mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
fc41c1a5eb
- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches - Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features - Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/ - Keep templates enabled; test test__chopped_dimer now passes
101 lines
3.2 KiB
JSON
Executable File
101 lines
3.2 KiB
JSON
Executable File
{
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"databases": {
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"UniProt": {
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"release_date": "2022-12-13 15:30:36",
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"version": null,
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"location_url": [
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"ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
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"ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
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]
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},
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"PDB seqres": {
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"release_date": "2024-07-01 03:36:14",
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"version": "546c661e9ffdb6f035040d28176f1c5a",
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"location_url": [
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"ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
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]
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},
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"ColabFold": {
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"version": "2024-07-29",
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"release_date": null,
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"location_url": [
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"https://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz"
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]
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}
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},
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"software": {
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"AlphaPulldown": {
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"version": "2.0.0.b2"
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},
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"AlphaFold": {
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"version": "2.3.2"
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},
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"jackhmmer": {
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"version": "3.4"
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},
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"hhblits": {
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"version": "3.3.0"
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},
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"hhsearch": {
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"version": "3.3.0"
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},
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"hmmsearch": {
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"version": "3.4"
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},
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"hmmbuild": {
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"version": "3.4"
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},
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"kalign": {
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"version": "2.04"
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}
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},
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"date": "2024-07-29 16:39:44",
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"other": {
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"logtostderr": "False",
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"alsologtostderr": "False",
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"log_dir": "",
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"v": "0",
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"verbosity": "0",
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"logger_levels": "{}",
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"stderrthreshold": "fatal",
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"showprefixforinfo": "True",
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"run_with_pdb": "False",
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"pdb_post_mortem": "False",
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"pdb": "False",
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"run_with_profiling": "False",
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"only_check_args": "False",
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"op_conversion_fallback_to_while_loop": "True",
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"delta_threshold": "0.5",
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"tt_check_filter": "False",
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"tt_single_core_summaries": "False",
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"runtime_oom_exit": "True",
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"hbm_oom_exit": "True",
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"xml_output_file": "",
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"fasta_paths": "['test/test_data/fastas/test.fasta']",
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"jackhmmer_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/jackhmmer",
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"hhblits_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hhblits",
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"hhsearch_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hhsearch",
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"hmmsearch_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hmmsearch",
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"hmmbuild_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hmmbuild",
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"kalign_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/kalign",
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"uniprot_database_path": "/scratch/AlphaFold_DBs/2.3.2/uniprot/uniprot.fasta",
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"pdb_seqres_database_path": "/scratch/AlphaFold_DBs/2.3.2/pdb_seqres/pdb_seqres.txt",
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"template_mmcif_dir": "/scratch/AlphaFold_DBs/2.3.2/pdb_mmcif/mmcif_files",
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"obsolete_pdbs_path": "/scratch/AlphaFold_DBs/2.3.2/pdb_mmcif/obsolete.dat",
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"db_preset": "full_dbs",
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"model_preset": "monomer",
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"benchmark": "False",
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"num_multimer_predictions_per_model": "5",
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"use_precomputed_msas": "False",
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"models_to_relax": "ModelsToRelax.BEST",
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"use_mmseqs2": "False",
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"save_msa_files": "False",
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"skip_existing": "False",
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"use_hhsearch": "False",
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"threshold_clashes": "1000.0",
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"hb_allowance": "0.4",
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"plddt_threshold": "0.0",
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"multiple_mmts": "False",
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"use_small_bfd": "False"
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}
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} |