Commit
·
e597249
1
Parent(s):
d0a41de
adds the load script
Browse filesminor change to the load script
minor change to the load script
- pubchemqc-pm6.py +2732 -0
pubchemqc-pm6.py
ADDED
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@@ -0,0 +1,2732 @@
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| 1 |
+
# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
|
| 2 |
+
#
|
| 3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
| 4 |
+
# you may not use this file except in compliance with the License.
|
| 5 |
+
# You may obtain a copy of the License at
|
| 6 |
+
#
|
| 7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
| 8 |
+
#
|
| 9 |
+
# Unless required by applicable law or agreed to in writing, software
|
| 10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
| 11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
| 12 |
+
# See the License for the specific language governing permissions and
|
| 13 |
+
# limitations under the License.
|
| 14 |
+
"""loading script for the pubchemqc-pm6 data"""
|
| 15 |
+
|
| 16 |
+
import ijson
|
| 17 |
+
import datasets
|
| 18 |
+
|
| 19 |
+
|
| 20 |
+
_CITATION = """\
|
| 21 |
+
@article{Nakata:2020:5891,
|
| 22 |
+
author = {Maho Nakata and Tomomi Shimazaki and Masatomo Hashimoto and Toshiyuki Maeda},
|
| 23 |
+
doi = {10.1021/acs.jcim.0c00740},
|
| 24 |
+
issn = {1549960X},
|
| 25 |
+
issue = {12},
|
| 26 |
+
journal = {Journal of Chemical Information and Modeling},
|
| 27 |
+
month = {12},
|
| 28 |
+
pages = {5891-5899},
|
| 29 |
+
pmid = {33104339},
|
| 30 |
+
publisher = {American Chemical Society},
|
| 31 |
+
title = {PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties},
|
| 32 |
+
volume = {60},
|
| 33 |
+
url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740},
|
| 34 |
+
year = {2020},
|
| 35 |
+
}
|
| 36 |
+
"""
|
| 37 |
+
|
| 38 |
+
_DESCRIPTION = """\
|
| 39 |
+
The PubChemQC PM6 dataset consists of optimized molecular geometries \
|
| 40 |
+
and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million \
|
| 41 |
+
molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to \
|
| 42 |
+
neutral states, the cationic, anionic, and spin flipped electronic states of respectively \
|
| 43 |
+
56.2%, 49.7%, and 41.3% of the molecules have also been studied. As such, the grand total \
|
| 44 |
+
of the PM6 calculations amounted to 221 million.
|
| 45 |
+
"""
|
| 46 |
+
|
| 47 |
+
_HOMEPAGE = "https://nakatamaho.riken.jp/pubchemqc.riken.jp/pm6_datasets.html"
|
| 48 |
+
|
| 49 |
+
_LICENSE = "https://creativecommons.org/licenses/by/4.0"
|
| 50 |
+
|
| 51 |
+
|
| 52 |
+
_BASE_DATA_URL_FORMAT_STR = "https://huggingface.co/datasets/molssiai-hub/pubchemqc-pm6/resolve/main/data/{name}/train/{range}.json"
|
| 53 |
+
|
| 54 |
+
_CONFIG_NAMES = [
|
| 55 |
+
"pm6opt",
|
| 56 |
+
"pm6opt_chon300nosalt",
|
| 57 |
+
"pm6opt_chon500nosalt",
|
| 58 |
+
"pm6opt_chnops500nosalt"
|
| 59 |
+
"pm6opt_chnopsfcl300nosalt",
|
| 60 |
+
"pm6opt_chnopsfcl500nosalt",
|
| 61 |
+
"pm6opt_chnopsfclnakmgca500"
|
| 62 |
+
]
|
| 63 |
+
|
| 64 |
+
_FEATURE_KEYS = [
|
| 65 |
+
'cid',
|
| 66 |
+
'state',
|
| 67 |
+
'pubchem-inchi',
|
| 68 |
+
'pubchem-charge',
|
| 69 |
+
'pubchem-version',
|
| 70 |
+
'name',
|
| 71 |
+
'coordinates',
|
| 72 |
+
'atomic-numbers',
|
| 73 |
+
'atom-count',
|
| 74 |
+
'heavy-atom-count',
|
| 75 |
+
'core-electrons',
|
| 76 |
+
'version',
|
| 77 |
+
'obabel-inchi',
|
| 78 |
+
'pm6-obabel-canonical-smiles',
|
| 79 |
+
'charge',
|
| 80 |
+
'energy-beta-gap',
|
| 81 |
+
'energy-beta-homo',
|
| 82 |
+
'energy-beta-lumo',
|
| 83 |
+
'energy-alpha-gap',
|
| 84 |
+
'energy-alpha-homo',
|
| 85 |
+
'energy-alpha-lumo',
|
| 86 |
+
'total-energy',
|
| 87 |
+
'enthalpy',
|
| 88 |
+
'homos',
|
| 89 |
+
'orbital-energies',
|
| 90 |
+
'mo-count',
|
| 91 |
+
'basis-count',
|
| 92 |
+
'temperature',
|
| 93 |
+
'multiplicity',
|
| 94 |
+
'number-of-atoms',
|
| 95 |
+
'mulliken-partial-charges',
|
| 96 |
+
'dipole-moment',
|
| 97 |
+
'frequencies',
|
| 98 |
+
'intensities',
|
| 99 |
+
'pubchem-multiplicity',
|
| 100 |
+
'pubchem-obabel-canonical-smiles',
|
| 101 |
+
'pubchem-isomeric-smiles',
|
| 102 |
+
'pubchem-molecular-weight',
|
| 103 |
+
'pubchem-molecular-formula'
|
| 104 |
+
]
|
| 105 |
+
|
| 106 |
+
_FEATURE_TYPES = datasets.Features(
|
| 107 |
+
{
|
| 108 |
+
'cid': datasets.Value(dtype='int64', id=None),
|
| 109 |
+
'state': datasets.Value(dtype='string', id=None),
|
| 110 |
+
'pubchem-inchi': datasets.Value(dtype='string', id=None),
|
| 111 |
+
'pubchem-charge': datasets.Value(dtype='int64', id=None),
|
| 112 |
+
'pubchem-version': datasets.Value(dtype='string', id=None),
|
| 113 |
+
'name': datasets.Value(dtype='string', id=None),
|
| 114 |
+
'coordinates': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None),
|
| 115 |
+
'atomic-numbers': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None),
|
| 116 |
+
'atom-count': datasets.Value(dtype='int64', id=None),
|
| 117 |
+
'heavy-atom-count': datasets.Value(dtype='int64', id=None),
|
| 118 |
+
'core-electrons': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None),
|
| 119 |
+
'version': datasets.Value(dtype='string', id=None),
|
| 120 |
+
'obabel-inchi': datasets.Value(dtype='string', id=None),
|
| 121 |
+
'pm6-obabel-canonical-smiles': datasets.Value(dtype='string', id=None),
|
| 122 |
+
'charge': datasets.Value(dtype='int64', id=None),
|
| 123 |
+
'energy-beta-gap': datasets.Value(dtype='float64', id=None),
|
| 124 |
+
'energy-beta-homo': datasets.Value(dtype='float64', id=None),
|
| 125 |
+
'energy-beta-lumo': datasets.Value(dtype='float64', id=None),
|
| 126 |
+
'energy-alpha-gap': datasets.Value(dtype='float64', id=None),
|
| 127 |
+
'energy-alpha-homo': datasets.Value(dtype='float64', id=None),
|
| 128 |
+
'energy-alpha-lumo': datasets.Value(dtype='float64', id=None),
|
| 129 |
+
'total-energy': datasets.Value(dtype='float64', id=None),
|
| 130 |
+
'enthalpy': datasets.Value(dtype='float64', id=None),
|
| 131 |
+
'homos': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None),
|
| 132 |
+
'orbital-energies': datasets.Sequence(feature=datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None), length=-1, id=None),
|
| 133 |
+
'mo-count': datasets.Value(dtype='int64', id=None),
|
| 134 |
+
'basis-count': datasets.Value(dtype='int64', id=None),
|
| 135 |
+
'temperature': datasets.Value(dtype='float64', id=None),
|
| 136 |
+
'multiplicity': datasets.Value(dtype='int64', id=None),
|
| 137 |
+
'number-of-atoms': datasets.Value(dtype='int64', id=None),
|
| 138 |
+
'mulliken-partial-charges': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None),
|
| 139 |
+
'dipole-moment': datasets.Value(dtype='float64', id=None),
|
| 140 |
+
'frequencies': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None),
|
| 141 |
+
'intensities': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None),
|
| 142 |
+
'pubchem-multiplicity': datasets.Value(dtype='int64', id=None),
|
| 143 |
+
'pubchem-obabel-canonical-smiles': datasets.Value(dtype='string', id=None),
|
| 144 |
+
'pubchem-isomeric-smiles': datasets.Value(dtype='string', id=None),
|
| 145 |
+
'pubchem-molecular-weight': datasets.Value(dtype='float64', id=None),
|
| 146 |
+
'pubchem-molecular-formula': datasets.Value(dtype='string', id=None)
|
| 147 |
+
}
|
| 148 |
+
)
|
| 149 |
+
|
| 150 |
+
_ID_RANGES_PM6OPT = [
|
| 151 |
+
"066015983-066097499"
|
| 152 |
+
"087000776-087089527"
|
| 153 |
+
"058677778-058765750"
|
| 154 |
+
"110162376-110239526"
|
| 155 |
+
"028335040-028468283"
|
| 156 |
+
"092243704-092322956"
|
| 157 |
+
"065860342-065940848"
|
| 158 |
+
"058940206-059028518"
|
| 159 |
+
"083580669-083651806"
|
| 160 |
+
"002863460-002944485"
|
| 161 |
+
"019303895-019404899"
|
| 162 |
+
"110472971-110547341"
|
| 163 |
+
"093654011-093728754"
|
| 164 |
+
"063053850-063129974"
|
| 165 |
+
"009057356-009150515"
|
| 166 |
+
"119450152-119540216"
|
| 167 |
+
"115923626-116001333"
|
| 168 |
+
"066820335-066901840"
|
| 169 |
+
"107230203-107308139"
|
| 170 |
+
"025163647-025254021"
|
| 171 |
+
"054951146-055029921"
|
| 172 |
+
"018914660-019029351"
|
| 173 |
+
"051326288-051439489"
|
| 174 |
+
"040446496-040597112"
|
| 175 |
+
"043611506-043687973"
|
| 176 |
+
"068165803-068243974"
|
| 177 |
+
"009630576-009755333"
|
| 178 |
+
"108566095-108637767"
|
| 179 |
+
"067562913-067648683"
|
| 180 |
+
"005662914-005773947"
|
| 181 |
+
"117704585-117791505"
|
| 182 |
+
"107783345-107859775"
|
| 183 |
+
"056383674-056463371"
|
| 184 |
+
"110610483-110686156"
|
| 185 |
+
"118456152-118542296"
|
| 186 |
+
"079169537-079246597"
|
| 187 |
+
"059468972-059556151"
|
| 188 |
+
"096462695-096541074"
|
| 189 |
+
"103873819-103951864"
|
| 190 |
+
"061048585-061128439"
|
| 191 |
+
"052496981-052594278"
|
| 192 |
+
"003035994-003129705"
|
| 193 |
+
"069398027-069481121"
|
| 194 |
+
"094038248-094115359"
|
| 195 |
+
"112552950-112629205"
|
| 196 |
+
"056063012-056144045"
|
| 197 |
+
"116330579-116409861"
|
| 198 |
+
"108637768-108709511"
|
| 199 |
+
"106764676-106840887"
|
| 200 |
+
"082159509-082236637"
|
| 201 |
+
"117097881-117170243"
|
| 202 |
+
"097905831-097987765"
|
| 203 |
+
"071334081-071415976"
|
| 204 |
+
"108108664-108186188"
|
| 205 |
+
"002778591-002863459"
|
| 206 |
+
"042742767-042821083"
|
| 207 |
+
"100571670-100662063"
|
| 208 |
+
"061205573-061281063"
|
| 209 |
+
"116081527-116165680"
|
| 210 |
+
"105111750-105193248"
|
| 211 |
+
"077030676-077419252"
|
| 212 |
+
"113501324-113579573"
|
| 213 |
+
"024282066-024380305"
|
| 214 |
+
"106292691-106373872"
|
| 215 |
+
"026275129-026476509"
|
| 216 |
+
"115445242-115521464"
|
| 217 |
+
"092082521-092162916"
|
| 218 |
+
"041564061-041960811"
|
| 219 |
+
"071840253-071918309"
|
| 220 |
+
"059906656-060001356"
|
| 221 |
+
"115291115-115366819"
|
| 222 |
+
"011070192-011156086"
|
| 223 |
+
"056881960-056962300"
|
| 224 |
+
"093418543-093497510"
|
| 225 |
+
"016095098-016248698"
|
| 226 |
+
"098942473-099021031"
|
| 227 |
+
"009755333-009874014"
|
| 228 |
+
"058156884-058243237"
|
| 229 |
+
"058500038-058586074"
|
| 230 |
+
"078862267-078938945"
|
| 231 |
+
"096315481-096387594"
|
| 232 |
+
"081481442-081562021"
|
| 233 |
+
"070846446-070926197"
|
| 234 |
+
"117465558-117542766"
|
| 235 |
+
"083941800-084015009"
|
| 236 |
+
"084015009-084088357"
|
| 237 |
+
"005287890-005374110"
|
| 238 |
+
"071415977-071501913"
|
| 239 |
+
"080563506-080643422"
|
| 240 |
+
"083651806-083724315"
|
| 241 |
+
"118542297-118624626"
|
| 242 |
+
"050506208-050617537"
|
| 243 |
+
"108788737-108859590"
|
| 244 |
+
"089587115-089669128"
|
| 245 |
+
"096387595-096462694"
|
| 246 |
+
"105654558-105729165"
|
| 247 |
+
"113816770-113895063"
|
| 248 |
+
"053802949-053907680"
|
| 249 |
+
"112315312-112394805"
|
| 250 |
+
"041097107-041265411"
|
| 251 |
+
"057469359-057556555"
|
| 252 |
+
"055582023-055662290"
|
| 253 |
+
"086662480-086746558"
|
| 254 |
+
"080722059-080795256"
|
| 255 |
+
"045517727-045615284"
|
| 256 |
+
"043840812-043932688"
|
| 257 |
+
"082456990-082528214"
|
| 258 |
+
"063129974-063203757"
|
| 259 |
+
"042388034-042563000"
|
| 260 |
+
"086918676-087000776"
|
| 261 |
+
"108491327-108566095"
|
| 262 |
+
"096759084-096834427"
|
| 263 |
+
"022010173-022119709"
|
| 264 |
+
"098314776-098407999"
|
| 265 |
+
"042821083-042896802"
|
| 266 |
+
"058243238-058329785"
|
| 267 |
+
"105504519-105581215"
|
| 268 |
+
"080331177-080405307"
|
| 269 |
+
"050079847-050161916"
|
| 270 |
+
"104571616-104647675"
|
| 271 |
+
"031569351-032148590"
|
| 272 |
+
"093880995-093960333"
|
| 273 |
+
"095797243-095873759"
|
| 274 |
+
"045088323-045185345"
|
| 275 |
+
"072070630-072147336"
|
| 276 |
+
"017405938-017488429"
|
| 277 |
+
"053169985-053249089"
|
| 278 |
+
"075363179-075441732"
|
| 279 |
+
"045706645-045795536"
|
| 280 |
+
"007153661-007252410"
|
| 281 |
+
"120962075-121046734"
|
| 282 |
+
"095190205-095265770"
|
| 283 |
+
"110761171-110836144"
|
| 284 |
+
"052089989-052187934"
|
| 285 |
+
"008658138-008761733"
|
| 286 |
+
"101039928-101134116"
|
| 287 |
+
"104415419-104492785"
|
| 288 |
+
"094344520-094420402"
|
| 289 |
+
"116409861-116490425"
|
| 290 |
+
"047092309-047472487"
|
| 291 |
+
"064686967-064762309"
|
| 292 |
+
"105968306-106053088"
|
| 293 |
+
"011580729-011665553"
|
| 294 |
+
"109841428-109925982"
|
| 295 |
+
"001065437-001153278"
|
| 296 |
+
"004378517-004469559"
|
| 297 |
+
"050808907-050886215"
|
| 298 |
+
"080863729-080939123"
|
| 299 |
+
"079324945-079401185"
|
| 300 |
+
"025372233-025520420"
|
| 301 |
+
"094729853-094802183"
|
| 302 |
+
"012549878-012827652"
|
| 303 |
+
"108342164-108419919"
|
| 304 |
+
"023110547-023253749"
|
| 305 |
+
"020741611-020841289"
|
| 306 |
+
"101428162-101519819"
|
| 307 |
+
"027823200-028162720"
|
| 308 |
+
"119717691-119804932"
|
| 309 |
+
"082672792-082749196"
|
| 310 |
+
"004103812-004196635"
|
| 311 |
+
"087563727-087658817"
|
| 312 |
+
"102451948-102541869"
|
| 313 |
+
"059383446-059468972"
|
| 314 |
+
"044214649-044313228"
|
| 315 |
+
"018221966-018303234"
|
| 316 |
+
"000551686-000635379"
|
| 317 |
+
"065072588-065153994"
|
| 318 |
+
"071676359-071758580"
|
| 319 |
+
"079401186-079481250"
|
| 320 |
+
"111283310-111379148"
|
| 321 |
+
"055741846-055820820"
|
| 322 |
+
"114448366-114523059"
|
| 323 |
+
"043457009-043535162"
|
| 324 |
+
"050980849-051084840"
|
| 325 |
+
"027437271-027823200"
|
| 326 |
+
"087280093-087372083"
|
| 327 |
+
"061281063-061357969"
|
| 328 |
+
"116717146-116792426"
|
| 329 |
+
"101709724-101804219"
|
| 330 |
+
"052003451-052089988"
|
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]
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_ID_RANGES_PM6OPT_CHNOPSFCL300NOSALT = [
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| 1876 |
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| 1880 |
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|
| 1882 |
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"118002778-119031056"
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| 1884 |
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"061540097-061792479"
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| 1885 |
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"065607315-065911788"
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| 1886 |
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"080035822-080294251"
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| 1887 |
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"104965124-105239608"
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| 1888 |
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"012201043-013408394"
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| 1889 |
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"043078546-043344201"
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"081062057-081336094"
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]
|
| 1901 |
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|
| 1902 |
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_ID_RANGES_PM6OPT_CHNOPSFCL500NOSALT = [
|
| 1903 |
+
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|
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|
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"033830709-035756683"
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| 1910 |
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"100470476-100799822"
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|
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"071175972-071510549"
|
| 1920 |
+
"025263589-025649816"
|
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"028940993-029782536"
|
| 1923 |
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"108635755-108896614"
|
| 1924 |
+
"002773739-003056628"
|
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"094481138-094694050"
|
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"117788974-118136146"
|
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|
| 1928 |
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"072044878-072698957"
|
| 1929 |
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"045171565-045601796"
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| 1930 |
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"090636785-091009860"
|
| 1931 |
+
"121020472-121265497"
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| 1932 |
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"102361195-102667531"
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| 1933 |
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"080193965-080417890"
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| 1934 |
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"020484148-020866292"
|
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"101972572-102361190"
|
| 1936 |
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"020866293-021159942"
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"080417891-080653038"
|
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"119104907-119401667"
|
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"052356345-052626206"
|
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"053175144-053493952"
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| 1941 |
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"096801832-097012252"
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"070856066-071175969"
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"005194415-005567108"
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"064991543-065225807"
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"083860456-084081311"
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"051193061-051452580"
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"075427456-076921648"
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"104177840-104424207"
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"084305460-084518952"
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|
| 1961 |
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"057143130-057462370"
|
| 1963 |
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"003056632-003350518"
|
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|
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"004277125-004600210"
|
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+
"070576665-070856065"
|
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+
"115131000-115360792"
|
| 1971 |
+
"069162721-069501916"
|
| 1972 |
+
"000877805-001149297"
|
| 1973 |
+
"008567590-008826056"
|
| 1974 |
+
"113875271-114136168"
|
| 1975 |
+
"115593143-115834250"
|
| 1976 |
+
"110217305-110425553"
|
| 1977 |
+
"041231455-042085866"
|
| 1978 |
+
"115834252-116070747"
|
| 1979 |
+
"026200489-026897956"
|
| 1980 |
+
"056373162-056594262"
|
| 1981 |
+
"109645991-109966162"
|
| 1982 |
+
"101186662-101594890"
|
| 1983 |
+
"120640762-121020471"
|
| 1984 |
+
"079488852-079725762"
|
| 1985 |
+
"030724063-031974690"
|
| 1986 |
+
"043768051-044071184"
|
| 1987 |
+
"105854095-106081187"
|
| 1988 |
+
"121265499-121494125"
|
| 1989 |
+
"105397830-105633044"
|
| 1990 |
+
"112942098-113152717"
|
| 1991 |
+
"003350519-003666543"
|
| 1992 |
+
"113628783-113875270"
|
| 1993 |
+
"116297939-116537976"
|
| 1994 |
+
"082078928-082291859"
|
| 1995 |
+
"000000001-000315275"
|
| 1996 |
+
"110425554-110635678"
|
| 1997 |
+
"068815653-069162720"
|
| 1998 |
+
"023238867-023610576"
|
| 1999 |
+
"095128964-095336949"
|
| 2000 |
+
"066425157-066733543"
|
| 2001 |
+
"060725895-060957780"
|
| 2002 |
+
"079254120-079488851"
|
| 2003 |
+
"013879953-015050535"
|
| 2004 |
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"052083913-052356344"
|
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"109317510-109645989"
|
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"108420534-108635754"
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"063178963-063397950"
|
| 2008 |
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"011701543-012102059"
|
| 2009 |
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"099349137-099581221"
|
| 2010 |
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"065934100-066174851"
|
| 2011 |
+
"055699689-055924493"
|
| 2012 |
+
"103703503-103950327"
|
| 2013 |
+
"047003844-048836659"
|
| 2014 |
+
"000315276-000644650"
|
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"046849965-047096534"
|
| 2349 |
+
"096167368-096374131"
|
| 2350 |
+
"019499639-019817677"
|
| 2351 |
+
"019163484-019499637"
|
| 2352 |
+
"088713208-089068368"
|
| 2353 |
+
"109083263-109290090"
|
| 2354 |
+
"119485424-119709724"
|
| 2355 |
+
"042775566-043004122"
|
| 2356 |
+
"054877869-055103282"
|
| 2357 |
+
"082299537-082510706"
|
| 2358 |
+
"023994172-024348023"
|
| 2359 |
+
"098876424-099103940"
|
| 2360 |
+
"068102007-068414459"
|
| 2361 |
+
"100778804-101156832"
|
| 2362 |
+
"025517537-025948785"
|
| 2363 |
+
"111809830-112200149"
|
| 2364 |
+
"112685457-112907921"
|
| 2365 |
+
"111111071-111462637"
|
| 2366 |
+
"045713236-045936295"
|
| 2367 |
+
"024348024-024566747"
|
| 2368 |
+
"063705547-063925549"
|
| 2369 |
+
"108866776-109083262"
|
| 2370 |
+
"113349095-113589080"
|
| 2371 |
+
"099333223-099555501"
|
| 2372 |
+
"043685335-043964411"
|
| 2373 |
+
"022363703-022715302"
|
| 2374 |
+
"106050295-106286232"
|
| 2375 |
+
"025143640-025517535"
|
| 2376 |
+
"055541456-055758720"
|
| 2377 |
+
"115092944-115321300"
|
| 2378 |
+
"056207100-056432219"
|
| 2379 |
+
"090106841-090460109"
|
| 2380 |
+
"120393315-120614110"
|
| 2381 |
+
"062777451-063001891"
|
| 2382 |
+
"003896331-004218885"
|
| 2383 |
+
"055984342-056207099"
|
| 2384 |
+
"015550301-016224480"
|
| 2385 |
+
"104397438-104627125"
|
| 2386 |
+
"093155911-093376208"
|
| 2387 |
+
"079498950-079737610"
|
| 2388 |
+
"091692063-091959633"
|
| 2389 |
+
"084088398-084312800"
|
| 2390 |
+
"094043598-094255997"
|
| 2391 |
+
"009541875-009924481"
|
| 2392 |
+
"035276903-037195982"
|
| 2393 |
+
"087562071-087957458"
|
| 2394 |
+
"011927481-012629148"
|
| 2395 |
+
"118386799-118730309"
|
| 2396 |
+
"094255998-094465999"
|
| 2397 |
+
"017032055-017374067"
|
| 2398 |
+
"040603662-041084773"
|
| 2399 |
+
"093604022-093826262"
|
| 2400 |
+
"056432220-056692569"
|
| 2401 |
+
"089068369-089423128"
|
| 2402 |
+
"018433701-018796616"
|
| 2403 |
+
"070943634-071258680"
|
| 2404 |
+
"000858465-001127153"
|
| 2405 |
+
"000000001-000298189"
|
| 2406 |
+
"007562989-007797449"
|
| 2407 |
+
"113835771-114099716"
|
| 2408 |
+
"114099717-114351120"
|
| 2409 |
+
"009924482-010263339"
|
| 2410 |
+
"021197931-021573920"
|
| 2411 |
+
"108087016-108379630"
|
| 2412 |
+
"039969566-040603658"
|
| 2413 |
+
"082087414-082299536"
|
| 2414 |
+
"008510331-008765938"
|
| 2415 |
+
"076945829-078822220"
|
| 2416 |
+
"058584084-058956679"
|
| 2417 |
+
"094902473-095114347"
|
| 2418 |
+
"030369115-031432227"
|
| 2419 |
+
"049711825-050779850"
|
| 2420 |
+
"095537291-095750869"
|
| 2421 |
+
"104884625-105125763"
|
| 2422 |
+
"052466944-052729525"
|
| 2423 |
+
"084312801-084525089"
|
| 2424 |
+
"051064901-051274609"
|
| 2425 |
+
"014622187-015550300"
|
| 2426 |
+
"042429279-042775565"
|
| 2427 |
+
"119932596-120168955"
|
| 2428 |
+
"073919013-075447598"
|
| 2429 |
+
"016224481-016464425"
|
| 2430 |
+
"107474532-107768729"
|
| 2431 |
+
"119264143-119485423"
|
| 2432 |
+
"071857206-072074043"
|
| 2433 |
+
"118730310-119026878"
|
| 2434 |
+
"063001892-063222622"
|
| 2435 |
+
"066472149-066786139"
|
| 2436 |
+
"113118767-113349094"
|
| 2437 |
+
"056919851-057211240"
|
| 2438 |
+
"012629153-013490466"
|
| 2439 |
+
"063222623-063463293"
|
| 2440 |
+
"043004123-043228657"
|
| 2441 |
+
"092481296-092700226"
|
| 2442 |
+
"062342013-062558470"
|
| 2443 |
+
"045936298-046222507"
|
| 2444 |
+
"046222508-046493015"
|
| 2445 |
+
"064818264-065047283"
|
| 2446 |
+
"028766925-029397691"
|
| 2447 |
+
"084757188-086604608"
|
| 2448 |
+
"089423129-089761378"
|
| 2449 |
+
"081872596-082087413"
|
| 2450 |
+
"092700227-092924466"
|
| 2451 |
+
"053036841-053270651"
|
| 2452 |
+
"116255202-116495191"
|
| 2453 |
+
"051274610-051599174"
|
| 2454 |
+
"087178776-087562070"
|
| 2455 |
+
"017597264-018130067"
|
| 2456 |
+
"002135339-002459085"
|
| 2457 |
+
"072074044-072837712"
|
| 2458 |
+
"004218886-004542390"
|
| 2459 |
+
"079264093-079498949"
|
| 2460 |
+
"000298192-000618347"
|
| 2461 |
+
"056692570-056919850"
|
| 2462 |
+
"099103941-099333222"
|
| 2463 |
+
"002459086-002750683"
|
| 2464 |
+
"051599175-051913068"
|
| 2465 |
+
"028318764-028766923"
|
| 2466 |
+
"044292533-044909316"
|
| 2467 |
+
"084525090-084757187"
|
| 2468 |
+
"066786142-067119443"
|
| 2469 |
+
"095114348-095322243"
|
| 2470 |
+
"120844197-121080503"
|
| 2471 |
+
"060322624-060540596"
|
| 2472 |
+
"027514494-028318763"
|
| 2473 |
+
"059675985-060042370"
|
| 2474 |
+
"026645133-027514492"
|
| 2475 |
+
"110604556-110810365"
|
| 2476 |
+
"067119444-067443371"
|
| 2477 |
+
"069056287-069377478"
|
| 2478 |
+
"021573921-021980476"
|
| 2479 |
+
"109290091-109601060"
|
| 2480 |
+
"050779851-051064899"
|
| 2481 |
+
"108607951-108866775"
|
| 2482 |
+
"052729526-053036840"
|
| 2483 |
+
"052188113-052466942"
|
| 2484 |
+
"013490470-014622182"
|
| 2485 |
+
"043228658-043456099"
|
| 2486 |
+
"005463110-005956813"
|
| 2487 |
+
"063463294-063705546"
|
| 2488 |
+
"006446616-006912168"
|
| 2489 |
+
"041757291-042429278"
|
| 2490 |
+
"112200151-112463911"
|
| 2491 |
+
"097208508-097421575"
|
| 2492 |
+
"000618348-000858464"
|
| 2493 |
+
"009023155-009281517"
|
| 2494 |
+
"068414460-068736100"
|
| 2495 |
+
"114351121-114594093"
|
| 2496 |
+
"063925551-064146771"
|
| 2497 |
+
"089761379-090106839"
|
| 2498 |
+
"119709725-119932593"
|
| 2499 |
+
"082992507-083220779"
|
| 2500 |
+
"064379458-064599710"
|
| 2501 |
+
"092924467-093155910"
|
| 2502 |
+
"107768730-108087015"
|
| 2503 |
+
"071258681-071577885"
|
| 2504 |
+
"091383793-091692062"
|
| 2505 |
+
"010263340-010590462"
|
| 2506 |
+
"103922104-104150891"
|
| 2507 |
+
"009281519-009541874"
|
| 2508 |
+
"053564053-053877584"
|
| 2509 |
+
"043964417-044292530"
|
| 2510 |
+
"055758721-055984341"
|
| 2511 |
+
"022715303-023142703"
|
| 2512 |
+
"005956815-006446615"
|
| 2513 |
+
"121080504-121338418"
|
| 2514 |
+
"102890635-103119776"
|
| 2515 |
+
"065975552-066217380"
|
| 2516 |
+
"110394420-110604555"
|
| 2517 |
+
"010915402-011256444"
|
| 2518 |
+
"011593760-011927480"
|
| 2519 |
+
"080683248-080903159"
|
| 2520 |
+
"008765939-009023151"
|
| 2521 |
+
"101156840-101560752"
|
| 2522 |
+
"060775110-061002140"
|
| 2523 |
+
"068736101-069056286"
|
| 2524 |
+
"062123188-062342012"
|
| 2525 |
+
"115551568-115783099"
|
| 2526 |
+
"072837713-073919012"
|
| 2527 |
+
"064599711-064818263"
|
| 2528 |
+
"102316362-102641049"
|
| 2529 |
+
"096374132-096582664"
|
| 2530 |
+
"044909320-045354865"
|
| 2531 |
+
"090460110-090704675"
|
| 2532 |
+
"081639112-081872594"
|
| 2533 |
+
"054236738-054594086"
|
| 2534 |
+
"058956680-059325141"
|
| 2535 |
+
"098219180-098630533"
|
| 2536 |
+
"001406672-001737952"
|
| 2537 |
+
"070366892-070671542"
|
| 2538 |
+
"117187178-117403054"
|
| 2539 |
+
"017374068-017597263"
|
| 2540 |
+
"103348550-103590208"
|
| 2541 |
+
"001127154-001406671"
|
| 2542 |
+
"094466000-094679458"
|
| 2543 |
+
"116721684-116956007"
|
| 2544 |
+
"079737611-079969460"
|
| 2545 |
+
"082510707-082730510"
|
| 2546 |
+
"091959634-092249523"
|
| 2547 |
+
"091053274-091383787"
|
| 2548 |
+
"105370850-105605696"
|
| 2549 |
+
"031432263-033082648"
|
| 2550 |
+
"097421583-097637261"
|
| 2551 |
+
"080903160-081126250"
|
| 2552 |
+
"061232897-061458747"
|
| 2553 |
+
"119026879-119264142"
|
| 2554 |
+
"110810366-111111070"
|
| 2555 |
+
"039134454-039969565"
|
| 2556 |
+
"097637262-097863454"
|
| 2557 |
+
"058237797-058584083"
|
| 2558 |
+
"020892923-021197930"
|
| 2559 |
+
"016749020-017032054"
|
| 2560 |
+
"003608817-003896329"
|
| 2561 |
+
"061458748-061681960"
|
| 2562 |
+
"116495192-116721683"
|
| 2563 |
+
"079969461-080205407"
|
| 2564 |
+
"037195989-039134452"
|
| 2565 |
+
"047096535-049711824"
|
| 2566 |
+
"071577886-071857205"
|
| 2567 |
+
"116956008-117187177"
|
| 2568 |
+
"115783100-116026043"
|
| 2569 |
+
"116026044-116255201"
|
| 2570 |
+
"108379631-108607950"
|
| 2571 |
+
"107237951-107474531"
|
| 2572 |
+
"103119777-103348549"
|
| 2573 |
+
"106521269-106751562"
|
| 2574 |
+
"075447600-076945828"
|
| 2575 |
+
"007280011-007562988"
|
| 2576 |
+
"004843212-005134964"
|
| 2577 |
+
"083646795-083868534"
|
| 2578 |
+
"005134965-005463109"
|
| 2579 |
+
"113589081-113835770"
|
| 2580 |
+
"095750870-095959827"
|
| 2581 |
+
"087957459-088344699"
|
| 2582 |
+
"018130068-018433700"
|
| 2583 |
+
"105605697-105826668"
|
| 2584 |
+
"008027595-008271155"
|
| 2585 |
+
"001737953-002135337"
|
| 2586 |
+
"106286233-106521268"
|
| 2587 |
+
"059325143-059675984"
|
| 2588 |
+
"080428165-080683247"
|
| 2589 |
+
"002750684-003003995"
|
| 2590 |
+
"121338419-121494125"
|
| 2591 |
+
"099555502-099859737"
|
| 2592 |
+
]
|
| 2593 |
+
|
| 2594 |
+
|
| 2595 |
+
class PubChemQCPM6Config(datasets.BuilderConfig):
|
| 2596 |
+
"""
|
| 2597 |
+
Configuration class for the PubChemQC PM6 dataset.
|
| 2598 |
+
Args:
|
| 2599 |
+
features (dict): A dictionary specifying the features of the dataset.
|
| 2600 |
+
data_url (str): The URL to download the dataset.
|
| 2601 |
+
url (str): The URL to the dataset homepage.
|
| 2602 |
+
citation (str): The citation for the dataset.
|
| 2603 |
+
**kwargs: Additional keyword arguments.
|
| 2604 |
+
Attributes:
|
| 2605 |
+
version (datasets.Version): The version of the dataset.
|
| 2606 |
+
"""
|
| 2607 |
+
|
| 2608 |
+
def __init__(self, features, url, citation, id_range, **kwargs):
|
| 2609 |
+
super(PubChemQCPM6Config, self).__init__(
|
| 2610 |
+
version=datasets.Version("2.0.0"), **kwargs
|
| 2611 |
+
)
|
| 2612 |
+
self.features = features
|
| 2613 |
+
self.url = url
|
| 2614 |
+
self.citation = citation
|
| 2615 |
+
self.id_range = id_range
|
| 2616 |
+
|
| 2617 |
+
|
| 2618 |
+
class PubChemQCPM6(datasets.GeneratorBasedBuilder):
|
| 2619 |
+
|
| 2620 |
+
BUILDER_CONFIG_CLASS = PubChemQCPM6Config
|
| 2621 |
+
|
| 2622 |
+
DEFAULT_CONFIG_NAME = "pm6opt"
|
| 2623 |
+
|
| 2624 |
+
VERSION = datasets.Version("2.0.0")
|
| 2625 |
+
|
| 2626 |
+
url = "https://huggingface.co/datasets/molssiai-hub/pubchemqc-pm6"
|
| 2627 |
+
|
| 2628 |
+
BUILDER_CONFIGS = [
|
| 2629 |
+
PubChemQCPM6Config(
|
| 2630 |
+
name="pm6opt",
|
| 2631 |
+
description=_DESCRIPTION,
|
| 2632 |
+
features=_FEATURE_KEYS,
|
| 2633 |
+
url=url,
|
| 2634 |
+
citation=_CITATION,
|
| 2635 |
+
id_range=_ID_RANGES_PM6OPT,
|
| 2636 |
+
),
|
| 2637 |
+
PubChemQCPM6Config(
|
| 2638 |
+
name="pm6opt_chon300nosalt",
|
| 2639 |
+
description=_DESCRIPTION,
|
| 2640 |
+
features=_FEATURE_KEYS,
|
| 2641 |
+
url=url,
|
| 2642 |
+
citation=_CITATION,
|
| 2643 |
+
id_range=_ID_RANGES_PM6OPT_CHON300NOSALT,
|
| 2644 |
+
),
|
| 2645 |
+
PubChemQCPM6Config(
|
| 2646 |
+
name="pm6opt_chon500nosalt",
|
| 2647 |
+
description=_DESCRIPTION,
|
| 2648 |
+
features=_FEATURE_KEYS,
|
| 2649 |
+
url=url,
|
| 2650 |
+
citation=_CITATION,
|
| 2651 |
+
id_range=_ID_RANGES_PM6OPT_CHON500NOSALT,
|
| 2652 |
+
),
|
| 2653 |
+
PubChemQCPM6Config(
|
| 2654 |
+
name="pm6opt_chnops500nosalt",
|
| 2655 |
+
description=_DESCRIPTION,
|
| 2656 |
+
features=_FEATURE_KEYS,
|
| 2657 |
+
url=url,
|
| 2658 |
+
citation=_CITATION,
|
| 2659 |
+
id_range=_ID_RANGES_PM6OPT_CHNOPS500NOSALT,
|
| 2660 |
+
),
|
| 2661 |
+
PubChemQCPM6Config(
|
| 2662 |
+
name="pm6opt_chnopsfcl300nosalt",
|
| 2663 |
+
description=_DESCRIPTION,
|
| 2664 |
+
features=_FEATURE_KEYS,
|
| 2665 |
+
url=url,
|
| 2666 |
+
citation=_CITATION,
|
| 2667 |
+
id_range=_ID_RANGES_PM6OPT_CHNOPSFCL300NOSALT,
|
| 2668 |
+
),
|
| 2669 |
+
PubChemQCPM6Config(
|
| 2670 |
+
name="pm6opt_chnopsfcl500nosalt",
|
| 2671 |
+
description=_DESCRIPTION,
|
| 2672 |
+
features=_FEATURE_KEYS,
|
| 2673 |
+
url=url,
|
| 2674 |
+
citation=_CITATION,
|
| 2675 |
+
id_range=_ID_RANGES_PM6OPT_CHNOPSFCL500NOSALT,
|
| 2676 |
+
),
|
| 2677 |
+
PubChemQCPM6Config(
|
| 2678 |
+
name="pm6opt_chnopsfclnakmgca500",
|
| 2679 |
+
description=_DESCRIPTION,
|
| 2680 |
+
features=_FEATURE_KEYS,
|
| 2681 |
+
url=url,
|
| 2682 |
+
citation=_CITATION,
|
| 2683 |
+
id_range=_ID_RANGES_PM6OPT_CHNOPSFCLNAKMGCA500,
|
| 2684 |
+
)
|
| 2685 |
+
]
|
| 2686 |
+
|
| 2687 |
+
def _info(self):
|
| 2688 |
+
if self.config.name in _CONFIG_NAMES:
|
| 2689 |
+
features = _FEATURE_TYPES
|
| 2690 |
+
else:
|
| 2691 |
+
raise NotImplementedError("Unknown configuration in _info")
|
| 2692 |
+
|
| 2693 |
+
return datasets.DatasetInfo(
|
| 2694 |
+
description=_DESCRIPTION,
|
| 2695 |
+
features=features,
|
| 2696 |
+
homepage=_HOMEPAGE,
|
| 2697 |
+
supervised_keys=None,
|
| 2698 |
+
license=_LICENSE,
|
| 2699 |
+
citation=_CITATION,
|
| 2700 |
+
)
|
| 2701 |
+
|
| 2702 |
+
def _split_generators(self, dl_manager):
|
| 2703 |
+
if self.config.name in _CONFIG_NAMES:
|
| 2704 |
+
file_list = []
|
| 2705 |
+
for range in self.config.id_range:
|
| 2706 |
+
file_list.append(_BASE_DATA_URL_FORMAT_STR.format(
|
| 2707 |
+
name=self.config.name, range=range))
|
| 2708 |
+
else:
|
| 2709 |
+
raise NotImplementedError(
|
| 2710 |
+
"Unknown configuration in _split_generators")
|
| 2711 |
+
|
| 2712 |
+
return [
|
| 2713 |
+
datasets.SplitGenerator(
|
| 2714 |
+
name=datasets.Split.TRAIN,
|
| 2715 |
+
gen_kwargs={
|
| 2716 |
+
"filepaths": dl_manager.download(sorted(file_list)),
|
| 2717 |
+
},
|
| 2718 |
+
)
|
| 2719 |
+
]
|
| 2720 |
+
|
| 2721 |
+
def _generate_examples(self, filepaths):
|
| 2722 |
+
if self.config.name in _CONFIG_NAMES:
|
| 2723 |
+
idx = 0
|
| 2724 |
+
for filepath in filepaths:
|
| 2725 |
+
with open(filepath, "rb") as f:
|
| 2726 |
+
items = ijson.items(f, "item", use_float=True)
|
| 2727 |
+
for data in items:
|
| 2728 |
+
yield idx, data
|
| 2729 |
+
idx += 1
|
| 2730 |
+
else:
|
| 2731 |
+
raise NotImplementedError(
|
| 2732 |
+
"Unknown configuration in _generate_examples")
|