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Functions1,008 in github.com/bytedance/dplm

⨍ Functions 1,008◇ Types & classes 149↳ Endpoints 2

Functionprot_to_torsion_angles

Calculate torsion angle features from protein features.

src/byprot/utils/protein/all_atom.py:129

Functionprot_to_torsion_angles

Calculate torsion angle features from protein features.

src/byprot/datamodules/pdb_dataset/all_atom.py:129

Functionprotein_metrics

( *, pdb_path, atom37_pos, gt_atom37_pos, gt_aatype, diffuse_mask, )

src/byprot/modules/protein_metrics.py:156

Methodpstream_common

analysis/TMscore.cpp:2231

Methodquantize_and_decode

( self, pre_quant, mask=None, aatype=None, decoder_kwargs={} )

src/byprot/models/structok/structok_lfq.py:178

analysis/TMscore.cpp:2210

Functionread_pkl

Read data from a pickle file.

src/byprot/datamodules/pdb_dataset/utils.py:349

Ensure a basic_ipstream will read from at least one pipe

analysis/TMscore.cpp:554

Functionrecursive_apply

src/byprot/utils/__init__.py:307

Functionrecursive_eval

src/byprot/utils/__init__.py:320

Functionregister_datamodule

src/byprot/datamodules/__init__.py:16

Functionregister_model

src/byprot/models/__init__.py:16

Functionregister_task

src/byprot/tasks/__init__.py:290

Methodremap_to_used

src/byprot/models/structok/modules/vqvae.py:500

src/byprot/utils/callbacks.py:99

Functionresolve_ckpt_path

(ckpt_dir, ckpt_path)

src/byprot/utils/__init__.py:270

Functionresolve_experiment_config

(config: DictConfig)

src/byprot/utils/config.py:72

(pred, target, mask=None)

src/byprot/modules/metrics.py:43

Methodrun_pmpnn

(self, input_dir, output_path)

src/byprot/utils/protein/folding_model.py:141

Functionrun_tmalign

(query, reference, fast=True)

analysis/cal_tmscore.py:18

Methodsafe_superimpose

(reference, coords, mask)

src/byprot/tasks/struct_tokenizer/structok.py:301

Functionsave_pdb

(path, coords, seq)

src/byprot/utils/io.py:141

Functionsave_traj

Writes final sample and reverse diffusion trajectory. Args: bb_prot_traj: [noisy_T, N, 37, 3] atom37 sampled diffusion states.

src/byprot/utils/protein/utils.py:296

Functionsequence_to_onehot

Maps the given sequence into a one-hot encoded matrix. Args: sequence: An amino acid sequence. mapping: A dictionary mapping amino ac

src/byprot/utils/protein/residue_constants.py:887

Functionsequence_to_onehot

Maps the given sequence into a one-hot encoded matrix. Args: sequence: An amino acid sequence. mapping: A dictionary mapping amino ac

src/byprot/datamodules/pdb_dataset/residue_constants.py:887

Methodset_chunk_size

(self, chunk_size: T.Optional[int])

src/byprot/models/structok/modules/folding_utils/decoder.py:419

Methodset_chunk_size

(self, chunk_size)

src/byprot/models/structok/modules/folding_utils/trunk.py:181

Methodset_epoch

src/byprot/datamodules/dataset/data_utils.py:488

Methodset_epoch

src/byprot/datamodules/dataset/tokenized_protein.py:146

Methodset_epoch

src/byprot/datamodules/dataset/uniref_hf.py:68

(self, stage=None)

src/byprot/tasks/__init__.py:124

(self, stage=None)

src/byprot/tasks/lm/dplm.py:65

(self, stage=None)

src/byprot/tasks/lm/mlm.py:71

(self, stage=None)

src/byprot/tasks/lm/dplm2.py:70

(self, stage=None)

src/byprot/tasks/lm/dplm_invfold.py:83

(self, stage=None)

src/byprot/tasks/struct_tokenizer/structok.py:67

Load data. Set variables: `self.data_train`, `self.data_val`, `self.data_test`. This method is called by lightning when doing `traine

src/byprot/datamodules/uniref50_hf.py:51

Load data. Set variables: `self.data_train`, `self.data_val`, `self.data_test`. This method is called by lightning when doing `traine

src/byprot/datamodules/tokenized_protein_datamodule.py:55

Load data. Set variables: `self.data_train`, `self.data_val`, `self.data_test`. This method is called by lightning when doing `traine

src/byprot/datamodules/uniref50.py:58

Load data. Set variables: `self.data_train`, `self.data_val`, `self.data_test`. This method is called by lightning when doing `traine

src/byprot/datamodules/cath_datamodule.py:55

(self, stage: str)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:77

Methodshowmanyc

analysis/TMscore.cpp:2064

Functionsinusoidal_encoding

Taken from GENIE. Args:

src/byprot/utils/protein/utils.py:540

analysis/TMalign.cpp:2392

analysis/TMscore.cpp:4622

Methodspecial_token_list

src/byprot/models/dplm2/dplm2.py:100

Functionsplit_white

split a long string into vectors by whitespace, return both whitespaces * and non-whitespaces * line - input string * line_vec - o

analysis/TMalign.cpp:370

src/byprot/tasks/__init__.py:134

analysis/TMscore.cpp:1879

Performs a single optimization step. Args: closure (callable, optional): A closure that reevaluates the model and

src/byprot/utils/optim.py:54

src/byprot/tasks/__init__.py:154

Methodstruct_cls_token

`str`: End of sentence token. Log an error if used while not having been set.

src/byprot/datamodules/dataset/tokenized_protein.py:464

Methodstruct_eos_token

`str`: End of sentence token. Log an error if used while not having been set.

src/byprot/datamodules/dataset/tokenized_protein.py:453

Methodstruct_mask_token

`str`: End of sentence token. Log an error if used while not having been set.

src/byprot/datamodules/dataset/tokenized_protein.py:486

Methodstruct_tokenizer

src/byprot/utils/protein/evaluator_dplm2.py:156

Methodstruct_tokenizer

src/byprot/models/dplm2/dplm2.py:198

Methodstruct_unk_token

`str`: End of sentence token. Log an error if used while not having been set.

src/byprot/datamodules/dataset/tokenized_protein.py:475

Functionsupervised_chi_loss

Implements Algorithm 27 (torsionAngleLoss) Args: angles_sin_cos: [*, N, 7, 2] predicted angles unnormalized_angles_si

src/byprot/models/structok/modules/loss.py:382

Methodswitch_read_buffer

analysis/TMscore.cpp:1726

analysis/TMscore.cpp:1970

Functiont_stratified_loss

Stratify loss by binning t.

src/byprot/utils/protein/utils.py:602

Methodtest_dataloader

src/byprot/datamodules/uniref50_hf.py:102

Methodtest_dataloader

src/byprot/datamodules/tokenized_protein_datamodule.py:140

Methodtest_dataloader

src/byprot/datamodules/uniref50.py:124

Methodtest_dataloader

src/byprot/datamodules/cath_datamodule.py:137

Methodtest_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/__init__.py:190

Methodtest_step_end

( self, *args, **kwargs )

src/byprot/tasks/__init__.py:193

Functionto_atom37

src/byprot/utils/protein/all_atom.py:44

Functionto_atom37

src/byprot/datamodules/pdb_dataset/all_atom.py:44

Functiontorsion_angle_loss

( a, # [*, N, 7, 2] a_gt, # [*, N, 7, 2] a_alt_gt, # [*, N, 7, 2] )

src/byprot/models/structok/modules/loss.py:150

Methodtrain_dataloader

src/byprot/datamodules/uniref50_hf.py:83

Methodtrain_dataloader

src/byprot/datamodules/tokenized_protein_datamodule.py:97

Methodtrain_dataloader

src/byprot/datamodules/uniref50.py:102

Methodtrain_dataloader

src/byprot/datamodules/cath_datamodule.py:109

Methodtrain_dataloader

(self, rank=None, num_replicas=None)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:89

Methodtraining_step

(self, batch: Any, batch_idx: int, **kwargs)

src/byprot/tasks/__init__.py:157

Methodtraining_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm.py:136

Methodtraining_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/mlm.py:188

Methodtraining_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm2.py:185

Methodtraining_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm_invfold.py:295

Methodtraining_step

(self, batch: Any, batch_idx: int, **kwargs)

src/byprot/tasks/struct_tokenizer/structok.py:160

Methodtraining_step_end

( self, step_output: Union[torch.Tensor, Dict[str, Any]] )

src/byprot/tasks/__init__.py:160

Functiontransrot_to_atom37

(transrot_traj, res_mask)

src/byprot/utils/protein/all_atom.py:250

Functiontransrot_to_atom37

(transrot_traj, res_mask)

src/byprot/datamodules/pdb_dataset/all_atom.py:250

Methodtrunk_iter

(s, z, residx, mask)

src/byprot/models/structok/modules/folding_utils/trunk.py:222

Methodunderflow

analysis/TMscore.cpp:2031

Methodunmap_to_all

src/byprot/models/structok/modules/vqvae.py:516

Methodval_dataloader

src/byprot/datamodules/uniref50_hf.py:94

Methodval_dataloader

src/byprot/datamodules/tokenized_protein_datamodule.py:131

Methodval_dataloader

src/byprot/datamodules/uniref50.py:114

Methodval_dataloader

src/byprot/datamodules/cath_datamodule.py:124

Methodval_dataloader

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:178

Methodvalidation_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm.py:165

Methodvalidation_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/mlm.py:217

Methodvalidation_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm2.py:211

Methodvalidation_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/lm/dplm_invfold.py:321

Methodvalidation_step

(self, batch: Any, batch_idx: int)

src/byprot/tasks/struct_tokenizer/structok.py:189

Functionvector_projection

Project the vector R_ab onto a plane with normal vector P_n. Parameters ---------- R_ab: Tensor, shape = (N,3) Vector fro

src/byprot/utils/protein/all_atom.py:230

Functionvector_projection

Project the vector R_ab onto a plane with normal vector P_n. Parameters ---------- R_ab: Tensor, shape = (N,3) Vector fro

src/byprot/datamodules/pdb_dataset/all_atom.py:230

Functionwrite_pkl

Serialize data into a pickle file.

src/byprot/datamodules/pdb_dataset/utils.py:334

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