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5a492032d5
* Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: src nest, rename rf2aa to modelhub * refactor: initial commit without projects * Initial commit of chiral changes * Initial checkin of chiral feature code * Add chiral metric * Remove option for double residual connection. Add kq_norm oiptions to base (20250125) config. * Restoring flag * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: new modelhub --------- Co-authored-by: fdimaio <dimaio@uw.edu> Co-authored-by: HaotianZhangAI4Science <haotianzhang@zju.edu.cn>
46 lines
1.5 KiB
YAML
46 lines
1.5 KiB
YAML
defaults:
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- base
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dataset:
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dataset_parser:
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_target_: datahub.datasets.parsers.InterfacesDFParser
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dataset:
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name: interface
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data: ${paths.data.pdb_data_dir}/interfaces_df_train.parquet
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filters:
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# filters common across all PDB datasets
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- "deposition_date < '2021-09-30'"
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- "resolution < 9.0"
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- "num_polymer_pn_units <= 300"
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- "cluster.notnull()"
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# interface specific filters
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- "~(pn_unit_1_non_polymer_res_names.notnull() and pn_unit_1_non_polymer_res_names.str.contains('${resolve_import:cifutils.constants,AF3_EXCLUDED_LIGANDS_REGEX}', regex=True))"
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- "~(pn_unit_2_non_polymer_res_names.notnull() and pn_unit_2_non_polymer_res_names.str.contains('${resolve_import:cifutils.constants,AF3_EXCLUDED_LIGANDS_REGEX}', regex=True))"
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- "is_inter_molecule"
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columns_to_load:
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# columns common across all PDB datasets
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- example_id
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- pdb_id
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- assembly_id
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- deposition_date
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- resolution
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- num_polymer_pn_units
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- method
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- cluster
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- n_prot
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- n_nuc
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- n_ligand
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- n_peptide
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# interface specific columns
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- pn_unit_1_iid
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- pn_unit_2_iid
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- pn_unit_1_non_polymer_res_names
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- pn_unit_2_non_polymer_res_names
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- is_inter_molecule
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- all_pn_unit_iids_after_processing
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- involves_loi
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transform:
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# interface-specific Transform pipeline parameters
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crop_contiguous_probability: 0.0
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crop_spatial_probability: 1.0
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