Download Alphafold files¶
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from pathlib import Path
from pprint import pprint
from protein_detective.alphafold import fetch_many, fetch_many_async
from pathlib import Path
from pprint import pprint
from protein_detective.alphafold import fetch_many, fetch_many_async
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save_dir = Path("alphafold_files")
save_dir = Path("alphafold_files")
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summaries = fetch_many(["A1YPR0", "O60481"], save_dir)
summaries = fetch_many(["A1YPR0", "O60481"], save_dir)
Fetching Alphafold summaries: 100%|██████████| 2/2 [00:00<00:00, 8.97it/s] Downloading AlphaFold files: 100%|██████████| 2/2 [00:00<00:00, 14847.09it/s]
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pprint(summaries)
pprint(summaries)
[AlphaFoldEntry(uniprot_acc='A1YPR0',
summary=EntrySummary(entryId='AF-A1YPR0-F1',
gene='ZBTB7C',
sequenceChecksum='73D82A34502B55BF',
sequenceVersionDate='2007-02-06',
uniprotAccession='A1YPR0',
uniprotId='ZBT7C_HUMAN',
uniprotDescription='Zinc finger and BTB '
'domain-containing '
'protein 7C',
taxId=9606,
organismScientificName='Homo sapiens',
uniprotStart=1,
uniprotEnd=619,
uniprotSequence='MANDIDELIGIPFPNHSSEVLCSLNEQRHDGLLCDVLLVVQEQEYRTHRSVLAACSKYFKKLFTAGTLASQPYVYEIDFVQPEALAAILEFAYTSTLTITAGNVKHILNAARMLEIQCIVNVCLEIMEPGGDGGEEDDKEDDDDDEDDDDEEDEEEEEEEEEDDDDDTEDFADQENLPDPQDISCHQSPSKTDHLTEKAYSDTPRDFPDSFQAGSPGHLGVIRDFSIESLLRENLYPKANIPDRRPSLSPFAPDFFPHLWPGDFGAFAQLPEQPMDSGPLDLVIKNRKIKEEEKEELPPPPPPPFPNDFFKDMFPDLPGGPLGPIKAENDYGAYLNFLSATHLGGLFPPWPLVEERKLKPKASQQCPICHKVIMGAGKLPRHMRTHTGEKPYMCTICEVRFTRQDKLKIHMRKHTGERPYLCIHCNAKFVHNYDLKNHMRIHTGVRPYQCEFCYKSFTRSDHLHRHIKRQSCRMARPRRGRKPAAWRAASLLFGPGGPAPDKAAFVMPPALGEVGGHLGGAAVCLPGPSPAKHFLAAPKGALSLQELERQFEETQMKLFGRAQLEAERNAGGLLAFALAENVAAARPYFPLPDPWAAGLAGLPGLAGLNHVASMSEANN',
modelCreatedDate='2022-06-01',
latestVersion=4,
allVersions=[1, 2, 3, 4],
bcifUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.bcif',
cifUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.cif',
pdbUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.pdb',
paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v4.png',
paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v4.json',
amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-aa-substitutions.csv',
amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg19.csv',
amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg38.csv',
isReviewed=True,
isReferenceProteome=True),
pdb_file=PosixPath('alphafold_files/AF-A1YPR0-F1-model_v4.pdb'),
pae_file=None,
bcif_file=None,
cif_file=None,
pae_image_file=None,
pae_doc_file=None,
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None),
AlphaFoldEntry(uniprot_acc='O60481',
summary=EntrySummary(entryId='AF-O60481-F1',
gene='ZIC3',
sequenceChecksum='3150CF13C0679568',
sequenceVersionDate='1998-08-01',
uniprotAccession='O60481',
uniprotId='ZIC3_HUMAN',
uniprotDescription='Zinc finger protein '
'ZIC 3',
taxId=9606,
organismScientificName='Homo sapiens',
uniprotStart=1,
uniprotEnd=467,
uniprotSequence='MTMLLDGGPQFPGLGVGSFGAPRHHEMPNREPAGMGLNPFGDSTHAAAAAAAAAAFKLSPAAAHDLSSGQSSAFTPQGSGYANALGHHHHHHHHHHHTSQVPSYGGAASAAFNSTREFLFRQRSSGLSEAASGGGQHGLFAGSASSLHAPAGIPEPPSYLLFPGLHEQGAGHPSPTGHVDNNQVHLGLRGELFGRADPYRPVASPRTDPYAAGAQFPNYSPMNMNMGVNVAAHHGPGAFFRYMRQPIKQELSCKWIDEAQLSRPKKSCDRTFSTMHELVTHVTMEHVGGPEQNNHVCYWEECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDKPYICKVCDKSYTHPSSLRKHMKVHESQGSDSSPAASSGYESSTPPAIASANSKDTTKTPSAVQTSTSHNPGLPPNFNEWYV',
modelCreatedDate='2022-06-01',
latestVersion=4,
allVersions=[1, 2, 3, 4],
bcifUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.bcif',
cifUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.cif',
pdbUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.pdb',
paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v4.png',
paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v4.json',
amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-aa-substitutions.csv',
amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg19.csv',
amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg38.csv',
isReviewed=True,
isReferenceProteome=True),
pdb_file=PosixPath('alphafold_files/AF-O60481-F1-model_v4.pdb'),
pae_file=None,
bcif_file=None,
cif_file=None,
pae_image_file=None,
pae_doc_file=None,
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None)]
Download more cif and peaDoc with async
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summaries2 = [s async for s in fetch_many_async(["P50613"], save_dir, what={"cif", "paeDoc"})]
pprint(summaries2)
summaries2 = [s async for s in fetch_many_async(["P50613"], save_dir, what={"cif", "paeDoc"})]
pprint(summaries2)
Fetching Alphafold summaries: 100%|██████████| 1/1 [00:00<00:00, 4.87it/s] Downloading AlphaFold files: 100%|██████████| 2/2 [00:00<00:00, 12520.31it/s]
[AlphaFoldEntry(uniprot_acc='P50613',
summary=EntrySummary(entryId='AF-P50613-F1',
gene='CDK7',
sequenceChecksum='0A94BFA7DD416CEB',
sequenceVersionDate='1996-10-01',
uniprotAccession='P50613',
uniprotId='CDK7_HUMAN',
uniprotDescription='Cyclin-dependent '
'kinase 7',
taxId=9606,
organismScientificName='Homo sapiens',
uniprotStart=1,
uniprotEnd=346,
uniprotSequence='MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF',
modelCreatedDate='2022-06-01',
latestVersion=4,
allVersions=[1, 2, 3, 4],
bcifUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.bcif',
cifUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.cif',
pdbUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.pdb',
paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v4.png',
paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v4.json',
amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-aa-substitutions.csv',
amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg19.csv',
amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg38.csv',
isReviewed=True,
isReferenceProteome=True),
pdb_file=None,
pae_file=None,
bcif_file=None,
cif_file=PosixPath('alphafold_files/AF-P50613-F1-model_v4.cif'),
pae_image_file=None,
pae_doc_file=PosixPath('alphafold_files/AF-P50613-F1-predicted_aligned_error_v4.json'),
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None)]
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!ls -sh {save_dir}
!ls -sh {save_dir}
total 1.3M 392K AF-A1YPR0-F1-model_v4.pdb 292K AF-O60481-F1-model_v4.pdb 320K AF-P50613-F1-model_v4.cif 280K AF-P50613-F1-predicted_aligned_error_v4.json
Apply density filter¶
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from protein_detective.alphafold.density import filter_out_low_confidence_residues, find_high_confidence_residues
from protein_detective.alphafold.density import filter_out_low_confidence_residues, find_high_confidence_residues
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pdb_file = summaries[0].pdb_file
if pdb_file is None:
raise ValueError("Summary has not been downloaded yet.") # noqa: EM101, TRY003
residues = set(find_high_confidence_residues(pdb_file, 70))
len(residues)
pdb_file = summaries[0].pdb_file
if pdb_file is None:
raise ValueError("Summary has not been downloaded yet.") # noqa: EM101, TRY003
residues = set(find_high_confidence_residues(pdb_file, 70))
len(residues)
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214
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out_dir = Path("density_filtered")
out_dir.mkdir(exist_ok=True, parents=True)
out_file = out_dir / pdb_file.name
out_file
out_dir = Path("density_filtered")
out_dir.mkdir(exist_ok=True, parents=True)
out_file = out_dir / pdb_file.name
out_file
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PosixPath('density_filtered/AF-A1YPR0-F1-model_v4.pdb')
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filter_out_low_confidence_residues(pdb_file, residues, out_file)
filter_out_low_confidence_residues(pdb_file, residues, out_file)
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!ls -sh {pdb_file} {out_file}
!ls -sh {pdb_file} {out_file}
392K alphafold_files/AF-A1YPR0-F1-model_v4.pdb 148K density_filtered/AF-A1YPR0-F1-model_v4.pdb
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residues50 = set(find_high_confidence_residues(pdb_file, 50))
len(residues50)
residues50 = set(find_high_confidence_residues(pdb_file, 50))
len(residues50)
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275
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residues90 = set(find_high_confidence_residues(pdb_file, 90))
len(residues90)
residues90 = set(find_high_confidence_residues(pdb_file, 90))
len(residues90)
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22
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filter_out_low_confidence_residues(pdb_file, residues90, out_file.with_suffix(".90.pdb"))
filter_out_low_confidence_residues(pdb_file, residues90, out_file.with_suffix(".90.pdb"))
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!ls -sh {pdb_file} {out_file} {out_file.with_suffix(".90.pdb")}
!ls -sh {pdb_file} {out_file} {out_file.with_suffix(".90.pdb")}
392K alphafold_files/AF-A1YPR0-F1-model_v4.pdb 24K density_filtered/AF-A1YPR0-F1-model_v4.90.pdb 148K density_filtered/AF-A1YPR0-F1-model_v4.pdb
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