rc-foundry 0.1.4__py3-none-any.whl → 0.1.6__py3-none-any.whl

foundry/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.4'
-__version_tuple__ = version_tuple = (0, 1, 4)
+__version__ = version = '0.1.6'
+__version_tuple__ = version_tuple = (0, 1, 6)
 
 __commit_id__ = commit_id = None

{rc_foundry-0.1.4.dist-info → rc_foundry-0.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.4
+Version: 0.1.6
 Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
 Author-email: Institute for Protein Design <contact@ipd.uw.edu>
 License: BSD 3-Clause License

{rc_foundry-0.1.4.dist-info → rc_foundry-0.1.6.dist-info}/RECORD

@@ -1,7 +1,7 @@
 foundry/__init__.py,sha256=H8S1nl5v6YeW8ggn1jKy4GdtH7c-FGS-j7CqUCAEnAU,1926
 foundry/common.py,sha256=Aur8mH-CNmcUqSsw7VgaCQSW5sH1Bqf8Da91jzxPV1Y,3035
 foundry/constants.py,sha256=0n1wBKCvNuw3QaQehSbmsHYkIdaGn3tLeRFItBrdeHY,913
-foundry/version.py,sha256=rLCrf4heo25FJtBY-2Ap7ZuWW-5FS7sqTjsolIUuI5c,704
+foundry/version.py,sha256=riGXiVTWXmtdoju9hVCWvTxpszEMAAIK0sZZWoLKlnU,704
 foundry/callbacks/__init__.py,sha256=VsRT1e4sqlJHPcTCsfupMEx82Iz-LoOAGPpwvf_OJeE,126
 foundry/callbacks/callback.py,sha256=xZBo_suP4bLrP6gl5uJPbaXm00DXigePa6dMeDxucgg,3890
 foundry/callbacks/health_logging.py,sha256=tEtkByOlaAA7nnelxb7PbM9_dcIgOsdbxCdQY3K5pMc,16664
@@ -117,10 +117,10 @@ rfd3/.gitignore,sha256=935nLWJz_oi5h-UjxP4L_ulsMpkbRIVsl0dgGCwTCbc,109
 rfd3/Makefile,sha256=_O87r1eIN7AmWWIqur3z0tLn1kgAPGEAGX2fcddarMs,2224
 rfd3/__init__.py,sha256=2Wto2IsUIj2lGag9m_gqgdCwBNl5p21-Xnr7W_RpU3c,348
 rfd3/callbacks.py,sha256=Zjt8RiaYWquoKOwRmC_wCUbRbov-V4zd2_73zjhgDHE,2783
-rfd3/cli.py,sha256=TZpZouXGmwAMFaH8hp4r3q9tbUi1xlcN8n_r8hO2q8c,1424
+rfd3/cli.py,sha256=ka3K5H117fzDYIDXFpOpJV21w_XBrHYJZdFE0thsGBI,1644
 rfd3/constants.py,sha256=wLvDzrThpOrK8T3wGFNQeGrhAXOJQze8l3v_7pjIdMM,13141
 rfd3/engine.py,sha256=La_dB48Ewz0IdY1ocxvSWg-PXVAsySm0OGvwyz42lI8,20824
-rfd3/run_inference.py,sha256=dubMwEFkNPOq_yYf0ny37qvvEkRjNNPRFksZgmEFkUc,1520
+rfd3/run_inference.py,sha256=ljzsCKEtrlfAvP0SDFPeQwTM3rV_X3ewHOhcRFVI37c,1258
 rfd3/train.py,sha256=rHswffIUhOae3_iYyvAiQ3jALoFuzrcRUgMlbJLinlI,7947
 rfd3/inference/datasets.py,sha256=u-2U7deHXu-iOs7doiKKynewP-NEyJfdORSTDzUSaQI,6538
 rfd3/inference/input_parsing.py,sha256=mk3HBvo7MPTFEET7NagCo5TSjb47w-hxUDoeQxUW_h4,45449
@@ -173,8 +173,139 @@ rfd3/transforms/virtual_atoms.py,sha256=UpmxzPPd5FaJigcRoxgLSHHrLLOqsCvZ5PPZfQSG
 rfd3/utils/inference.py,sha256=RQp5CCy6Z6uHVZ2Mx0zmmGluYEOrASke4bABtfRjpy0,26448
 rfd3/utils/io.py,sha256=wbdjUTQkDc3RCSM7gdogA-XOKR68HeQ-cfvyN4pP90w,9849
 rfd3/utils/vizualize.py,sha256=HPlczrA3zkOuxV5X05eOvy_Oga9e3cPnFUXOEP4RR_g,11046
-rc_foundry-0.1.4.dist-info/METADATA,sha256=hzcS1buvLzRRAv7rPRgKwYjeNDL_iTGyR6u8CRpL-Ic,10585
-rc_foundry-0.1.4.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rc_foundry-0.1.4.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
-rc_foundry-0.1.4.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
-rc_foundry-0.1.4.dist-info/RECORD,,
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rf3/configs/callbacks/default.yaml

@@ -0,0 +1,5 @@
+defaults:
+  - train_logging
+  - metrics_logging
+  - dump_validation_structures
+  - _self_

rf3/configs/callbacks/dump_validation_structures.yaml

@@ -0,0 +1,6 @@
+dump_validation_structures_callback:
+    _target_: rf3.callbacks.dump_validation_structures.DumpValidationStructuresCallback
+    save_dir: ${paths.output_dir}/val_structures
+    dump_predictions: True
+    one_model_per_file: False
+    dump_trajectories: False

rf3/configs/callbacks/metrics_logging.yaml

@@ -0,0 +1,10 @@
+store_validation_metrics_in_df_callback:
+    _target_: rf3.callbacks.metrics_logging.StoreValidationMetricsInDFCallback
+    save_dir: ${paths.output_dir}/val_metrics
+    metrics_to_save: "all"
+
+log_af3_validation_metrics_callback:
+    _target_: rf3.callbacks.metrics_logging.LogAF3ValidationMetricsCallback
+    # Only logs if present in the metric output dictionary
+    # Must be subset of metrics_to_save
+    metrics_to_log:  "all"

rf3/configs/callbacks/train_logging.yaml

@@ -0,0 +1,16 @@
+log_af3_training_losses_callback:
+    _target_: foundry.callbacks.train_logging.LogAF3TrainingLossesCallback
+    log_every_n: 10
+    log_full_batch_losses: true
+
+log_learning_rate_callback:
+    _target_: foundry.callbacks.train_logging.LogLearningRateCallback
+    log_every_n: 10
+
+log_model_parameters_callback:
+    _target_: foundry.callbacks.train_logging.LogModelParametersCallback
+
+log_dataset_sampling_ratios_callback:
+    _target_: foundry.callbacks.train_logging.LogDatasetSamplingRatiosCallback
+
+

rf3/configs/dataloader/default.yaml

@@ -0,0 +1,15 @@
+train: 
+  dataloader_params:
+    # These parameters will be unpacked as kwargs for the DataLoader
+    batch_size: 1
+    num_workers: 2
+    prefetch_factor: 3
+  n_fallback_retries: 4
+
+val: 
+  dataloader_params:
+    # These parameters will be unpacked as kwargs for the DataLoader
+    batch_size: 1
+    num_workers: 2
+    prefetch_factor: 3
+  n_fallback_retries: 0 # Disable fallback retries for validation

rf3/configs/datasets/base.yaml

@@ -0,0 +1,31 @@
+# Base Transform defaults
+diffusion_batch_size_train: 48
+diffusion_batch_size_inference: 5
+
+n_recycles_train: 4
+n_recycles_validation: 10
+
+run_confidence_head: false
+
+# Conditioning
+p_unconditional: 0.9
+
+# Embeddings
+p_dropout_atom_level_embeddings: 0.5
+
+n_msa: 1024
+crop_size: 384
+max_atoms_in_crop: 5000 
+
+key_to_balance: n_tokens_total
+
+take_first_chiral_subordering: false
+use_element_for_atom_names_of_atomized_tokens: true
+mirror_prob: 0.02
+atomization_prob: 0.02
+ligand_dropout_prob: 0.0
+
+add_residue_is_paired_feature: true
+
+add_cyclic_bonds: true
+

rf3/configs/datasets/pdb_and_distillation.yaml

@@ -0,0 +1,58 @@
+# AF3 dataset configuration with monomer distillation
+
+defaults:
+  - base
+  # The @ symbol specifies the tree under which the item will be attached to the config
+  - train/pdb/train_interface@train.pdb.sub_datasets.interface
+  - train/pdb/train_pn_unit@train.pdb.sub_datasets.pn_unit
+  - train:
+    - monomer_distillation
+    - na_complex_distillation
+    - disorder_distillation
+    # - domain_distillation
+    # - rna_monomer_distillation
+  - val/af3_validation@val.af3_validation
+  - val/af3_validation@val.quick_af3_validation_with_templating
+  - _self_
+
+# Dataloading pipeline to use
+pipeline_target: rf3.data.pipelines.build_af3_transform_pipeline
+
+# Dataset weighting
+train: 
+  pdb:
+    probability: 0.50
+  monomer_distillation:
+    probability: 0.46
+  na_complex_distillation:
+    probability: 0.02
+  disorder_distillation:
+    probability: 0.02
+  # multidomain_distillation:
+  #   probability: 0.06
+  # rna_monomer_distillation:
+  #   probability: 0.04
+
+val:
+  quick_af3_validation_with_templating:
+    dataset:
+      dataset:
+        filters:
+          # Only score examples with protein-ligand interfaces
+          - "interfaces_to_score.str.contains('protein-ligand')"
+          # Small examples only - very fast
+          - "n_tokens_total < 400"
+      transform:
+        # +-- Conditioning --+
+        p_unconditional: 0.0 # Always show conditioning
+        # (Templates)
+        template_noise_scales:
+          not_atomized: 1e-4 # No noise on polymer atoms (epsilon to avoid division by zero)
+          atomized: 1e-4 # No noise on ligand atoms (epsilon to avoid division by zero)
+        allowed_chain_types_for_conditioning:
+          _target_: atomworks.enums.ChainType.get_all_types
+        p_condition_per_token: 1.0 # Always condition
+        p_provide_inter_molecule_distances: 0.0 # No inter-chain distances
+        # (Reference conformer)
+        p_give_non_polymer_ref_conf: 1.0 # Always give non-polymer reference conformers
+        p_give_polymer_ref_conf: 1.0 # Always give polymer reference conformers

rf3/configs/datasets/pdb_only.yaml

@@ -0,0 +1,17 @@
+# AF3 dataset configuration with monomer distillation
+
+defaults:
+  - base
+  # The @ symbol specifies the tree under which the item will be attached to the config
+  - train/pdb/train_interface@train.pdb.sub_datasets.interface
+  - train/pdb/train_pn_unit@train.pdb.sub_datasets.pn_unit
+  - val/af3_validation@val.af3_validation
+  - _self_
+
+# Dataloading pipeline to use
+pipeline_target: rf3.data.pipelines.build_af3_transform_pipeline
+
+# Dataset weighting
+train: 
+  pdb:
+    probability: 1.0

rf3/configs/datasets/train/disorder_distillation.yaml

@@ -0,0 +1,48 @@
+# TODO: Inherit from common config with default Transform pipeline
+
+disorder_distillation:
+  dataset:
+    _target_: atomworks.ml.datasets.StructuralDatasetWrapper
+    save_failed_examples_to_dir: null
+
+    # cif parser arguments
+    cif_parser_args:
+      cache_dir: null
+      load_from_cache: False
+      save_to_cache: False 
+
+    # metadata parser
+    dataset_parser:
+      _target_: atomworks.ml.datasets.parsers.GenericDFParser
+      pn_unit_iid_colnames: null
+
+    # metadata dataset
+    dataset:
+      _target_: atomworks.ml.datasets.PandasDataset
+      name: pdb_diso_distillation
+      id_column: example_id
+      data: ${paths.data.disorder_distill_parquet_dir}/disorderDistillation.csv
+      columns_to_load:
+        - example_id
+        - path
+    transform:
+      _target_: ${datasets.pipeline_target}
+      is_inference: False
+      protein_msa_dirs: ${paths.data.protein_msa_dirs}
+      rna_msa_dirs: ${paths.data.rna_msa_dirs}
+      n_recycles: ${datasets.n_recycles_train}
+      crop_size: ${datasets.crop_size}
+      n_msa: ${datasets.n_msa}
+      diffusion_batch_size: ${datasets.diffusion_batch_size_train}
+      max_atoms_in_crop: ${datasets.max_atoms_in_crop}
+      crop_contiguous_probability: 0.25
+      crop_spatial_probability: 0.75
+      run_confidence_head: ${datasets.run_confidence_head}
+      take_first_chiral_subordering: ${datasets.take_first_chiral_subordering}
+      use_element_for_atom_names_of_atomized_tokens: ${datasets.use_element_for_atom_names_of_atomized_tokens}
+      mirror_prob: ${datasets.mirror_prob}
+      atomization_prob: ${datasets.atomization_prob}
+      ligand_dropout_prob: ${datasets.ligand_dropout_prob}
+      p_unconditional: ${datasets.p_unconditional}
+      p_dropout_atom_level_embeddings: ${datasets.p_dropout_atom_level_embeddings}
+      add_residue_is_paired_feature: ${datasets.add_residue_is_paired_feature}

rf3/configs/datasets/train/domain_distillation.yaml

@@ -0,0 +1,50 @@
+# TODO: Inherit from common config with default Transform pipeline
+
+multidomain_distillation:
+  dataset:
+    _target_: rf3.data.paired_msa.MultiInputDatasetWrapper
+    save_failed_examples_to_dir: null
+
+    # cif parser
+    cif_parser_args:
+      #assume_residues_all_resolved: true
+      cache_dir: null
+      load_from_cache: false
+      save_to_cache: false 
+
+    # metadata parser
+    dataset_parser:
+      _target_: rf3.data.paired_msa.MultidomainDFParser
+
+    # metadata dataset
+    dataset:
+      _target_: atomworks.ml.datasets.PandasDataset
+      name: multidomain_distillation
+      id_column: example_id
+      data: /projects/ml/datahub/dfs/domain_domain/domain_domain_dataset.DIGS.parquet
+      columns_to_load:
+        - example_id
+        - pdb_path
+        - msa_path
+    transform:
+      _target_: ${datasets.pipeline_target}
+      is_inference: False
+      input_contains_explicit_msa: True
+      protein_msa_dirs: []
+      rna_msa_dirs: []
+      n_recycles: ${datasets.n_recycles_train}
+      crop_size: ${datasets.crop_size}
+      n_msa: ${datasets.n_msa}
+      diffusion_batch_size: ${datasets.diffusion_batch_size_train}
+      max_atoms_in_crop: ${datasets.max_atoms_in_crop}
+      crop_contiguous_probability: 0.25
+      crop_spatial_probability: 0.75
+      run_confidence_head: ${datasets.run_confidence_head}
+      take_first_chiral_subordering: ${datasets.take_first_chiral_subordering}
+      use_element_for_atom_names_of_atomized_tokens: ${datasets.use_element_for_atom_names_of_atomized_tokens}
+      mirror_prob: 0.0
+      atomization_prob: ${datasets.atomization_prob}
+      ligand_dropout_prob: 0.0
+      p_unconditional: ${datasets.p_unconditional}
+      p_dropout_atom_level_embeddings: ${datasets.p_dropout_atom_level_embeddings}
+      add_residue_is_paired_feature: ${datasets.add_residue_is_paired_feature}

rf3/configs/datasets/train/monomer_distillation.yaml

@@ -0,0 +1,49 @@
+# TODO: Inherit from common config with default Transform pipeline
+
+monomer_distillation:
+  dataset:
+    _target_: atomworks.ml.datasets.StructuralDatasetWrapper
+    save_failed_examples_to_dir: ${paths.data.failed_examples_dir}
+
+    # cif parser arguments
+    cif_parser_args:
+      cache_dir: null
+      load_from_cache: False
+      save_to_cache: False 
+
+    # metadata parser
+    dataset_parser:
+      _target_: atomworks.ml.datasets.parsers.GenericDFParser
+      pn_unit_iid_colnames: null
+
+    # metadata dataset
+    dataset:
+      _target_: atomworks.ml.datasets.PandasDataset
+      name: af2fb_distillation
+      id_column: example_id
+      data: ${paths.data.monomer_distillation_parquet_dir}/af2_distillation_facebook.parquet
+      columns_to_load:
+        - example_id
+        - path
+    transform:
+      _target_: ${datasets.pipeline_target}
+      is_inference: False
+      protein_msa_dirs: [{"dir": "${paths.data.monomer_distillation_data_dir}/msa", "extension": ".a3m", "directory_depth": 2}]
+      rna_msa_dirs: []
+      n_recycles: ${datasets.n_recycles_train}
+      crop_size: ${datasets.crop_size}
+      n_msa: ${datasets.n_msa}
+      diffusion_batch_size: ${datasets.diffusion_batch_size_train}
+      max_atoms_in_crop: ${datasets.max_atoms_in_crop}
+      crop_contiguous_probability: 0.25
+      crop_spatial_probability: 0.75
+      b_factor_min: 70.0
+      run_confidence_head: ${datasets.run_confidence_head}
+      take_first_chiral_subordering: ${datasets.take_first_chiral_subordering}
+      use_element_for_atom_names_of_atomized_tokens: ${datasets.use_element_for_atom_names_of_atomized_tokens}
+      mirror_prob: ${datasets.mirror_prob}
+      atomization_prob: ${datasets.atomization_prob}
+      ligand_dropout_prob: ${datasets.ligand_dropout_prob}
+      p_unconditional: ${datasets.p_unconditional}
+      p_dropout_atom_level_embeddings: ${datasets.p_dropout_atom_level_embeddings}
+      add_residue_is_paired_feature: ${datasets.add_residue_is_paired_feature}

rf3/configs/datasets/train/na_complex_distillation.yaml

@@ -0,0 +1,50 @@
+# TODO: Inherit from common config with default Transform pipeline
+
+na_complex_distillation:
+  dataset:
+    _target_: atomworks.ml.datasets.StructuralDatasetWrapper
+    save_failed_examples_to_dir: null
+
+    # cif parser
+    cif_parser_args:
+      #assume_residues_all_resolved: true
+      cache_dir: null
+      load_from_cache: false
+      save_to_cache: false
+
+    # metadata parser
+    dataset_parser:
+      _target_: atomworks.ml.datasets.parsers.GenericDFParser
+      pn_unit_iid_colnames: null #[]
+
+    # metadata dataset
+    dataset:
+      _target_: atomworks.ml.datasets.PandasDataset
+      name: tf_distillation
+      id_column: example_id
+      data: ${paths.data.na_complex_distillation_parquet_dir}/transcriptionFactor_distillation_rf3.newDL.csv
+      columns_to_load:
+        - example_id
+        - path
+    transform:
+      _target_: ${datasets.pipeline_target}
+      is_inference: False
+      protein_msa_dirs: [{"dir": "${paths.data.na_complex_distillation_data_dir}/a3m/", "extension": ".a3m", "directory_depth": 1}]
+      rna_msa_dirs: []
+      n_recycles: ${datasets.n_recycles_train}
+      crop_size: ${datasets.crop_size}
+      n_msa: ${datasets.n_msa}
+      diffusion_batch_size: ${datasets.diffusion_batch_size_train}
+      max_atoms_in_crop: ${datasets.max_atoms_in_crop}
+      crop_contiguous_probability: 0.25
+      crop_spatial_probability: 0.75
+      pad_dna_p_skip: 0.0
+      run_confidence_head: ${datasets.run_confidence_head}
+      take_first_chiral_subordering: ${datasets.take_first_chiral_subordering}
+      use_element_for_atom_names_of_atomized_tokens: ${datasets.use_element_for_atom_names_of_atomized_tokens}
+      mirror_prob: 0.0
+      atomization_prob: ${datasets.atomization_prob}
+      ligand_dropout_prob: ${datasets.ligand_dropout_prob}
+      p_unconditional: ${datasets.p_unconditional}
+      p_dropout_atom_level_embeddings: ${datasets.p_dropout_atom_level_embeddings}
+      add_residue_is_paired_feature: ${datasets.add_residue_is_paired_feature}

rf3/configs/datasets/train/pdb/af3_weighted_sampling.yaml

@@ -0,0 +1,8 @@
+weights:
+  _target_: atomworks.ml.samplers.calculate_weights_for_pdb_dataset_df
+  # We do not include beta here, since it is different for interfaces and chains
+  alphas:
+    a_prot: 3.0 # 3 for AF-3
+    a_nuc: 3.0 # 3 for AF-3
+    a_ligand: 1.0 # 1 for AF-3
+    a_loi: 5.0 # 5 for AF-3

rf3/configs/datasets/train/pdb/base.yaml

@@ -0,0 +1,32 @@
+dataset:
+  _target_: atomworks.ml.datasets.StructuralDatasetWrapper
+  save_failed_examples_to_dir: ${paths.data.failed_examples_dir}
+  cif_parser_args:
+    cache_dir: null
+    load_from_cache: false
+    save_to_cache: false
+  dataset:
+    _target_: atomworks.ml.datasets.PandasDataset
+    # we will use the example_id as the unique column
+    id_column: example_id
+  transform:
+    # common Transform pipeline components for all PDB datasets
+    _target_: ${datasets.pipeline_target}
+    is_inference: False
+    protein_msa_dirs: ${paths.data.protein_msa_dirs}
+    rna_msa_dirs: ${paths.data.rna_msa_dirs}
+    n_recycles: ${datasets.n_recycles_train}
+    crop_size: ${datasets.crop_size}
+    n_msa: ${datasets.n_msa}
+    diffusion_batch_size: ${datasets.diffusion_batch_size_train}
+    max_atoms_in_crop: ${datasets.max_atoms_in_crop}
+    run_confidence_head: ${datasets.run_confidence_head}
+    p_unconditional: ${datasets.p_unconditional}
+    p_dropout_atom_level_embeddings: ${datasets.p_dropout_atom_level_embeddings}
+    take_first_chiral_subordering: ${datasets.take_first_chiral_subordering}
+    use_element_for_atom_names_of_atomized_tokens: ${datasets.use_element_for_atom_names_of_atomized_tokens}
+    mirror_prob: ${datasets.mirror_prob}
+    atomization_prob: ${datasets.atomization_prob}
+    ligand_dropout_prob: ${datasets.ligand_dropout_prob}
+    add_residue_is_paired_feature: ${datasets.add_residue_is_paired_feature}
+    add_cyclic_bonds: ${datasets.add_cyclic_bonds}