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Functions1,008 in github.com/bytedance/dplm

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

↓ 1 callersMethodinitialize_output_tokens

( self, batch, encoder_out, partial_masks=None, use_draft_seq=False,

src/byprot/models/dplm/dplm_invfold.py:242

↓ 1 callersMethodinitialize_output_tokens

( self, batch, encoder_out, partial_masks=None, **kwargs )

src/byprot/models/dplm/modules/dplm_modeling_esm.py:381

↓ 1 callersMethodinject_noise

( self, tokens, coord_mask, noise=None, sel_mask=None, mask_by_unk=False )

src/byprot/tasks/lm/dplm_invfold.py:164

↓ 1 callersFunctioninverse_sqrt_lr_schedule

( step, warmup_steps, warmup_init_lr, lr_step, decay_step )

src/byprot/utils/lr_scheduler.py:76

↓ 1 callersFunctionlength_cropping

(dataset_pandas, epoch, min_crop_length=60)

src/byprot/datamodules/tokenized_protein_datamodule.py:151

↓ 1 callersFunctionlm_loss

Computes BERT-style masked MSA loss. Implements subsection 1.9.9. Args: logits: [*, N_seq, N_res, 23] predicted residue distribution

src/byprot/models/structok/modules/loss.py:1631

↓ 1 callersFunctionload_dataset_from_hf

(data_path, split)

src/byprot/datamodules/dataset/tokenized_protein.py:643

↓ 1 callersFunctionload_dataset_from_hf

(data_path, split)

src/byprot/datamodules/dataset/uniref_hf.py:331

↓ 1 callersMethodload_from_ckpt

(self, ckpt_path, not_load=False)

src/byprot/tasks/lm/dplm2.py:112

↓ 1 callersMethodload_from_ckpt

(self, ckpt_path)

src/byprot/tasks/struct_tokenizer/structok.py:84

↓ 1 callersFunctionload_from_pdb

(pdb_path, process_chain=PdbDataset.process_chain)

src/byprot/utils/protein/tokenize_pdb.py:29

↓ 1 callersMethodload_metadata

src/byprot/utils/protein/evaluator_dplm2.py:122

↓ 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

src/byprot/utils/protein/residue_constants.py:438

↓ 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

src/byprot/datamodules/pdb_dataset/residue_constants.py:438

↓ 1 callersFunctionload_structure

Args: fpath: filepath to either pdb or cif file chain: the chain id or list of chain ids to load Returns: biotite.str

src/byprot/utils/io.py:52

↓ 1 callersFunctionload_vocab_file

src/byprot/datamodules/dataset/tokenized_protein.py:22

↓ 1 callersFunctionluost_rmsd

(res_list1: list, res_list2: list)

src/byprot/modules/metrics.py:13

↓ 1 callersFunctionmain

(config: DictConfig)

↓ 1 callersFunctionmain

(config: DictConfig)

↓ 1 callersFunctionmain

generate_dplm.py:118

↓ 1 callersFunctionmain

generate_dplm2.py:462

↓ 1 callersFunctionmain

analysis/cal_tmscore.py:78

↓ 1 callersFunctionmain

analysis/cal_plddt_dir.py:285

↓ 1 callersFunctionmain

src/byprot/utils/protein/tokenize_pdb.py:89

↓ 1 callersFunctionmain

run/scaffold_generate_dplm2.py:188

↓ 1 callersFunctionmain

run/scaffold_generate_dplm.py:88

↓ 1 callersFunctionmeasure_perplexity

(predicted_indices, n_embed)

src/byprot/models/structok/modules/loss.py:1690

↓ 1 callersFunctionmult_along_first_dims

returns x * y elementwise along the leading dimensions of y

src/byprot/models/structok/modules/lfq.py:69

↓ 1 callersFunctionnew_arange

Return a Tensor of `size` filled with a range function on the device of x. If size is empty, using the size of the variable x.

src/byprot/tasks/lm/dplm_invfold.py:26

↓ 1 callersFunctionnew_arange

Return a Tensor of `size` filled with a range function on the device of x. If size is empty, using the size of the variable x.

src/byprot/datamodules/dataset/cath.py:327

↓ 1 callersFunctionnoam_lr_schedule

(step, warmup_steps, factor, model_size)

src/byprot/utils/lr_scheduler.py:116

↓ 1 callersMethodon_predict_epoch_end

src/byprot/tasks/lm/mlm.py:313

↓ 1 callersMethodon_predict_epoch_end

src/byprot/tasks/lm/dplm_invfold.py:500

↓ 1 callersFunctionon_prediction_mode

(pl_module: LightningModule, enable=True)

src/byprot/tasks/__init__.py:33

↓ 1 callersMethodon_validation_epoch_end

src/byprot/tasks/__init__.py:183

↓ 1 callersFunctionoutput_TMscore_results

analysis/TMscore.cpp:6638

↓ 1 callersFunctionoutput_pymol

analysis/TMscore.cpp:4666

↓ 1 callersFunctionoutput_rasmol

analysis/TMscore.cpp:4992

↓ 1 callersFunctionoutput_results

output the final results

analysis/TMalign.cpp:3696

↓ 1 callersFunctionoutput_rotation_matrix

extract rotation matrix based on TMscore8 */

analysis/TMalign.cpp:3666

↓ 1 callersFunctionoutput_rotation_matrix

extract rotation matrix based on TMscore8 */

analysis/TMscore.cpp:5648

↓ 1 callersFunctionoutput_superpose

analysis/TMalign.cpp:3047

↓ 1 callersMethodoutput_to_pdb

Returns the pbd (file) string from the model given the model output.

src/byprot/models/structok/modules/folding_utils/decoder.py:403

↓ 1 callersMethodoutput_to_pdb

Returns the pbd (file) string from the model given the model output.

src/byprot/models/structok/modules/folding_utils/esmfold.py:332

↓ 1 callersFunctionpack_one

src/byprot/models/structok/modules/lfq.py:51

↓ 1 callersFunctionpad_rigid

(rigid: torch.tensor, max_len: int)

src/byprot/datamodules/pdb_dataset/utils.py:110

↓ 1 callersFunctionparameter_set4final_C3prime

analysis/TMalign.cpp:1669

↓ 1 callersFunctionparameter_set4final_C3prime

analysis/TMscore.cpp:3101

↓ 1 callersFunctionparameter_set4scale

analysis/TMalign.cpp:1707

↓ 1 callersFunctionparameter_set4scale

analysis/TMscore.cpp:3139

↓ 1 callersFunctionparameter_set4search

analysis/TMalign.cpp:1647

↓ 1 callersFunctionparameter_set4search

analysis/TMscore.cpp:3079

↓ 1 callersMethodparse_PDB

( self, path_to_pdb, input_chain_list=None, masked_chain_list=None, ca

src/byprot/datamodules/dataset/data_utils.py:128

↓ 1 callersMethodparse_PDB_biounits

input: x = PDB filename atoms = atoms to extract (optional) output: (length, atoms, coords=(x,y,z)), sequence

src/byprot/datamodules/dataset/data_utils.py:260

↓ 1 callersFunctionparse_cli_override_args

src/byprot/utils/config.py:58

↓ 1 callersMethodpeof

analysis/TMscore.cpp:1900

↓ 1 callersFunctionpolynomial_lr_schedule

( step, total_steps, warmup_steps, warmup_init_lr, lr, lr_end, power )

src/byprot/utils/lr_scheduler.py:145

↓ 1 callersMethodpredict_step

( self, batch: Any, batch_idx: int, dataloader_idx: int = 0, log_metri

src/byprot/tasks/lm/mlm.py:296

↓ 1 callersMethodpredict_step

( self, batch: Any, batch_idx: int, dataloader_idx: int = 0, log_metri

src/byprot/tasks/lm/dplm_invfold.py:439

↓ 1 callersMethodprepare_for_struct_tokenizer

(self, decoder_out, non_special_sym_mask)

src/byprot/models/dplm2/dplm2_bit.py:438

↓ 1 callersFunctionpreprocess_dataset

(csv_path, data_bin, split)

src/byprot/datamodules/dataset/tokenized_protein.py:28

↓ 1 callersFunctionprint_config

Prints content of DictConfig using Rich library and its tree structure. Args: config (DictConfig): Configuration composed by Hydra.

src/byprot/utils/__init__.py:103

↓ 1 callersFunctionprint_extra_help

analysis/TMalign.cpp:98

↓ 1 callersFunctionprint_extra_help

analysis/TMscore.cpp:88

↓ 1 callersMethodq_sample

(self, x_0, t1, maskable_mask)

src/byprot/models/dplm/dplm.py:135

↓ 1 callersMethodq_sample_coupled

(self, x_0, t1, t2, maskable_mask)

src/byprot/models/dplm/dplm.py:109

↓ 1 callersMethodq_sample_coupled

(self, x_0, t1, t2, maskable_mask)

src/byprot/models/dplm/modules/dplm_adapter.py:151

↓ 1 callersMethodrdbuf

analysis/TMscore.cpp:2362

↓ 1 callersFunctionread_alignment_lines

( lines, keep_gaps=True, keep_insertions=True, to_upper=False, )

analysis/cal_plddt_dir.py:65

↓ 1 callersFunctionread_fasta

( path, keep_gaps=True, keep_insertions=True, to_upper=False, )

analysis/cal_plddt_dir.py:49

↓ 1 callersFunctionread_user_alignment

read user specified pairwise alignment from 'fname_lign' to 'sequence'. * This function should only be called by main function, as it will * termi

analysis/TMalign.cpp:905

↓ 1 callersMethodremap_to_used

src/byprot/models/structok/modules/vqvae.py:176

↓ 1 callersMethodremap_to_used

src/byprot/models/structok/modules/vqvae.py:306

↓ 1 callersMethodresample

Rejection sampling for eliminating the unexpected repeat patterns in generation results, e.g., GGGGG.... We first calculate the frequency of

src/byprot/models/dplm/dplm.py:220

↓ 1 callersMethodrestore

Restore the parameters stored with the `store` method. Useful to validate the model with EMA parameters without affecting the origina

src/byprot/models/structok/modules/ema.py:82

↓ 1 callersFunctionrigid_transform_3D

(A, B, verbose=False)

src/byprot/modules/protein_metrics.py:96

↓ 1 callersFunctionrun

analysis/cal_plddt_dir.py:198

↓ 1 callersFunctionrun

(cfg: DictConfig)

src/byprot/utils/protein/evaluator_dplm2.py:1123

↓ 1 callersMethodrun_detokenize_from_fasta

(self, fasta_path)

src/byprot/utils/protein/evaluator_dplm2.py:193

↓ 1 callersFunctionrun_easy_cluster

(designable_dir, output_dir)

src/byprot/utils/protein/utils.py:105

↓ 1 callersMethodrun_pmpnn

( self, write_dir, pdb_input_path, )

src/byprot/utils/protein/evaluator_dplm2.py:806

↓ 1 callersFunctionrun_tokenize

(struct_tokenizer, input_pdb_folder, output_dir)

src/byprot/utils/protein/tokenize_pdb.py:37

↓ 1 callersMethodrun_tokenize

(self, pdb_folder, output_dir)

src/byprot/utils/protein/evaluator_dplm2.py:307

↓ 1 callersFunctionsample_cluster

(dataset_pandas, epoch)

src/byprot/datamodules/tokenized_protein_datamodule.py:167

↓ 1 callersMethodsample_cluster

(self, pdb_csv, seed)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:335

↓ 1 callersMethodsave_prediction

(self, results, saveto=None)

src/byprot/tasks/lm/dplm_invfold.py:567

↓ 1 callersFunctionsave_results

( tokenizer, struct_tokenizer, save_dir, output_tokens, headers=None, save_pdb=False,

run/scaffold_generate_dplm2.py:130

↓ 1 callersFunctionscore_matrix_rmsd_sec

analysis/TMalign.cpp:2613

↓ 1 callersFunctionsec_str

analysis/TMalign.cpp:2436

↓ 1 callersMethodself_mixup

(self, x_t, single_modality_index, bsz, seq_len)

src/byprot/models/dplm2/dplm2_bit.py:222

↓ 1 callersMethodself_mixup

(self, x_t, single_modality_index)

src/byprot/models/dplm2/dplm2.py:272

↓ 1 callersMethodset_chunk_size

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

src/byprot/models/structok/modules/folding_utils/esmfold.py:345

↓ 1 callersMethodset_epoch

src/byprot/datamodules/dataset/uniref.py:79

↓ 1 callersMethodsetup_inference_dir

(self, ckpt_path)

src/byprot/utils/protein/evaluator_dplm2.py:180

↓ 1 callersFunctionsidechain_loss

( sidechain_frames: torch.Tensor, sidechain_atom_pos: torch.Tensor, rigidgroups_gt_frames: torch.T

src/byprot/models/structok/modules/loss.py:305

↓ 1 callersFunctionsigmoid_cross_entropy

(logits, labels)

src/byprot/models/structok/modules/loss.py:137

↓ 1 callersFunctionstandard_TMscore

analysis/TMscore.cpp:5677

↓ 1 callersMethodstore

Save the current parameters for restoring later. Args: parameters: Iterable of `torch.nn.Parameter`; the parameters to be

src/byprot/models/structok/modules/ema.py:73

↓ 1 callersFunctiontest

Contains minimal example of the testing/prediction pipeline. Evaluates given checkpoint on a testset. Args: config (DictConfig): Conf

src/byprot/testing_pipeline.py:25

↓ 1 callersFunctiontm_loss

( logits, final_affine_tensor, backbone_rigid_tensor, backbone_rigid_mask, resolution,

src/byprot/models/structok/modules/loss.py:754

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