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"""loading script for the pubchemqc-b3lyp data""" |
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import ijson |
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import datasets |
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_CITATION = """\ |
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@article{Nakata2023, |
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abstract = {The presented “PubChemQC B3LYP/6-31G*//PM6” data set is composed of the electronic properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from essential compounds to biomolecules with a molecular weight up to 1000. These molecules account for 94.0% of the original PubChem Compound catalog as of August 29, 2016. The electronic properties, including orbitals, orbital energies, total energies, dipole moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6 methods. The data set, available in three formats, namely, GAMESS quantum chemistry program files, selected JSON output files, and a PostgreSQL database, provides researchers with the ability to query molecular properties. It is further subdivided into five subdata sets for more specific data. The first two subsets encompass molecules with carbon, hydrogen, oxygen, and nitrogen with molecular weights under 300 and 500, respectively. The third and fourth subsets incorporate molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, and chlorine, with molecular weights under 300 and 500, respectively. The fifth subset comprises molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, chlorine, sodium, potassium, magnesium, and calcium, with a molecular weight of under 500. The coefficients of determination for the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap range from 0.892 (for CHON500) to 0.803 (for the whole data set). These comprehensive results pave the way for applications in drug discovery and materials science, among others. The data sets can be accessed under the Creative Commons Attribution 4.0 International license at the following web address: https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html.}, |
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author = {Maho Nakata and Toshiyuki Maeda}, |
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doi = {10.1021/ACS.JCIM.3C00899/ASSET/IMAGES/MEDIUM/CI3C00899_0012.GIF}, |
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issn = {1549960X}, |
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issue = {18}, |
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journal = {Journal of Chemical Information and Modeling}, |
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month = {9}, |
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pages = {5734-5754}, |
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pmid = {37677147}, |
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publisher = {American Chemical Society}, |
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title = {PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations}, |
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volume = {63}, |
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url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00899}, |
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year = {2023}, |
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} |
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""" |
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_DESCRIPTION = """\ |
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The presented “PubChemQC B3LYP/6-31G*//PM6” data set is composed of the electronic \ |
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properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from \ |
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essential compounds to biomolecules with a molecular weight up to 1000. These molecules \ |
|
account for 94.0% of the original PubChem Compound catalog as of August 29, 2016. \ |
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The electronic properties, including orbitals, orbital energies, total energies, dipole \ |
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moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6 \ |
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methods. |
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""" |
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_HOMEPAGE = "https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html" |
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_LICENSE = "https://creativecommons.org/licenses/by/4.0" |
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_BASE_DATA_URL_FORMAT_STR = "https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp/resolve/main/data/{name}/train/{range}.json" |
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_CONFIG_NAMES = [ |
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"b3lyp_pm6", |
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"b3lyp_pm6_chon300nosalt", |
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"b3lyp_pm6_chon500nosalt", |
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"b3lyp_pm6_chnopsfcl300nosalt", |
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"b3lyp_pm6_chnopsfcl500nosalt", |
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"b3lyp_pm6_chnopsfclnakmgca500" |
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] |
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_FEATURE_KEYS = [ |
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'cid', |
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'state', |
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'pubchem-inchi', |
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'pubchem-charge', |
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'pubchem-version', |
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'name', |
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'coordinates', |
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'atomic-numbers', |
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'atom-count', |
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'heavy-atom-count', |
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'core-electrons', |
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'bond-order', |
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'connection-indices', |
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'formula', |
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'version', |
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'obabel-inchi', |
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'pm6-obabel-canonical-smiles', |
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'charge', |
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'energy-beta-gap', |
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'energy-beta-homo', |
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'energy-beta-lumo', |
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'energy-alpha-gap', |
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'energy-alpha-homo', |
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'energy-alpha-lumo', |
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'total-energy', |
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'homos', |
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'orbital-energies', |
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'mo-count', |
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'basis-count', |
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'multiplicity', |
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'molecular-mass', |
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'number-of-atoms', |
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'lowdin-partial-charges', |
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'mulliken-partial-charges', |
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'dipole-moment', |
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'pubchem-multiplicity', |
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'pubchem-obabel-canonical-smiles', |
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'pubchem-isomeric-smiles', |
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'pubchem-molecular-weight', |
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'pubchem-molecular-formula' |
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] |
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|
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_FEATURE_TYPES = datasets.Features( |
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{ |
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"cid": datasets.Value(dtype="int64", id=None), |
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"state": datasets.Value(dtype="string", id=None), |
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"pubchem-inchi": datasets.Value(dtype="string", id=None), |
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"pubchem-charge": datasets.Value(dtype="int64", id=None), |
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"pubchem-version": datasets.Value(dtype="string", id=None), |
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"name": datasets.Value(dtype="string", id=None), |
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"coordinates": datasets.Sequence(feature=datasets.Value(dtype="float64", 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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"atom-count": datasets.Value(dtype="int64", id=None), |
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"heavy-atom-count": datasets.Value(dtype="int64", id=None), |
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"core-electrons": datasets.Sequence(feature=datasets.Value(dtype="int64", id=None), length=-1, id=None), |
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"bond-order": datasets.Sequence(feature=datasets.Value(dtype="int64", id=None), length=-1, id=None), |
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"connection-indices": datasets.Sequence(feature=datasets.Value(dtype="int64", id=None), length=-1, id=None), |
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"formula": datasets.Value(dtype="string", id=None), |
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"version": datasets.Value(dtype="string", id=None), |
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"obabel-inchi": datasets.Value(dtype="string", id=None), |
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"pm6-obabel-canonical-smiles": datasets.Value(dtype="string", id=None), |
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"charge": datasets.Value(dtype="int64", id=None), |
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"energy-beta-gap": datasets.Value(dtype="float64", id=None), |
|
"energy-beta-homo": datasets.Value(dtype="float64", id=None), |
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"energy-beta-lumo": datasets.Value(dtype="float64", id=None), |
|
"energy-alpha-gap": datasets.Value(dtype="float64", id=None), |
|
"energy-alpha-homo": datasets.Value(dtype="float64", id=None), |
|
"energy-alpha-lumo": datasets.Value(dtype="float64", id=None), |
|
"total-energy": datasets.Value(dtype="float64", id=None), |
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"homos": datasets.Sequence(feature=datasets.Value(dtype="int64", id=None), length=-1, id=None), |
|
"orbital-energies": datasets.Sequence(feature=datasets.Sequence(feature=datasets.Value(dtype="float64", id=None), length=-1, id=None), length=-1, id=None), |
|
"mo-count": datasets.Value(dtype="int64", id=None), |
|
"basis-count": datasets.Value(dtype="int64", id=None), |
|
"multiplicity": datasets.Value(dtype="int64", id=None), |
|
"molecular-mass": datasets.Value(dtype="float64", id=None), |
|
"number-of-atoms": datasets.Value(dtype="int64", id=None), |
|
"lowdin-partial-charges": datasets.Sequence(feature=datasets.Value(dtype="float64", id=None), length=-1, id=None), |
|
"mulliken-partial-charges": datasets.Sequence(feature=datasets.Value(dtype="float64", id=None), length=-1, id=None), |
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"dipole-moment": datasets.Value(dtype="float64", id=None), |
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"pubchem-multiplicity": datasets.Value(dtype="int64", id=None), |
|
"pubchem-obabel-canonical-smiles": datasets.Value(dtype="string", id=None), |
|
'pubchem-isomeric-smiles': datasets.Value(dtype="string", id=None), |
|
"pubchem-molecular-weight": datasets.Value(dtype="float64", id=None), |
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"pubchem-molecular-formula": datasets.Value(dtype="string", id=None), |
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} |
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) |
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|
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_ID_RANGES_B3LYP_PM6 = [ |
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"069838214-070067759", |
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"016418668-016622411", |
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"018248993-018501518", |
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"080598281-080799107", |
|
"050460404-050669555", |
|
"089044623-089269002", |
|
"052430628-052673047", |
|
"050245960-050460403", |
|
"083205711-083406375", |
|
"068061518-068284290", |
|
"027714325-028367889", |
|
"000000001-000253696", |
|
"097278004-097482378", |
|
"001687096-002009718", |
|
"093246646-093447393", |
|
"074250632-075507818", |
|
"109698559-109914622", |
|
"095261252-095462819", |
|
"081801790-082002124", |
|
"043121110-043321695", |
|
"066926358-067148252", |
|
"039406497-040154274", |
|
"062875058-063075606", |
|
"043522281-043722983", |
|
"004997250-005220177", |
|
"094253942-094454501", |
|
"081601176-081801789", |
|
"068502199-068722952", |
|
"097886617-098106994", |
|
"101520800-101784274", |
|
"075507819-076965970", |
|
"062072696-062273137", |
|
"045586430-045805292", |
|
"108469989-108670985", |
|
"082604005-082804581", |
|
"120069554-120278439", |
|
"008835467-009074444", |
|
"112655106-112856951", |
|
"103158479-103359312", |
|
"056146357-056347853", |
|
"019488508-019703067", |
|
"020253760-020549110", |
|
"107664738-107866036", |
|
"083807474-084008211", |
|
"040154275-040743801", |
|
"020823895-021041615", |
|
"087551363-087800478", |
|
"068284291-068502198", |
|
"097482379-097684978", |
|
"023098136-023422039", |
|
"017379703-017584491", |
|
"109274931-109483471", |
|
"116076960-116277746", |
|
"023695704-023957050", |
|
"054938049-055138612", |
|
"009317711-009561456", |
|
"073213210-074250631", |
|
"110729402-110932217", |
|
"082403521-082604004", |
|
"044139774-044414522", |
|
"070541718-070768491", |
|
"057707755-057938179", |
|
"116478905-116680795", |
|
"004562802-004786579", |
|
"070305863-070541717", |
|
"071874892-072076290", |
|
"001194894-001426768", |
|
"079595038-079795541", |
|
"060266706-060467686", |
|
"005220178-005478786", |
|
"079996245-080196714", |
|
"106255750-106457061", |
|
"105451910-105653107", |
|
"087050400-087301606", |
|
"036185344-038234901", |
|
"042391117-042714925", |
|
"102042996-102298261", |
|
"112856952-113058407", |
|
"121337267-121494125", |
|
"066085824-066286345", |
|
"079394423-079595037", |
|
"006826337-007176354", |
|
"084208787-084410291", |
|
"063476623-063677410", |
|
"105250935-105451909", |
|
"046008145-046227079", |
|
"050669556-050873793", |
|
"059789367-060039314", |
|
"121123661-121337266", |
|
"059559916-059789366", |
|
"003242748-003461775", |
|
"007176355-007449540", |
|
"119643196-119851991", |
|
"023422041-023695669", |
|
"097684979-097886616", |
|
"107463348-107664737", |
|
"005862345-006190260", |
|
"083406376-083606831", |
|
"096269672-096471110", |
|
"069612798-069838213", |
|
"002552285-002804369", |
|
"080799108-080999622", |
|
"003899016-004119706", |
|
"104849339-105050142", |
|
"109483473-109698558", |
|
"043722984-043926848", |
|
"006504211-006826336", |
|
"010542013-010773379", |
|
"038234918-039406494", |
|
"118143532-118360971", |
|
"005478787-005862344", |
|
"117086426-117288091", |
|
"063677411-063879293", |
|
"106054712-106255749", |
|
"067148253-067368219", |
|
"118801814-119014242", |
|
"107262257-107463347", |
|
"084008212-084208786", |
|
"108670986-108872508", |
|
"070067760-070305862", |
|
"086827832-087050399", |
|
"018501519-018777647", |
|
"079194099-079394422", |
|
"018777648-019029724", |
|
"098855980-099060097", |
|
"041733630-042391116", |
|
"112024942-112245949", |
|
"106457062-106657998", |
|
"007683236-007896656", |
|
"017584492-018042736", |
|
"007896657-008126070", |
|
"012519140-013258253", |
|
"119224645-119431401", |
|
"066487152-066703856", |
|
"067591395-067830698", |
|
"000738833-000967529", |
|
"120914890-121123660", |
|
"052673048-052915909", |
|
"052915910-053168351", |
|
"004341752-004562801", |
|
"109914623-110118745", |
|
"067368220-067591394", |
|
"064280438-064480989", |
|
"022774226-023098135", |
|
"025069870-025340337", |
|
"105653108-105853686", |
|
"000967530-001194893", |
|
"062674137-062875057", |
|
"090159716-090383532", |
|
"092639644-092841886", |
|
"010773380-011009162", |
|
"079795542-079996244", |
|
"047007890-048201959", |
|
"119851992-120069553", |
|
"057002094-057226938", |
|
"119431402-119643195", |
|
"119014243-119224644", |
|
"093044840-093246645", |
|
"100331198-100532635", |
|
"065684618-065885224", |
|
"054189379-054472509", |
|
"106657999-106860006", |
|
"055742931-055944904", |
|
"072545233-073213209", |
|
"061471322-061671774", |
|
"078792790-078993619", |
|
"096068544-096269671", |
|
"024843983-025069869", |
|
"088315671-088567103", |
|
"060869412-061069970", |
|
"003461778-003683221", |
|
"093649966-093851046", |
|
"067830699-068061517", |
|
"105050143-105250934", |
|
"114869070-115070740", |
|
"082202929-082403520", |
|
"019703069-019986827", |
|
"091074701-091308340", |
|
"069164715-069386128", |
|
"102298264-102548258", |
|
"111804560-112024940", |
|
"057473634-057707754", |
|
"061069971-061270556", |
|
"051662685-051906947", |
|
"015767396-016203391", |
|
"108872509-109073823", |
|
"011474898-011701281", |
|
"051906948-052163952", |
|
"014116820-015061896", |
|
"055138613-055340010", |
|
"117489164-117702788", |
|
"120701700-120914889", |
|
"093447394-093649965", |
|
"066703857-066926357", |
|
"113460821-113662218", |
|
"063276177-063476622", |
|
"102957567-103158478", |
|
"064480990-064682056", |
|
"108269163-108469988", |
|
"013258290-014116756", |
|
"019264034-019488507", |
|
"043321696-043522280", |
|
"100130172-100331197", |
|
"087301607-087551362", |
|
"053906020-054189377", |
|
"049808870-050033093", |
|
"116881648-117086425", |
|
"026862533-027714305", |
|
"029340288-030252867", |
|
"098635916-098855979", |
|
"089938436-090159715", |
|
"071427538-071658020", |
|
"008584963-008835466", |
|
"110118746-110326719", |
|
"078993620-079194098", |
|
"099060098-099266087", |
|
"102756503-102957566", |
|
"072076291-072545232", |
|
"055541373-055742930", |
|
"034626922-036185297", |
|
"024209591-024428440", |
|
"053623448-053906019", |
|
"057226939-057473633", |
|
"096672925-096874348", |
|
"048201980-049808869", |
|
"111370237-111583698", |
|
"050873794-051123310", |
|
"111583699-111804559", |
|
"098388562-098635915", |
|
"019986828-020253759", |
|
"095059742-095261251", |
|
"120278440-120490161", |
|
"064682057-064882517", |
|
"011244432-011474897", |
|
"061270557-061471321", |
|
"056347854-056549247", |
|
"100532636-100737716", |
|
"024629876-024843982", |
|
"044414525-044667922", |
|
"087800479-088065439", |
|
"061872192-062072695", |
|
"055340011-055541372", |
|
"117288092-117489163", |
|
"025340338-025684809", |
|
"095664613-095867002", |
|
"098106995-098388561", |
|
"070768492-070982906", |
|
"041114773-041733629", |
|
"117702789-117926586", |
|
"084410292-084611212", |
|
"092436183-092639643", |
|
"100737717-100988360", |
|
"081400427-081601175", |
|
"006190261-006504210", |
|
"054472510-054726377", |
|
"070982907-071200898", |
|
"002804370-003018593", |
|
"060039315-060266705", |
|
"001426770-001687095", |
|
"016888133-017126668", |
|
"058859492-059101427", |
|
"083005157-083205710", |
|
"115070741-115271900", |
|
"060467687-060668792", |
|
"063075607-063276176", |
|
"008348112-008584961", |
|
"056549248-056784475", |
|
"026210317-026862532", |
|
"089269003-089495112", |
|
"068722953-068943375", |
|
"082002125-082202928", |
|
"114667779-114869069", |
|
"118581018-118801813", |
|
"008126072-008348110", |
|
"053399292-053623447", |
|
"118360972-118581017", |
|
"066286346-066487151", |
|
"045805293-046008144", |
|
"046227080-046449704", |
|
"084812012-086604548", |
|
"115876156-116076959", |
|
"071200899-071427537", |
|
"101253713-101520799", |
|
"059101428-059330760", |
|
"051123311-051324457", |
|
"104045737-104246570", |
|
"114064430-114265517", |
|
"105853687-106054711", |
|
"086604549-086827831", |
|
"031128104-032521525", |
|
"113259602-113460820", |
|
"032521528-034626919", |
|
"092229790-092436182", |
|
"016203393-016418667", |
|
"064079771-064280437", |
|
"095867003-096068543", |
|
"099916491-100130171", |
|
"092841887-093044839", |
|
"069386129-069612797", |
|
"000253697-000507790", |
|
"080999623-081200048", |
|
"117926588-118143531", |
|
"065283562-065484049", |
|
"104246571-104447580", |
|
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] |
|
|
|
_ID_RANGES_B3LYP_PM6_CHNOPSFCL300NOSALT = [ |
|
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'101169290-101572732', |
|
'107775979-108095759', |
|
'066476638-066792162', |
|
'045357623-045715560', |
|
'111118503-111470416', |
|
'116729001-116963620', |
|
'033102034-035285652', |
|
'113596433-113844800', |
|
'080687797-080907642', |
|
'025953040-026657400', |
|
'061685173-061905269', |
|
'120621697-120852767', |
|
'025520310-025953038', |
|
'115560695-115793408', |
|
'072841924-073923983', |
|
'007563494-007797980', |
|
'052732428-053039586', |
|
'045940252-046225539', |
|
'105134113-105378591', |
|
'060047877-060325850', |
|
'059681228-060047876', |
|
'094050018-094262260', |
|
'022718817-023144726', |
|
'093610266-093832639', |
|
'067124107-067449218', |
|
'041767798-042432543', |
|
'046225540-046496602', |
|
'051067845-051276686', |
|
'065270161-065522981', |
|
'092707152-092930834', |
|
'009925192-010264132', |
|
'105833886-106058014', |
|
'058588405-058960656', |
|
'009543538-009925191', |
|
'117196011-117410861', |
|
'088722857-089078823', |
|
'064821472-065050471', |
|
'104892236-105134112', |
|
'030375495-031443940', |
|
'078826650-079051187', |
|
'061461898-061685172', |
|
'114107968-114358771', |
|
'069707216-070030624', |
|
'013494628-014626827', |
|
'064149910-064382645', |
|
'055105777-055329428', |
|
'009023949-009282357', |
|
'118740678-119034741', |
|
'058960660-059332184', |
|
'020182243-020539032', |
|
'005463609-005957981', |
|
'014626829-015555902', |
|
'098638434-098883662', |
|
'029406694-030375494', |
|
'082303867-082514991', |
|
'009282358-009543537', |
|
'071584857-071861576', |
|
'022369275-022718816', |
|
'106294038-106528438', |
|
'026657408-027519630', |
|
'008271715-008510844', |
|
'116035959-116262367', |
|
'108875090-109090169', |
|
'117410862-117715654', |
|
'003609073-003896627', |
|
'081643739-081877353', |
|
'103127339-103357682', |
|
'097003652-097214852', |
|
'039148386-039975107', |
|
'056922219-057214545', |
|
'092256407-092487890', |
|
'037219244-039148383', |
|
'097214853-097428416', |
|
'086901806-087187340', |
|
'082092007-082303866', |
|
'095966292-096173691', |
|
'109945408-110190397', |
|
'081372533-081643738', |
|
'081877354-082092006', |
|
'002135498-002459353', |
|
'062561664-062780618', |
|
'090714365-091062980', |
|
'121088365-121350293', |
|
'119717131-119940490', |
|
'102648505-102897872', |
|
'063708754-063928701', |
|
'011257492-011594734', |
|
'103930055-104158155', |
|
'092487891-092707151', |
|
'076953047-078826649', |
|
'040607279-041088427', |
|
'117715655-118065783', |
|
'073923984-075452115', |
|
'069061811-069382794', |
|
'096793559-097003651', |
|
'046496605-046853486', |
|
'100108373-100453638', |
|
'020894254-021200486', |
|
'070678846-070949551', |
|
'052469408-052732427', |
|
'021200489-021576697', |
|
'091966387-092256406', |
|
'080907643-081131075', |
|
'082735049-082997273', |
|
'106759014-107006886', |
|
'069382795-069707214', |
|
'049713835-050781944', |
|
'081131076-081372532', |
|
'017598382-018131160', |
|
'084761484-086612140', |
|
'028770555-029406691', |
|
'084529439-084761483', |
|
'057906408-058242734', |
|
'116262368-116502752', |
|
'044921804-045357622', |
|
'097644346-097870019', |
|
'004219206-004542690', |
|
'080210897-080432986', |
|
'062345259-062561663', |
|
'107006887-107245301', |
|
'086612146-086901804', |
|
'120852768-121088364', |
|
'119493610-119717130', |
|
'003896628-004219205', |
|
'042432545-042778230', |
|
'053272798-053566230', |
|
'097428417-097644345', |
|
'008028391-008271714', |
|
'094685731-094909221', |
|
'043458122-043687291', |
|
'099111472-099339947', |
|
'082997274-083225650', |
|
'103357683-103598066', |
|
'102329721-102648504', |
|
'056695884-056922218', |
|
'042778231-043006092', |
|
'083225651-083444545', |
|
'010591399-010916593', |
|
'110611813-110817324', |
|
'091062983-091393652', |
|
'096380371-096589163', |
|
'079503818-079743704', |
|
'079974156-080210896', |
|
'112915012-113125714', |
|
'011594735-011928545', |
|
'002459354-002750887', |
|
'094909222-095120707', |
|
'000298224-000618477', |
|
'024810909-025146188', |
|
'093162838-093383628', |
|
'055986804-056209547', |
|
'083444546-083651135', |
|
'121350295-121494125', |
|
'015555903-016226454', |
|
'114358772-114602668', |
|
'067779308-068107950', |
|
'016466303-016750753', |
|
'059332185-059681216', |
|
'106058015-106294037', |
|
'088354178-088722855', |
|
'060779725-061005376', |
|
'010916594-011257491', |
|
'104636076-104892234', |
|
'058242737-058588403', |
|
'079268577-079503817', |
|
'035285656-037219240', |
|
'087570116-087967059', |
|
'084092656-084317515', |
|
'023996570-024349963', |
|
'065522982-065748172', |
|
'067449219-067779306', |
|
'102897873-103127338', |
|
'062780619-063005032', |
|
'023144727-023545686', |
|
'075452116-076953046', |
|
'044296703-044921803', |
|
'003004169-003292922', |
|
'054880555-055105776', |
|
'061005377-061236109', |
|
'017375386-017598381', |
|
'057548651-057906406', |
|
'099562280-099869411', |
|
'094262261-094472394', |
|
'119940492-120177048', |
|
'007797981-008028389', |
|
'055329429-055543937', |
|
'008510845-008766470', |
|
'105378592-105612897', |
|
'115793409-116035958', |
|
'111470417-111823937', |
|
'028320848-028770553', |
|
'071266170-071584856', |
|
'018798361-019164754', |
|
'068419396-068741466', |
|
'003292923-003609072', |
|
'024349964-024568623', |
|
'079051188-079268576', |
|
'113125715-113357213', |
|
'115329503-115560694', |
|
'065748173-065978765', |
|
'087187341-087570115', |
|
'083872784-084092655', |
|
'070030625-070372990', |
|
'053881443-054240679', |
|
'090115964-090469582', |
|
'107482228-107775978', |
|
'051276687-051606947', |
|
'012633972-013494620', |
|
'064602910-064821471', |
|
'119034742-119271886', |
|
'108095761-108386993', |
|
'089078824-089434140', |
|
'089434141-089770210', |
|
'099339948-099562279', |
|
'114602669-114850966', |
|
'061905270-062126390', |
|
'043006093-043231326', |
|
'025146189-025520308', |
|
'001406787-001738122', |
|
'046853491-047101465', |
|
'057214549-057548649', |
|
'089770211-090115963', |
|
'007280731-007563493', |
|
'095328582-095543490', |
|
'001738123-002135497', |
|
'080432987-080687796', |
|
'054240683-054596966', |
|
'054596967-054880553', |
|
'106528440-106759013', |
|
'066220658-066476637', |
|
'053566231-053881442', |
|
'004542691-004843500', |
|
'096173692-096380370', |
|
'021983600-022369270', |
|
'027519631-028320847', |
|
'024568624-024810908', |
|
'056434706-056695883', |
|
'108615516-108875089', |
|
'112470993-112692811', |
|
'005135518-005463608', |
|
'000618478-000858562', |
|
'072079001-072841923', |
|
'084317516-084529438', |
|
'053039587-053272797', |
|
'001127278-001406786', |
|
'094472395-094685730', |
|
'019164755-019501105', |
|
'060325851-060543825', |
|
'101572734-101947010', |
|
'066792163-067124104', |
|
'107245302-107482227', |
|
'120401133-120621696', |
|
'114850967-115100358', |
|
'109297177-109614742', |
|
'051606949-051915361', |
|
'055543938-055761163', |
|
'052191076-052469407', |
|
'118399418-118740677', |
|
'083651136-083872783', |
|
'095543491-095757752', |
|
'065978766-066220657', |
|
'070372992-070678837', |
|
'021576698-021983599', |
|
'062126391-062345258', |
|
'064382646-064602909', |
|
'098883663-099111471', |
|
'113844801-114107967', |
|
'019819596-020182242', |
|
'108386994-108615515', |
|
'004843501-005135514', |
|
'043687292-043967597', |
|
'095757753-095966291', |
|
'017033260-017375385', |
|
'068741468-069061806', |
|
'005957982-006447338', |
|
'110817325-111118502', |
|
'100453641-100785895', |
|
'116963621-117196010', |
|
'071861577-072079000', |
|
'115100359-115329501', |
|
'093383629-093610265', |
|
'063005033-063225851', |
|
'070949552-071266169', |
|
'099869413-100108372', |
|
'019501106-019819591', |
|
'065050472-065270160', |
|
'010264133-010591398', |
|
'111823939-112214079', |
|
'050781945-051067844', |
|
'068107951-068419395', |
|
'092930835-093162837', |
|
'020539033-020894253', |
|
'087967060-088354176', |
|
'120177049-120401132', |
|
'016750754-017033259', |
|
'041088428-041767797', |
|
'112692812-112915011', |
|
'063928702-064149909', |
|
'016226455-016466302', |
|
'063225852-063467303', |
|
'055761164-055986803', |
|
'096589164-096793558', |
|
'116502753-116729000', |
|
'113357214-113596431', |
|
'100785896-101169282' |
|
] |
|
|
|
|
|
class PubChemQCB3LYPConfig(datasets.BuilderConfig): |
|
""" |
|
Configuration class for the PubChemQCB3LYP 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(PubChemQCB3LYPConfig, self).__init__( |
|
version=datasets.Version("0.0.0"), **kwargs |
|
) |
|
self.features = features |
|
self.url = url |
|
self.citation = citation |
|
self.id_range = id_range |
|
|
|
|
|
class PubChemQCB3LYP(datasets.GeneratorBasedBuilder): |
|
|
|
BUILDER_CONFIG_CLASS = PubChemQCB3LYPConfig |
|
|
|
DEFAULT_CONFIG_NAME = "b3lyp_pm6" |
|
|
|
VERSION = datasets.Version("0.0.0") |
|
|
|
url = "https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp" |
|
|
|
BUILDER_CONFIGS = [ |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6, |
|
), |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6_chon300nosalt", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6_CHON300NOSALT, |
|
), |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6_chon500nosalt", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6_CHON500NOSALT, |
|
), |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6_chnopsfcl300nosalt", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6_CHNOPSFCL300NOSALT, |
|
), |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6_chnopsfcl500nosalt", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6_CHNOPSFCL500NOSALT, |
|
), |
|
PubChemQCB3LYPConfig( |
|
name="b3lyp_pm6_chnopsfclnakmgca500", |
|
description=_DESCRIPTION, |
|
features=_FEATURE_KEYS, |
|
url=url, |
|
citation=_CITATION, |
|
id_range=_ID_RANGES_B3LYP_PM6_CHNOPSFCLNAKMGCA500, |
|
) |
|
] |
|
|
|
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") |
|
|
