Creating Datasets from the PDB¶
Graphein provides a utility for curating and splitting datasets from the RCSB PDB.
Initialising a PDBManager will download PDB Metadata which we can use to make complex selections of protein structures.
[1]:
!pip install graphein
!pip install torch_geometric
from rich import inspect
from graphein.ml.datasets import PDBManager
manager = PDBManager(root_dir=".")
inspect(manager, methods=True)
[03/30/23 20:26:33] WARNING To use the Graphein submodule embeddings.py:44 graphein.protein.features.sequence.embeddings, you need to install: biovec biovec cannot be installed via conda Alternatively, you can install graphein with the extras: pip install graphein[extras]
[03/30/23 20:26:40] INFO Found 3749 PDB files unavailable for download. pdb_data.py:527
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'7scc': False, '7sfd': False, '7sfr': False, '7sn4': False, '7sn9': False, '7soe': False, '7sof': False, '7som': False, '7sp4': False, '7spb': False, '7spc': False, '7spi': False, '7spj': False, '7spk': False, '7spu': False, '7sqc': False, '7sqd': False, '7sqf': False, '7sqh': False, '7sqq': False, '7sqt': False, '7ss9': False, '7ssd': False, '7ssh': False, '7ssl': False, '7ssn': False, '7sso': False, '7ssw': False, '7st2': False, '7st3': False, '7st6': False, '7st7': False, '7stg': False, '7su4': False, '7su7': False, '7suk': False, '7sxn': False, '7sxr': False, '7sxx': False, '7sxz': False, '7sy1': False, '7sy7': False, '7t0w': False, '7t0z': False, '7t1w': False, '7t1x': False, '7t3p': False, '7t3q': False, '7t3r': False, '7t3t': False, '7t64': False, '7t65': False, '7t66': False, '7t68': False, '7t6w': False, '7t73': False, '7t74': False, '7t75': False, '7t76': False, '7t77': False, '7t7c': False, '7t81': False, '7t8n': False, '7t8o': False, '7t8v': False, '7t9a': False, '7t9b': False, '7t9e': False, '7tau': False, '7tbi': False, '7tbj': False, '7tbk': False, '7tbl': False, '7tbm': False, '7tcv': False, '7td9': False, '7tdg': False, '7tdh': False, '7tdi': False, '7tdj': False, '7tdk': False, '7tdv': False, '7tdz': False, '7tei': False, '7ten': False, '7tf6': False, '7tf7': False, '7tfa': False, '7tfb': False, '7tfc': False, '7tfd': False, '7tfo': False, '7tgh': False, '7thr': False, '7ti4': False, '7ti5': False, '7tjs': False, '7tjt': False, '7tjv': False, '7tjy': False, '7tk0': False, '7tk3': False, '7tk6': False, '7tkm': False, '7tkq': False, '7tms': False, '7tmt': False, '7tnb': False, '7tnq': False, '7tns': False, '7tnt': False, '7tok': False, '7too': False, '7top': False, '7toq': False, '7tor': False, '7tos': False, '7tr6': False, '7tr8': False, '7tr9': False, '7tra': False, '7tw2': False, '7tzc': False, '7u05': False, '7u06': False, '7u0h': False, '7u0l': False, '7u0p': False, '7u0q': False, '7u1i': False, '7u1j': False, '7u2h': False, '7u2i': False, '7u2j': False, '7u4p': False, '7u4t': False, '7u6f': False, '7u71': False, '7u8c': False, '7u8o': False, '7u8p': False, '7u8q': False, '7u8r': False, '7u94': False, '7u95': False, '7u96': False, '7u97': False, '7u9q': False, '7u9r': False, '7u9t': False, '7u9x': False, '7u9z': False, '7ua1': False, '7ua3': False, '7ua4': False, '7ua5': False, '7ua9': False, '7uc3': False, '7ucj': False, '7uck': False, '7ud4': False, '7ueb': False, '7ug6': False, '7ug7': False, '7uhz': False, '7ui0': False, '7ui9': False, '7uif': False, '7uig': False, '7uio': False, '7uli': False, '7ums': False, '7umt': False, '7un1': False, '7unc': False, '7und': False, '7une': False, '7unf': False, '7ung': False, '7unr': False, '7unu': False, '7unv': False, '7unw': False, '7uom': False, '7uoo': False, '7uph': False, '7uqb': False, '7uqz': False, '7usa': False, '7uti': False, '7utl': False, '7uvl': False, '7uw9': False, '7uwa': False, '7uwb': False, '7uwc': False, '7uwd': False, '7uxh': False, '7uxx': False, '7uxz': False, '7v08': False, '7v0k': False, '7v0t': False, '7v3u': False, '7v3v': False, '7v7h': False, '7v7i': False, '7v7j': False, '7v93': False, '7va9': False, '7vai': False, '7vaj': False, '7vak': False, '7val': False, '7vam': False, '7van': False, '7vao': False, '7vap': False, '7vaq': False, '7var': False, '7vas': False, '7vat': False, '7vau': False, '7vav': False, '7vaw': False, '7vax': False, '7vay': False, '7vb0': False, '7vb9': False, '7vba': False, '7vbb': False, '7vbc': False, '7vci': False, '7vd5': False, '7vd6': False, '7vea': False, '7vml': False, '7vmm': False, '7vmn': False, '7vmo': False, '7vmp': False, '7vmq': False, '7vmr': False, '7vms': False, '7vop': False, '7vor': False, '7vot': False, '7vrt': False, '7vs5': False, '7vu9': False, '7vub': False, '7vul': False, '7vum': False, '7vw7': False, '7vwy': False, '7vy2': False, '7w1c': False, '7w1d': False, '7w1e': False, '7w1y': False, '7w37': False, '7w38': False, '7w39': False, '7w3a': False, '7w3b': False, '7w3c': False, '7w3f': False, '7w3g': False, '7w3h': False, '7w3i': False, '7w3j': False, '7w3k': False, '7w3m': False, '7w5b': False, '7w5z': False, '7w85': False, '7w8g': False, '7wfd': False, '7wfe': False, '7wg5': False, '7wjw': False, '7wns': False, '7wot': False, '7wpr': False, '7wps': False, '7wqo': False, '7wqt': False, '7wtl': False, '7wtm': False, '7wtn': False, '7wto': False, '7wtp': False, '7wtq': False, '7wtr': False, '7wvh': False, '7wz8': False, '7x2g': False, '7x37': False, '7x38': False, '7x3f': False, '7x4k': False, '7x5a': False, '7x5t': False, '7x7q': False, '7xi9': False, '7xib': False, '7xm1': False, '7xn7': False, '7xse': False, '7xsx': False, '7xsz': False, '7xt7': False, '7xtd': False, '7xti': False, '7y4l': False, '7y5e': False, '7y6s': False, '7y7a': False, '7ycx': False, '7yfz': False, '7yla': False, '7yvq': False, '7ywt': False, '7yyp': False, '7yzh': False, '7yzs': False, '7z0n': False, '7z0p': False, '7z13': False, '7z1d': False, '7z1e': False, '7z1l': False, '7z1m': False, '7z1o': False, '7z1r': False, '7z34': False, '7z37': False, '7z3a': False, '7z3k': False, '7z3l': False, '7z3y': False, '7z43': False, '7z49': False, '7z4b': False, '7z4o': False, '7z55': False, '7z56': False, '7z5d': False, '7z5e': False, '7z5f': False, '7z5o': False, '7z5s': False, '7z5t': False, '7z62': False, '7z63': False, '7z66': False, '7z6t': False, '7z89': False, '7z8a': False, '7z8f': False, '7z9a': False, '7z9b': False, '7z9h': False, '7z9i': False, '7z9j': False, '7z9n': False, '7z9o': False, '7z9s': False, '7z9u': False, '7z9w': False, '7z9y': False, '7za6': False, '7za7': False, '7za8': False, '7za9': False, '7zaa': False, '7zab': False, '7zac': False, '7zad': False, '7zae': False, '7zaf': False, '7zaj': False, '7zal': False, '7zam': False, '7zar': False, '7zat': False, '7zaz': False, '7zb2': False, '7zc0': False, '7ze0': False, '7ze7': False, '7ze9': False, '7zen': False, '7zfn': False, '7zfo': False, '7zfs': False, '7zft': False, '7zfu': False, '7zfw': False, '7zfy': False, '7zfz': False, '7zg1': False, '7zg2': False, '7zg8': False, '7zgx': False, '7zgy': False, '7zhj': False, '7zil': False, '7zim': False, '7zin': False, '7zio': False, '7zip': False, '7ziq': False, '7zjw': False, '7zjx': False, '7zn2': False, '7zn4': False, '7zpq': False, '7zq9': False, '7zqb': False, '7zqc': False, '7zqd': False, '7zqn': False, '7zqo': False, '7zra': False, '7zrs': False, '7zs5': False, '7zs6': False, '7zts': False, '7zuf': False, '7zuh': False, '7zui': False, '7zuj': False, '7zuk': False, '7zul': False, '7zus': False, '7zuw': False, '7zux': False, '7zw0': False, '7zwd': False, '7zx0': False, '7zx1': False, '7zx7': False, '7zx8': False, '8a1d': False, '8a1s': False, '8a22': False, '8a2l': False, '8a2m': False, '8a3d': False, '8a3k': False, '8a47': False, '8a5n': False, '8a60': False, '8a9a': False, '8aa5': False, '8aaf': False, '8agb': False, '8agh': False, '8agk': False, '8ago': False, '8agt': False, '8agu': False, '8agv': False, '8agw': False, '8agx': False, '8agz': False, '8ah0': False, '8ah1': False, '8aij': False, '8aiy': False, '8aj4': False, '8aj5': False, '8akn': False, '8alp': False, '8am9': False, '8amt': False, '8anx': False, '8aoz': False, '8ap0': False, '8ap6': False, '8apa': False, '8apb': False, '8apc': False, '8apd': False, '8ape': False, '8apf': False, '8apg': False, '8aph': False, '8apj': False, '8apk': False, '8apn': False, '8ash': False, '8ask': False, '8atj': False, '8atm': False, '8ato': False, '8atu': False, '8atx': False, '8au1': False, '8auk': False, '8auw': False, '8axk': False, '8axl': False, '8axn': False, '8aye': False, '8b0b': False, '8b0c': False, '8b0d': False, '8b0e': False, '8b0f': False, '8b0g': False, '8b0h': False, '8b0x': False, '8b2a': False, '8b2b': False, '8b2c': False, '8b4n': False, '8b5g': False, '8b5h': False, '8b5i': False, '8b5j': False, '8b5l': False, '8b6c': False, '8b7l': False, '8b7o': False, '8b7y': False, '8bac': False, '8bfl': False, '8bfp': False, '8bip': False, '8bjq': False, '8bov': False, '8boy': False, '8bp2': False, '8bpx': False, '8bq5': False, '8bqd': False, '8bqx': False, '8br8': False, '8brm': False, '8bsi': False, '8bsj': False, '8btd': False, '8btr': False, '8bxu': False, '8bxv': False, '8bxw': False, '8bxx': False, '8c5c': False, '8cen': False, '8ceo': False, '8ci0': False, '8crx': False, '8cs9': False, '8csl': False, '8csy': False, '8cue': False, '8cvj': False, '8cvk': False, '8cvl': False, '8cvt': False, '8cw4': False, '8cwm': False, '8cxm': False, '8cxp': False, '8d3c': False, '8d3d': False, '8d6x': False, '8d6y': False, '8d9t': False, '8d9u': False, '8d9v': False, '8dbp': False, '8dbq': False, '8dbr': False, '8dbt': False, '8dbu': False, '8dbv': False, '8dbw': False, '8dd3': False, '8de6': False, '8dli': False, '8dlt': False, '8dlu': False, '8dlx': False, '8dlz': False, '8dp8': False, '8dp9': False, '8dpa': False, '8dv6': False, '8dvd': False, '8dwb': False, '8e2d': False, '8e2e': False, '8e2i': False, '8e2k': False, '8e3j': False, '8e3p': False, '8e4i': False, '8e4k': False, '8e4z': False, '8e52': False, '8e53': False, '8e54': False, '8e5u': False, '8e6g': False, '8e73': False, '8eaf': False, '8eag': False, '8eah': False, '8eai': False, '8eaj': False, '8eak': False, '8eal': False, '8eam': False, '8eaq': False, '8ecw': False, '8ed0': False, '8edk': False, '8edx': False, '8eey': False, '8egv': False, '8ehp': False, '8eid': False, '8eiu': False, '8ej4': False, '8ekb': False, '8ekc': False, '8ekf': False, '8ekn': False, '8ele': False, '8emy': False, '8en1': False, '8en4': False, '8en5': False, '8en6': False, '8ep2': False, '8ep9': False, '8epj': False, '8epo': False, '8epr': False, '8eq4': False, '8eq7': False, '8eq9': False, '8eqd': False, '8eqe': False, '8eqx': False, '8er4': False, '8esq': False, '8esr': False, '8eth': False, '8etl': False, '8eto': False, '8eu8': False, '8eud': False, '8eug': False, '8eui': False, '8eur': False, '8eut': False, '8eux': False, '8fbd': False, '8fbf': False, '8fbl': False, '8fjk': False, '8fjl': False, '8fnw': False, '8fq4': False, '8fv5': False, '8fwi': False, '8g08': False, '8g09': False, '8g0a': False, '8g0d': False, '8g0e': False, '8g5e': False, '8gms': False, '8gpu': False, '8gwa': False, '8gxq': False, '8gxs': False, '8gxu': False, '8gxw': False, '8gxx': False, '8gxy': False, '8gxz': False, '8h2i': False, '8hdr': False, '8hr7': False, '8ika': False}
╭────────────────────────────── <class 'graphein.ml.datasets.pdb_data.PDBManager'> ───────────────────────────────╮ │ A utility for creating selections of experimental PDB structures. │ │ │ │ ╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ │ │ <graphein.ml.datasets.pdb_data.PDBManager object at 0x7f63a02e5190> │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ df = id pdb chain length molecule_type \ │ │ 0 100d_A 100d A 10 na │ │ 1 100d_B 100d B 10 na │ │ 2 101d_A 101d A 12 na │ │ 3 101d_B 101d B 12 na │ │ 4 101m_A 101m A 154 protein │ │ ... ... ... ... ... ... │ │ 780157 9xia_A 9xia A 388 protein │ │ 780158 9xim_A 9xim A 393 protein │ │ 780159 9xim_B 9xim B 393 protein │ │ 780160 9xim_C 9xim C 393 protein │ │ 780161 9xim_D 9xim D 393 protein │ │ │ │ name \ │ │ 0 DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... │ │ 1 DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... │ │ 2 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... │ │ 3 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... │ │ 4 MYOGLOBIN │ │ ... ... │ │ 780157 XYLOSE ISOMERASE │ │ 780158 D-XYLOSE ISOMERASE │ │ 780159 D-XYLOSE ISOMERASE │ │ 780160 D-XYLOSE ISOMERASE │ │ 780161 D-XYLOSE ISOMERASE │ │ │ │ sequence split │ │ n_chains \ │ │ 0 CCGGCGCCGG N/A │ │ 2 │ │ 1 CCGGCGCCGG N/A │ │ 2 │ │ 2 CGCGAATTCGCG N/A │ │ 2 │ │ 3 CGCGAATTCGCG N/A │ │ 2 │ │ 4 MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR... N/A │ │ 1 │ │ ... ... ... │ │ ... │ │ 780157 MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVQRLAEL... N/A │ │ 1 │ │ 780158 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780159 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780160 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780161 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ │ │ ligands source resolution \ │ │ 0 [SPM] 1.90 │ │ 1 [SPM] 1.90 │ │ 2 [CBR, MG, NT] 2.25 │ │ 3 [CBR, MG, NT] 2.25 │ │ 4 [HEM, NBN, SO4] Physeter catodon 2.07 │ │ ... ... ... ... │ │ 780157 [DFR, MN] Streptomyces rubiginosus 1.90 │ │ 780158 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780159 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780160 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780161 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ │ │ deposition_date experiment_type pdb_file_available │ │ 0 1994-12-05 diffraction True │ │ 1 1994-12-05 diffraction True │ │ 2 1994-12-14 diffraction True │ │ 3 1994-12-14 diffraction True │ │ 4 1997-12-13 diffraction True │ │ ... ... ... ... │ │ 780157 1990-10-11 diffraction True │ │ 780158 1992-04-03 diffraction True │ │ 780159 1992-04-03 diffraction True │ │ 780160 1992-04-03 diffraction True │ │ 780161 1992-04-03 diffraction True │ │ │ │ [780162 rows x 15 columns] │ │ ligand_map_filename = 'cc-to-pdb.tdd' │ │ ligand_map_url = 'http://ligand-expo.rcsb.org/dictionaries/cc-to-pdb.tdd' │ │ list_columns = ['ligands'] │ │ pdb_availability_filename = 'pdb_bundle_index.txt' │ │ pdb_availability_url = 'https://files.wwpdb.org/pub/pdb/compatible/pdb_bundle/pdb_bundle_ind… │ │ pdb_deposition_date_filename = 'entries.idx' │ │ pdb_deposition_date_url = 'https://files.wwpdb.org/pub/pdb/derived_data/index/entries.idx' │ │ pdb_dir = PosixPath('pdb') │ │ pdb_entry_type_filename = 'pdb_entry_type.txt' │ │ pdb_entry_type_url = 'https://files.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt' │ │ pdb_seqres_archive_filename = 'pdb_seqres.txt.gz' │ │ pdb_seqres_filename = 'pdb_seqres.txt' │ │ pdb_sequences_url = 'https://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz' │ │ resolution_filename = 'resolu.idx' │ │ resolution_url = 'https://files.wwpdb.org/pub/pdb/derived_data/index/resolu.idx' │ │ root_dir = PosixPath('.') │ │ source = id pdb chain length molecule_type \ │ │ 0 100d_A 100d A 10 na │ │ 1 100d_B 100d B 10 na │ │ 2 101d_A 101d A 12 na │ │ 3 101d_B 101d B 12 na │ │ 4 101m_A 101m A 154 protein │ │ ... ... ... ... ... ... │ │ 780157 9xia_A 9xia A 388 protein │ │ 780158 9xim_A 9xim A 393 protein │ │ 780159 9xim_B 9xim B 393 protein │ │ 780160 9xim_C 9xim C 393 protein │ │ 780161 9xim_D 9xim D 393 protein │ │ │ │ name \ │ │ 0 DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... │ │ 1 DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... │ │ 2 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... │ │ 3 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... │ │ 4 MYOGLOBIN │ │ ... ... │ │ 780157 XYLOSE ISOMERASE │ │ 780158 D-XYLOSE ISOMERASE │ │ 780159 D-XYLOSE ISOMERASE │ │ 780160 D-XYLOSE ISOMERASE │ │ 780161 D-XYLOSE ISOMERASE │ │ │ │ sequence split │ │ n_chains \ │ │ 0 CCGGCGCCGG N/A │ │ 2 │ │ 1 CCGGCGCCGG N/A │ │ 2 │ │ 2 CGCGAATTCGCG N/A │ │ 2 │ │ 3 CGCGAATTCGCG N/A │ │ 2 │ │ 4 MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR... N/A │ │ 1 │ │ ... ... ... │ │ ... │ │ 780157 MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVQRLAEL... N/A │ │ 1 │ │ 780158 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780159 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780160 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ 780161 SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... N/A │ │ 4 │ │ │ │ ligands source resolution \ │ │ 0 [SPM] 1.90 │ │ 1 [SPM] 1.90 │ │ 2 [CBR, MG, NT] 2.25 │ │ 3 [CBR, MG, NT] 2.25 │ │ 4 [HEM, NBN, SO4] Physeter catodon 2.07 │ │ ... ... ... ... │ │ 780157 [DFR, MN] Streptomyces rubiginosus 1.90 │ │ 780158 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780159 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780160 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ 780161 [MN, XLS] Actinoplanes missouriensis 2.40 │ │ │ │ deposition_date experiment_type pdb_file_available │ │ 0 1994-12-05 diffraction True │ │ 1 1994-12-05 diffraction True │ │ 2 1994-12-14 diffraction True │ │ 3 1994-12-14 diffraction True │ │ 4 1997-12-13 diffraction True │ │ ... ... ... ... │ │ 780157 1990-10-11 diffraction True │ │ 780158 1992-04-03 diffraction True │ │ 780159 1992-04-03 diffraction True │ │ 780160 1992-04-03 diffraction True │ │ 780161 1992-04-03 diffraction True │ │ │ │ [780162 rows x 15 columns] │ │ source_map_filename = 'source.idx' │ │ source_map_url = 'https://files.wwpdb.org/pub/pdb/derived_data/index/source.idx' │ │ splits_provided = False │ │ cluster = def cluster(min_seq_id: float = 0.3, coverage: float = 0.8, update: │ │ bool = False, fasta_fname: Optional[str] = None, cluster_fname: │ │ Optional[str] = None, overwrite: bool = False) -> │ │ Union[pandas.core.frame.DataFrame, Dict[str, │ │ pandas.core.frame.DataFrame]]: Cluster sequences in selection using │ │ MMseqs2. │ │ compare_length = def compare_length(length: int, comparison: str = 'equal', │ │ compare_pdb_groups: bool = False, splits: Optional[List[str]] = None, │ │ update: bool = False): Select molecules with a given length. │ │ download_metadata = def download_metadata(): Download all PDB metadata. │ │ download_pdbs = def download_pdbs(out_dir='.', format='pdb', splits: │ │ Optional[List[str]] = None, overwrite: bool = False, max_workers: int │ │ = 8, chunksize: int = 32): Download PDB files in the current │ │ selection. │ │ experiment_type = def experiment_type(type: str = 'diffraction', splits: │ │ Optional[List[str]] = None, update: bool = False) -> │ │ pandas.core.frame.DataFrame: Select molecules by experiment type. │ │ [`diffraction`, `NMR`, `EM`, `other`] │ │ export_pdbs = def export_pdbs(pdb_dir: str, splits: Optional[List[str]] = None, │ │ max_num_chains_per_pdb_code: int = 1, force: bool = False): Write the │ │ selection as a collection of PDB files. │ │ filter_by_deposition_date = def filter_by_deposition_date(max_deposition_date: numpy.datetime64, │ │ update: bool = False) -> Union[pandas.core.frame.DataFrame, Dict[str, │ │ pandas.core.frame.DataFrame]]: Select molecules deposited on or before │ │ a given date. │ │ from_fasta = def from_fasta(ids: str, filename: str, splits: Optional[List[str]] = │ │ None) -> pandas.core.frame.DataFrame: Create a selection from a FASTA │ │ file. │ │ get_best_resolution = def get_best_resolution(splits: Optional[List[str]] = None) -> float: │ │ Return the best resolution in the dataset. │ │ get_experiment_types = def get_experiment_types(splits: Optional[List[str]] = None) -> │ │ List[str]: Return list of different experiment types in the dataset. │ │ get_longest_chain = def get_longest_chain(splits: Optional[List[str]] = None) -> int: │ │ Return the length of the longest chain in the dataset. │ │ get_molecule_names = def get_molecule_names(splits: Optional[List[str]] = None) -> │ │ List[str]: Return list of molecule names in the dataset. │ │ get_molecule_types = def get_molecule_types(splits: Optional[List[str]] = None) -> │ │ List[str]: Return list of different molecule types in the dataset. │ │ get_num_chains = def get_num_chains(splits: Optional[List[str]] = None) -> int: Return │ │ the number of chains in the dataset. │ │ get_num_unique_pdbs = def get_num_unique_pdbs(splits: Optional[List[str]] = None) -> int: │ │ Return the number of unique PDB IDs in the dataset. │ │ get_shortest_chain = def get_shortest_chain(splits: Optional[List[str]] = None) -> int: │ │ Return the length of the shortest chain in the dataset. │ │ get_splits = def get_splits(splits: Optional[List[str]] = None, df_splits: │ │ Optional[Dict[str, pandas.core.frame.DataFrame]] = None, source: bool │ │ = False) -> pandas.core.frame.DataFrame: Return DataFrame entries │ │ belonging to the splits given. │ │ get_unavailable_pdb_files = def get_unavailable_pdb_files(splits: Optional[List[str]] = None) -> │ │ List[str]: Returns a list of PDB files unavailable for download. │ │ get_unique_pdbs = def get_unique_pdbs(splits: Optional[List[str]] = None) -> List[str]: │ │ Return a list of unique PDB IDs in the dataset. │ │ get_worst_resolution = def get_worst_resolution(splits: Optional[List[str]] = None) -> float: │ │ Return the worst resolution in the dataset. │ │ has_ligand = def has_ligand(ligand: str, splits: Optional[List[str]] = None, │ │ update: bool = False) -> pandas.core.frame.DataFrame: Select molecules │ │ that contain a given ligand. │ │ has_ligands = def has_ligands(ligands: List[str], splits: Optional[List[str]] = │ │ None, inverse: bool = False, update: bool = False): Select molecules │ │ that contain all ligands in the provided list. │ │ length_equal_to = def length_equal_to(length: int, splits: Optional[List[str]] = None, │ │ update: bool = False) -> pandas.core.frame.DataFrame: Select molecules │ │ equal to a given length. │ │ length_longer_than = def length_longer_than(length: int, splits: Optional[List[str]] = │ │ None, update: bool = False) -> pandas.core.frame.DataFrame: Select │ │ molecules longer than a given length. │ │ length_shorter_than = def length_shorter_than(length: int, splits: Optional[List[str]] = │ │ None, update: bool = False) -> pandas.core.frame.DataFrame: Select │ │ molecules shorter than a given length. │ │ merge_df_splits = def merge_df_splits(first_df_split: pandas.core.frame.DataFrame, │ │ second_df_split: pandas.core.frame.DataFrame, split: str) -> │ │ pandas.core.frame.DataFrame: Reconcile an existing DataFrame split │ │ with a new split. │ │ merge_pdb_chain_groups = def merge_pdb_chain_groups(group: │ │ pandas.core.groupby.generic.DataFrameGroupBy) -> │ │ pandas.core.frame.DataFrame: Combine groups of chains associated with │ │ the same PDB code. │ │ molecule_type = def molecule_type(type: str = 'protein', splits: Optional[List[str]] = │ │ None, update: bool = False) -> pandas.core.frame.DataFrame: Select │ │ molecules by molecule type. [`protein`, `dna`, `rna`] │ │ oligomeric = def oligomeric(oligomer: int = 1, comparison: str = 'equal', splits: │ │ Optional[List[str]] = None, update: bool = False) -> │ │ pandas.core.frame.DataFrame: │ │ Select molecules with a given oligmeric length. │ │ I.e. ``df.n_chains ==/</> oligomer`` │ │ parse = def parse() -> pandas.core.frame.DataFrame: Parse all PDB sequence │ │ records. │ │ remove_non_standard_alphabet_sequences = def remove_non_standard_alphabet_sequences(splits: Optional[List[str]] │ │ = None, update: bool = False): Remove sequences with non-standard │ │ characters. │ │ remove_unavailable_pdbs = def remove_unavailable_pdbs(splits: Optional[List[str]] = None, │ │ update: bool = False) -> pandas.core.frame.DataFrame: │ │ Removes PDB files that are not available for download from the │ │ selection. │ │ reset = def reset() -> pandas.core.frame.DataFrame: Reset the dataset to the │ │ original DataFrame source. │ │ resolution_better_than_or_equal_to = def resolution_better_than_or_equal_to(resolution: float, splits: │ │ Optional[List[str]] = None, update: bool = False) -> │ │ pandas.core.frame.DataFrame: Select molecules with a resolution better │ │ than or equal to the given value. │ │ resolution_worse_than_or_equal_to = def resolution_worse_than_or_equal_to(resolution: int, splits: │ │ Optional[List[str]] = None, update: bool = False) -> │ │ pandas.core.frame.DataFrame: Select molecules with a resolution worse │ │ than or equal to the given value. │ │ sample = def sample(n: Optional[int] = None, frac: Optional[float] = None, │ │ splits: Optional[List[str]] = None, replace: bool = False, update: │ │ bool = False) -> pandas.core.frame.DataFrame: Sample a subset of the │ │ dataset. │ │ select_pdb_by_criterion = def select_pdb_by_criterion(pdb: biopandas.pdb.pandas_pdb.PandasPdb, │ │ field: str, field_values: List[Any]) -> │ │ biopandas.pdb.pandas_pdb.PandasPdb: Filter a PDB using a field │ │ selection. │ │ split_by_deposition_date = def split_by_deposition_date(df: pandas.core.frame.DataFrame, update: │ │ bool = False) -> Dict[str, pandas.core.frame.DataFrame]: Split │ │ molecules based on their deposition date. │ │ split_clusters = def split_clusters(df: pandas.core.frame.DataFrame, update: bool = │ │ False) -> Dict[str, pandas.core.frame.DataFrame]: Split clusters │ │ derived by MMseqs2. │ │ split_df_into_time_frames = def split_df_into_time_frames(df: pandas.core.frame.DataFrame, splits: │ │ List[str], split_time_frames: List[numpy.datetime64]) -> Dict[str, │ │ pandas.core.frame.DataFrame]: Split the provided DataFrame │ │ sequentially according to given time frames. │ │ split_df_proportionally = def split_df_proportionally(df: pandas.core.frame.DataFrame, splits: │ │ List[str], split_ratios: List[float], assign_leftover_rows_to_split_n: │ │ int = 0, random_state: int = 42) -> Dict[str, │ │ pandas.core.frame.DataFrame]: Split the provided DataFrame iteratively │ │ according to given proportions. │ │ to_chain_sequence_mapping_dict = def to_chain_sequence_mapping_dict(splits: Optional[List[str]]) -> │ │ Dict[str, str]: Return a dictionary of sequences indexed by chains. │ │ to_csv = def to_csv(fname: str, splits: Optional[List[str]] = None): Write the │ │ selection to a CSV file. │ │ to_fasta = def to_fasta(filename: str, splits: Optional[List[str]] = None): Write │ │ the dataset to a FASTA file (indexed by chain id). │ │ write_chains = def write_chains(splits: Optional[List[str]] = None, models: List[int] │ │ = [1], force: bool = False) -> List[pathlib.Path]: │ │ Write chains in current selection to disk. e.g., we create a file │ │ of the form ``4hbb_A.pdb`` for chain ``A`` of PDB file ``4hhb.pdb``. │ │ write_df_pdbs = def write_df_pdbs(pdb_dir: str, df: pandas.core.frame.DataFrame, │ │ out_dir: str = 'collated_pdb', splits: Optional[List[str]] = None, │ │ max_num_chains_per_pdb_code: int = 1): Write the given selection as a │ │ collection of PDB files. │ │ write_out_pdb_chain_groups = def write_out_pdb_chain_groups(df: pandas.core.frame.DataFrame, │ │ pdb_dir: str, out_dir: str, split: str, merge_fn: Callable, │ │ max_num_chains_per_pdb_code: int = 1): │ │ Record groups of PDB codes and associated chains │ │ as collated PDB files. │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
The manager wraps two dataframes:
manager.df- your working selection.manager.source- A clean copy of the original metadata.
[2]:
manager.df
[2]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 100d_A | 100d | A | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 1 | 100d_B | 100d | B | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 2 | 101d_A | 101d | A | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 3 | 101d_B | 101d | B | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 4 | 101m_A | 101m | A | 154 | protein | MYOGLOBIN | MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR... | N/A | 1 | [HEM, NBN, SO4] | Physeter catodon | 2.07 | 1997-12-13 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 780157 | 9xia_A | 9xia | A | 388 | protein | XYLOSE ISOMERASE | MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVQRLAEL... | N/A | 1 | [DFR, MN] | Streptomyces rubiginosus | 1.90 | 1990-10-11 | diffraction | True |
| 780158 | 9xim_A | 9xim | A | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780159 | 9xim_B | 9xim | B | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780160 | 9xim_C | 9xim | C | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780161 | 9xim_D | 9xim | D | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
780162 rows × 15 columns
[3]:
manager.source
[3]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 100d_A | 100d | A | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 1 | 100d_B | 100d | B | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 2 | 101d_A | 101d | A | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 3 | 101d_B | 101d | B | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 4 | 101m_A | 101m | A | 154 | protein | MYOGLOBIN | MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR... | N/A | 1 | [HEM, NBN, SO4] | Physeter catodon | 2.07 | 1997-12-13 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 780157 | 9xia_A | 9xia | A | 388 | protein | XYLOSE ISOMERASE | MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVQRLAEL... | N/A | 1 | [DFR, MN] | Streptomyces rubiginosus | 1.90 | 1990-10-11 | diffraction | True |
| 780158 | 9xim_A | 9xim | A | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780159 | 9xim_B | 9xim | B | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780160 | 9xim_C | 9xim | C | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780161 | 9xim_D | 9xim | D | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
780162 rows × 15 columns
Selection Properties¶
[4]:
print("Num chains: ", manager.get_num_chains())
print("Num unique pdbs: ", manager.get_num_unique_pdbs())
print("Longest chain: ", manager.get_longest_chain())
print("Shortest chain: ", manager.get_shortest_chain())
print("Best Resolution: ", manager.get_best_resolution())
print("Worst Resolution: ", manager.get_worst_resolution())
print("Experiment Types: ", manager.get_experiment_types())
print("Molecule Types: ", manager.get_molecule_types())
Num chains: 780162
Num unique pdbs: 202738
Longest chain: 16181
Shortest chain: 1
Best Resolution: -1.0
Worst Resolution: 70.0
Experiment Types: ['diffraction' 'NMR' 'other' 'EM']
Molecule Types: ['na' 'protein']
Making Selections¶
Selection functions return a pd.DataFrame. All selection functions provide an update: bool argument controlling whether or not manager.df is updated in place:
[5]:
Number of chains: 780162
Hi res structure: 202476
Not modified: 780162
Modified inplace: 202476
If you want to reset the selection:
780162
Here is an example selection:
[7]:
manager.length_shorter_than(6, update=True)
manager.length_longer_than(4, update=True)
manager.molecule_type("protein", update=True)
manager.resolution_better_than_or_equal_to(1.5, update=True)
manager.experiment_type("diffraction", update=True)
manager.remove_non_standard_alphabet_sequences(update=True)
manager.df
[7]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 19383 | 1hhz_D | 1hhz | D | 5 | protein | CELL WALL PEPTIDE | AEKAA | N/A | 6 | [3FG, DAL, DVC, FGA, GHP, MLU, OMY, OMZ, PGR] | 0.99 | 2000-12-29 | diffraction | True | |
| 19384 | 1hhz_E | 1hhz | E | 5 | protein | CELL WALL PEPTIDE | AEKAA | N/A | 6 | [3FG, DAL, DVC, FGA, GHP, MLU, OMY, OMZ, PGR] | 0.99 | 2000-12-29 | diffraction | True | |
| 19385 | 1hhz_F | 1hhz | F | 5 | protein | CELL WALL PEPTIDE | AEKAA | N/A | 6 | [3FG, DAL, DVC, FGA, GHP, MLU, OMY, OMZ, PGR] | 0.99 | 2000-12-29 | diffraction | True | |
| 50598 | 1sha_B | 1sha | B | 5 | protein | PHOSPHOPEPTIDE A | YVPML | N/A | 2 | [PTR] | Rous sarcoma virus | 1.50 | 1992-08-18 | diffraction | True |
| 50810 | 1skg_B | 1skg | B | 5 | protein | VAFRS | VAFRS | N/A | 2 | [MOH, SO4] | Daboia russellii pulchella; SYNTHETIC CONSTRUCT | 1.21 | 2004-03-04 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 653289 | 7kpu_B | 7kpu | B | 5 | protein | bisubstrate analogue (CMC-ACE-SER-GLY-ARG-GLY-... | SGRGK | N/A | 4 | [ACE, BTB, GOL, NH2, SO4, WZG] | Homo sapiens; SYNTHETIC CONSTRUCT | 1.43 | 2020-11-12 | diffraction | True |
| 682420 | 7oju_H | 7oju | H | 5 | protein | MVNAL Peptide | MVNAL | N/A | 2 | [CMC, GOL, P6G] | Chaetomium thermophilum (strain DSM 1495 / CBS... | 1.10 | 2021-05-17 | diffraction | True |
| 694077 | 7pul_P | 7pul | P | 5 | protein | GLY-ALA-GLY-ALA-ALA | GAGAA | N/A | 2 | [CA, MG] | Enterococcus faecalis | 1.40 | 2021-09-30 | diffraction | True |
| 745627 | 7x70_B | 7x70 | B | 5 | protein | peptide | AVKLQ | N/A | 2 | [] | Homo sapiens; SYNTHETIC CONSTRUCT | 1.25 | 2022-03-08 | diffraction | True |
| 755416 | 7z5z_C | 7z5z | C | 5 | protein | UDP-MurNAc-pentapeptide | AECAA | N/A | 3 | [A9Z, DAL, FGA, GOL, MUB, UDP] | Weissella viridescens; SYNTHETIC CONSTRUCT | 1.49 | 2022-03-10 | diffraction | True |
80 rows × 15 columns
Creating train/val/test splits¶
Splits can be created with through a few different strategies:
temporal
sequence similarity (using MMSeqs2)
structural similarity (coming soon)
Multiple types of splitting operations can be composed. For example, one can perform a time-based split after clustering sequences into train/val/test splits without corrupting the sequence-based splits.
Temporal splits¶
We can create train, val and test splits based on deposition time:
[8]:
import numpy as np
splits = ["train", "val", "test"]
pdb_manager = PDBManager(
root_dir=".",
splits=splits,
split_ratios=[0.8, 0.1, 0.1],
split_time_frames=[
np.datetime64("2020-01-01"),
np.datetime64("2021-01-01"),
np.datetime64("2023-03-01"),
],
)
pdb_manager.split_by_deposition_date(df=pdb_manager.df, update=True)
pdb_manager.df_splits["train"]
[03/30/23 20:27:05] INFO Found 3749 PDB files unavailable for download. pdb_data.py:527
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'7qv1': False, '7qv2': False, '7qv3': False, '7qvk': False, '7qvp': False, '7qvr': False, '7qvw': False, '7qw3': False, '7qwh': False, '7qwi': False, '7qwo': False, '7qwq': False, '7qwr': False, '7qws': False, '7qx1': False, '7qxc': False, '7qxd': False, '7qxe': False, '7qxn': False, '7qxp': False, '7qxt': False, '7qxu': False, '7qxw': False, '7qxx': False, '7qy6': False, '7qya': False, '7qyb': False, '7qyh': False, '7qyk': False, '7qyl': False, '7qym': False, '7qyx': False, '7qyy': False, '7qzm': False, '7qzx': False, '7qzy': False, '7qzz': False, '7r00': False, '7r05': False, '7r0p': False, '7r0y': False, '7r1g': False, '7r1n': False, '7r1o': False, '7r1p': False, '7r1q': False, '7r1x': False, '7r2y': False, '7r2z': False, '7r30': False, '7r31': False, '7r32': False, '7r3d': False, '7r3n': False, '7r55': False, '7r5c': False, '7r5j': False, '7r5k': False, '7r5t': False, '7r5x': False, '7r6j': False, '7r7a': False, '7r81': False, '7r8u': False, '7rd1': False, '7rd2': False, '7rev': False, '7rf1': False, '7rf2': False, '7rf3': False, '7rf4': False, '7rf5': False, '7rf6': False, '7rf7': False, '7rf8': False, '7ri8': False, '7rk8': False, '7rk9': False, '7rl0': False, '7rl1': False, '7rl5': False, '7rmc': False, '7rmf': False, '7rmk': False, '7rmo': False, '7rnl': False, '7rnr': False, '7rq8': False, '7rq9': False, '7rqa': False, '7rqb': False, '7rqc': False, '7rqd': False, '7rqe': False, '7rr5': False, '7rro': False, '7rs5': False, '7rs6': False, '7rsx': False, '7rsy': False, '7rsz': False, '7rte': False, '7rti': False, '7rwl': False, '7rwt': False, '7rxy': False, '7ry5': False, '7ryd': False, '7ryf': False, '7ryg': False, '7ryh': False, '7ryj': False, '7ryk': False, '7rz0': False, '7rz2': False, '7s0p': False, '7s0s': False, '7s1g': False, '7s1h': False, '7s1i': False, '7s1j': False, '7s1k': False, '7s1w': False, '7s64': False, '7s78': False, '7s9v': False, '7sa4': False, '7sbq': False, '7sc7': False, '7sc8': False, '7sc9': False, '7sca': False, '7scb': False, '7scc': False, '7sfd': False, '7sfr': False, '7sn4': False, '7sn9': False, '7soe': False, '7sof': False, '7som': False, '7sp4': False, '7spb': False, '7spc': False, '7spi': False, '7spj': False, '7spk': False, '7spu': False, '7sqc': False, '7sqd': False, '7sqf': False, '7sqh': False, '7sqq': False, '7sqt': False, '7ss9': False, '7ssd': False, '7ssh': False, '7ssl': False, '7ssn': False, '7sso': False, '7ssw': False, '7st2': False, '7st3': False, '7st6': False, '7st7': False, '7stg': False, '7su4': False, '7su7': False, '7suk': False, '7sxn': False, '7sxr': False, '7sxx': False, '7sxz': False, '7sy1': False, '7sy7': False, '7t0w': False, '7t0z': False, '7t1w': False, '7t1x': False, '7t3p': False, '7t3q': False, '7t3r': False, '7t3t': False, '7t64': False, '7t65': False, '7t66': False, '7t68': False, '7t6w': False, '7t73': False, '7t74': False, '7t75': False, '7t76': False, '7t77': False, '7t7c': False, '7t81': False, '7t8n': False, '7t8o': False, '7t8v': False, '7t9a': False, '7t9b': False, '7t9e': False, '7tau': False, '7tbi': False, '7tbj': False, '7tbk': False, '7tbl': False, '7tbm': False, '7tcv': False, '7td9': False, '7tdg': False, '7tdh': False, '7tdi': False, '7tdj': False, '7tdk': False, '7tdv': False, '7tdz': False, '7tei': False, '7ten': False, '7tf6': False, '7tf7': False, '7tfa': False, '7tfb': False, '7tfc': False, '7tfd': False, '7tfo': False, '7tgh': False, '7thr': False, '7ti4': False, '7ti5': False, '7tjs': False, '7tjt': False, '7tjv': False, '7tjy': False, '7tk0': False, '7tk3': False, '7tk6': False, '7tkm': False, '7tkq': False, '7tms': False, '7tmt': False, '7tnb': False, '7tnq': False, '7tns': False, '7tnt': False, '7tok': False, '7too': False, '7top': False, '7toq': False, '7tor': False, '7tos': False, '7tr6': False, '7tr8': False, '7tr9': False, '7tra': False, '7tw2': False, '7tzc': False, '7u05': False, '7u06': False, '7u0h': False, '7u0l': False, '7u0p': False, '7u0q': False, '7u1i': False, '7u1j': False, '7u2h': False, '7u2i': False, '7u2j': False, '7u4p': False, '7u4t': False, '7u6f': False, '7u71': False, '7u8c': False, '7u8o': False, '7u8p': False, '7u8q': False, '7u8r': False, '7u94': False, '7u95': False, '7u96': False, '7u97': False, '7u9q': False, '7u9r': False, '7u9t': False, '7u9x': False, '7u9z': False, '7ua1': False, '7ua3': False, '7ua4': False, '7ua5': False, '7ua9': False, '7uc3': False, '7ucj': False, '7uck': False, '7ud4': False, '7ueb': False, '7ug6': False, '7ug7': False, '7uhz': False, '7ui0': False, '7ui9': False, '7uif': False, '7uig': False, '7uio': False, '7uli': False, '7ums': False, '7umt': False, '7un1': False, '7unc': False, '7und': False, '7une': False, '7unf': False, '7ung': False, '7unr': False, '7unu': False, '7unv': False, '7unw': False, '7uom': False, '7uoo': False, '7uph': False, '7uqb': False, '7uqz': False, '7usa': False, '7uti': False, '7utl': False, '7uvl': False, '7uw9': False, '7uwa': False, '7uwb': False, '7uwc': False, '7uwd': False, '7uxh': False, '7uxx': False, '7uxz': False, '7v08': False, '7v0k': False, '7v0t': False, '7v3u': False, '7v3v': False, '7v7h': False, '7v7i': False, '7v7j': False, '7v93': False, '7va9': False, '7vai': False, '7vaj': False, '7vak': False, '7val': False, '7vam': False, '7van': False, '7vao': False, '7vap': False, '7vaq': False, '7var': False, '7vas': False, '7vat': False, '7vau': False, '7vav': False, '7vaw': False, '7vax': False, '7vay': False, '7vb0': False, '7vb9': False, '7vba': False, '7vbb': False, '7vbc': False, '7vci': False, '7vd5': False, '7vd6': False, '7vea': False, '7vml': False, '7vmm': False, '7vmn': False, '7vmo': False, '7vmp': False, '7vmq': False, '7vmr': False, '7vms': False, '7vop': False, '7vor': False, '7vot': False, '7vrt': False, '7vs5': False, '7vu9': False, '7vub': False, '7vul': False, '7vum': False, '7vw7': False, '7vwy': False, '7vy2': False, '7w1c': False, '7w1d': False, '7w1e': False, '7w1y': False, '7w37': False, '7w38': False, '7w39': False, '7w3a': False, '7w3b': False, '7w3c': False, '7w3f': False, '7w3g': False, '7w3h': False, '7w3i': False, '7w3j': False, '7w3k': False, '7w3m': False, '7w5b': False, '7w5z': False, '7w85': False, '7w8g': False, '7wfd': False, '7wfe': False, '7wg5': False, '7wjw': False, '7wns': False, '7wot': False, '7wpr': False, '7wps': False, '7wqo': False, '7wqt': False, '7wtl': False, '7wtm': False, '7wtn': False, '7wto': False, '7wtp': False, '7wtq': False, '7wtr': False, '7wvh': False, '7wz8': False, '7x2g': False, '7x37': False, '7x38': False, '7x3f': False, '7x4k': False, '7x5a': False, '7x5t': False, '7x7q': False, '7xi9': False, '7xib': False, '7xm1': False, '7xn7': False, '7xse': False, '7xsx': False, '7xsz': False, '7xt7': False, '7xtd': False, '7xti': False, '7y4l': False, '7y5e': False, '7y6s': False, '7y7a': False, '7ycx': False, '7yfz': False, '7yla': False, '7yvq': False, '7ywt': False, '7yyp': False, '7yzh': False, '7yzs': False, '7z0n': False, '7z0p': False, '7z13': False, '7z1d': False, '7z1e': False, '7z1l': False, '7z1m': False, '7z1o': False, '7z1r': False, '7z34': False, '7z37': False, '7z3a': False, '7z3k': False, '7z3l': False, '7z3y': False, '7z43': False, '7z49': False, '7z4b': False, '7z4o': False, '7z55': False, '7z56': False, '7z5d': False, '7z5e': False, '7z5f': False, '7z5o': False, '7z5s': False, '7z5t': False, '7z62': False, '7z63': False, '7z66': False, '7z6t': False, '7z89': False, '7z8a': False, '7z8f': False, '7z9a': False, '7z9b': False, '7z9h': False, '7z9i': False, '7z9j': False, '7z9n': False, '7z9o': False, '7z9s': False, '7z9u': False, '7z9w': False, '7z9y': False, '7za6': False, '7za7': False, '7za8': False, '7za9': False, '7zaa': False, '7zab': False, '7zac': False, '7zad': False, '7zae': False, '7zaf': False, '7zaj': False, '7zal': False, '7zam': False, '7zar': False, '7zat': False, '7zaz': False, '7zb2': False, '7zc0': False, '7ze0': False, '7ze7': False, '7ze9': False, '7zen': False, '7zfn': False, '7zfo': False, '7zfs': False, '7zft': False, '7zfu': False, '7zfw': False, '7zfy': False, '7zfz': False, '7zg1': False, '7zg2': False, '7zg8': False, '7zgx': False, '7zgy': False, '7zhj': False, '7zil': False, '7zim': False, '7zin': False, '7zio': False, '7zip': False, '7ziq': False, '7zjw': False, '7zjx': False, '7zn2': False, '7zn4': False, '7zpq': False, '7zq9': False, '7zqb': False, '7zqc': False, '7zqd': False, '7zqn': False, '7zqo': False, '7zra': False, '7zrs': False, '7zs5': False, '7zs6': False, '7zts': False, '7zuf': False, '7zuh': False, '7zui': False, '7zuj': False, '7zuk': False, '7zul': False, '7zus': False, '7zuw': False, '7zux': False, '7zw0': False, '7zwd': False, '7zx0': False, '7zx1': False, '7zx7': False, '7zx8': False, '8a1d': False, '8a1s': False, '8a22': False, '8a2l': False, '8a2m': False, '8a3d': False, '8a3k': False, '8a47': False, '8a5n': False, '8a60': False, '8a9a': False, '8aa5': False, '8aaf': False, '8agb': False, '8agh': False, '8agk': False, '8ago': False, '8agt': False, '8agu': False, '8agv': False, '8agw': False, '8agx': False, '8agz': False, '8ah0': False, '8ah1': False, '8aij': False, '8aiy': False, '8aj4': False, '8aj5': False, '8akn': False, '8alp': False, '8am9': False, '8amt': False, '8anx': False, '8aoz': False, '8ap0': False, '8ap6': False, '8apa': False, '8apb': False, '8apc': False, '8apd': False, '8ape': False, '8apf': False, '8apg': False, '8aph': False, '8apj': False, '8apk': False, '8apn': False, '8ash': False, '8ask': False, '8atj': False, '8atm': False, '8ato': False, '8atu': False, '8atx': False, '8au1': False, '8auk': False, '8auw': False, '8axk': False, '8axl': False, '8axn': False, '8aye': False, '8b0b': False, '8b0c': False, '8b0d': False, '8b0e': False, '8b0f': False, '8b0g': False, '8b0h': False, '8b0x': False, '8b2a': False, '8b2b': False, '8b2c': False, '8b4n': False, '8b5g': False, '8b5h': False, '8b5i': False, '8b5j': False, '8b5l': False, '8b6c': False, '8b7l': False, '8b7o': False, '8b7y': False, '8bac': False, '8bfl': False, '8bfp': False, '8bip': False, '8bjq': False, '8bov': False, '8boy': False, '8bp2': False, '8bpx': False, '8bq5': False, '8bqd': False, '8bqx': False, '8br8': False, '8brm': False, '8bsi': False, '8bsj': False, '8btd': False, '8btr': False, '8bxu': False, '8bxv': False, '8bxw': False, '8bxx': False, '8c5c': False, '8cen': False, '8ceo': False, '8ci0': False, '8crx': False, '8cs9': False, '8csl': False, '8csy': False, '8cue': False, '8cvj': False, '8cvk': False, '8cvl': False, '8cvt': False, '8cw4': False, '8cwm': False, '8cxm': False, '8cxp': False, '8d3c': False, '8d3d': False, '8d6x': False, '8d6y': False, '8d9t': False, '8d9u': False, '8d9v': False, '8dbp': False, '8dbq': False, '8dbr': False, '8dbt': False, '8dbu': False, '8dbv': False, '8dbw': False, '8dd3': False, '8de6': False, '8dli': False, '8dlt': False, '8dlu': False, '8dlx': False, '8dlz': False, '8dp8': False, '8dp9': False, '8dpa': False, '8dv6': False, '8dvd': False, '8dwb': False, '8e2d': False, '8e2e': False, '8e2i': False, '8e2k': False, '8e3j': False, '8e3p': False, '8e4i': False, '8e4k': False, '8e4z': False, '8e52': False, '8e53': False, '8e54': False, '8e5u': False, '8e6g': False, '8e73': False, '8eaf': False, '8eag': False, '8eah': False, '8eai': False, '8eaj': False, '8eak': False, '8eal': False, '8eam': False, '8eaq': False, '8ecw': False, '8ed0': False, '8edk': False, '8edx': False, '8eey': False, '8egv': False, '8ehp': False, '8eid': False, '8eiu': False, '8ej4': False, '8ekb': False, '8ekc': False, '8ekf': False, '8ekn': False, '8ele': False, '8emy': False, '8en1': False, '8en4': False, '8en5': False, '8en6': False, '8ep2': False, '8ep9': False, '8epj': False, '8epo': False, '8epr': False, '8eq4': False, '8eq7': False, '8eq9': False, '8eqd': False, '8eqe': False, '8eqx': False, '8er4': False, '8esq': False, '8esr': False, '8eth': False, '8etl': False, '8eto': False, '8eu8': False, '8eud': False, '8eug': False, '8eui': False, '8eur': False, '8eut': False, '8eux': False, '8fbd': False, '8fbf': False, '8fbl': False, '8fjk': False, '8fjl': False, '8fnw': False, '8fq4': False, '8fv5': False, '8fwi': False, '8g08': False, '8g09': False, '8g0a': False, '8g0d': False, '8g0e': False, '8g5e': False, '8gms': False, '8gpu': False, '8gwa': False, '8gxq': False, '8gxs': False, '8gxu': False, '8gxw': False, '8gxx': False, '8gxy': False, '8gxz': False, '8h2i': False, '8hdr': False, '8hr7': False, '8ika': False}
INFO Splitting sequences into time frames: 2020-01-01 2021-01-01 pdb_data.py:1391 2023-03-01
[03/30/23 20:27:08] INFO Deposition date-derived dataset splits of sizes: 563693 78973 137323 pdb_data.py:1361
INFO Done splitting sequences pdb_data.py:1395
[8]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 100d_A | 100d | A | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 1 | 100d_B | 100d | B | 10 | na | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP... | CCGGCGCCGG | N/A | 2 | [SPM] | 1.90 | 1994-12-05 | diffraction | True | |
| 2 | 101d_A | 101d | A | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 3 | 101d_B | 101d | B | 12 | na | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*C... | CGCGAATTCGCG | N/A | 2 | [CBR, MG, NT] | 2.25 | 1994-12-14 | diffraction | True | |
| 4 | 101m_A | 101m | A | 154 | protein | MYOGLOBIN | MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR... | N/A | 1 | [HEM, NBN, SO4] | Physeter catodon | 2.07 | 1997-12-13 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 780157 | 9xia_A | 9xia | A | 388 | protein | XYLOSE ISOMERASE | MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVQRLAEL... | N/A | 1 | [DFR, MN] | Streptomyces rubiginosus | 1.90 | 1990-10-11 | diffraction | True |
| 780158 | 9xim_A | 9xim | A | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780159 | 9xim_B | 9xim | B | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780160 | 9xim_C | 9xim | C | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
| 780161 | 9xim_D | 9xim | D | 393 | protein | D-XYLOSE ISOMERASE | SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIG... | N/A | 4 | [MN, XLS] | Actinoplanes missouriensis | 2.40 | 1992-04-03 | diffraction | True |
563693 rows × 15 columns
[9]:
pdb_manager.df_splits["val"]
[9]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 408858 | 5qub_A | 5qub | A | 229 | protein | RadA | MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA... | N/A | 1 | [D48, PO4] | Pyrococcus furiosus | 1.35 | 2020-01-27 | diffraction | True |
| 408859 | 5quc_A | 5quc | A | 229 | protein | RadA | MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA... | N/A | 1 | [D48, PO4] | Pyrococcus furiosus | 1.43 | 2020-01-27 | diffraction | True |
| 408860 | 5qud_A | 5qud | A | 229 | protein | RadA | MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA... | N/A | 1 | [D48, PO4] | Pyrococcus furiosus | 1.30 | 2020-01-27 | diffraction | True |
| 408861 | 5que_A | 5que | A | 229 | protein | RadA | MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA... | N/A | 1 | [D48, PO4] | Pyrococcus furiosus | 1.30 | 2020-01-27 | diffraction | True |
| 408862 | 5quf_A | 5quf | A | 229 | protein | RadA | MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA... | N/A | 1 | [D48, PO4] | Pyrococcus furiosus | 1.35 | 2020-01-27 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 656479 | 7l8t_B | 7l8t | B | 153 | protein | BG505 SOSIP.v5.2 N241/N289 - gp41 | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLR... | N/A | 8 | [BMA, MAN, NAG] | Human immunodeficiency virus 1; Macaca mulatta | 3.70 | 2020-12-31 | EM | True |
| 656480 | 7l8t_D | 7l8t | D | 153 | protein | BG505 SOSIP.v5.2 N241/N289 - gp41 | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLR... | N/A | 8 | [BMA, MAN, NAG] | Human immunodeficiency virus 1; Macaca mulatta | 3.70 | 2020-12-31 | EM | True |
| 656481 | 7l8t_F | 7l8t | F | 153 | protein | BG505 SOSIP.v5.2 N241/N289 - gp41 | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLR... | N/A | 8 | [BMA, MAN, NAG] | Human immunodeficiency virus 1; Macaca mulatta | 3.70 | 2020-12-31 | EM | True |
| 656482 | 7l8t_H | 7l8t | H | 116 | protein | Rh.33311 pAbC-1 - Heavy Chain | XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... | N/A | 8 | [BMA, MAN, NAG] | Human immunodeficiency virus 1; Macaca mulatta | 3.70 | 2020-12-31 | EM | True |
| 656483 | 7l8t_L | 7l8t | L | 102 | protein | Rh.33311 pAbC-1 - Light Chain | XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... | N/A | 8 | [BMA, MAN, NAG] | Human immunodeficiency virus 1; Macaca mulatta | 3.70 | 2020-12-31 | EM | True |
78973 rows × 15 columns
[10]:
pdb_manager.df_splits["test"]
[10]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 340899 | 5bkf_A | 5bkf | A | 364 | protein | Glycine receptor subunit alpha-2 | KDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNV... | N/A | 5 | [NAG] | Aequorea victoria; Homo sapiens | 3.60 | 2021-03-19 | EM | True |
| 340900 | 5bkf_B | 5bkf | B | 364 | protein | Glycine receptor subunit alpha-2 | KDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNV... | N/A | 5 | [NAG] | Aequorea victoria; Homo sapiens | 3.60 | 2021-03-19 | EM | True |
| 340901 | 5bkf_C | 5bkf | C | 364 | protein | Glycine receptor subunit alpha-2 | KDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNV... | N/A | 5 | [NAG] | Aequorea victoria; Homo sapiens | 3.60 | 2021-03-19 | EM | True |
| 340902 | 5bkf_D | 5bkf | D | 364 | protein | Glycine receptor subunit alpha-2 | KDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNV... | N/A | 5 | [NAG] | Aequorea victoria; Homo sapiens | 3.60 | 2021-03-19 | EM | True |
| 340903 | 5bkf_E | 5bkf | E | 702 | protein | Glycine receptor subunit beta,Green fluorescen... | GVAMPGAEDDVVAALEVLFQGPKSSKKGKGKKKQYLCPSQQSAEDL... | N/A | 5 | [NAG] | Aequorea victoria; Homo sapiens | 3.60 | 2021-03-19 | EM | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 779966 | 8ika_Au | 8ika | Au | 265 | protein | Type 1 encapsulin shell protein | MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPV... | N/A | 60 | [] | Mycobacterium tuberculosis (strain ATCC 25618 ... | 2.75 | 2023-02-28 | EM | False |
| 779967 | 8ika_Av | 8ika | Av | 265 | protein | Type 1 encapsulin shell protein | MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPV... | N/A | 60 | [] | Mycobacterium tuberculosis (strain ATCC 25618 ... | 2.75 | 2023-02-28 | EM | False |
| 779968 | 8ika_Aw | 8ika | Aw | 265 | protein | Type 1 encapsulin shell protein | MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPV... | N/A | 60 | [] | Mycobacterium tuberculosis (strain ATCC 25618 ... | 2.75 | 2023-02-28 | EM | False |
| 779969 | 8ika_Ax | 8ika | Ax | 265 | protein | Type 1 encapsulin shell protein | MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPV... | N/A | 60 | [] | Mycobacterium tuberculosis (strain ATCC 25618 ... | 2.75 | 2023-02-28 | EM | False |
| 779970 | 8ika_Ay | 8ika | Ay | 265 | protein | Type 1 encapsulin shell protein | MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPV... | N/A | 60 | [] | Mycobacterium tuberculosis (strain ATCC 25618 ... | 2.75 | 2023-02-28 | EM | False |
137323 rows × 15 columns
We can also perform additional structural filters:
[11]:
pdb_manager.molecule_type(type="protein", update=True)
pdb_manager.experiment_type(type="diffraction", update=True)
pdb_manager.resolution_better_than_or_equal_to(2.0, update=True)
pdb_manager.length_longer_than(40, update=True)
pdb_manager.length_shorter_than(401, update=True)
pdb_manager.has_ligands(["SO4"], update=True) # Must contain an SO4 ligand
pdb_manager.oligomeric(1, update=True) # Get only monomers
print("Number of chains: ", len(pdb_manager.df))
Number of chains: 5547
We also want to restrict ourselves to proteins that contain standard residues & are available to download in PDB format
[12]:
Number of chains: 5461
Sequence Similarity Splits¶
We can cluster sequences by sequence similarity using MMSeqs2:
(install: conda install -c conda-forge -c bioconda mmseqs2)
[13]:
[03/30/23 20:28:24] INFO Overwriting. Removing old cluster file pdb_data.py:1259 pdb_cluster_rep_seq_id_0.3_c_0.8.fasta
INFO Creating clusters... pdb_data.py:1265
INFO Writing current selection (5461 chains) to FASTA... pdb_data.py:1267
INFO Clustering with: mmseqs easy-cluster pdb.fasta pdb_cluster tmp pdb_data.py:1278 --min-seq-id 0.3 -c 0.8 --cov-mode 1
easy-cluster pdb.fasta pdb_cluster tmp --min-seq-id 0.3 -c 0.8 --cov-mode 1
MMseqs Version: 14.7e284
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
Sensitivity 4
k-mer length 0
k-score seq:2147483647,prof:2147483647
Alphabet size aa:21,nucl:5
Max sequence length 65535
Max results per query 20
Split database 0
Split mode 2
Split memory limit 0
Coverage threshold 0.8
Coverage mode 1
Compositional bias 1
Compositional bias 1
Diagonal scoring true
Exact k-mer matching 0
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Minimum diagonal score 15
Selected taxa
Include identical seq. id. false
Spaced k-mers 1
Preload mode 0
Pseudo count a substitution:1.100,context:1.400
Pseudo count b substitution:4.100,context:5.800
Spaced k-mer pattern
Local temporary path
Threads 64
Compressed 0
Verbosity 3
Add backtrace false
Alignment mode 3
Alignment mode 0
Allow wrapped scoring false
E-value threshold 0.001
Seq. id. threshold 0.3
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Max reject 2147483647
Max accept 2147483647
Score bias 0
Realign hits false
Realign score bias -0.2
Realign max seqs 2147483647
Correlation score weight 0
Gap open cost aa:11,nucl:5
Gap extension cost aa:1,nucl:2
Zdrop 40
Rescore mode 0
Remove hits by seq. id. and coverage false
Sort results 0
Cluster mode 0
Max connected component depth 1000
Similarity type 2
Single step clustering false
Cascaded clustering steps 3
Cluster reassign false
Remove temporary files true
Force restart with latest tmp false
MPI runner
k-mers per sequence 21
Scale k-mers per sequence aa:0.000,nucl:0.200
Adjust k-mer length false
Shift hash 67
Include only extendable false
Skip repeating k-mers false
Database type 0
Shuffle input database true
Createdb mode 1
Write lookup file 0
Offset of numeric ids 0
createdb pdb.fasta tmp/2979816542525769739/input --dbtype 0 --shuffle 1 --createdb-mode 1 --write-lookup 0 --id-offset 0 --compressed 0 -v 3
Shuffle database cannot be combined with --createdb-mode 0
We recompute with --shuffle 0
Converting sequences
[
Time for merging to input_h: 0h 0m 0s 0ms
Time for merging to input: 0h 0m 0s 0ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 2ms
Create directory tmp/2979816542525769739/clu_tmp
cluster tmp/2979816542525769739/input tmp/2979816542525769739/clu tmp/2979816542525769739/clu_tmp --max-seqs 20 -c 0.8 --cov-mode 1 --spaced-kmer-mode 1 --alignment-mode 3 -e 0.001 --min-seq-id 0.3 --remove-tmp-files 1
Set cluster sensitivity to -s 5.000000
Set cluster mode GREEDY MEM
Set cluster iterations to 3
linclust tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --alph-size aa:13,nucl:5 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 -k 0 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --rescore-mode 0 --filter-hits 0 --sort-results 0 --remove-tmp-files 1 --force-reuse 0
kmermatcher tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.3 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 64 --compressed 0 -v 3
kmermatcher tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.3 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 64 --compressed 0 -v 3
Database size: 5461 type: Aminoacid
Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X)
Generate k-mers list for 1 split
[=================================================================] 5.46K 0s 7ms
Sort kmer 0h 0m 0s 2ms
Sort by rep. sequence 0h 0m 0s 2ms
Time for fill: 0h 0m 0s 0ms
Time for merging to pref: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 50ms
rescorediagonal tmp/2979816542525769739/input tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 0 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 0.8 -a 0 --cov-mode 1 --min-seq-id 0.5 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 64 --compressed 0 -v 3
[=================================================================] 5.46K 0s 3ms
Time for merging to pref_rescore1: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 126ms
clust tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore1 tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pre_clust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3
Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 10ms
Size of the sequence database: 5461
Size of the alignment database: 5461
Number of clusters: 1679
Writing results 0h 0m 0s 0ms
Time for merging to pre_clust: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 36ms
createsubdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/order_redundancy tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy -v 3 --subdb-mode 1
Time for merging to input_step_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 7ms
createsubdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/order_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter1 -v 3 --subdb-mode 1
Time for merging to pref_filter1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 5ms
filterdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter1 tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter2 --filter-file tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/order_redundancy --threads 64 --compressed 0 -v 3
Filtering using file(s)
[=================================================================] 1.68K 0s 3ms
Time for merging to pref_filter2: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 146ms
rescorediagonal tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter2 tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 1 --wrapped-scoring 0 --filter-hits 1 -e 0.001 -c 0.8 -a 0 --cov-mode 1 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 64 --compressed 0 -v 3
[=================================================================] 1.68K 0s 27ms
Time for merging to pref_rescore2: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 203ms
align tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore2 tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/aln --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 1679 type: Aminoacid
Target database size: 1679 type: Aminoacid
Calculation of alignments
[=================================================================] 1.68K 0s 20ms
Time for merging to aln: 0h 0m 0s 3ms
1788 alignments calculated
1743 sequence pairs passed the thresholds (0.974832 of overall calculated)
1.038118 hits per query sequence
Time for processing: 0h 0m 0s 200ms
clust tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/aln tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/clust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3
Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 23ms
Size of the sequence database: 1679
Size of the alignment database: 1679
Number of clusters: 1619
Writing results 0h 0m 0s 0ms
Time for merging to clust: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 54ms
mergeclusters tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pre_clust tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/clust --threads 64 --compressed 0 -v 3
Clustering step 1
[=================================================================] 1.68K 0s 3ms
Clustering step 2
[=================================================================] 1.62K 0s 38ms
Write merged clustering
[=================================================================] 5.46K 0s 177ms
Time for merging to clu_redundancy: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 206ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter1 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore1 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pre_clust -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/input_step_redundancy_h -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_filter2 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/pref_rescore2 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/aln -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/linclust/4027551054934845650/clust -v 3
Time for processing: 0h 0m 0s 0ms
createsubdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_redundancy tmp/2979816542525769739/input tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy -v 3 --subdb-mode 1
Time for merging to input_step_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 6ms
prefilter tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 1 --comp-bias-corr 0 --comp-bias-corr-scale 1 --diag-score 0 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 0 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 64 --compressed 0 -v 3
Query database size: 1619 type: Aminoacid
Estimated memory consumption: 984M
Target database size: 1619 type: Aminoacid
Index table k-mer threshold: 154 at k-mer size 6
Index table: counting k-mers
[=================================================================] 1.62K 0s 24ms
Index table: Masked residues: 5374
Index table: fill
[=================================================================] 1.62K 0s 12ms
Index statistics
Entries: 168376
DB size: 489 MB
Avg k-mer size: 0.002631
Top 10 k-mers
SGVRHM 56
DLTNFQ 24
SSRNFQ 12
GLPGMT 10
GGDCDS 7
SCGSPL 5
ENYQAM 5
RELFHM 5
GLPGMM 5
GLPGMS 5
Time for index table init: 0h 0m 0s 411ms
Process prefiltering step 1 of 1
k-mer similarity threshold: 154
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 1619
Target db start 1 to 1619
[=================================================================] 1.62K 0s 6ms
2.180235 k-mers per position
111 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
2 sequences passed prefiltering per query sequence
1 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step0: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 720ms
align tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step0 tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 0 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 1619 type: Aminoacid
Target database size: 1619 type: Aminoacid
Calculation of alignments
[=================================================================] 1.62K 0s 36ms
Time for merging to aln_step0: 0h 0m 0s 3ms
3245 alignments calculated
2026 sequence pairs passed the thresholds (0.624345 of overall calculated)
1.251390 hits per query sequence
Time for processing: 0h 0m 0s 159ms
clust tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step0 tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step0 --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3
Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 11ms
Size of the sequence database: 1619
Size of the alignment database: 1619
Number of clusters: 1483
Writing results 0h 0m 0s 0ms
Time for merging to clu_step0: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 31ms
createsubdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step0 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 -v 3 --subdb-mode 1
Time for merging to input_step1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
prefilter tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 3 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 64 --compressed 0 -v 3
Query database size: 1483 type: Aminoacid
Estimated memory consumption: 984M
Target database size: 1483 type: Aminoacid
Index table k-mer threshold: 136 at k-mer size 6
Index table: counting k-mers
[=================================================================] 1.48K 0s 19ms
Index table: Masked residues: 4877
Index table: fill
[=================================================================] 1.48K 0s 8ms
Index statistics
Entries: 300450
DB size: 490 MB
Avg k-mer size: 0.004695
Top 10 k-mers
SSLPSH 55
SGVRHM 51
GVLTLY 24
LGELQS 23
SMGQGR 9
GLPGMT 9
IHDKNI 5
SASPEK 5
ASSPEK 5
ENYQAM 5
Time for index table init: 0h 0m 0s 373ms
Process prefiltering step 1 of 1
k-mer similarity threshold: 136
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 1483
Target db start 1 to 1483
[=================================================================] 1.48K 0s 19ms
24.103790 k-mers per position
219 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
2 sequences passed prefiltering per query sequence
1 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step1: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 717ms
align tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 1483 type: Aminoacid
Target database size: 1483 type: Aminoacid
Calculation of alignments
[=================================================================] 1.48K 0s 20ms
Time for merging to aln_step1: 0h 0m 0s 3ms
3282 alignments calculated
1688 sequence pairs passed the thresholds (0.514321 of overall calculated)
1.138233 hits per query sequence
Time for processing: 0h 0m 0s 102ms
clust tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step1 --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3
Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 50ms
Size of the sequence database: 1483
Size of the alignment database: 1483
Number of clusters: 1396
Writing results 0h 0m 0s 0ms
Time for merging to clu_step1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 68ms
createsubdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 -v 3 --subdb-mode 1
Time for merging to input_step2: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 13ms
prefilter tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 5 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 64 --compressed 0 -v 3
Query database size: 1396 type: Aminoacid
Estimated memory consumption: 983M
Target database size: 1396 type: Aminoacid
Index table k-mer threshold: 118 at k-mer size 6
Index table: counting k-mers
[=================================================================] 1.40K 0s 31ms
Index table: Masked residues: 4780
Index table: fill
[=================================================================] 1.40K 0s 6ms
Index statistics
Entries: 295758
DB size: 489 MB
Avg k-mer size: 0.004621
Top 10 k-mers
SSLPSH 55
SGVRHM 51
SSVLEN 24
GVLTLY 24
LGELQS 23
GLPGMT 9
SASPEK 5
ASSPEK 5
ENYQAM 5
RELFHM 5
Time for index table init: 0h 0m 0s 352ms
Process prefiltering step 1 of 1
k-mer similarity threshold: 118
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 1396
Target db start 1 to 1396
[=================================================================] 1.40K 0s 88ms
181.906698 k-mers per position
395 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
3 sequences passed prefiltering per query sequence
2 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step2: 0h 0m 0s 4ms
Time for processing: 0h 0m 0s 781ms
align tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.3 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 1396 type: Aminoacid
Target database size: 1396 type: Aminoacid
Calculation of alignments
[=================================================================] 1.40K 0s 33ms
Time for merging to aln_step2: 0h 0m 0s 3ms
4453 alignments calculated
1490 sequence pairs passed the thresholds (0.334606 of overall calculated)
1.067335 hits per query sequence
Time for processing: 0h 0m 0s 158ms
clust tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step2 tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step2 --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 64 --compressed 0 -v 3
Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 11ms
Size of the sequence database: 1396
Size of the alignment database: 1396
Number of clusters: 1346
Writing results 0h 0m 0s 0ms
Time for merging to clu_step2: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 64ms
mergeclusters tmp/2979816542525769739/input tmp/2979816542525769739/clu tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_redundancy tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step0 tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step1 tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step2 --threads 64 --compressed 0 -v 3
Clustering step 1
[=================================================================] 1.62K 0s 27ms
Clustering step 2
[=================================================================] 1.48K 0s 64ms
Clustering step 3
[=================================================================] 1.40K 0s 76ms
Clustering step 4
[=================================================================] 1.35K 0s 77ms
Write merged clustering
[=================================================================] 5.46K 0s 224ms
Time for merging to clu: 0h 0m 0s 1ms
Time for processing: 0h 0m 0s 230ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_redundancy -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step_redundancy_h -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step0 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step1 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step1 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step1 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/pref_step2 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/aln_step2 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/clu_step2 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step1_h -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2 -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_tmp/9750242695871741645/input_step2_h -v 3
Time for processing: 0h 0m 0s 0ms
createtsv tmp/2979816542525769739/input tmp/2979816542525769739/input tmp/2979816542525769739/clu tmp/2979816542525769739/cluster.tsv --threads 64 -v 3
Time for merging to cluster.tsv: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 108ms
result2repseq tmp/2979816542525769739/input tmp/2979816542525769739/clu tmp/2979816542525769739/clu_rep --db-load-mode 0 --compressed 0 --threads 64 -v 3
[=================================================================] 1.35K 0s 11ms
Time for merging to clu_rep: 0h 0m 0s 26ms
Time for processing: 0h 0m 0s 137ms
result2flat tmp/2979816542525769739/input tmp/2979816542525769739/input tmp/2979816542525769739/clu_rep tmp/2979816542525769739/rep_seq.fasta --use-fasta-header -v 3
Time for processing: 0h 0m 0s 6ms
createseqfiledb tmp/2979816542525769739/input tmp/2979816542525769739/clu tmp/2979816542525769739/clu_seqs --threads 64 -v 3
[=================================================================] 1.35K 0s 2ms
Time for merging to clu_seqs: 0h 0m 0s 7ms
Time for processing: 0h 0m 0s 145ms
result2flat tmp/2979816542525769739/input tmp/2979816542525769739/input tmp/2979816542525769739/clu_seqs tmp/2979816542525769739/all_seqs.fasta -v 3
Time for processing: 0h 0m 0s 21ms
rmdb tmp/2979816542525769739/input -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/input_h -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu_seqs -v 3
Time for processing: 0h 0m 0s 1ms
rmdb tmp/2979816542525769739/clu_rep -v 3
Time for processing: 0h 0m 0s 0ms
rmdb tmp/2979816542525769739/clu -v 3
Time for processing: 0h 0m 0s 1ms
[03/30/23 20:28:29] INFO Done clustering! pdb_data.py:1283
INFO Randomly splitting clusters into ratios: 0.8 0.1 0.1... pdb_data.py:1187
INFO Proportionally-derived dataset splits of sizes: 1078 134 134 pdb_data.py:1114
INFO Done splitting clusters pdb_data.py:1196
Number of chains: 1346
[16]:
splits = pdb_manager.split_clusters(pdb_manager.df)
[03/30/23 20:42:36] INFO Randomly splitting clusters into ratios: 0.8 0.1 0.1... pdb_data.py:1187
INFO Proportionally-derived dataset splits of sizes: 1078 134 134 pdb_data.py:1114
INFO Done splitting clusters pdb_data.py:1196
[18]:
splits["train"]
[18]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 279258 | 4pqa_A | 4pqa | A | 381 | protein | Succinyl-diaminopimelate desuccinylase | MTETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHF... | N/A | 1 | [SO4, X8Z, ZN] | Neisseria meningitidis | 1.780 | 2014-03-01 | diffraction | True |
| 486946 | 6hpf_A | 6hpf | A | 312 | protein | endo-b-mannanase | APSTTPVNEKATDAAKNLLSYLVEQAANGVTLSGQQDLESAQWVSD... | N/A | 1 | [ACY, BMA, CL, GLA, MAN, NAG, SO4] | Yunnania penicillata | 1.360 | 2018-09-20 | diffraction | True |
| 93196 | 2hm7_A | 2hm7 | A | 310 | protein | Carboxylesterase | MPLDPVIQQVLDQLNRMPAPDYKHLSAQQFRSQQSLFPPVKKEPVA... | N/A | 1 | [SO4] | Alicyclobacillus acidocaldarius | 2.000 | 2006-07-11 | diffraction | True |
| 209977 | 3u62_A | 3u62 | A | 253 | protein | Shikimate dehydrogenase | MKFCIIGYPVRHSISPRLYNEYFKRAGMNHSYGMEEIPPESFDTEI... | N/A | 1 | [SO4] | Thermotoga maritima | 1.450 | 2011-10-12 | diffraction | True |
| 75453 | 2b1y_A | 2b1y | A | 104 | protein | hypothetical protein Atu1913 | MARPNFRYTHYDLKELRAGTTLEISLSSVNNVRLMTGANFQRFTEL... | N/A | 1 | [SO4] | Agrobacterium tumefaciens str. | 1.800 | 2005-09-16 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 510388 | 6mgc_A | 6mgc | A | 361 | protein | Capsule polysaccharide export protein KpsC | MGIGIYSPGIWRIPHLEKFLAQPCQKLSLLRPVPQEVNAIAVWGHR... | N/A | 1 | [C5P, CL, SO4] | Escherichia coli O1:K1 / APEC | 1.350 | 2018-09-13 | diffraction | True |
| 772192 | 8dv0_A | 8dv0 | A | 199 | protein | Dephospho-CoA kinase | MAHHHHHHMLAIGITGSYASGKTFILDYLAEKGYKTFCADRCIKEL... | N/A | 1 | [EDO, SO4] | Rickettsia felis URRWXCal2 | 1.400 | 2022-07-27 | diffraction | True |
| 471269 | 6evl_A | 6evl | A | 102 | protein | Prolyl 4-hydroxylase subunit alpha-2 | MHHHHHHMLSVDDCFGMGRSAYNEGDYYHTVLWMEQVLKQLDAGEE... | N/A | 1 | [DMS, SO4] | Homo sapiens | 1.870 | 2017-11-02 | diffraction | True |
| 151770 | 3exq_A | 3exq | A | 161 | protein | NUDIX family hydrolase | MSLTRTQPVELVTMVMVTDPETQRVLVEDKVNVPWKAGHSFPGGHV... | N/A | 1 | [SO4] | Lactobacillus brevis ATCC 367 | 2.000 | 2008-10-16 | diffraction | True |
| 432667 | 5wl5_A | 5wl5 | A | 223 | protein | Engineered Chalcone Isomerase ancR5 | SHGMAVTKVTVDGIEFPPTITPPGSSKSLTLLGAGVRGIEIEAIQI... | N/A | 1 | [CL, SO4] | unidentified | 1.513 | 2017-07-25 | diffraction | True |
1078 rows × 15 columns
[19]:
splits["val"]
[19]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 131877 | 2z0z_A | 2z0z | A | 194 | protein | Putative uncharacterized protein TTHA1799 | MWAFPERFEGRHVRLEPLALAHLPAFLRHYDPEVYRFLSRAPVAPT... | N/A | 1 | [SO4] | Thermus thermophilus | 2.000 | 2007-05-07 | diffraction | True |
| 43204 | 1py0_A | 1py0 | A | 125 | protein | Pseudoazurin | ASENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVES... | N/A | 1 | [SO4, Y1, YMA, ZN] | Alcaligenes faecalis | 2.000 | 2003-07-07 | diffraction | True |
| 4961 | 1bx0_A | 1bx0 | A | 314 | protein | PROTEIN (FERREDOXIN:NADP+ OXIDOREDUCTASE) | QIASDVEAPPPAPAKVEKHSKKMEEGITVNKFKPKTPYVGRCLLNT... | N/A | 1 | [FAD, PO4, SO4] | Spinacia oleracea | 1.900 | 1998-10-10 | diffraction | True |
| 436695 | 5xj5_A | 5xj5 | A | 201 | protein | Glycerol-3-phosphate acyltransferase | MGSALFLVIFAYLLGSITFGEVIAKLKGVDLRNVGSGNVGATNVTR... | N/A | 1 | [78M, FME, PGE, SO4] | Aquifex aeolicus | 1.481 | 2017-04-30 | diffraction | True |
| 159885 | 3hbm_A | 3hbm | A | 282 | protein | UDP-sugar hydrolase | MKVLFRSDSSSQIGFGHIKRDLVLAKQYSDVSFACLPLEGSLIDEI... | N/A | 1 | [SO4] | Campylobacter jejuni subsp. jejuni | 1.800 | 2009-05-04 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 422066 | 5uqj_A | 5uqj | A | 221 | protein | U6 snRNA phosphodiesterase | GMSRFWRSFTYFEWRPTPAIHRQLQKIICKYKETFMKQEYTNPYQL... | N/A | 1 | [ACT, GOL, SO4] | Saccharomyces cerevisiae | 1.800 | 2017-02-08 | diffraction | True |
| 158414 | 3gy9_A | 3gy9 | A | 150 | protein | GCN5-related N-acetyltransferase | GMDVTIERVNDFDGYNWLPLLAKSSQEGFQLVERMLRNRREESFQE... | N/A | 1 | [COA, GOL, SO4] | Exiguobacterium sibiricum 255-15 | 1.520 | 2009-04-03 | diffraction | True |
| 540484 | 6qu6_A | 6qu6 | A | 212 | protein | Fiber | MRGSHHHHHHGSGDLVAWNKKDDRRTLWTTPDTSPNCKMSTEKDSK... | N/A | 1 | [EDO, PEG, SIA, SLB, SO4] | Human adenovirus 26 | 1.030 | 2019-02-26 | diffraction | True |
| 231831 | 4cg3_A | 4cg3 | A | 313 | protein | CUTINASE | MKYLLPTAAAGLLLLAAQPAMAMDIGINSDPANPYERGPNPTDALL... | N/A | 1 | [SO4] | THERMOBIFIDA FUSCA | 1.550 | 2013-11-20 | diffraction | True |
| 610378 | 7a1h_A | 7a1h | A | 64 | protein | Subtilisin-chymotrypsin inhibitor-2A | MKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDR... | N/A | 1 | [SO4] | Hordeum vulgare | 1.900 | 2020-08-13 | diffraction | True |
134 rows × 15 columns
[20]:
splits["test"]
[20]:
| id | pdb | chain | length | molecule_type | name | sequence | split | n_chains | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 137068 | 3al2_A | 3al2 | A | 235 | protein | DNA topoisomerase 2-binding protein 1 | GPLGSLKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTC... | N/A | 1 | [SO4] | Homo sapiens | 2.000 | 2010-07-22 | diffraction | True |
| 25399 | 1jov_A | 1jov | A | 270 | protein | HI1317 | MKTTLLKTLTPELHLVQHNDIPVLHLKHAVGTAKISLQGAQLISWK... | N/A | 1 | [SO4, TRS] | Haemophilus influenzae | 1.570 | 2001-07-31 | diffraction | True |
| 381776 | 5kta_A | 5kta | A | 188 | protein | FdhC | MVNFNLKANTTYLRLVEENDAEFICTLRNNDKLNTYISKSTGDIKS... | N/A | 1 | [CSX, DMS, SO4] | Acinetobacter nosocomialis | 1.890 | 2016-07-11 | diffraction | True |
| 165255 | 3iwl_A | 3iwl | A | 68 | protein | Copper transport protein ATOX1 | MPKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEH... | N/A | 1 | [PT, SO4, TCE] | Homo sapiens | 1.600 | 2009-09-02 | diffraction | True |
| 228154 | 4bi7_A | 4bi7 | A | 257 | protein | TRIOSEPHOSPHATE ISOMERASE | MPARRPFIGGNFKCNGSLDFIKSHVAAIAAHKIPDSVDVVIAPSAV... | N/A | 1 | [PGA, SO4] | GIARDIA INTESTINALIS | 1.600 | 2013-04-09 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 454968 | 6btd_A | 6btd | A | 222 | protein | Fuculose phosphate aldolase | MLLQKEREEIVAYGKKMISSGLTKGTGGNISIFNREQGLVAISPSG... | N/A | 1 | [MN, SO4] | Bacillus thuringiensis | 1.551 | 2017-12-06 | diffraction | True |
| 479055 | 6gg1_A | 6gg1 | A | 154 | protein | Interleukin-24 | AFHFGPCRVEGVVPQELWEAFWAVRDTLQAQDNITDVRLLRAEVLQ... | N/A | 1 | [NI, SO4] | Homo sapiens | 1.300 | 2018-05-02 | diffraction | True |
| 696311 | 7q68_A | 7q68 | A | 172 | protein | Thioredoxin domain-containing protein | MAPLQPGDSFPANVVFSYIPPTGSLDLTVCGRPIEYNASEALAKGT... | N/A | 1 | [GOL, SO4] | Chaetomium thermophilum var. thermophilum DSM ... | 1.750 | 2021-11-05 | diffraction | True |
| 269201 | 4n02_A | 4n02 | A | 357 | protein | Isopentenyl-diphosphate delta-isomerase | MRGSHHHHHHGSGSGSGIEGRITTNRKDEHILYALEQKSSYNSFDE... | N/A | 1 | [FNR, SO4] | Streptococcus pneumoniae | 1.400 | 2013-09-30 | diffraction | True |
| 475304 | 6fsg_A | 6fsg | A | 147 | protein | Flavodoxin | SKLVMIFASMSGNTEEMADHIAGVIRETENEIEVIDIMDSPEASIL... | N/A | 1 | [FMN, GLC, SO4] | Bacillus cereus (strain ATCC 14579 / DSM 31 / ... | 1.270 | 2018-02-19 | diffraction | True |
134 rows × 15 columns
Finally, we can export and download our splits
[21]:
pdb_manager.download_pdbs("./pdb", splits=splits)
pdb_manager.export_pdbs(
pdb_dir="./pdb", splits=splits, max_num_chains_per_pdb_code=3
)
[03/30/23 20:43:24] INFO Downloading 994 PDB files... pdb_data.py:1476
I/O¶
We can write our selections as FASTA files or download and write the relevant PDBs in our selection to disk:
CSV¶
[15]:
import os
import pandas as pd
os.makedirs("tmp/", exist_ok=True)
# Write selection to disk
manager.to_csv("tmp/test.csv")
# Read selection from disk
sel = pd.read_csv("tmp/test.csv")
sel
[03/29/23 01:39:08] WARNING You are exporting a selection that contains 1 PDB(s) unavailable for pdb_data.py:1611 download in PDB format: ['6t9m']
INFO Writing selection (80 chains) to CSV file: tmp/test.csv pdb_data.py:1626
[15]:
| id | pdb | chain | length | molecule_type | name | sequence | split | ligands | source | resolution | deposition_date | experiment_type | pdb_file_available | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1hhz_D | 1hhz | D | 5 | protein | CELL WALL PEPTIDE | AEKAA | NaN | ['3FG', 'DAL', 'DVC', 'FGA', 'GHP', 'MLU', 'OM... | NaN | 0.99 | 2000-12-29 | diffraction | True |
| 1 | 1hhz_E | 1hhz | E | 5 | protein | CELL WALL PEPTIDE | AEKAA | NaN | ['3FG', 'DAL', 'DVC', 'FGA', 'GHP', 'MLU', 'OM... | NaN | 0.99 | 2000-12-29 | diffraction | True |
| 2 | 1hhz_F | 1hhz | F | 5 | protein | CELL WALL PEPTIDE | AEKAA | NaN | ['3FG', 'DAL', 'DVC', 'FGA', 'GHP', 'MLU', 'OM... | NaN | 0.99 | 2000-12-29 | diffraction | True |
| 3 | 1sha_B | 1sha | B | 5 | protein | PHOSPHOPEPTIDE A | YVPML | NaN | ['PTR'] | Rous sarcoma virus | 1.50 | 1992-08-18 | diffraction | True |
| 4 | 1skg_B | 1skg | B | 5 | protein | VAFRS | VAFRS | NaN | ['MOH', 'SO4'] | Daboia russellii pulchella; SYNTHETIC CONSTRUCT | 1.21 | 2004-03-04 | diffraction | True |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 75 | 7kpu_B | 7kpu | B | 5 | protein | bisubstrate analogue (CMC-ACE-SER-GLY-ARG-GLY-... | SGRGK | NaN | ['ACE', 'BTB', 'GOL', 'NH2', 'SO4', 'WZG'] | Homo sapiens; SYNTHETIC CONSTRUCT | 1.43 | 2020-11-12 | diffraction | True |
| 76 | 7oju_H | 7oju | H | 5 | protein | MVNAL Peptide | MVNAL | NaN | ['CMC', 'GOL', 'P6G'] | Chaetomium thermophilum (strain DSM 1495 / CBS... | 1.10 | 2021-05-17 | diffraction | True |
| 77 | 7pul_P | 7pul | P | 5 | protein | GLY-ALA-GLY-ALA-ALA | GAGAA | NaN | ['CA', 'MG'] | Enterococcus faecalis | 1.40 | 2021-09-30 | diffraction | True |
| 78 | 7x70_B | 7x70 | B | 5 | protein | peptide | AVKLQ | NaN | [] | Homo sapiens; SYNTHETIC CONSTRUCT | 1.25 | 2022-03-08 | diffraction | True |
| 79 | 7z5z_C | 7z5z | C | 5 | protein | UDP-MurNAc-pentapeptide | AECAA | NaN | ['A9Z', 'DAL', 'FGA', 'GOL', 'MUB', 'UDP'] | Weissella viridescens; SYNTHETIC CONSTRUCT | 1.49 | 2022-03-10 | diffraction | True |
80 rows × 14 columns
FASTA¶
[17]:
from graphein.protein.utils import read_fasta
# Write selection to a fasta file
manager.to_fasta("tmp/test.fasta")
# Load selection from a fasta file
fs = read_fasta("tmp/test.fasta")
print(fs)
[03/29/23 01:40:04] WARNING You are exporting a selection that contains 1 PDB(s) unavailable for pdb_data.py:1611 download in PDB format: ['6t9m']
WARNING You are exporting a selection that contains 1 PDB(s) unavailable for pdb_data.py:1611 download in PDB format: ['6t9m']
{'1hhz_D': 'AEKAA', '1hhz_E': 'AEKAA', '1hhz_F': 'AEKAA', '1sha_B': 'YVPML', '1skg_B': 'VAFRS', '1tjk_I': 'FLSTK', '2d5w_C': 'ASKPK', '2d5w_D': 'ASKTK', '3drj_B': 'AHAKA', '3hds_E': 'ASWSA', '3hds_F': 'ASWSA', '4j78_B': 'KTKLL', '4j82_C': 'KSHQE', '4j82_D': 'KSHQE', '4j84_C': 'ARKLD', '4j84_D': 'ARKLD', '4l9p_C': 'KCVVM', '4olr_A': 'YVVFV', '4olr_B': 'YVVFV', '4qxx_Z': 'GNLVS', '4v3i_B': 'DLTRP', '4x3o_C': 'PKKTG', '4zhb_B': 'VDAVN', '5ctv_C': 'AEKAA', '5ctv_E': 'AEKAA', '5n99_C': 'NQPWQ', '5n99_E': 'NQPWQ', '5n99_F': 'NQPWQ', '5n99_H': 'NQPWQ', '5n99_J': 'NQPWQ', '5n99_L': 'NQPWQ', '5n99_N': 'NQPWQ', '5n99_P': 'NQPWQ', '5n99_R': 'NQPWQ', '5n99_T': 'NQPWQ', '5n99_V': 'NQPWQ', '5n99_X': 'NQPWQ', '5nf0_F': 'GGGGG', '5njf_E': 'AAAAA', '5njf_F': 'AAAAA', '5onp_B': 'GAIIG', '5onq_B': 'GAIIG', '5r42_E': 'TPGVY', '5r43_E': 'TPGVY', '5r44_E': 'TPGVY', '5r45_E': 'TPGVY', '5r46_E': 'TPGVY', '5r47_E': 'TPGVY', '5r48_E': 'TPGVY', '5r49_E': 'TPGVY', '5r4a_E': 'TPGVY', '5r4b_E': 'TPGVY', '5r4c_E': 'TPGVY', '5r4d_D': 'GSWPW', '5r4d_E': 'TPGVY', '6ax4_C': 'PLHST', '6diy_A': 'YTFGQ', '6eaw_I': 'CTKSI', '6f4r_B': 'CARAY', '6f4s_B': 'CARAY', '6f4t_B': 'CARAY', '6fbb_P': 'SRSSP', '6rd2_C': 'TEDEL', '6rd2_D': 'TEDEL', '6slg_B': 'AALAF', '6t9m_BBB': 'GPAMK', '6y3m_P': 'QSYTV', '6z00_C': 'MVNAL', '6z00_D': 'MVNAL', '7ett_B': 'QFPFV', '7etu_B': 'SFPFT', '7etv_B': 'DFPFV', '7kd7_E': 'SGRGK', '7kd7_B': 'SGRGK', '7kpu_E': 'SGRGK', '7kpu_B': 'SGRGK', '7oju_H': 'MVNAL', '7pul_P': 'GAGAA', '7x70_B': 'AVKLQ', '7z5z_C': 'AECAA'}
Downloading PDBs¶
[18]:
manager.download_pdbs("tmp/pdbs/")
[03/29/23 01:40:19] INFO Downloading 55 PDB files... pdb_data.py:1456
[19]:
os.listdir("tmp/pdbs")
[19]:
['5r46.pdb',
'4j84.pdb',
'6y3m.pdb',
'5ctv.pdb',
'4qxx.pdb',
'5njf.pdb',
'7etu.pdb',
'6f4s.pdb',
'6z00.pdb',
'7oju.pdb',
'1hhz.pdb',
'4j82.pdb',
'5r48.pdb',
'1skg.pdb',
'5r45.pdb',
'4zhb.pdb',
'5r42.pdb',
'4v3i.pdb',
'5onp.pdb',
'5r47.pdb',
'1sha.pdb',
'4x3o.pdb',
'5r4c.pdb',
'5onq.pdb',
'5n99.pdb',
'3drj.pdb',
'7kd7.pdb',
'5r4a.pdb',
'7z5z.pdb',
'7kpu.pdb',
'5r4b.pdb',
'5r4d.pdb',
'3hds.pdb',
'5r44.pdb',
'6diy.pdb',
'6rd2.pdb',
'6fbb.pdb',
'5r43.pdb',
'6f4r.pdb',
'2d5w.pdb',
'7ett.pdb',
'5r49.pdb',
'7etv.pdb',
'6eaw.pdb',
'7pul.pdb',
'6slg.pdb',
'6ax4.pdb',
'6f4t.pdb',
'1tjk.pdb',
'4l9p.pdb',
'5nf0.pdb',
'4olr.pdb',
'4j78.pdb',
'7x70.pdb']
Writing Individual Chains¶
We can also extract the individual chains from the PDB files in our selection
[21]:
manager.remove_unavailable_pdbs(update=True)
manager.write_chains()
[03/29/23 01:45:08] INFO Downloading 54 PDB files... pdb_data.py:1504
[03/29/23 01:46:00] INFO Done downloading PDB files pdb_data.py:1508
INFO Extracting chains... pdb_data.py:1511
0%| | 0/54 [00:00<?, ?it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
6%|▌ | 3/54 [00:00<00:02, 22.50it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
11%|█ | 6/54 [00:00<00:03, 14.05it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
15%|█▍ | 8/54 [00:00<00:03, 13.76it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
19%|█▊ | 10/54 [00:00<00:03, 11.58it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
22%|██▏ | 12/54 [00:01<00:04, 10.14it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
28%|██▊ | 15/54 [00:01<00:03, 12.66it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
31%|███▏ | 17/54 [00:01<00:02, 13.81it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
35%|███▌ | 19/54 [00:01<00:04, 8.09it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
39%|███▉ | 21/54 [00:02<00:05, 6.18it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
43%|████▎ | 23/54 [00:02<00:05, 5.58it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
46%|████▋ | 25/54 [00:02<00:04, 6.78it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
50%|█████ | 27/54 [00:03<00:03, 8.10it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
54%|█████▎ | 29/54 [00:03<00:02, 9.42it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
57%|█████▋ | 31/54 [00:03<00:02, 10.56it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
61%|██████ | 33/54 [00:03<00:01, 11.51it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
65%|██████▍ | 35/54 [00:03<00:01, 11.68it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
69%|██████▊ | 37/54 [00:03<00:01, 13.27it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
72%|███████▏ | 39/54 [00:03<00:01, 11.92it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
76%|███████▌ | 41/54 [00:04<00:01, 11.53it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
80%|███████▉ | 43/54 [00:04<00:00, 11.41it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
83%|████████▎ | 45/54 [00:04<00:00, 12.32it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
91%|█████████ | 49/54 [00:04<00:00, 14.77it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
94%|█████████▍| 51/54 [00:04<00:00, 13.33it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
98%|█████████▊| 53/54 [00:04<00:00, 13.44it/s]/home/atj39/mambaforge/envs/graphein/lib/python3.9/site-packages/biopandas/pdb/pandas_pdb.py:624: UserWarning: Column model_id is not an expected column and will be skipped.
warn(
100%|██████████| 54/54 [00:05<00:00, 10.80it/s]
[03/29/23 01:46:05] INFO Done extracting chains pdb_data.py:1520
[21]:
[PosixPath('pdb/1hhz_D.pdb'),
PosixPath('pdb/1hhz_E.pdb'),
PosixPath('pdb/1hhz_F.pdb'),
PosixPath('pdb/1sha_B.pdb'),
PosixPath('pdb/1skg_B.pdb'),
PosixPath('pdb/1tjk_I.pdb'),
PosixPath('pdb/2d5w_C.pdb'),
PosixPath('pdb/2d5w_D.pdb'),
PosixPath('pdb/3drj_B.pdb'),
PosixPath('pdb/3hds_E.pdb'),
PosixPath('pdb/3hds_F.pdb'),
PosixPath('pdb/4j78_B.pdb'),
PosixPath('pdb/4j82_C.pdb'),
PosixPath('pdb/4j82_D.pdb'),
PosixPath('pdb/4j84_C.pdb'),
PosixPath('pdb/4j84_D.pdb'),
PosixPath('pdb/4l9p_C.pdb'),
PosixPath('pdb/4olr_A.pdb'),
PosixPath('pdb/4olr_B.pdb'),
PosixPath('pdb/4qxx_Z.pdb'),
PosixPath('pdb/4v3i_B.pdb'),
PosixPath('pdb/4x3o_C.pdb'),
PosixPath('pdb/4zhb_B.pdb'),
PosixPath('pdb/5ctv_C.pdb'),
PosixPath('pdb/5ctv_E.pdb'),
PosixPath('pdb/5n99_C.pdb'),
PosixPath('pdb/5n99_E.pdb'),
PosixPath('pdb/5n99_F.pdb'),
PosixPath('pdb/5n99_H.pdb'),
PosixPath('pdb/5n99_J.pdb'),
PosixPath('pdb/5n99_L.pdb'),
PosixPath('pdb/5n99_N.pdb'),
PosixPath('pdb/5n99_P.pdb'),
PosixPath('pdb/5n99_R.pdb'),
PosixPath('pdb/5n99_T.pdb'),
PosixPath('pdb/5n99_V.pdb'),
PosixPath('pdb/5n99_X.pdb'),
PosixPath('pdb/5nf0_F.pdb'),
PosixPath('pdb/5njf_E.pdb'),
PosixPath('pdb/5njf_F.pdb'),
PosixPath('pdb/5onp_B.pdb'),
PosixPath('pdb/5onq_B.pdb'),
PosixPath('pdb/5r42_E.pdb'),
PosixPath('pdb/5r43_E.pdb'),
PosixPath('pdb/5r44_E.pdb'),
PosixPath('pdb/5r45_E.pdb'),
PosixPath('pdb/5r46_E.pdb'),
PosixPath('pdb/5r47_E.pdb'),
PosixPath('pdb/5r48_E.pdb'),
PosixPath('pdb/5r49_E.pdb'),
PosixPath('pdb/5r4a_E.pdb'),
PosixPath('pdb/5r4b_E.pdb'),
PosixPath('pdb/5r4c_E.pdb'),
PosixPath('pdb/5r4d_D.pdb'),
PosixPath('pdb/5r4d_E.pdb'),
PosixPath('pdb/6ax4_C.pdb'),
PosixPath('pdb/6diy_A.pdb'),
PosixPath('pdb/6eaw_I.pdb'),
PosixPath('pdb/6f4r_B.pdb'),
PosixPath('pdb/6f4s_B.pdb'),
PosixPath('pdb/6f4t_B.pdb'),
PosixPath('pdb/6fbb_P.pdb'),
PosixPath('pdb/6rd2_C.pdb'),
PosixPath('pdb/6rd2_D.pdb'),
PosixPath('pdb/6slg_B.pdb'),
PosixPath('pdb/6y3m_P.pdb'),
PosixPath('pdb/6z00_C.pdb'),
PosixPath('pdb/6z00_D.pdb'),
PosixPath('pdb/7ett_B.pdb'),
PosixPath('pdb/7etu_B.pdb'),
PosixPath('pdb/7etv_B.pdb'),
PosixPath('pdb/7kd7_E.pdb'),
PosixPath('pdb/7kd7_B.pdb'),
PosixPath('pdb/7kpu_E.pdb'),
PosixPath('pdb/7kpu_B.pdb'),
PosixPath('pdb/7oju_H.pdb'),
PosixPath('pdb/7pul_P.pdb'),
PosixPath('pdb/7x70_B.pdb'),
PosixPath('pdb/7z5z_C.pdb')]