| _target_: onescience.datapipes.simplefold.train_datamodule.SimpleFoldTrainingDataModule |
|
|
| datasets: |
| - _target_: onescience.datapipes.simplefold.train_datamodule.DatasetConfig |
| data_name: rcsb_protein |
| tokenized_dir: data/rcsb_protein_tokenized |
| target_dir: data/rcsb_processed_targets |
| manifest_path: data/rcsb_protein_tokenized/manifest.json |
| cropper: |
| _target_: onescience.datapipes.boltz_data_pipeline.crop.boltz.BoltzCropper |
| min_neighborhood: 0 |
| max_neighborhood: 40 |
| filters: |
| - _target_: onescience.datapipes.boltz_data_pipeline.filter.dynamic.resolution.ResolutionFilter |
| resolution: 5.0 |
| - _target_: onescience.datapipes.boltz_data_pipeline.filter.dynamic.date.DateFilter |
| date: "2020-05-01" |
| ref: released |
|
|
| - _target_: onescience.datapipes.simplefold.train_datamodule.DatasetConfig |
| data_name: swissprot |
| tokenized_dir: data/swissprot_tokenized |
| target_dir: data/swissprot_pdb_v4_boltz |
| manifest_path: data/swissprot_tokenized/manifest.json |
| record_list: data/swissprot_filtered.txt |
| cropper: |
| _target_: onescience.datapipes.boltz_data_pipeline.crop.boltz.BoltzCropper |
| min_neighborhood: 0 |
| max_neighborhood: 40 |
|
|
| - _target_: onescience.datapipes.simplefold.train_datamodule.DatasetConfig |
| data_name: processed_afesm |
| tokenized_dir: data/processed_afesm |
| target_dir: data/processed_afesm |
| manifest_path: data/processed_afesm/manifest.json |
| cropper: |
| _target_: onescience.datapipes.boltz_data_pipeline.crop.boltz.BoltzCropper |
| min_neighborhood: 0 |
| max_neighborhood: 40 |
|
|
| filters: |
| - _target_: onescience.datapipes.boltz_data_pipeline.filter.dynamic.size.SizeFilter |
| min_chains: 1 |
| max_chains: 300 |
|
|
| tokenizer: |
| _target_: onescience.datapipes.boltz_data_pipeline.tokenize.boltz_protein.BoltzTokenizer |
|
|
| featurizer: |
| _target_: onescience.datapipes.boltz_data_pipeline.feature.featurizer.BoltzFeaturizer |
|
|
| symmetries: data/symmetry.pkl |
| max_tokens: 256 |
| max_atoms: 2304 |
| pad_to_max_tokens: False |
| pad_to_max_atoms: False |
| batch_size: 256 |
| num_workers: 16 |
| pin_memory: True |
| return_train_symmetries: False |
| min_dist: 2.0 |
| max_dist: 22.0 |
| num_bins: 64 |
| atoms_per_window_queries: 32 |
| rotation_augment_ref_pos: False |
| rotation_augment_coords: True |
