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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>
42 lines
1.2 KiB
YAML
42 lines
1.2 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.PNUnitsDFParser
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dataset:
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name: pn_unit
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data: ${paths.data.pdb_data_dir}/pn_units_df_train.parquet
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filters:
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# filters common across all PDB datasets
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- "deposition_date < '2021-09-30'"
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- "resolution < 9.0"
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- "num_polymer_pn_units <= 300"
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- "cluster.notnull()"
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# pn_unit specific filters
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- "~(q_pn_unit_non_polymer_res_names.notnull() and q_pn_unit_non_polymer_res_names.str.contains('${resolve_import:cifutils.constants,AF3_EXCLUDED_LIGANDS_REGEX}', regex=True))"
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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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- total_num_atoms_in_unprocessed_assembly
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# pn_unit specific columns
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- q_pn_unit_iid
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- q_pn_unit_non_polymer_res_names
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- all_pn_unit_iids_after_processing
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- q_pn_unit_is_loi
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transform:
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# pn_unit-specific Transform pipeline parameters
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crop_contiguous_probability: 0.3333333333333333
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crop_spatial_probability: 0.6666666666666667
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