tensor, mask: torch.Tensor, chunk_size: int, )

openfold/model/evoformer.py:75

↓ 1 callersMethod_chunk

(self, m: torch.Tensor, biases: List[torch.Tensor], chunk_size: int, )

openfold/model/msa.py:86

↓ 1 callersMethod_chunk

(self, m: torch.Tensor, mask: torch.Tensor, chunk_size: int, )

openfold/model/msa.py:345

↓ 1 callersMethod_chunk

(self, z: torch.Tensor, mask: torch.Tensor, chunk_size: int, )

openfold/model/pair_transition.py:59

↓ 1 callersMethod_chunk

(self, a: torch.Tensor, b: torch.Tensor, chunk_size: int )

openfold/model/outer_product_mean.py:66

↓ 1 callersMethod_chunk

(self, z: torch.Tensor, t: torch.Tensor, biases: List[torch.Tensor], chunk_siz

openfold/model/template.py:75

↓ 1 callersMethod_chunked_msa_attn

(self, m: torch.Tensor, z: Optional[torch.Tensor], mask: Optional[torch.Tensor],

openfold/model/msa.py:140

↓ 1 callersMethod_combine_projections

(self, a: torch.Tensor, b: torch.Tensor, )

openfold/model/triangular_multiplicative_update.py:55

↓ 1 callersMethod_compute_language_model_representations

Adds bos/eos tokens for the language model, since the structure module doesn't use these.

model/strcture2seq.py:58

↓ 1 callersFunction_convert_sto_seq_to_a3m

( query_non_gaps: Sequence[bool], sto_seq: str )

openfold/data/parsers.py:164

↓ 1 callersMethod_corrupt_rotmats

(self, rotmats_1, t, res_mask)

data/interpolant.py:81

↓ 1 callersMethod_corrupt_trans

trans_t = (1 - t) * noise + t * trans_1

data/interpolant.py:49

↓ 1 callersMethod_cross_concat

(self, feats_1d, num_batch, num_res)

model/score_network.py:140

↓ 1 callersMethod_disable_activation_checkpointing

(self)

openfold/model/model.py:342

↓ 1 callersMethod_dist

Pairwise euclidean distances

ProteinMPNN/protein_mpnn_utils.py:889

↓ 1 callersMethod_dist

(self, X, mask, eps=1E-6)

ProteinMPNN/protein_mpnn_utils.py:987

↓ 1 callersMethod_dist

(self, X, mask, eps=1E-6)

ProteinMPNN/training/model_utils.py:314

↓ 1 callersMethod_enable_activation_checkpointing

(self)

openfold/model/model.py:349

↓ 1 callersFunction_extract_template_features

Parses atom positions in the target structure and aligns with the query. Atoms for each residue in the template structure are indexed to coincide

openfold/data/templates.py:521

↓ 1 callersFunction_fetch_dims

(tree)

openfold/utils/tensor_utils.py:110

↓ 1 callersFunction_find_template_in_pdb

Tries to find the template chain in the given pdb file. This method tries the three following things in order: 1. Tries if there is an ex

openfold/data/templates.py:266

↓ 1 callersFunction_flash_attn

(q, k, v, kv_mask)

model/msa.py:32

↓ 1 callersFunction_get_atom_positions

Gets atom positions and mask from a list of Biopython Residues.

openfold/data/templates.py:502

↓ 1 callersFunction_get_atom_site_list

Returns list of atom sites; contains data not present in the structure.

openfold/data/mmcif_parsing.py:356

↓ 1 callersFunction_get_atom_site_list

Returns list of atom sites; contains data not present in the structure.

data/mmcif_parsing.py:326

↓ 1 callersMethod_get_cache_name

Auxiliary function for determining the cache file name based on the parameters (sigma, omega, l, etc.) used for generating the lookup

data/so3_utils.py:871

↓ 1 callersFunction_get_first_model

Returns the first model in a Biopython structure.

openfold/data/mmcif_parsing.py:306

↓ 1 callersFunction_get_first_model

Returns the first model in a Biopython structure.

data/mmcif_parsing.py:284

↓ 1 callersFunction_get_header

Returns a basic header containing method, release date and resolution.

openfold/data/mmcif_parsing.py:320

↓ 1 callersFunction_get_header

Returns a basic header containing method, release date and resolution.

data/mmcif_parsing.py:297

↓ 1 callersFunction_get_module_device

Fetches the device of a module, assuming that all of the module's parameters reside on a single device Args: module: A torch.nn.

openfold/model/torchscript.py:75

↓ 1 callersFunction_get_protein_chains

Extracts polymer information for protein chains only. Args: parsed_info: _mmcif_dict produced by the Biopython parser. Returns:

openfold/data/mmcif_parsing.py:373

↓ 1 callersFunction_get_protein_chains

Extracts polymer information for protein chains only. Args: parsed_info: _mmcif_dict produced by the Biopython parser. Returns: A dict m

data/mmcif_parsing.py:340

↓ 1 callersFunction_is_after_cutoff

Checks if the template date is after the release date cutoff. Args: pdb_id: 4 letter pdb code. release_dates: Dictionary mapping

openfold/data/templates.py:104

↓ 1 callersFunction_is_set

Returns False if data is a special mmCIF character indicating 'unset'.

openfold/data/mmcif_parsing.py:427

↓ 1 callersFunction_is_set

Returns False if data is a special mmCIF character indicating 'unset'.

data/mmcif_parsing.py:417

↓ 1 callersFunction_lma

( q: torch.Tensor, k: torch.Tensor, v: torch.Tensor, biases: List[torch.Tensor], q_chu

openfold/model/primitives.py:539

↓ 1 callersFunction_make_atom14_ambiguity_feats

()

openfold/np/residue_constants.py:1287

↓ 1 callersFunction_make_rigid_group_constants

Fill the arrays above.

openfold/np/residue_constants.py:1133

↓ 1 callersFunction_make_rigid_group_constants

Fill the arrays above.

data/residue_constants.py:829

↓ 1 callersFunction_make_standard_atom_mask

Returns [num_res_types, num_atom_types] mask array.

openfold/np/residue_constants.py:1037

↓ 1 callersFunction_make_standard_atom_mask

Returns [num_res_types, num_atom_types] mask array.

data/residue_constants.py:740

↓ 1 callersMethod_mpnn_idx_to_esm_idx

(self, aa, mask)

model/strcture2seq.py:54

↓ 1 callersMethod_mpnn_to_esm

(d: Alphabet)

model/strcture2seq.py:40

↓ 1 callersFunction_openmm_minimize

Minimize energy via openmm.

openfold/np/relax/amber_minimize.py:79

↓ 1 callersMethod_opm

(self, a, b)

openfold/model/outer_product_mean.py:53

↓ 1 callersMethod_orientations_coarse

(self, X, E_idx, eps=1e-6)

ProteinMPNN/protein_mpnn_utils.py:839

↓ 1 callersFunction_parse_hhr_hit

Parses the detailed HMM HMM comparison section for a single Hit. This works on .hhr files generated from both HHBlits and HHSearch. Args:

openfold/data/parsers.py:250

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