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Lines for PAE for multimers. Test data for a trimer
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@DimaMolod
DimaMolod committed Aug 30, 2024
1 parent 13adee0 commit b6ce664
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2 changes: 1 addition & 1 deletion alphapulldown/utils/plotting.py
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Expand Up @@ -33,7 +33,7 @@ def plot_pae_from_matrix(seqs, pae_matrix, figure_name='', ranking: int = 0):
fig.colorbar(pos).ax.set_title("unit: Angstrom")

# Draw black lines at sequence boundaries
for t in range(1, len(xticks), 2): # Draw lines at the end of each sequence
for t in range(1, len(xticks)): # Draw lines at the end of each sequence
ax1.axhline(xticks[t], color="black", linewidth=3.5)
ax1.axvline(xticks[t], color="black", linewidth=3.5)

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1 change: 1 addition & 0 deletions test/check_predict_structure.py
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Expand Up @@ -126,6 +126,7 @@ def tearDown(self) -> None:
@parameterized.named_parameters(
{'testcase_name': 'monomer', 'protein_list': 'test_monomer.txt', 'mode': 'custom'},
{'testcase_name': 'dimer', 'protein_list': 'test_dimer.txt', 'mode': 'custom'},
{'testcase_name': 'trimer', 'protein_list': 'test_trimer.txt', 'mode': 'custom'},
{'testcase_name': 'homo_oligomer', 'protein_list': "test_homooligomer.txt", 'mode': 'homo-oligomer'},
{'testcase_name': 'chopped_dimer', 'protein_list': 'test_dimer_chopped.txt', 'mode': 'custom'}
)
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Binary file added ...predictions/TEST_and_TEST_and_TEST/TEST_and_TEST_and_TEST_PAE_plot_ranked_1.png
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Binary file added ...predictions/TEST_and_TEST_and_TEST/TEST_and_TEST_and_TEST_PAE_plot_ranked_2.png
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101 changes: 101 additions & 0 deletions test/test_data/predictions/TEST_and_TEST_and_TEST/TEST_feature_metadata_2024-07-29.json
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{
"databases": {
"UniProt": {
"release_date": "2022-12-13 15:30:36",
"version": null,
"location_url": [
"ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
"ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
]
},
"PDB seqres": {
"release_date": "2024-07-01 03:36:14",
"version": "546c661e9ffdb6f035040d28176f1c5a",
"location_url": [
"ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
]
},
"ColabFold": {
"version": "2024-07-29",
"release_date": null,
"location_url": [
"https://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz"
]
}
},
"software": {
"AlphaPulldown": {
"version": "2.0.0.b2"
},
"AlphaFold": {
"version": "2.3.2"
},
"jackhmmer": {
"version": "3.4"
},
"hhblits": {
"version": "3.3.0"
},
"hhsearch": {
"version": "3.3.0"
},
"hmmsearch": {
"version": "3.4"
},
"hmmbuild": {
"version": "3.4"
},
"kalign": {
"version": "2.04"
}
},
"date": "2024-07-29 16:39:44",
"other": {
"logtostderr": "False",
"alsologtostderr": "False",
"log_dir": "",
"v": "0",
"verbosity": "0",
"logger_levels": "{}",
"stderrthreshold": "fatal",
"showprefixforinfo": "True",
"run_with_pdb": "False",
"pdb_post_mortem": "False",
"pdb": "False",
"run_with_profiling": "False",
"only_check_args": "False",
"op_conversion_fallback_to_while_loop": "True",
"delta_threshold": "0.5",
"tt_check_filter": "False",
"tt_single_core_summaries": "False",
"runtime_oom_exit": "True",
"hbm_oom_exit": "True",
"xml_output_file": "",
"fasta_paths": "['test/test_data/fastas/test.fasta']",
"jackhmmer_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/jackhmmer",
"hhblits_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hhblits",
"hhsearch_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hhsearch",
"hmmsearch_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hmmsearch",
"hmmbuild_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/hmmbuild",
"kalign_binary_path": "/home/dmolodenskiy/.conda/envs/AlphaPulldownMamba/bin/kalign",
"uniprot_database_path": "/scratch/AlphaFold_DBs/2.3.2/uniprot/uniprot.fasta",
"pdb_seqres_database_path": "/scratch/AlphaFold_DBs/2.3.2/pdb_seqres/pdb_seqres.txt",
"template_mmcif_dir": "/scratch/AlphaFold_DBs/2.3.2/pdb_mmcif/mmcif_files",
"obsolete_pdbs_path": "/scratch/AlphaFold_DBs/2.3.2/pdb_mmcif/obsolete.dat",
"db_preset": "full_dbs",
"model_preset": "monomer",
"benchmark": "False",
"num_multimer_predictions_per_model": "5",
"use_precomputed_msas": "False",
"models_to_relax": "ModelsToRelax.BEST",
"use_mmseqs2": "False",
"save_msa_files": "False",
"skip_existing": "False",
"use_hhsearch": "False",
"threshold_clashes": "1000.0",
"hb_allowance": "0.4",
"plddt_threshold": "0.0",
"multiple_mmts": "False",
"use_small_bfd": "False"
}
}
1 change: 1 addition & 0 deletions test/test_data/predictions/TEST_and_TEST_and_TEST/confidence_model_1_multimer_v3_pred_0.json
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1 change: 1 addition & 0 deletions test/test_data/predictions/TEST_and_TEST_and_TEST/confidence_model_2_multimer_v3_pred_0.json
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1 change: 1 addition & 0 deletions test/test_data/predictions/TEST_and_TEST_and_TEST/confidence_model_3_multimer_v3_pred_0.json
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1 change: 1 addition & 0 deletions test/test_data/predictions/TEST_and_TEST_and_TEST/confidence_model_4_multimer_v3_pred_0.json
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