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"""loading script for the pubchem-10-15-2024 data""" |
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import ijson |
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import datasets |
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_CITATION = """\ |
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@article{Kim:2022:D1373, |
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author = {Kim, Sunghwan and Chen, Jie and Cheng, Tiejun and Gindulyte, Asta and He, Jia and He, Siqian and Li, Qingliang and Shoemaker, Benjamin A and Thiessen, Paul A and Yu, Bo and Zaslavsky, Leonid and Zhang, Jian and Bolton, Evan E}, |
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title = "{PubChem 2023 update}", |
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journal = {Nucleic Acids Research}, |
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volume = {51}, |
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pages = {D1373-D1380}, |
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year = {2022}, |
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doi = {10.1093/nar/gkac956} |
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} |
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""" |
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_DESCRIPTION = """\ |
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PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information \ |
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resource that serves a wide range of use cases. In the past \ |
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two years, a number of changes were made to PubChem. Data from more than 120 \ |
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data sources was added to PubChem. Some major highlights include: the \ |
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integration of Google Patents data into PubChem, which greatly expanded the \ |
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coverage of the PubChem Patent data collection; the creation of the Cell Line \ |
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and Taxonomy data collections, which provide quick and easy access to chemical \ |
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information for a given cell line and taxon, respectively; and the update of \ |
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the bioassay data model. In addition, new functionalities were added to the \ |
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PubChem programmatic access protocols, PUG-REST and PUG-View, including support \ |
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for target-centric data download for a given protein, gene, pathway, cell line, \ |
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and taxon and the addition of the `standardize` option to PUG-REST, which \ |
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returns the standardized form of an input chemical structure. A significant \ |
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update was also made to PubChemRDF. The present paper provides an overview of \ |
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these changes. |
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""" |
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_HOMEPAGE = "https://pubchem.ncbi.nlm.nih.gov" |
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_LICENSE = "https://www.ncbi.nlm.nih.gov/home/about/policies/#data" |
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_BASE_DATA_URL_FORMAT_STR = "https://huggingface.co/datasets/molssiai-hub/pubchem-10-15-2024/resolve/main/data/train/Compound_{range}.json" |
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|
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_CONFIG_NAMES = [ |
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"pubchem-10-15-2024" |
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] |
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_FEATURE_KEYS = [ |
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'PUBCHEM_COMPOUND_CID', |
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'PUBCHEM_COMPOUND_CANONICALIZED', |
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'PUBCHEM_CACTVS_COMPLEXITY', |
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'PUBCHEM_CACTVS_HBOND_ACCEPTOR', |
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'PUBCHEM_CACTVS_HBOND_DONOR', |
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'PUBCHEM_CACTVS_ROTATABLE_BOND', |
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'PUBCHEM_CACTVS_SUBSKEYS', |
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'PUBCHEM_IUPAC_OPENEYE_NAME', |
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'PUBCHEM_IUPAC_CAS_NAME', |
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'PUBCHEM_IUPAC_NAME_MARKUP', |
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'PUBCHEM_IUPAC_NAME', |
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'PUBCHEM_IUPAC_SYSTEMATIC_NAME', |
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'PUBCHEM_IUPAC_TRADITIONAL_NAME', |
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'PUBCHEM_IUPAC_INCHI', |
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'PUBCHEM_IUPAC_INCHIKEY', |
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'PUBCHEM_XLOGP3_AA', |
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'PUBCHEM_EXACT_MASS', |
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'PUBCHEM_MOLECULAR_FORMULA', |
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'PUBCHEM_MOLECULAR_WEIGHT', |
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'PUBCHEM_OPENEYE_CAN_SMILES', |
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'PUBCHEM_OPENEYE_ISO_SMILES', |
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'PUBCHEM_CACTVS_TPSA', |
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'PUBCHEM_MONOISOTOPIC_WEIGHT', |
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'PUBCHEM_TOTAL_CHARGE', |
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'PUBCHEM_HEAVY_ATOM_COUNT', |
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'PUBCHEM_ATOM_DEF_STEREO_COUNT', |
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'PUBCHEM_ATOM_UDEF_STEREO_COUNT', |
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'PUBCHEM_BOND_DEF_STEREO_COUNT', |
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'PUBCHEM_BOND_UDEF_STEREO_COUNT', |
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'PUBCHEM_ISOTOPIC_ATOM_COUNT', |
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'PUBCHEM_COMPONENT_COUNT', |
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'PUBCHEM_CACTVS_TAUTO_COUNT', |
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'PUBCHEM_COORDINATE_TYPE', |
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'PUBCHEM_BONDANNOTATIONS', |
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'COORDS', |
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'ATOMIC_INDICES', |
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'ATOMIC_SYMBOLS', |
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'ATOMIC_NUMBERS', |
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'ATOMIC_FORMAL_CHARGES', |
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'BOND_ORDERS', |
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'PUBCHEM_XLOGP3', |
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'PUBCHEM_NONSTANDARDBOND', |
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'PUBCHEM_REFERENCE_STANDARDIZATION' |
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] |
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|
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_FEATURE_TYPES = datasets.Features( |
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{ |
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'PUBCHEM_COMPOUND_CID': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_COMPOUND_CANONICALIZED': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_CACTVS_COMPLEXITY': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_CACTVS_HBOND_ACCEPTOR': datasets.Value(dtype='int64', id=None), |
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'PUBCHEM_CACTVS_HBOND_DONOR': datasets.Value(dtype='int64', id=None), |
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'PUBCHEM_CACTVS_ROTATABLE_BOND': datasets.Value(dtype='int64', id=None), |
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'PUBCHEM_CACTVS_SUBSKEYS': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_OPENEYE_NAME': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_CAS_NAME': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_NAME_MARKUP': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_NAME': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_SYSTEMATIC_NAME': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_TRADITIONAL_NAME': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_INCHI': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_IUPAC_INCHIKEY': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_XLOGP3_AA': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_EXACT_MASS': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_MOLECULAR_FORMULA': datasets.Value(dtype='string', id=None), |
|
'PUBCHEM_MOLECULAR_WEIGHT': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_OPENEYE_CAN_SMILES': datasets.Value(dtype='string', id=None), |
|
'PUBCHEM_OPENEYE_ISO_SMILES': datasets.Value(dtype='string', id=None), |
|
'PUBCHEM_CACTVS_TPSA': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_MONOISOTOPIC_WEIGHT': datasets.Value(dtype='float64', id=None), |
|
'PUBCHEM_TOTAL_CHARGE': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_HEAVY_ATOM_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_ATOM_DEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_ATOM_UDEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_BOND_DEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_BOND_UDEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_ISOTOPIC_ATOM_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_COMPONENT_COUNT': datasets.Value(dtype='int64', id=None), |
|
'PUBCHEM_CACTVS_TAUTO_COUNT': datasets.Value(dtype='int64', id=None), |
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'PUBCHEM_COORDINATE_TYPE': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'PUBCHEM_BONDANNOTATIONS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'COORDS': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None), |
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'ATOMIC_INDICES': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'ATOMIC_SYMBOLS': datasets.Sequence(feature=datasets.Value(dtype='string', id=None), length=-1, id=None), |
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'ATOMIC_NUMBERS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'ATOMIC_FORMAL_CHARGES': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'BOND_ORDERS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), |
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'PUBCHEM_XLOGP3': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_NONSTANDARDBOND': datasets.Value(dtype='string', id=None), |
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'PUBCHEM_REFERENCE_STANDARDIZATION': datasets.Value(dtype='string', id=None) |
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} |
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) |
|
|
|
_ID_RANGES = [ |
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'000000001_000500000', |
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'000500001_001000000', |
|
'001000001_001500000', |
|
'001500001_002000000', |
|
'002000001_002500000', |
|
'002500001_003000000', |
|
'003000001_003500000', |
|
'003500001_004000000', |
|
'004000001_004500000', |
|
'004500001_005000000', |
|
'005000001_005500000', |
|
'005500001_006000000', |
|
'006000001_006500000', |
|
'006500001_007000000', |
|
'007000001_007500000', |
|
'007500001_008000000', |
|
'008000001_008500000', |
|
'008500001_009000000', |
|
'009000001_009500000', |
|
'009500001_010000000', |
|
'010000001_010500000', |
|
'010500001_011000000', |
|
'011000001_011500000', |
|
'011500001_012000000', |
|
'012000001_012500000', |
|
'012500001_013000000', |
|
'013000001_013500000', |
|
'013500001_014000000', |
|
'014000001_014500000', |
|
'014500001_015000000', |
|
'015000001_015500000', |
|
'015500001_016000000', |
|
'016000001_016500000', |
|
'016500001_017000000', |
|
'017000001_017500000', |
|
'017500001_018000000', |
|
'018000001_018500000', |
|
'018500001_019000000', |
|
'019000001_019500000', |
|
'019500001_020000000', |
|
'020000001_020500000', |
|
'020500001_021000000', |
|
'021000001_021500000', |
|
'021500001_022000000', |
|
'022000001_022500000', |
|
'022500001_023000000', |
|
'023000001_023500000', |
|
'023500001_024000000', |
|
'024000001_024500000', |
|
'024500001_025000000', |
|
'025000001_025500000', |
|
'025500001_026000000', |
|
'026000001_026500000', |
|
'026500001_027000000', |
|
'027000001_027500000', |
|
'027500001_028000000', |
|
'028000001_028500000', |
|
'028500001_029000000', |
|
'029000001_029500000', |
|
'029500001_030000000', |
|
'030000001_030500000', |
|
'030500001_031000000', |
|
'031000001_031500000', |
|
'031500001_032000000', |
|
'032000001_032500000', |
|
'032500001_033000000', |
|
'033000001_033500000', |
|
'033500001_034000000', |
|
'034000001_034500000', |
|
'034500001_035000000', |
|
'035000001_035500000', |
|
'035500001_036000000', |
|
'036000001_036500000', |
|
'036500001_037000000', |
|
'037000001_037500000', |
|
'037500001_038000000', |
|
'038000001_038500000', |
|
'038500001_039000000', |
|
'039000001_039500000', |
|
'039500001_040000000', |
|
'040000001_040500000', |
|
'040500001_041000000', |
|
'041000001_041500000', |
|
'041500001_042000000', |
|
'042000001_042500000', |
|
'042500001_043000000', |
|
'043000001_043500000', |
|
'043500001_044000000', |
|
'044000001_044500000', |
|
'044500001_045000000', |
|
'045000001_045500000', |
|
'045500001_046000000', |
|
'046000001_046500000', |
|
'046500001_047000000', |
|
'047000001_047500000', |
|
'047500001_048000000', |
|
'048000001_048500000', |
|
'048500001_049000000', |
|
'049000001_049500000', |
|
'049500001_050000000', |
|
'050000001_050500000', |
|
'050500001_051000000', |
|
'051000001_051500000', |
|
'051500001_052000000', |
|
'052000001_052500000', |
|
'052500001_053000000', |
|
'053000001_053500000', |
|
'053500001_054000000', |
|
'054000001_054500000', |
|
'054500001_055000000', |
|
'055000001_055500000', |
|
'055500001_056000000', |
|
'056000001_056500000', |
|
'056500001_057000000', |
|
'057000001_057500000', |
|
'057500001_058000000', |
|
'058000001_058500000', |
|
'058500001_059000000', |
|
'059000001_059500000', |
|
'059500001_060000000', |
|
'060000001_060500000', |
|
'060500001_061000000', |
|
'061000001_061500000', |
|
'061500001_062000000', |
|
'062000001_062500000', |
|
'062500001_063000000', |
|
'063000001_063500000', |
|
'063500001_064000000', |
|
'064000001_064500000', |
|
'064500001_065000000', |
|
'065000001_065500000', |
|
'065500001_066000000', |
|
'066000001_066500000', |
|
'066500001_067000000', |
|
'067000001_067500000', |
|
'067500001_068000000', |
|
'068000001_068500000', |
|
'068500001_069000000', |
|
'069000001_069500000', |
|
'069500001_070000000', |
|
'070000001_070500000', |
|
'070500001_071000000', |
|
'071000001_071500000', |
|
'071500001_072000000', |
|
'072000001_072500000', |
|
'072500001_073000000', |
|
'073000001_073500000', |
|
'073500001_074000000', |
|
'074000001_074500000', |
|
'074500001_075000000', |
|
'075000001_075500000', |
|
'075500001_076000000', |
|
'076000001_076500000', |
|
'076500001_077000000', |
|
'077000001_077500000', |
|
'077500001_078000000', |
|
'078000001_078500000', |
|
'078500001_079000000', |
|
'079000001_079500000', |
|
'079500001_080000000', |
|
'080000001_080500000', |
|
'080500001_081000000', |
|
'081000001_081500000', |
|
'081500001_082000000', |
|
'082000001_082500000', |
|
'082500001_083000000', |
|
'083000001_083500000', |
|
'083500001_084000000', |
|
'084000001_084500000', |
|
'084500001_085000000', |
|
'085000001_085500000', |
|
'085500001_086000000', |
|
'086000001_086500000', |
|
'086500001_087000000', |
|
'087000001_087500000', |
|
'087500001_088000000', |
|
'088000001_088500000', |
|
'088500001_089000000', |
|
'089000001_089500000', |
|
'089500001_090000000', |
|
'090000001_090500000', |
|
'090500001_091000000', |
|
'091000001_091500000', |
|
'091500001_092000000', |
|
'092000001_092500000', |
|
'092500001_093000000', |
|
'093000001_093500000', |
|
'093500001_094000000', |
|
'094000001_094500000', |
|
'094500001_095000000', |
|
'095000001_095500000', |
|
'095500001_096000000', |
|
'096000001_096500000', |
|
'096500001_097000000', |
|
'097000001_097500000', |
|
'097500001_098000000', |
|
'098000001_098500000', |
|
'098500001_099000000', |
|
'099000001_099500000', |
|
'099500001_100000000', |
|
'100000001_100500000', |
|
'100500001_101000000', |
|
'101000001_101500000', |
|
'101500001_102000000', |
|
'102000001_102500000', |
|
'102500001_103000000', |
|
'103000001_103500000', |
|
'103500001_104000000', |
|
'104000001_104500000', |
|
'104500001_105000000', |
|
'105000001_105500000', |
|
'105500001_106000000', |
|
'106000001_106500000', |
|
'106500001_107000000', |
|
'107000001_107500000', |
|
'107500001_108000000', |
|
'108000001_108500000', |
|
'108500001_109000000', |
|
'109000001_109500000', |
|
'109500001_110000000', |
|
'110000001_110500000', |
|
'110500001_111000000', |
|
'111000001_111500000', |
|
'111500001_112000000', |
|
'112000001_112500000', |
|
'112500001_113000000', |
|
'113000001_113500000', |
|
'113500001_114000000', |
|
'114000001_114500000', |
|
'114500001_115000000', |
|
'115000001_115500000', |
|
'115500001_116000000', |
|
'116000001_116500000', |
|
'116500001_117000000', |
|
'117000001_117500000', |
|
'117500001_118000000', |
|
'118000001_118500000', |
|
'118500001_119000000', |
|
'119000001_119500000', |
|
'119500001_120000000', |
|
'120000001_120500000', |
|
'120500001_121000000', |
|
'121000001_121500000', |
|
'121500001_122000000', |
|
'122000001_122500000', |
|
'122500001_123000000', |
|
'123000001_123500000', |
|
'123500001_124000000', |
|
'124000001_124500000', |
|
'124500001_125000000', |
|
'125000001_125500000', |
|
'125500001_126000000', |
|
'126000001_126500000', |
|
'126500001_127000000', |
|
'127000001_127500000', |
|
'127500001_128000000', |
|
'128000001_128500000', |
|
'128500001_129000000', |
|
'129000001_129500000', |
|
'129500001_130000000', |
|
'130000001_130500000', |
|
'130500001_131000000', |
|
'131000001_131500000', |
|
'131500001_132000000', |
|
'132000001_132500000', |
|
'132500001_133000000', |
|
'133000001_133500000', |
|
'133500001_134000000', |
|
'134000001_134500000', |
|
'134500001_135000000', |
|
'135000001_135500000', |
|
'135500001_136000000', |
|
'136000001_136500000', |
|
'136500001_137000000', |
|
'137000001_137500000', |
|
'137500001_138000000', |
|
'138000001_138500000', |
|
'138500001_139000000', |
|
'139000001_139500000', |
|
'139500001_140000000', |
|
'140000001_140500000', |
|
'140500001_141000000', |
|
'141000001_141500000', |
|
'141500001_142000000', |
|
'142000001_142500000', |
|
'142500001_143000000', |
|
'143000001_143500000', |
|
'143500001_144000000', |
|
'144000001_144500000', |
|
'144500001_145000000', |
|
'145000001_145500000', |
|
'145500001_146000000', |
|
'146000001_146500000', |
|
'146500001_147000000', |
|
'147000001_147500000', |
|
'147500001_148000000', |
|
'148000001_148500000', |
|
'148500001_149000000', |
|
'149000001_149500000', |
|
'149500001_150000000', |
|
'150000001_150500000', |
|
'150500001_151000000', |
|
'151000001_151500000', |
|
'151500001_152000000', |
|
'152000001_152500000', |
|
'152500001_153000000', |
|
'153000001_153500000', |
|
'153500001_154000000', |
|
'154000001_154500000', |
|
'154500001_155000000', |
|
'155000001_155500000', |
|
'155500001_156000000', |
|
'156000001_156500000', |
|
'156500001_157000000', |
|
'157000001_157500000', |
|
'157500001_158000000', |
|
'158000001_158500000', |
|
'158500001_159000000', |
|
'159000001_159500000', |
|
'159500001_160000000', |
|
'160000001_160500000', |
|
'160500001_161000000', |
|
'161000001_161500000', |
|
'161500001_162000000', |
|
'162000001_162500000', |
|
'162500001_163000000', |
|
'163000001_163500000', |
|
'163500001_164000000', |
|
'164000001_164500000', |
|
'164500001_165000000', |
|
'165000001_165500000', |
|
'165500001_166000000', |
|
'166000001_166500000', |
|
'166500001_167000000', |
|
'167000001_167500000', |
|
'167500001_168000000', |
|
'168000001_168500000', |
|
'168500001_169000000', |
|
'169000001_169500000', |
|
'169500001_170000000', |
|
'170000001_170500000', |
|
'170500001_171000000', |
|
'171000001_171500000', |
|
'171500001_172000000', |
|
'172000001_172500000' |
|
] |
|
|
|
|
|
class PubChemConfig(datasets.BuilderConfig): |
|
""" |
|
Configuration class for the PubChem dataset. |
|
Args: |
|
features (dict): A dictionary specifying the features of the dataset. |
|
data_url (str): The URL to download the dataset. |
|
url (str): The URL to the dataset homepage. |
|
citation (str): The citation for the dataset. |
|
**kwargs: Additional keyword arguments. |
|
Attributes: |
|
version (datasets.Version): The version of the dataset. |
|
""" |
|
|
|
def __init__(self, features, url, citation, id_range, **kwargs): |
|
super(PubChemConfig, self).__init__( |
|
version=datasets.Version("0.0.0"), **kwargs |
|
) |
|
self.features = features |
|
self.url = url |
|
self.citation = citation |
|
self.id_range = id_range |
|
|
|
|
|
class PubChem(datasets.GeneratorBasedBuilder): |
|
|
|
BUILDER_CONFIG_CLASS = PubChemConfig |
|
|
|
DEFAULT_CONFIG_NAME = "pubchem-10-15-2024" |
|
|
|
VERSION = datasets.Version("0.0.0") |
|
|
|
url = "https://huggingface.co/datasets/molssiai-hub/pubchem-10-15-2024" |
|
|
|
BUILDER_CONFIGS = [ |
|
PubChemConfig( |
|
name="pubchem-10-15-2024", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES, |
|
) |
|
] |
|
|
|
def _info(self): |
|
if self.config.name in _CONFIG_NAMES: |
|
features = _FEATURE_TYPES |
|
else: |
|
raise NotImplementedError("Unknown configuration in _info") |
|
|
|
return datasets.DatasetInfo( |
|
description=_DESCRIPTION, |
|
features=features, |
|
homepage=_HOMEPAGE, |
|
supervised_keys=None, |
|
license=_LICENSE, |
|
citation=_CITATION, |
|
) |
|
|
|
def _split_generators(self, dl_manager): |
|
if self.config.name in _CONFIG_NAMES: |
|
file_list = [] |
|
for range in self.config.id_range: |
|
file_list.append(_BASE_DATA_URL_FORMAT_STR.format( |
|
name=self.config.name, range=range)) |
|
else: |
|
raise NotImplementedError( |
|
"Unknown configuration in _split_generators") |
|
|
|
return [ |
|
datasets.SplitGenerator( |
|
name=datasets.Split.TRAIN, |
|
gen_kwargs={ |
|
"filepaths": dl_manager.download(sorted(file_list)), |
|
}, |
|
) |
|
] |
|
|
|
def _generate_examples(self, filepaths): |
|
if self.config.name in _CONFIG_NAMES: |
|
idx = 0 |
|
for filepath in filepaths: |
|
with open(filepath, "rb") as f: |
|
items = ijson.items(f, "item", use_float=True) |
|
for data in items: |
|
yield idx, data |
|
idx += 1 |
|
else: |
|
raise NotImplementedError( |
|
"Unknown configuration in _generate_examples") |
|
|
