├── .coveragerc ├── .github └── workflows │ ├── docs.yaml │ ├── main.yaml │ └── pr.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE.txt ├── NOTICE ├── README.md ├── docker-compose.yml ├── dockerfiles ├── base │ ├── Dockerfile │ ├── env.yml │ └── requirements.txt ├── main │ └── Dockerfile └── test │ └── Dockerfile ├── docs ├── api │ └── index.md ├── apidoc.py ├── citation.md ├── conf.py ├── contribution │ ├── development.md │ ├── documentation.md │ ├── index.md │ ├── pipeline.md │ ├── release.md │ └── workflow.png ├── dataset.md ├── evaluation.md ├── examples │ ├── 1_download.ipynb │ ├── 2_query_filter_index.ipynb │ ├── 3_access_system_files.ipynb │ ├── 4_align_mask_crop.ipynb │ ├── 5_dataset_and_loader.ipynb │ ├── 6_custom_split.ipynb │ ├── index.md │ ├── mlsb_challenge.md │ └── split_plots │ │ ├── chain_composition.png │ │ ├── domain_classifications.png │ │ ├── ligand_types.png │ │ ├── molecular_descriptors.png │ │ ├── plinder_clusters.png │ │ ├── priorities.png │ │ └── split_proportions.png ├── index.md ├── static │ ├── assets │ │ └── general │ │ │ ├── plinder_data_hierarchy.png │ │ │ ├── plinder_icon.png │ │ │ └── plinder_logo.png │ └── plinder.css ├── tablegen.py ├── tutorial │ ├── api.ipynb │ ├── dataset.md │ └── index.md └── viewcode.py ├── environment.yml ├── flows ├── configs │ ├── split_configs │ │ ├── batch_0 │ │ │ ├── 1.yaml │ │ │ ├── 2.yaml │ │ │ ├── 3.yaml │ │ │ ├── 4.yaml │ │ │ ├── 5.yaml │ │ │ └── 6.yaml │ │ ├── batch_1 │ │ │ ├── 1.yaml │ │ │ ├── 2.yaml │ │ │ ├── 3.yaml │ │ │ ├── 4.yaml │ │ │ ├── 5.yaml │ │ │ └── 6.yaml │ │ ├── batch_2 │ │ │ ├── 0_5.yaml │ │ │ └── 1_5.yaml │ │ ├── batch_3 │ │ │ ├── 1.yaml │ │ │ ├── 10.yaml │ │ │ ├── 11.yaml │ │ │ ├── 12.yaml │ │ │ ├── 13.yaml │ │ │ ├── 14.yaml │ │ │ ├── 2.yaml │ │ │ ├── 3.yaml │ │ │ ├── 5.yaml │ │ │ ├── 6.yaml │ │ │ ├── 7.yaml │ │ │ └── 9.yaml │ │ ├── batch_4 │ │ │ ├── 4.yaml │ │ │ └── 8.yaml │ │ ├── batch_5 │ │ │ ├── 10.yaml │ │ │ ├── 9.yaml │ │ │ ├── batch_11.yaml │ │ │ └── batch_12.yaml │ │ └── batch_6 │ │ │ ├── 10.yaml │ │ │ ├── 2.yaml │ │ │ ├── 7.yaml │ │ │ └── 9.yaml │ └── v2 │ │ ├── download_and_make_dbs.yaml │ │ ├── make_batch_scores_only.yaml │ │ ├── make_components.yaml │ │ ├── make_entries_ligands.yaml │ │ ├── make_leakage.yaml │ │ ├── make_protein_scores.yaml │ │ ├── make_splits.yaml │ │ ├── split_multi_graph.yaml │ │ └── split_single_graph.yaml ├── data_ingest.py ├── data_ingest_report.py ├── docker.py ├── proc.py ├── report.py └── split_eval.py ├── mypy.ini ├── pyproject.toml ├── pytest.ini ├── requirements_data.txt ├── scripts └── write_data_dicionary.py ├── src └── plinder │ ├── __init__.py │ ├── _version.py │ ├── core │ ├── __init__.py │ ├── index │ │ ├── __init__.py │ │ ├── system.py │ │ └── utils.py │ ├── loader │ │ ├── __init__.py │ │ ├── dataset.py │ │ ├── featurizer.py │ │ ├── transforms.py │ │ └── utils.py │ ├── scores │ │ ├── __init__.py │ │ ├── clusters.py │ │ ├── index.py │ │ ├── ligand.py │ │ ├── links.py │ │ ├── protein.py │ │ └── query.py │ ├── split │ │ ├── __init__.py │ │ ├── plot.py │ │ └── utils.py │ ├── structure │ │ ├── __init__.py │ │ ├── atoms.py │ │ ├── contacts.py │ │ ├── diffdock_utils.py │ │ ├── models.py │ │ ├── smallmols_similarity.py │ │ ├── smallmols_utils.py │ │ ├── structure.py │ │ ├── superimpose.py │ │ ├── surgery.py │ │ └── vendored.py │ └── utils │ │ ├── __init__.py │ │ ├── config.py │ │ ├── constants.py │ │ ├── cpl.py │ │ ├── dataclass.py │ │ ├── dec.py │ │ ├── gcs.py │ │ ├── io.py │ │ ├── load_systems.py │ │ ├── log.py │ │ ├── schemas.py │ │ └── unpack.py │ ├── data │ ├── __init__.py │ ├── _version.py │ ├── clusters.py │ ├── column_descriptions │ │ ├── __init__.py │ │ ├── entry.tsv │ │ ├── entry_validation.tsv │ │ ├── extra.tsv │ │ ├── ligand_interacting_ligand_chains.tsv │ │ ├── ligand_interacting_ligand_chains_validation.tsv │ │ ├── ligand_neighboring_ligand_chains.tsv │ │ ├── ligand_neighboring_ligand_chains_validation.tsv │ │ ├── ligand_protein_chains.tsv │ │ ├── ligand_protein_chains_validation.tsv │ │ ├── ligands.tsv │ │ ├── posebusters_checks.tsv │ │ ├── qc.tsv │ │ ├── similarity_clusters.tsv │ │ ├── system.tsv │ │ ├── system_ligand_chains.tsv │ │ ├── system_ligand_chains_validation.tsv │ │ ├── system_ligand_validation.tsv │ │ ├── system_pocket.tsv │ │ ├── system_pocket_validation.tsv │ │ ├── system_protein_chains.tsv │ │ └── system_protein_chains_validation.tsv │ ├── common │ │ ├── __init__.py │ │ ├── _version.py │ │ ├── constants.py │ │ └── log.py │ ├── databases.py │ ├── docs.py │ ├── final_structure_qc.py │ ├── get_system_annotations.py │ ├── leakage.py │ ├── pipeline │ │ ├── __init__.py │ │ ├── config.py │ │ ├── io.py │ │ ├── mpqueue.py │ │ ├── pipeline.py │ │ ├── tasks.py │ │ ├── transform.py │ │ └── utils.py │ ├── save_linked_structures.py │ ├── splits.py │ ├── structure │ │ ├── __init__.py │ │ ├── atoms.py │ │ └── contacts.py │ └── utils │ │ ├── __init__.py │ │ └── annotations │ │ ├── __init__.py │ │ ├── aggregate_annotations.py │ │ ├── get_ligand_validation.py │ │ ├── get_similarity_scores.py │ │ ├── interaction_utils.py │ │ ├── interface_gap.py │ │ ├── ligand_utils.py │ │ ├── mmpdb_utils.py │ │ ├── protein_utils.py │ │ ├── rdkit_utils.py │ │ ├── save_utils.py │ │ ├── static_files │ │ ├── artifacts_badlist.csv │ │ ├── cofactors.json │ │ ├── dates.csv │ │ ├── ligand_list.tsv │ │ └── prdcc.chemlib │ │ └── utils.py │ ├── eval │ ├── __init__.py │ └── docking │ │ ├── __init__.py │ │ ├── make_plots.py │ │ ├── stratify_test_set.py │ │ ├── utils.py │ │ └── write_scores.py │ └── methods │ └── __init__.py ├── tests ├── __init__.py ├── conftest.py ├── core │ ├── test_atoms.py │ ├── test_core_config.py │ ├── test_core_scores.py │ ├── test_core_system.py │ ├── test_data_loader.py │ ├── test_dataclass.py │ ├── test_gcs.py │ ├── test_index_utils.py │ ├── test_smallmols_utils.py │ ├── test_split_plot.py │ ├── test_superimpose.py │ └── test_transforms.py ├── data │ ├── pipeline │ │ ├── test_config.py │ │ ├── test_end_to_end.py │ │ ├── test_io.py │ │ ├── test_pipeline.py │ │ ├── test_tasks.py │ │ ├── test_transform.py │ │ └── test_utils.py │ ├── test_clusters.py │ ├── test_docs.py │ ├── test_plinder_data.py │ └── test_save_linked_structures.py ├── test_annotations.py ├── test_data │ ├── 2g.zip │ ├── 7nac.json │ ├── components.cif │ ├── components.cif.gz │ ├── components.parquet │ ├── ecod_mini.tsv │ ├── eval │ │ ├── fingerprints │ │ │ └── ligands_per_system.parquet │ │ ├── index │ │ │ └── annotation_table.parquet │ │ ├── predicted_poses │ │ │ ├── 1a3b__1__1.B__1.D │ │ │ │ ├── rank1.sdf │ │ │ │ └── rank1_named.sdf │ │ │ └── 1ai5__1__1.A_1.B__1.D │ │ │ │ └── rank1.sdf │ │ ├── predictions.csv │ │ ├── results.csv │ │ ├── scores │ │ │ └── search_db=holo │ │ │ │ └── small_score.parquet │ │ ├── splits │ │ │ └── split.parquet │ │ └── systems │ │ │ ├── a3.zip │ │ │ └── ai.zip │ ├── kinase_ligand_ccd_codes.parquet │ ├── kinase_uniprotac.parquet │ ├── mini_all_entries.json │ ├── mini_score_dataset.parquet │ ├── mini_score_seq_dataset.parquet │ ├── mini_structure_checks_report.tsv │ ├── mini_system_files_new │ │ ├── 1fbh__1__1.A_1.B__1.E_1.F │ │ │ ├── chain_mapping.json │ │ │ ├── ligand_files │ │ │ │ ├── 1.E.sdf │ │ │ │ └── 1.F.sdf │ │ │ ├── sequences.fasta │ │ │ ├── system.cif │ │ │ └── system.pdb │ │ ├── 1fbz__1__1.A__1.C │ │ │ ├── chain_mapping.json │ │ │ ├── ligand_files │ │ │ │ └── 1.C.sdf │ │ │ ├── sequences.fasta │ │ │ ├── system.cif │ │ │ └── system.pdb │ │ └── 3fbp__1__1.A_1.B__1.C │ │ │ ├── chain_mapping.json │ │ │ ├── ligand_files │ │ │ └── 1.C.sdf │ │ │ ├── sequences.fasta │ │ │ ├── system.cif │ │ │ └── system.pdb │ ├── mmp │ │ ├── mini_clusters │ │ │ └── cluster=components │ │ │ │ ├── directed=False │ │ │ │ └── metric=protein_fident_weighted_sum │ │ │ │ │ └── threshold=95.parquet │ │ │ │ └── directed=True │ │ │ │ └── metric=pocket_fident │ │ │ │ └── threshold=100.parquet │ │ ├── mmp_mini_data.tsv │ │ ├── mmp_test_pocket_fident_weighted_sum__1.0__strong__component.csv │ │ ├── mmp_test_protein_fident_weighted_sum__0.95__weak__component.csv │ │ └── tiny_mmp_index.csv.gz │ ├── panther_classifications_mini.tar.gz │ ├── panther_raw.tar.gz │ ├── pdb_seqres.txt.gz │ ├── plinder │ │ └── mount │ │ │ ├── clusters │ │ │ └── subdir │ │ │ │ └── clusters.parquet │ │ │ ├── entries │ │ │ ├── 9h.zip │ │ │ ├── av.zip │ │ │ ├── ng.zip │ │ │ └── v2.zip │ │ │ ├── fingerprints │ │ │ └── ligands_per_system.parquet │ │ │ ├── index │ │ │ └── annotation_table.parquet │ │ │ ├── ligand_scores │ │ │ └── ligand_scores.parquet │ │ │ ├── links │ │ │ └── kind=apo │ │ │ │ └── links.parquet │ │ │ ├── manifest │ │ │ └── manifest.parquet │ │ │ ├── mmp │ │ │ └── plinder_mmp_series.parquet │ │ │ ├── scores │ │ │ ├── search_db=apo │ │ │ │ ├── pocket_lddt.parquet │ │ │ │ └── protein_fident_qcov_weighted_sum.parquet │ │ │ ├── search_db=holo │ │ │ │ ├── pocket_lddt.parquet │ │ │ │ └── protein_fident_qcov_weighted_sum.parquet │ │ │ └── search_db=pred │ │ │ │ ├── pocket_lddt.parquet │ │ │ │ └── protein_fident_qcov_weighted_sum.parquet │ │ │ ├── splits │ │ │ └── split.parquet │ │ │ ├── strat │ │ │ └── val_vs_test_data │ │ │ │ ├── max_similarities__test_vs_val__pli_unique_qcov.parquet │ │ │ │ ├── max_similarities__test_vs_val__pocket_fident_qcov.parquet │ │ │ │ ├── max_similarities__test_vs_val__pocket_lddt.parquet │ │ │ │ ├── max_similarities__test_vs_val__pocket_lddt_qcov.parquet │ │ │ │ ├── max_similarities__test_vs_val__pocket_qcov.parquet │ │ │ │ ├── max_similarities__test_vs_val__protein_fident_weighted_sum.parquet │ │ │ │ ├── max_similarities__test_vs_val__protein_lddt_weighted_sum.parquet │ │ │ │ ├── max_similarities__test_vs_val__protein_seqsim_weighted_sum.parquet │ │ │ │ ├── max_similarities__test_vs_val__tanimoto_similarity_max.parquet │ │ │ │ └── test_set.parquet │ │ │ └── systems │ │ │ ├── 9h.zip │ │ │ ├── av.zip │ │ │ ├── ng.zip │ │ │ └── v2.zip │ ├── smiles_from_nextgen_bonds_data.csv │ ├── split_challenge │ │ ├── eval_metrics_config.yaml │ │ ├── test_lig_profile.csv │ │ ├── test_source_file.csv │ │ └── test_submission.csv │ ├── split_plot_split.parquet │ ├── system_instance_dataframe │ │ ├── instance_dataframe7.csv │ │ ├── plinder_final_dir_structure │ │ │ ├── apo │ │ │ │ ├── 6S8O__1__1.A.cif │ │ │ │ ├── 6S8O__1__1.A.pdb │ │ │ │ ├── 7OS1__1__1.A.cif │ │ │ │ └── 7OS1__1__1.A.pdb │ │ │ ├── holo │ │ │ │ ├── 2Y4I__1__1.B__1.E_1.F__ATP_MG │ │ │ │ │ ├── chain_mapping.json │ │ │ │ │ ├── ligand_files │ │ │ │ │ │ ├── 1.E.sdf │ │ │ │ │ │ └── 1.F.sdf │ │ │ │ │ ├── sequences.fasta │ │ │ │ │ ├── system.cif │ │ │ │ │ └── system.pdb │ │ │ │ └── 8BCH__1__1.A__1.B__QA9 │ │ │ │ │ ├── chain_mapping.json │ │ │ │ │ ├── ligand_files │ │ │ │ │ └── 1.B.sdf │ │ │ │ │ ├── sequences.fasta │ │ │ │ │ ├── system.cif │ │ │ │ │ └── system.pdb │ │ │ └── predicted │ │ │ │ ├── AF-O75643.cif │ │ │ │ └── AF-O75643.pdb │ │ └── system_dataframe7.csv │ ├── test_kinase_klifs.csv │ ├── validation │ │ ├── 1qz5_validation.xml.gz │ │ ├── 2dty_validation.xml.gz │ │ ├── 2e84_validation.xml.gz │ │ ├── 2ixb_validation.xml.gz │ │ ├── 2leb_validation.xml.gz │ │ ├── 2y4i_validation.xml.gz │ │ ├── 4fxd_validation.xml.gz │ │ ├── 5lwx_validation.xml.gz │ │ ├── 6fx1_validation.xml.gz │ │ ├── 6lu7_validation.xml.gz │ │ ├── 6m92_validation.xml.gz │ │ ├── 8a7u_validation.xml.gz │ │ └── 8pn3_validation.xml.gz │ └── xx │ │ ├── output │ │ ├── 4ci1-assembly.cif │ │ └── 5a7w-assembly.cif │ │ ├── pdb_00001ngx │ │ └── pdb_00001ngx_xyz-enrich.cif.gz │ │ ├── pdb_00001ppc │ │ └── pdb_00001ppc_xyz-enrich.cif.gz │ │ ├── pdb_00001qz5 │ │ ├── 1qz5-assembly.cif │ │ ├── pdb_00001qz5_xyz-enrich.cif │ │ └── pdb_00001qz5_xyz-enrich.cif.gz │ │ ├── pdb_00002dty │ │ └── pdb_00002dty_xyz-enrich.cif.gz │ │ ├── pdb_00002e84 │ │ └── pdb_00002e84_xyz-enrich.cif.gz │ │ ├── pdb_00002gdo │ │ └── pdb_00002gdo_xyz-enrich.cif.gz │ │ ├── pdb_00002hyy │ │ └── pdb_00002hyy_xyz-enrich.cif.gz │ │ ├── pdb_00002ixb │ │ └── pdb_00002ixb_xyz-enrich.cif.gz │ │ ├── pdb_00002leb │ │ └── pdb_00002leb_xyz-enrich.cif.gz │ │ ├── pdb_00002p1q │ │ └── pdb_00002p1q_xyz-enrich.cif.gz │ │ ├── pdb_00002y4i │ │ └── pdb_00002y4i_xyz-enrich.cif.gz │ │ ├── pdb_00003cyh │ │ └── pdb_00003cyh_xyz-enrich.cif.gz │ │ ├── pdb_00003cz3 │ │ └── pdb_00003cz3_xyz-enrich.cif.gz │ │ ├── pdb_00003g32 │ │ └── pdb_00003g32_xyz-enrich.cif.gz │ │ ├── pdb_00003grt │ │ └── pdb_00003grt_xyz-enrich.cif.gz │ │ ├── pdb_00003ot7 │ │ └── pdb_00003ot7_xyz-enrich.cif.gz │ │ ├── pdb_00004ci1 │ │ ├── 4ci1-assembly.cif │ │ ├── pdb_00004ci1_xyz-enrich.cif │ │ └── pdb_00004ci1_xyz-enrich.cif.gz │ │ ├── pdb_00004fxd │ │ └── pdb_00004fxd_xyz-enrich.cif.gz │ │ ├── pdb_00004jvn │ │ └── pdb_00004jvn_xyz-enrich.cif.gz │ │ ├── pdb_00004nhc │ │ └── pdb_00004nhc_xyz-enrich.cif.gz │ │ ├── pdb_00004qyf │ │ └── pdb_00004qyf_xyz-enrich.cif.gz │ │ ├── pdb_00004tz4 │ │ └── pdb_00004tz4_xyz-enrich.cif.gz │ │ ├── pdb_00005a7w │ │ ├── 5a7w-assembly.cif │ │ ├── 5a7w_A_35M.sdf │ │ ├── 5a7w_A_hyd.pdb │ │ ├── 5a7w_interactions.txt │ │ └── pdb_00005a7w_xyz-enrich.cif.gz │ │ ├── pdb_00005fkw │ │ └── pdb_00005fkw_xyz-enrich.cif.gz │ │ ├── pdb_00005lwx │ │ └── pdb_00005lwx_xyz-enrich.cif.gz │ │ ├── pdb_00006f6r │ │ └── pdb_00006f6r_xyz-enrich.cif.gz │ │ ├── pdb_00006fx1 │ │ └── pdb_00006fx1_xyz-enrich.cif.gz │ │ ├── pdb_00006i41 │ │ └── pdb_00006i41_xyz-enrich.cif.gz │ │ ├── pdb_00006lu7 │ │ └── pdb_00006lu7_xyz-enrich.cif.gz │ │ ├── pdb_00006m92 │ │ └── pdb_00006m92_xyz-enrich.cif.gz │ │ ├── pdb_00006ntj │ │ └── pdb_00006ntj_xyz-enrich.cif.gz │ │ ├── pdb_00006u6k │ │ └── pdb_00006u6k_xyz-enrich.cif.gz │ │ ├── pdb_00007az3 │ │ └── pdb_00007az3_xyz-enrich.cif.gz │ │ ├── pdb_00007bqu │ │ └── pdb_00007bqu_xyz-enrich.cif.gz │ │ ├── pdb_00007gj7 │ │ └── pdb_00007gj7_xyz-enrich.cif.gz │ │ ├── pdb_00007gl9 │ │ └── pdb_00007gl9_xyz-enrich.cif.gz │ │ └── pdb_00008pn3 │ │ └── pdb_00008pn3_xyz-enrich.cif.gz ├── test_eval.py └── test_final_structure_checks.py 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