molSimplify 1.7.4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (651) hide show
  1. docs/source/conf.py +224 -0
  2. molSimplify/Classes/__init__.py +6 -0
  3. molSimplify/Classes/atom3D.py +235 -0
  4. molSimplify/Classes/dft_obs.py +130 -0
  5. molSimplify/Classes/globalvars.py +827 -0
  6. molSimplify/Classes/helpers.py +161 -0
  7. molSimplify/Classes/ligand.py +2330 -0
  8. molSimplify/Classes/mGUI.py +2493 -0
  9. molSimplify/Classes/mWidgets.py +438 -0
  10. molSimplify/Classes/miniGUI.py +41 -0
  11. molSimplify/Classes/mol2D.py +260 -0
  12. molSimplify/Classes/mol3D.py +5846 -0
  13. molSimplify/Classes/monomer3D.py +253 -0
  14. molSimplify/Classes/partialcharges.py +226 -0
  15. molSimplify/Classes/protein3D.py +1178 -0
  16. molSimplify/Classes/rundiag.py +151 -0
  17. molSimplify/Data/ML.dat +212 -0
  18. molSimplify/Data/MLS_FSR_for_inter.dat +23 -0
  19. molSimplify/Data/MLS_FSR_for_inter2.dat +23 -0
  20. molSimplify/Data/MLS_angle_for_click.dat +8 -0
  21. molSimplify/Data/MLS_angle_for_inter.dat +23 -0
  22. molSimplify/Data/MLS_angle_for_inter2.dat +48 -0
  23. molSimplify/Data/MLS_angle_for_intra.dat +10 -0
  24. molSimplify/Data/MLS_angle_for_intra2.dat +6 -0
  25. molSimplify/Data/MLS_angle_for_oa.dat +18 -0
  26. molSimplify/Data/ML_FSR_for_inter.dat +112 -0
  27. molSimplify/Data/ML_FSR_for_inter2.dat +110 -0
  28. molSimplify/Data/ML_bond_for_cat.dat +8 -0
  29. molSimplify/Data/ML_bond_for_click.dat +8 -0
  30. molSimplify/Data/ML_bond_for_inter.dat +48 -0
  31. molSimplify/Data/ML_bond_for_inter2.dat +48 -0
  32. molSimplify/Data/ML_bond_for_intra.dat +10 -0
  33. molSimplify/Data/ML_bond_for_intra2.dat +6 -0
  34. molSimplify/Data/ML_bond_for_oa.dat +18 -0
  35. molSimplify/Data/bp1.dat +21 -0
  36. molSimplify/Data/li.dat +3 -0
  37. molSimplify/Data/no.dat +2 -0
  38. molSimplify/Data/oct.dat +7 -0
  39. molSimplify/Data/pbp.dat +8 -0
  40. molSimplify/Data/spy.dat +6 -0
  41. molSimplify/Data/sqap.dat +9 -0
  42. molSimplify/Data/sqp.dat +5 -0
  43. molSimplify/Data/tbp.dat +6 -0
  44. molSimplify/Data/tdhd.dat +9 -0
  45. molSimplify/Data/thd.dat +5 -0
  46. molSimplify/Data/tpl.dat +4 -0
  47. molSimplify/Data/tpr.dat +7 -0
  48. molSimplify/Informatics/HFXsensitivity/__init__.py +0 -0
  49. molSimplify/Informatics/HFXsensitivity/measure_HFX_sensitivity_oxo_hat_reb_rel.py +443 -0
  50. molSimplify/Informatics/HFXsensitivity/measure_HFX_stable.py +346 -0
  51. molSimplify/Informatics/MOF/Linker_rotation.py +179 -0
  52. molSimplify/Informatics/MOF/MOF_descriptors.py +1299 -0
  53. molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py +589 -0
  54. molSimplify/Informatics/MOF/MOF_functionalizer.py +1648 -0
  55. molSimplify/Informatics/MOF/PBC_functions.py +1347 -0
  56. molSimplify/Informatics/MOF/__init__.py +0 -0
  57. molSimplify/Informatics/MOF/atomic.py +267 -0
  58. molSimplify/Informatics/MOF/cluster_extraction.py +388 -0
  59. molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py +895 -0
  60. molSimplify/Informatics/MOF/monofunctionalized_BDC/index_information.py +10 -0
  61. molSimplify/Informatics/Mol2Parser.py +46 -0
  62. molSimplify/Informatics/RACassemble.py +408 -0
  63. molSimplify/Informatics/__init__.py +0 -0
  64. molSimplify/Informatics/active_learning/__init__.py +0 -0
  65. molSimplify/Informatics/active_learning/expected_improvement.py +269 -0
  66. molSimplify/Informatics/autocorrelation.py +1930 -0
  67. molSimplify/Informatics/clean_autocorrelation.py +778 -0
  68. molSimplify/Informatics/coulomb_analyze.py +67 -0
  69. molSimplify/Informatics/decoration_manager.py +193 -0
  70. molSimplify/Informatics/geo_analyze.py +88 -0
  71. molSimplify/Informatics/geometrics.py +56 -0
  72. molSimplify/Informatics/graph_analyze.py +163 -0
  73. molSimplify/Informatics/graph_racs.py +288 -0
  74. molSimplify/Informatics/jupyter_vis.py +172 -0
  75. molSimplify/Informatics/lacRACAssemble.py +2192 -0
  76. molSimplify/Informatics/lacRACAssemble_bisdithiolenes.py +236 -0
  77. molSimplify/Informatics/misc_descriptors.py +198 -0
  78. molSimplify/Informatics/organic_fingerprints.py +61 -0
  79. molSimplify/Informatics/partialcharges.py +345 -0
  80. molSimplify/Informatics/protein/activesite.py +53 -0
  81. molSimplify/Informatics/protein/pymol_add_hs.py +33 -0
  82. molSimplify/Informatics/rac155_geo.py +48 -0
  83. molSimplify/Ligands/(1_methylbenzimidazol_2_yl)pyridine.xyz +45 -0
  84. molSimplify/Ligands/1-4-dimethyl-1-2-3-triazole.xyz +15 -0
  85. molSimplify/Ligands/12crown4.mol +62 -0
  86. molSimplify/Ligands/Antipyrine.mol +58 -0
  87. molSimplify/Ligands/BPAbipy.mol +106 -0
  88. molSimplify/Ligands/Hpyrrole.mol +26 -0
  89. molSimplify/Ligands/N-quinolinylbutyramidate.xyz +31 -0
  90. molSimplify/Ligands/N-quinolinylmethylmethinylacetamidate.xyz +30 -0
  91. molSimplify/Ligands/NMe2_-1.xyz +11 -0
  92. molSimplify/Ligands/PCy3.mol +111 -0
  93. molSimplify/Ligands/PMe3.xyz +15 -0
  94. molSimplify/Ligands/PPh3.mol +76 -0
  95. molSimplify/Ligands/Propyphenazone.mol +77 -0
  96. molSimplify/Ligands/acac.mol +33 -0
  97. molSimplify/Ligands/acacen.mol +76 -0
  98. molSimplify/Ligands/acetate.smi +1 -0
  99. molSimplify/Ligands/acetate.xyz +9 -0
  100. molSimplify/Ligands/aceticacidbipyridine.mol +70 -0
  101. molSimplify/Ligands/acetonitrile.mol +17 -0
  102. molSimplify/Ligands/alanine.mol +30 -0
  103. molSimplify/Ligands/alphabetizer.py +21 -0
  104. molSimplify/Ligands/amine.mol +11 -0
  105. molSimplify/Ligands/ammonia.mol +12 -0
  106. molSimplify/Ligands/arginine.mol +58 -0
  107. molSimplify/Ligands/asparagine.mol +38 -0
  108. molSimplify/Ligands/aspartic_acid.mol +35 -0
  109. molSimplify/Ligands/azide.mol +11 -0
  110. molSimplify/Ligands/benzene.mol +28 -0
  111. molSimplify/Ligands/benzene_pi.mol +30 -0
  112. molSimplify/Ligands/benzenedithiol.mol +30 -0
  113. molSimplify/Ligands/benzenethiol.mol +30 -0
  114. molSimplify/Ligands/benzylisocy.mol +38 -0
  115. molSimplify/Ligands/bidiazine.mol +42 -0
  116. molSimplify/Ligands/bidiazole.mol +38 -0
  117. molSimplify/Ligands/bifuran.mol +38 -0
  118. molSimplify/Ligands/bihydrodiazine.mol +58 -0
  119. molSimplify/Ligands/bihydrodiazole.mol +46 -0
  120. molSimplify/Ligands/bihydrooxazine.mol +54 -0
  121. molSimplify/Ligands/bihydrooxazole.mol +42 -0
  122. molSimplify/Ligands/bihydrothiazine.mol +54 -0
  123. molSimplify/Ligands/bihydrothiazole.mol +42 -0
  124. molSimplify/Ligands/biimidazole.mol +38 -0
  125. molSimplify/Ligands/bioxazole.mol +34 -0
  126. molSimplify/Ligands/bipy.mol +46 -0
  127. molSimplify/Ligands/bipyrazine.xyz +20 -0
  128. molSimplify/Ligands/bipyrimidine.mol +42 -0
  129. molSimplify/Ligands/bipyrrole.mol +42 -0
  130. molSimplify/Ligands/bisnapthyridylpyridine.mol +111 -0
  131. molSimplify/Ligands/bithiazole.mol +34 -0
  132. molSimplify/Ligands/bromide.mol +7 -0
  133. molSimplify/Ligands/bromide.smi +1 -0
  134. molSimplify/Ligands/c2.mol +9 -0
  135. molSimplify/Ligands/caprolactone.mol +41 -0
  136. molSimplify/Ligands/carbonyl.mol +8 -0
  137. molSimplify/Ligands/carboxyl.mol +13 -0
  138. molSimplify/Ligands/cat.mol +30 -0
  139. molSimplify/Ligands/chloride.mol +7 -0
  140. molSimplify/Ligands/chloride.smi +1 -0
  141. molSimplify/Ligands/chloropyridine.mol +27 -0
  142. molSimplify/Ligands/co2.mol +10 -0
  143. molSimplify/Ligands/corrolazine.mol +72 -0
  144. molSimplify/Ligands/cs.mol +8 -0
  145. molSimplify/Ligands/cyanate.xyz +5 -0
  146. molSimplify/Ligands/cyanide.mol +9 -0
  147. molSimplify/Ligands/cyanoaceticporphyrin.mol +114 -0
  148. molSimplify/Ligands/cyanopyridine.mol +29 -0
  149. molSimplify/Ligands/cyclam.mol +81 -0
  150. molSimplify/Ligands/cyclen.mol +69 -0
  151. molSimplify/Ligands/cyclopentadienyl.mol +26 -0
  152. molSimplify/Ligands/cysteine.mol +32 -0
  153. molSimplify/Ligands/diaminomethyl.mol +19 -0
  154. molSimplify/Ligands/diazine.mol +25 -0
  155. molSimplify/Ligands/diazole.mol +23 -0
  156. molSimplify/Ligands/dicyanamide.mol +15 -0
  157. molSimplify/Ligands/dihydrofuran.mol +27 -0
  158. molSimplify/Ligands/dmap.xyz +35 -0
  159. molSimplify/Ligands/dmf.mol +28 -0
  160. molSimplify/Ligands/dmi.mol +41 -0
  161. molSimplify/Ligands/dmpe.mol +52 -0
  162. molSimplify/Ligands/dpmu.mol +47 -0
  163. molSimplify/Ligands/dppe.mol +112 -0
  164. molSimplify/Ligands/edta.mol +69 -0
  165. molSimplify/Ligands/en.mol +28 -0
  166. molSimplify/Ligands/ethanethiol.mol +21 -0
  167. molSimplify/Ligands/ethanolamine.mol +26 -0
  168. molSimplify/Ligands/ethbipy.mol +70 -0
  169. molSimplify/Ligands/ethyl.mol +19 -0
  170. molSimplify/Ligands/ethylamine.mol +24 -0
  171. molSimplify/Ligands/ethylene.mol +16 -0
  172. molSimplify/Ligands/ethylesteracac.mol +57 -0
  173. molSimplify/Ligands/fluoride.mol +7 -0
  174. molSimplify/Ligands/fluoride.smi +1 -0
  175. molSimplify/Ligands/formaldehyde.mol +12 -0
  176. molSimplify/Ligands/formamidate.xyz +8 -0
  177. molSimplify/Ligands/formate.xyz +6 -0
  178. molSimplify/Ligands/furan.mol +23 -0
  179. molSimplify/Ligands/glutamic_acid.mol +42 -0
  180. molSimplify/Ligands/glutamine.mol +44 -0
  181. molSimplify/Ligands/glycinate.mol +23 -0
  182. molSimplify/Ligands/glycine.mol +24 -0
  183. molSimplify/Ligands/h2s.mol +10 -0
  184. molSimplify/Ligands/helium.mol +6 -0
  185. molSimplify/Ligands/histidine.mol +45 -0
  186. molSimplify/Ligands/hmpa.mol +62 -0
  187. molSimplify/Ligands/hs-.mol +9 -0
  188. molSimplify/Ligands/hydride.mol +7 -0
  189. molSimplify/Ligands/hydrocarboxyacetylide.xyz +8 -0
  190. molSimplify/Ligands/hydrocyanide.mol +10 -0
  191. molSimplify/Ligands/hydrodiazine.mol +33 -0
  192. molSimplify/Ligands/hydrodiazole.mol +27 -0
  193. molSimplify/Ligands/hydrogensulfide.mol +10 -0
  194. molSimplify/Ligands/hydroisocyanide.mol +11 -0
  195. molSimplify/Ligands/hydrooxazine.mol +31 -0
  196. molSimplify/Ligands/hydrooxazole.mol +25 -0
  197. molSimplify/Ligands/hydrothiazine.mol +31 -0
  198. molSimplify/Ligands/hydrothiazole.mol +25 -0
  199. molSimplify/Ligands/hydroxyl.mol +9 -0
  200. molSimplify/Ligands/imidazole.mol +23 -0
  201. molSimplify/Ligands/imidazolidinone.mol +29 -0
  202. molSimplify/Ligands/imine.mol +13 -0
  203. molSimplify/Ligands/iminodiacetic.mol +33 -0
  204. molSimplify/Ligands/iodide.mol +7 -0
  205. molSimplify/Ligands/iodobenzene.xyz +14 -0
  206. molSimplify/Ligands/isoleucine.mol +48 -0
  207. molSimplify/Ligands/isothiocyanate.mol +11 -0
  208. molSimplify/Ligands/leucine.mol +48 -0
  209. molSimplify/Ligands/ligands.dict +257 -0
  210. molSimplify/Ligands/lysine.mol +54 -0
  211. molSimplify/Ligands/mebenzenedithiol.mol +36 -0
  212. molSimplify/Ligands/mebim_py.xyz +29 -0
  213. molSimplify/Ligands/mebim_pz.xyz +28 -0
  214. molSimplify/Ligands/mebipy.mol +58 -0
  215. molSimplify/Ligands/mecat.mol +36 -0
  216. molSimplify/Ligands/methanal.mol +11 -0
  217. molSimplify/Ligands/methanethiol.mol +15 -0
  218. molSimplify/Ligands/methanol.mol +16 -0
  219. molSimplify/Ligands/methionine.mol +44 -0
  220. molSimplify/Ligands/methyl.mol +13 -0
  221. molSimplify/Ligands/methylacetylide.xyz +8 -0
  222. molSimplify/Ligands/methylamine.mol +19 -0
  223. molSimplify/Ligands/methylazide.xyz +9 -0
  224. molSimplify/Ligands/methylisocy.mol +17 -0
  225. molSimplify/Ligands/methylpyridine.mol +33 -0
  226. molSimplify/Ligands/n2.mol +8 -0
  227. molSimplify/Ligands/n4py.xyz +51 -0
  228. molSimplify/Ligands/nch.mol +10 -0
  229. molSimplify/Ligands/nco-.mol +11 -0
  230. molSimplify/Ligands/nethanolamine.mol +26 -0
  231. molSimplify/Ligands/nitrate.mol +14 -0
  232. molSimplify/Ligands/nitrite.mol +11 -0
  233. molSimplify/Ligands/nitro.mol +11 -0
  234. molSimplify/Ligands/nitrobipy.mol +54 -0
  235. molSimplify/Ligands/nitroso.mol +8 -0
  236. molSimplify/Ligands/nme3.mol +30 -0
  237. molSimplify/Ligands/no-.mol +10 -0
  238. molSimplify/Ligands/no2-.mol +11 -0
  239. molSimplify/Ligands/noxygen.mol +8 -0
  240. molSimplify/Ligands/ns-.mol +10 -0
  241. molSimplify/Ligands/o-pyridylbenzene.xyz +23 -0
  242. molSimplify/Ligands/o-pyridylphenylanion.xyz +22 -0
  243. molSimplify/Ligands/o2-.mol +9 -0
  244. molSimplify/Ligands/o2.xyz +4 -0
  245. molSimplify/Ligands/och2.mol +12 -0
  246. molSimplify/Ligands/oethanolamine.mol +26 -0
  247. molSimplify/Ligands/ome2.mol +22 -0
  248. molSimplify/Ligands/ooh.xyz +5 -0
  249. molSimplify/Ligands/oxalate.mol +17 -0
  250. molSimplify/Ligands/oxalate.smi +1 -0
  251. molSimplify/Ligands/oxygen.mol +7 -0
  252. molSimplify/Ligands/pentacyanocyclopentadienide.mol +36 -0
  253. molSimplify/Ligands/ph2-.mol +11 -0
  254. molSimplify/Ligands/ph3.mol +12 -0
  255. molSimplify/Ligands/phen.mol +51 -0
  256. molSimplify/Ligands/phenacac.mol +63 -0
  257. molSimplify/Ligands/phenalalanine.mol +51 -0
  258. molSimplify/Ligands/phendione.mol +51 -0
  259. molSimplify/Ligands/phenphen.mol +75 -0
  260. molSimplify/Ligands/phenylbenzoxazole.mol +54 -0
  261. molSimplify/Ligands/phenylcyc.mol +99 -0
  262. molSimplify/Ligands/phenylenediamine.mol +37 -0
  263. molSimplify/Ligands/phenylisocy.mol +32 -0
  264. molSimplify/Ligands/phosacidbipy.mol +66 -0
  265. molSimplify/Ligands/phosphine.mol +13 -0
  266. molSimplify/Ligands/phosphorine.mol +27 -0
  267. molSimplify/Ligands/phosphorustrifluoride.mol +12 -0
  268. molSimplify/Ligands/phthalocyanine.mol +126 -0
  269. molSimplify/Ligands/pme3o.mol +32 -0
  270. molSimplify/Ligands/porphyrin.mol +82 -0
  271. molSimplify/Ligands/pph3o.mol +77 -0
  272. molSimplify/Ligands/proline.mol +39 -0
  273. molSimplify/Ligands/propdiol.mol +21 -0
  274. molSimplify/Ligands/propylene.mol +23 -0
  275. molSimplify/Ligands/pyridine.mol +27 -0
  276. molSimplify/Ligands/pyrimidone.mol +27 -0
  277. molSimplify/Ligands/pyrrole.mol +24 -0
  278. molSimplify/Ligands/quinoxalinedithiol.mol +39 -0
  279. molSimplify/Ligands/s2-.mol +9 -0
  280. molSimplify/Ligands/salen.mol +75 -0
  281. molSimplify/Ligands/salphen.mol +84 -0
  282. molSimplify/Ligands/serine.mol +32 -0
  283. molSimplify/Ligands/simple_ligands.dict +14 -0
  284. molSimplify/Ligands/sulfacidbipy.mol +63 -0
  285. molSimplify/Ligands/tbucat.mol +54 -0
  286. molSimplify/Ligands/tbuphisocy.mol +56 -0
  287. molSimplify/Ligands/tbutylcyclen.mol +166 -0
  288. molSimplify/Ligands/tbutylisocy.mol +35 -0
  289. molSimplify/Ligands/tbutylthiol.mol +33 -0
  290. molSimplify/Ligands/tcnoet.mol +43 -0
  291. molSimplify/Ligands/tcnoetOH.mol +45 -0
  292. molSimplify/Ligands/terpy.mol +65 -0
  293. molSimplify/Ligands/tetrahydrofuran.mol +31 -0
  294. molSimplify/Ligands/thiane.mol +37 -0
  295. molSimplify/Ligands/thiazole.mol +21 -0
  296. molSimplify/Ligands/thiocyanate.mol +11 -0
  297. molSimplify/Ligands/thiol.mol +9 -0
  298. molSimplify/Ligands/thiophene.mol +23 -0
  299. molSimplify/Ligands/thiopyridine.mol +29 -0
  300. molSimplify/Ligands/threonine.mol +38 -0
  301. molSimplify/Ligands/tpp.mol +165 -0
  302. molSimplify/Ligands/tricyanomethyl.mol +19 -0
  303. molSimplify/Ligands/trifluoromethyl.mol +13 -0
  304. molSimplify/Ligands/tryptophan.mol +60 -0
  305. molSimplify/Ligands/tyrosine.mol +53 -0
  306. molSimplify/Ligands/uthiol.mol +11 -0
  307. molSimplify/Ligands/uthiolme2.mol +23 -0
  308. molSimplify/Ligands/valine.mol +42 -0
  309. molSimplify/Ligands/water.mol +10 -0
  310. molSimplify/Ligands/x.mol +6 -0
  311. molSimplify/Scripts/__init__.py +0 -0
  312. molSimplify/Scripts/addtodb.py +308 -0
  313. molSimplify/Scripts/cellbuilder.py +1592 -0
  314. molSimplify/Scripts/cellbuilder_tools.py +701 -0
  315. molSimplify/Scripts/chains.py +342 -0
  316. molSimplify/Scripts/convert_2to3.py +23 -0
  317. molSimplify/Scripts/dbinteract.py +631 -0
  318. molSimplify/Scripts/distgeom.py +617 -0
  319. molSimplify/Scripts/findcorrelations.py +287 -0
  320. molSimplify/Scripts/generator.py +267 -0
  321. molSimplify/Scripts/geometry.py +1224 -0
  322. molSimplify/Scripts/grabguivars.py +845 -0
  323. molSimplify/Scripts/in_b3lyp_usetc.py +141 -0
  324. molSimplify/Scripts/inparse.py +1673 -0
  325. molSimplify/Scripts/io.py +1149 -0
  326. molSimplify/Scripts/isomers.py +415 -0
  327. molSimplify/Scripts/jobgen.py +247 -0
  328. molSimplify/Scripts/krr_prep.py +1262 -0
  329. molSimplify/Scripts/molSimplify_io.py +18 -0
  330. molSimplify/Scripts/molden2psi4wfn.py +166 -0
  331. molSimplify/Scripts/namegen.py +32 -0
  332. molSimplify/Scripts/nn_prep.py +561 -0
  333. molSimplify/Scripts/oct_check_mols.py +782 -0
  334. molSimplify/Scripts/periodic_QE.py +97 -0
  335. molSimplify/Scripts/postmold.py +304 -0
  336. molSimplify/Scripts/postmwfn.py +709 -0
  337. molSimplify/Scripts/postparse.py +488 -0
  338. molSimplify/Scripts/postproc.py +139 -0
  339. molSimplify/Scripts/qcgen.py +1450 -0
  340. molSimplify/Scripts/rmsd.py +489 -0
  341. molSimplify/Scripts/rungen.py +670 -0
  342. molSimplify/Scripts/structgen.py +3040 -0
  343. molSimplify/Scripts/tf_nn_prep.py +894 -0
  344. molSimplify/Scripts/tsgen.py +295 -0
  345. molSimplify/Scripts/uq_calibration.py +69 -0
  346. molSimplify/__init__.py +0 -0
  347. molSimplify/__main__.py +197 -0
  348. molSimplify/icons/chemdb.png +0 -0
  349. molSimplify/icons/hjklogo.png +0 -0
  350. molSimplify/icons/icon.png +0 -0
  351. molSimplify/icons/logo.png +0 -0
  352. molSimplify/icons/logo_old.png +0 -0
  353. molSimplify/icons/petachem.png +0 -0
  354. molSimplify/icons/petachem2.png +0 -0
  355. molSimplify/icons/petachem_full.png +0 -0
  356. molSimplify/icons/pythonlogo.png +0 -0
  357. molSimplify/icons/sge copy.png +0 -0
  358. molSimplify/icons/sge.png +0 -0
  359. molSimplify/icons/slurm.png +0 -0
  360. molSimplify/icons/wft1.png +0 -0
  361. molSimplify/icons/wft2.png +0 -0
  362. molSimplify/icons/wft3.png +0 -0
  363. molSimplify/ml/__init__.py +0 -0
  364. molSimplify/ml/kernels.py +36 -0
  365. molSimplify/ml/layers.py +29 -0
  366. molSimplify/molscontrol/__init__.py +14 -0
  367. molSimplify/molscontrol/_version.py +521 -0
  368. molSimplify/molscontrol/clf_tools.py +144 -0
  369. molSimplify/molscontrol/data/README.md +21 -0
  370. molSimplify/molscontrol/data/look_and_say.dat +15 -0
  371. molSimplify/molscontrol/dynamic_classifier.py +514 -0
  372. molSimplify/molscontrol/io_tools.py +363 -0
  373. molSimplify/molscontrol/molscontrol.py +49 -0
  374. molSimplify/molscontrol/terachem/jobscript_control.sh +31 -0
  375. molSimplify/molscontrol/terachem/terachem_input +22 -0
  376. molSimplify/python_krr/X_train_TS.csv +535 -0
  377. molSimplify/python_krr/__init__.py +0 -0
  378. molSimplify/python_krr/hat2_X_mean_std.csv +3 -0
  379. molSimplify/python_krr/hat2_feature_names.csv +1 -0
  380. molSimplify/python_krr/hat2_y_mean_std.csv +2 -0
  381. molSimplify/python_krr/hat_X_mean_std.csv +6 -0
  382. molSimplify/python_krr/hat_feature_names.csv +1 -0
  383. molSimplify/python_krr/hat_krr_X_train.csv +5205 -0
  384. molSimplify/python_krr/hat_krr_dual_coef.csv +1 -0
  385. molSimplify/python_krr/hat_y_mean_std.csv +2 -0
  386. molSimplify/python_krr/sklearn_models.py +34 -0
  387. molSimplify/python_krr/y_train_TS.csv +535 -0
  388. molSimplify/python_nn/ANN.py +198 -0
  389. molSimplify/python_nn/__init__.py +0 -0
  390. molSimplify/python_nn/clf_analysis_tool.py +125 -0
  391. molSimplify/python_nn/dictionary_toolbox.py +49 -0
  392. molSimplify/python_nn/ensemble_test.py +309 -0
  393. molSimplify/python_nn/hs_center.csv +26 -0
  394. molSimplify/python_nn/hs_scale.csv +26 -0
  395. molSimplify/python_nn/ls_center.csv +26 -0
  396. molSimplify/python_nn/ls_scale.csv +26 -0
  397. molSimplify/python_nn/ms_hs_b1.csv +50 -0
  398. molSimplify/python_nn/ms_hs_b2.csv +50 -0
  399. molSimplify/python_nn/ms_hs_b3.csv +1 -0
  400. molSimplify/python_nn/ms_hs_w1.csv +50 -0
  401. molSimplify/python_nn/ms_hs_w2.csv +50 -0
  402. molSimplify/python_nn/ms_hs_w3.csv +1 -0
  403. molSimplify/python_nn/ms_ls_b1.csv +50 -0
  404. molSimplify/python_nn/ms_ls_b2.csv +50 -0
  405. molSimplify/python_nn/ms_ls_b3.csv +1 -0
  406. molSimplify/python_nn/ms_ls_w1.csv +50 -0
  407. molSimplify/python_nn/ms_ls_w2.csv +50 -0
  408. molSimplify/python_nn/ms_ls_w3.csv +1 -0
  409. molSimplify/python_nn/ms_slope_b1.csv +50 -0
  410. molSimplify/python_nn/ms_slope_b2.csv +50 -0
  411. molSimplify/python_nn/ms_slope_b3.csv +1 -0
  412. molSimplify/python_nn/ms_slope_w1.csv +50 -0
  413. molSimplify/python_nn/ms_slope_w2.csv +50 -0
  414. molSimplify/python_nn/ms_slope_w3.csv +1 -0
  415. molSimplify/python_nn/ms_split_b1.csv +50 -0
  416. molSimplify/python_nn/ms_split_b2.csv +50 -0
  417. molSimplify/python_nn/ms_split_b3.csv +1 -0
  418. molSimplify/python_nn/ms_split_w1.csv +50 -0
  419. molSimplify/python_nn/ms_split_w2.csv +50 -0
  420. molSimplify/python_nn/ms_split_w3.csv +1 -0
  421. molSimplify/python_nn/slope_center.csv +25 -0
  422. molSimplify/python_nn/slope_scale.csv +25 -0
  423. molSimplify/python_nn/split_center.csv +26 -0
  424. molSimplify/python_nn/split_scale.csv +26 -0
  425. molSimplify/python_nn/tf_ANN.py +762 -0
  426. molSimplify/python_nn/train_data.csv +1211 -0
  427. molSimplify/tf_nn/__init__.py +0 -0
  428. molSimplify/tf_nn/geo_static_clf/geo_static_clf_model.h5 +0 -0
  429. molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_name.csv +1591 -0
  430. molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_x.csv +2790 -0
  431. molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_y.csv +2790 -0
  432. molSimplify/tf_nn/geo_static_clf/geo_static_clf_vars.csv +154 -0
  433. molSimplify/tf_nn/geos/hs_ii_bl_x.csv +1577 -0
  434. molSimplify/tf_nn/geos/hs_ii_bl_y.csv +1577 -0
  435. molSimplify/tf_nn/geos/hs_ii_model.h5 +0 -0
  436. molSimplify/tf_nn/geos/hs_ii_model.json +1 -0
  437. molSimplify/tf_nn/geos/hs_ii_vars.csv +154 -0
  438. molSimplify/tf_nn/geos/hs_iii_bl_x.csv +1659 -0
  439. molSimplify/tf_nn/geos/hs_iii_bl_y.csv +1659 -0
  440. molSimplify/tf_nn/geos/hs_iii_model.h5 +0 -0
  441. molSimplify/tf_nn/geos/hs_iii_model.json +1 -0
  442. molSimplify/tf_nn/geos/hs_iii_vars.csv +154 -0
  443. molSimplify/tf_nn/geos/ls_ii_bl_x.csv +1374 -0
  444. molSimplify/tf_nn/geos/ls_ii_bl_y.csv +1374 -0
  445. molSimplify/tf_nn/geos/ls_ii_model.h5 +0 -0
  446. molSimplify/tf_nn/geos/ls_ii_model.json +1 -0
  447. molSimplify/tf_nn/geos/ls_ii_vars.csv +154 -0
  448. molSimplify/tf_nn/geos/ls_iii_bl_x.csv +1364 -0
  449. molSimplify/tf_nn/geos/ls_iii_bl_y.csv +1364 -0
  450. molSimplify/tf_nn/geos/ls_iii_model.h5 +0 -0
  451. molSimplify/tf_nn/geos/ls_iii_model.json +1 -0
  452. molSimplify/tf_nn/geos/ls_iii_vars.csv +154 -0
  453. molSimplify/tf_nn/homolumo/gap_model.h5 +0 -0
  454. molSimplify/tf_nn/homolumo/gap_model.json +1 -0
  455. molSimplify/tf_nn/homolumo/gap_test_names.csv +175 -0
  456. molSimplify/tf_nn/homolumo/gap_test_x.csv +176 -0
  457. molSimplify/tf_nn/homolumo/gap_test_y.csv +176 -0
  458. molSimplify/tf_nn/homolumo/gap_train_names.csv +699 -0
  459. molSimplify/tf_nn/homolumo/gap_train_x.csv +700 -0
  460. molSimplify/tf_nn/homolumo/gap_train_y.csv +700 -0
  461. molSimplify/tf_nn/homolumo/gap_vars.csv +153 -0
  462. molSimplify/tf_nn/homolumo/homo_model.h5 +0 -0
  463. molSimplify/tf_nn/homolumo/homo_model.json +126 -0
  464. molSimplify/tf_nn/homolumo/homo_test_names.csv +175 -0
  465. molSimplify/tf_nn/homolumo/homo_test_x.csv +176 -0
  466. molSimplify/tf_nn/homolumo/homo_test_y.csv +176 -0
  467. molSimplify/tf_nn/homolumo/homo_train_names.csv +699 -0
  468. molSimplify/tf_nn/homolumo/homo_train_x.csv +700 -0
  469. molSimplify/tf_nn/homolumo/homo_train_y.csv +700 -0
  470. molSimplify/tf_nn/homolumo/homo_vars.csv +153 -0
  471. molSimplify/tf_nn/oxoandhomo/homo_empty_info.json +7 -0
  472. molSimplify/tf_nn/oxoandhomo/homo_empty_model.h5 +0 -0
  473. molSimplify/tf_nn/oxoandhomo/homo_empty_model.json +1 -0
  474. molSimplify/tf_nn/oxoandhomo/homo_empty_test_names.csv +143 -0
  475. molSimplify/tf_nn/oxoandhomo/homo_empty_test_x.csv +144 -0
  476. molSimplify/tf_nn/oxoandhomo/homo_empty_test_y.csv +144 -0
  477. molSimplify/tf_nn/oxoandhomo/homo_empty_train_names.csv +513 -0
  478. molSimplify/tf_nn/oxoandhomo/homo_empty_train_x.csv +514 -0
  479. molSimplify/tf_nn/oxoandhomo/homo_empty_train_y.csv +514 -0
  480. molSimplify/tf_nn/oxoandhomo/homo_empty_val_names.csv +143 -0
  481. molSimplify/tf_nn/oxoandhomo/homo_empty_val_x.csv +58 -0
  482. molSimplify/tf_nn/oxoandhomo/homo_empty_val_y.csv +58 -0
  483. molSimplify/tf_nn/oxoandhomo/homo_empty_vars.csv +155 -0
  484. molSimplify/tf_nn/oxoandhomo/oxo20_info.json +7 -0
  485. molSimplify/tf_nn/oxoandhomo/oxo20_model.h5 +0 -0
  486. molSimplify/tf_nn/oxoandhomo/oxo20_model.json +1 -0
  487. molSimplify/tf_nn/oxoandhomo/oxo20_test_names.csv +143 -0
  488. molSimplify/tf_nn/oxoandhomo/oxo20_test_x.csv +144 -0
  489. molSimplify/tf_nn/oxoandhomo/oxo20_test_y.csv +144 -0
  490. molSimplify/tf_nn/oxoandhomo/oxo20_train_names.csv +513 -0
  491. molSimplify/tf_nn/oxoandhomo/oxo20_train_x.csv +514 -0
  492. molSimplify/tf_nn/oxoandhomo/oxo20_train_y.csv +514 -0
  493. molSimplify/tf_nn/oxoandhomo/oxo20_val_names.csv +143 -0
  494. molSimplify/tf_nn/oxoandhomo/oxo20_val_x.csv +58 -0
  495. molSimplify/tf_nn/oxoandhomo/oxo20_val_y.csv +58 -0
  496. molSimplify/tf_nn/oxoandhomo/oxo20_vars.csv +154 -0
  497. molSimplify/tf_nn/oxocatalysis/hat_model.h5 +0 -0
  498. molSimplify/tf_nn/oxocatalysis/hat_model.json +1 -0
  499. molSimplify/tf_nn/oxocatalysis/hat_test_names.csv +419 -0
  500. molSimplify/tf_nn/oxocatalysis/hat_test_x.csv +420 -0
  501. molSimplify/tf_nn/oxocatalysis/hat_test_y.csv +420 -0
  502. molSimplify/tf_nn/oxocatalysis/hat_train_names.csv +1507 -0
  503. molSimplify/tf_nn/oxocatalysis/hat_train_x.csv +1508 -0
  504. molSimplify/tf_nn/oxocatalysis/hat_train_y.csv +1508 -0
  505. molSimplify/tf_nn/oxocatalysis/hat_val_x.csv +169 -0
  506. molSimplify/tf_nn/oxocatalysis/hat_val_y.csv +169 -0
  507. molSimplify/tf_nn/oxocatalysis/hat_vars.csv +162 -0
  508. molSimplify/tf_nn/oxocatalysis/oxo_model.h5 +0 -0
  509. molSimplify/tf_nn/oxocatalysis/oxo_model.json +1 -0
  510. molSimplify/tf_nn/oxocatalysis/oxo_test_names.csv +527 -0
  511. molSimplify/tf_nn/oxocatalysis/oxo_test_x.csv +528 -0
  512. molSimplify/tf_nn/oxocatalysis/oxo_test_y.csv +528 -0
  513. molSimplify/tf_nn/oxocatalysis/oxo_train_names.csv +1897 -0
  514. molSimplify/tf_nn/oxocatalysis/oxo_train_x.csv +1898 -0
  515. molSimplify/tf_nn/oxocatalysis/oxo_train_y.csv +1898 -0
  516. molSimplify/tf_nn/oxocatalysis/oxo_val_x.csv +212 -0
  517. molSimplify/tf_nn/oxocatalysis/oxo_val_y.csv +212 -0
  518. molSimplify/tf_nn/oxocatalysis/oxo_vars.csv +162 -0
  519. molSimplify/tf_nn/rescaling_data/gap_mean_x.csv +153 -0
  520. molSimplify/tf_nn/rescaling_data/gap_mean_y.csv +1 -0
  521. molSimplify/tf_nn/rescaling_data/gap_var_x.csv +153 -0
  522. molSimplify/tf_nn/rescaling_data/gap_var_y.csv +1 -0
  523. molSimplify/tf_nn/rescaling_data/geo_static_clf_mean_x.csv +154 -0
  524. molSimplify/tf_nn/rescaling_data/geo_static_clf_mean_y.csv +1 -0
  525. molSimplify/tf_nn/rescaling_data/geo_static_clf_var_x.csv +154 -0
  526. molSimplify/tf_nn/rescaling_data/geo_static_clf_var_y.csv +1 -0
  527. molSimplify/tf_nn/rescaling_data/hat_mean_x.csv +162 -0
  528. molSimplify/tf_nn/rescaling_data/hat_mean_y.csv +1 -0
  529. molSimplify/tf_nn/rescaling_data/hat_var_x.csv +162 -0
  530. molSimplify/tf_nn/rescaling_data/hat_var_y.csv +1 -0
  531. molSimplify/tf_nn/rescaling_data/homo_empty_mean_x.csv +155 -0
  532. molSimplify/tf_nn/rescaling_data/homo_empty_mean_y.csv +1 -0
  533. molSimplify/tf_nn/rescaling_data/homo_empty_var_x.csv +155 -0
  534. molSimplify/tf_nn/rescaling_data/homo_empty_var_y.csv +1 -0
  535. molSimplify/tf_nn/rescaling_data/homo_mean_x.csv +153 -0
  536. molSimplify/tf_nn/rescaling_data/homo_mean_y.csv +1 -0
  537. molSimplify/tf_nn/rescaling_data/homo_var_x.csv +153 -0
  538. molSimplify/tf_nn/rescaling_data/homo_var_y.csv +1 -0
  539. molSimplify/tf_nn/rescaling_data/hs_ii_mean_x.csv +154 -0
  540. molSimplify/tf_nn/rescaling_data/hs_ii_mean_y.csv +3 -0
  541. molSimplify/tf_nn/rescaling_data/hs_ii_var_x.csv +154 -0
  542. molSimplify/tf_nn/rescaling_data/hs_ii_var_y.csv +3 -0
  543. molSimplify/tf_nn/rescaling_data/hs_iii_mean_x.csv +154 -0
  544. molSimplify/tf_nn/rescaling_data/hs_iii_mean_y.csv +3 -0
  545. molSimplify/tf_nn/rescaling_data/hs_iii_var_x.csv +154 -0
  546. molSimplify/tf_nn/rescaling_data/hs_iii_var_y.csv +3 -0
  547. molSimplify/tf_nn/rescaling_data/ls_ii_mean_x.csv +154 -0
  548. molSimplify/tf_nn/rescaling_data/ls_ii_mean_y.csv +3 -0
  549. molSimplify/tf_nn/rescaling_data/ls_ii_var_x.csv +154 -0
  550. molSimplify/tf_nn/rescaling_data/ls_ii_var_y.csv +3 -0
  551. molSimplify/tf_nn/rescaling_data/ls_iii_mean_x.csv +154 -0
  552. molSimplify/tf_nn/rescaling_data/ls_iii_mean_y.csv +3 -0
  553. molSimplify/tf_nn/rescaling_data/ls_iii_var_x.csv +154 -0
  554. molSimplify/tf_nn/rescaling_data/ls_iii_var_y.csv +3 -0
  555. molSimplify/tf_nn/rescaling_data/oxo20_mean_x.csv +154 -0
  556. molSimplify/tf_nn/rescaling_data/oxo20_mean_y.csv +1 -0
  557. molSimplify/tf_nn/rescaling_data/oxo20_var_x.csv +154 -0
  558. molSimplify/tf_nn/rescaling_data/oxo20_var_y.csv +1 -0
  559. molSimplify/tf_nn/rescaling_data/oxo_mean_x.csv +162 -0
  560. molSimplify/tf_nn/rescaling_data/oxo_mean_y.csv +1 -0
  561. molSimplify/tf_nn/rescaling_data/oxo_var_x.csv +162 -0
  562. molSimplify/tf_nn/rescaling_data/oxo_var_y.csv +1 -0
  563. molSimplify/tf_nn/rescaling_data/sc_static_clf_mean_x.csv +154 -0
  564. molSimplify/tf_nn/rescaling_data/sc_static_clf_mean_y.csv +1 -0
  565. molSimplify/tf_nn/rescaling_data/sc_static_clf_var_x.csv +154 -0
  566. molSimplify/tf_nn/rescaling_data/sc_static_clf_var_y.csv +1 -0
  567. molSimplify/tf_nn/rescaling_data/split_mean_x.csv +155 -0
  568. molSimplify/tf_nn/rescaling_data/split_mean_y.csv +1 -0
  569. molSimplify/tf_nn/rescaling_data/split_var_x.csv +155 -0
  570. molSimplify/tf_nn/rescaling_data/split_var_y.csv +1 -0
  571. molSimplify/tf_nn/sc_static_clf/sc_static_clf_model.h5 +0 -0
  572. molSimplify/tf_nn/sc_static_clf/sc_static_clf_train_name.csv +1591 -0
  573. molSimplify/tf_nn/sc_static_clf/sc_static_clf_train_x.csv +1592 -0
  574. molSimplify/tf_nn/sc_static_clf/sc_static_clf_train_y.csv +1592 -0
  575. molSimplify/tf_nn/sc_static_clf/sc_static_clf_vars.csv +154 -0
  576. molSimplify/tf_nn/split/split_model.h5 +0 -0
  577. molSimplify/tf_nn/split/split_model.json +1 -0
  578. molSimplify/tf_nn/split/split_vars.csv +155 -0
  579. molSimplify/tf_nn/split/split_x.csv +1902 -0
  580. molSimplify/tf_nn/split/split_y.csv +1902 -0
  581. molSimplify/tf_nn/split/train_names.csv +1901 -0
  582. molSimplify/utils/__init__.py +0 -0
  583. molSimplify/utils/decorators.py +16 -0
  584. molSimplify/utils/metaclasses.py +12 -0
  585. molSimplify/utils/tensorflow.py +23 -0
  586. molSimplify/utils/timer.py +16 -0
  587. molSimplify-1.7.4.dist-info/LICENSE +674 -0
  588. molSimplify-1.7.4.dist-info/METADATA +821 -0
  589. molSimplify-1.7.4.dist-info/RECORD +651 -0
  590. molSimplify-1.7.4.dist-info/WHEEL +5 -0
  591. molSimplify-1.7.4.dist-info/entry_points.txt +3 -0
  592. molSimplify-1.7.4.dist-info/top_level.txt +4 -0
  593. tests/generateTests.py +122 -0
  594. tests/helperFuncs.py +658 -0
  595. tests/informatics/test_MOF_descriptors.py +128 -0
  596. tests/informatics/test_active_learning.py +113 -0
  597. tests/informatics/test_coulomb_analyze.py +24 -0
  598. tests/informatics/test_graph_racs.py +193 -0
  599. tests/ml/test_kernels.py +20 -0
  600. tests/ml/test_layers.py +47 -0
  601. tests/runtest.py +10 -0
  602. tests/test_Mol2D.py +128 -0
  603. tests/test_basic_imports.py +62 -0
  604. tests/test_bidentate.py +25 -0
  605. tests/test_cli.py +20 -0
  606. tests/test_distgeom.py +106 -0
  607. tests/test_example_1.py +29 -0
  608. tests/test_example_3.py +31 -0
  609. tests/test_example_5.py +43 -0
  610. tests/test_example_7.py +28 -0
  611. tests/test_example_8.py +15 -0
  612. tests/test_example_tbp.py +15 -0
  613. tests/test_ff_xtb.py +111 -0
  614. tests/test_geocheck_oct.py +26 -0
  615. tests/test_geocheck_one_empty.py +15 -0
  616. tests/test_geometry.py +44 -0
  617. tests/test_inparse.py +76 -0
  618. tests/test_io.py +84 -0
  619. tests/test_jobgen.py +84 -0
  620. tests/test_joption_pythonic.py +27 -0
  621. tests/test_ligand_assign.py +58 -0
  622. tests/test_ligand_assign_consistent.py +60 -0
  623. tests/test_ligand_class.py +26 -0
  624. tests/test_ligand_from_mol_file.py +35 -0
  625. tests/test_ligands.py +86 -0
  626. tests/test_mol3D.py +337 -0
  627. tests/test_molcas_caspt2.py +15 -0
  628. tests/test_molcas_casscf.py +15 -0
  629. tests/test_old_ANNs.py +68 -0
  630. tests/test_orca_ccsdt.py +15 -0
  631. tests/test_orca_dft.py +15 -0
  632. tests/test_qcgen.py +50 -0
  633. tests/test_racs.py +124 -0
  634. tests/test_rmsd.py +68 -0
  635. tests/test_structgen_functions.py +198 -0
  636. tests/test_tetrahedral.py +29 -0
  637. tests/test_tutorial_10_part_one.py +16 -0
  638. tests/test_tutorial_10_part_two.py +15 -0
  639. tests/test_tutorial_2.py +11 -0
  640. tests/test_tutorial_3.py +15 -0
  641. tests/test_tutorial_4.py +57 -0
  642. tests/test_tutorial_6.py +10 -0
  643. tests/test_tutorial_8.py +29 -0
  644. tests/test_tutorial_9_part_one.py +15 -0
  645. tests/test_tutorial_9_part_two.py +15 -0
  646. tests/test_tutorial_qm9_part_one.py +6 -0
  647. tests/testresources/refs/racs/generate_references.py +85 -0
  648. workflows/NandyJACSAu2022/bridge_functionalizer.py +253 -0
  649. workflows/NandyJACSAu2022/frag_functionalizer.py +242 -0
  650. workflows/NandyJACSAu2022/fragment_classes.py +586 -0
  651. workflows/NandyJACSAu2022/macrocycle_synthesis.py +179 -0
molSimplify/tf_nn/rescaling_data/ls_ii_mean_x.csv ADDED
@@ -0,0 +1,154 @@
1
+ [ 0.16015385]
2
+ [ 1.15487179]
3
+ [ 1.4974359]
4
+ [ 55.11276205]
5
+ [ 105.05423149]
6
+ [ 148.47981436]
7
+ [ 164.16456892]
8
+ [ 241.08102564]
9
+ [ 401.49333333]
10
+ [ 473.31487179]
11
+ [ 415.13641026]
12
+ [ 8.69076923]
13
+ [ 16.22564103]
14
+ [ 24.15589744]
15
+ [ 26.93641026]
16
+ [ 40.38153846]
17
+ [ 94.16820513]
18
+ [ 120.15384615]
19
+ [ 117.33025641]
20
+ [ 3.42727256]
21
+ [ 7.25708944]
22
+ [ 9.33622759]
23
+ [ 9.63783303]
24
+ [ 71.24750872]
25
+ [ 141.51366051]
26
+ [ 210.22724164]
27
+ [ 234.52803446]
28
+ [ 290.65846154]
29
+ [ 541.6225641]
30
+ [ 688.73846154]
31
+ [ 614.07794872]
32
+ [ 11.21435897]
33
+ [ 21.81538462]
34
+ [ 33.58974359]
35
+ [ 37.75794872]
36
+ [ 55.40512821]
37
+ [ 131.42153846]
38
+ [ 168.84307692]
39
+ [ 160.51487179]
40
+ [ 4.42061333]
41
+ [ 9.89493272]
42
+ [ 13.39553785]
43
+ [ 13.59648903]
44
+ [ 8.63793154]
45
+ [ 11.3068281]
46
+ [ 9.45368021]
47
+ [ 10.76327451]
48
+ [ 63.53897436]
49
+ [ 48.26564103]
50
+ [ 48.36666667]
51
+ [ 37.31282051]
52
+ [ 1.47794872]
53
+ [ 1.25128205]
54
+ [ 1.46923077]
55
+ [ 2.73641026]
56
+ [ 4.8625641]
57
+ [ 4.7774359]
58
+ [ 4.0625641]
59
+ [ 0.60179621]
60
+ [ 0.70294313]
61
+ [ 0.63502836]
62
+ [ 0.62314185]
63
+ [ 9.30211251]
64
+ [ 12.03713128]
65
+ [ 13.94757918]
66
+ [ 18.24935467]
67
+ [ 57.53435897]
68
+ [ 52.64205128]
69
+ [ 68.32051282]
70
+ [ 61.98307692]
71
+ [ 1.55384615]
72
+ [ 1.79282051]
73
+ [ 2.37282051]
74
+ [ 2.93230769]
75
+ [ 6.15179487]
76
+ [ 7.66564103]
77
+ [ 6.86051282]
78
+ [ 0.576064]
79
+ [ 0.75817262]
80
+ [ 0.9069439]
81
+ [ 0.97778487]
82
+ [ 3.07643426]
83
+ [ 31.38494123]
84
+ [ 41.05796974]
85
+ [ 34.16569292]
86
+ [ 675.71692308]
87
+ [ 1155.49230769]
88
+ [ 1123.01333333]
89
+ [ 1020.32512821]
90
+ [ 9.16923077]
91
+ [ 7.88410256]
92
+ [ 91.02769231]
93
+ [ 113.05230769]
94
+ [ 107.95692308]
95
+ [ 1.69199795]
96
+ [ 5.9424321]
97
+ [ 7.62970749]
98
+ [ 6.65913928]
99
+ [ 273.06610021]
100
+ [ 576.94163774]
101
+ [ 1076.28940862]
102
+ [ 1506.43750441]
103
+ [ 1842.29025641]
104
+ [ 4252.04717949]
105
+ [ 6234.35487179]
106
+ [ 6852.38358974]
107
+ [ 43.48307692]
108
+ [ 91.23282051]
109
+ [ 165.82358974]
110
+ [ 230.21538462]
111
+ [ 257.0625641]
112
+ [ 676.35282051]
113
+ [ 1046.46564103]
114
+ [ 1256.45333333]
115
+ [ 18.41122533]
116
+ [ 47.23989108]
117
+ [ 77.90027856]
118
+ [ 99.89482667]
119
+ [ 0.57374872]
120
+ [ 0.70345128]
121
+ [ 0.8243641]
122
+ [ 3.85025641]
123
+ [ 2.9]
124
+ [ 5.18564103]
125
+ [ 0.00717949]
126
+ [-0.81230769]
127
+ [-0.49179487]
128
+ [ 0.19989231]
129
+ [ 0.11606667]
130
+ [ 0.28355385]
131
+ [ 0.79492308]
132
+ [ 1.13054872]
133
+ [ 1.56535385]
134
+ [ 3.86564103]
135
+ [ 3.97692308]
136
+ [ 8.91384615]
137
+ [-0.41435897]
138
+ [-1.25487179]
139
+ [-0.31897436]
140
+ [ 0.16110769]
141
+ [ 0.13379487]
142
+ [ 0.46472821]
143
+ [-7.47264615]
144
+ [-7.52603077]
145
+ [-5.69283077]
146
+ [ 111.37333333]
147
+ [ 194.89846154]
148
+ [ 165.68410256]
149
+ [ 20.82871795]
150
+ [ 36.17333333]
151
+ [ 29.31179487]
152
+ [ 3.21932308]
153
+ [ 6.05706667]
154
+ [ 5.09632821]
molSimplify/tf_nn/rescaling_data/ls_ii_mean_y.csv ADDED
@@ -0,0 +1,3 @@
1
+ [ 2.09137144]
2
+ [ 2.08600641]
3
+ [ 2.06514693]
molSimplify/tf_nn/rescaling_data/ls_ii_var_x.csv ADDED
@@ -0,0 +1,154 @@
1
+ [ 0.00808664]
2
+ [ 0.13088652]
3
+ [ 0.49614727]
4
+ [ 2331.65426525]
5
+ [ 11985.05751733]
6
+ [ 35111.27852217]
7
+ [ 58047.40989309]
8
+ [ 33903.85087074]
9
+ [ 195794.40585299]
10
+ [ 404646.80649678]
11
+ [ 450592.8152384]
12
+ [ 67.42668402]
13
+ [ 307.65985536]
14
+ [ 932.88031137]
15
+ [ 1564.00621275]
16
+ [ 2309.36006943]
17
+ [ 14715.4732455]
18
+ [ 30658.2922288]
19
+ [ 37710.20887942]
20
+ [ 9.33801008]
21
+ [ 63.76867162]
22
+ [ 153.54409795]
23
+ [ 220.89649225]
24
+ [ 3200.16435271]
25
+ [ 17488.7485822]
26
+ [ 49976.08193552]
27
+ [ 77795.56706902]
28
+ [ 45376.54694122]
29
+ [ 293223.61959342]
30
+ [ 685063.4957002]
31
+ [ 687192.5190522]
32
+ [ 89.06892202]
33
+ [ 437.01207101]
34
+ [ 1268.28707429]
35
+ [ 2036.8644881]
36
+ [ 3189.87381986]
37
+ [ 20746.90640789]
38
+ [ 44219.46152899]
39
+ [ 49566.6641378]
40
+ [ 14.27659471]
41
+ [ 99.17246227]
42
+ [ 243.60372976]
43
+ [ 307.29339229]
44
+ [ 3.65637667]
45
+ [ 23.49609357]
46
+ [ 112.29011668]
47
+ [ 181.44495271]
48
+ [ 3311.93642972]
49
+ [ 579.16892202]
50
+ [ 2432.8391453]
51
+ [ 2823.39034845]
52
+ [ 0.51361631]
53
+ [ 1.93531887]
54
+ [ 3.08161736]
55
+ [ 6.54949481]
56
+ [ 18.86367548]
57
+ [ 40.97610625]
58
+ [ 35.36890625]
59
+ [ 0.01283817]
60
+ [ 0.06599493]
61
+ [ 0.42113424]
62
+ [ 0.58390573]
63
+ [ 4.1813051]
64
+ [ 23.43324451]
65
+ [ 140.55884]
66
+ [ 277.39324836]
67
+ [ 1631.827281]
68
+ [ 547.30059066]
69
+ [ 2908.21239974]
70
+ [ 4521.86920079]
71
+ [ 0.51684418]
72
+ [ 2.39194845]
73
+ [ 4.57151769]
74
+ [ 6.98105878]
75
+ [ 29.86977883]
76
+ [ 65.89846049]
77
+ [ 61.88413307]
78
+ [ 0.00719256]
79
+ [ 0.07883036]
80
+ [ 0.53859992]
81
+ [ 0.8274861]
82
+ [ 0.25311734]
83
+ [ 14.5471018]
84
+ [ 164.28913649]
85
+ [ 648.7059728]
86
+ [ 2421.91371361]
87
+ [ 62942.25199211]
88
+ [ 148434.7741812]
89
+ [ 520298.81429165]
90
+ [ 11.3077712]
91
+ [ 36.09836266]
92
+ [ 406.61154083]
93
+ [ 2847.42187929]
94
+ [ 7396.98275976]
95
+ [ 0.03056993]
96
+ [ 0.18725947]
97
+ [ 5.1611493]
98
+ [ 22.03567785]
99
+ [ 20229.40708439]
100
+ [ 112473.2749112]
101
+ [ 361075.89836354]
102
+ [ 658828.57432172]
103
+ [ 319939.3978025]
104
+ [ 1795024.8880305]
105
+ [ 6176863.67304036]
106
+ [ 12931996.84567942]
107
+ [ 637.97073925]
108
+ [ 2996.3755382]
109
+ [ 9711.33708455]
110
+ [ 18574.83360947]
111
+ [ 23441.8001883]
112
+ [ 161322.75551769]
113
+ [ 436350.26112715]
114
+ [ 771114.43243761]
115
+ [ 83.90584441]
116
+ [ 603.04508322]
117
+ [ 1678.89662462]
118
+ [ 3226.83559542]
119
+ [ 1.271785]
120
+ [ 1.15939293]
121
+ [ 2.00351324]
122
+ [ 41.63655122]
123
+ [ 44.70461538]
124
+ [ 77.07169126]
125
+ [ 5.04251256]
126
+ [ 2.46938698]
127
+ [ 2.84608652]
128
+ [ 0.14009201]
129
+ [ 0.08221481]
130
+ [ 0.20836483]
131
+ [ 1.11388381]
132
+ [ 1.44940988]
133
+ [ 3.74882913]
134
+ [ 35.46194767]
135
+ [ 50.94690335]
136
+ [ 112.46591085]
137
+ [ 4.4847169]
138
+ [ 5.02452755]
139
+ [ 4.26594767]
140
+ [ 0.12373129]
141
+ [ 0.10815586]
142
+ [ 0.3114838]
143
+ [ 3.34894623]
144
+ [ 5.70146127]
145
+ [ 18.62253086]
146
+ [ 127.48523761]
147
+ [ 7458.34558738]
148
+ [ 18913.65200368]
149
+ [ 11.29476502]
150
+ [ 257.58328889]
151
+ [ 567.10278396]
152
+ [ 0.23650005]
153
+ [ 11.61972514]
154
+ [ 20.36451924]
molSimplify/tf_nn/rescaling_data/ls_ii_var_y.csv ADDED
@@ -0,0 +1,3 @@
1
+ [ 0.03892314]
2
+ [ 0.03805995]
3
+ [ 0.01681942]
molSimplify/tf_nn/rescaling_data/ls_iii_mean_x.csv ADDED
@@ -0,0 +1,154 @@
1
+ [ 0.15965909]
2
+ [ 1.14152893]
3
+ [ 1.4535124]
4
+ [ 51.40380093]
5
+ [ 96.49722893]
6
+ [ 135.0537875]
7
+ [ 147.59978233]
8
+ [ 238.91012397]
9
+ [ 370.31508264]
10
+ [ 426.36880165]
11
+ [ 368.28822314]
12
+ [ 8.07592975]
13
+ [ 14.88016529]
14
+ [ 21.9927686]
15
+ [ 24.28719008]
16
+ [ 36.87293388]
17
+ [ 85.45971074]
18
+ [ 107.24380165]
19
+ [ 102.62706612]
20
+ [ 3.20612665]
21
+ [ 6.63517128]
22
+ [ 8.42140795]
23
+ [ 8.57145455]
24
+ [ 64.3700689]
25
+ [ 124.32084463]
26
+ [ 181.91961839]
27
+ [ 200.88897025]
28
+ [ 279.20557851]
29
+ [ 479.53305785]
30
+ [ 601.76446281]
31
+ [ 529.11570248]
32
+ [ 9.98553719]
33
+ [ 19.07644628]
34
+ [ 28.98347107]
35
+ [ 32.04338843]
36
+ [ 48.05991736]
37
+ [ 112.81404959]
38
+ [ 142.37603306]
39
+ [ 133.54545455]
40
+ [ 3.98106498]
41
+ [ 8.65179483]
42
+ [ 11.50986756]
43
+ [ 11.53931839]
44
+ [ 8.57593858]
45
+ [ 10.91460599]
46
+ [ 8.91901746]
47
+ [ 9.99695413]
48
+ [ 77.53719008]
49
+ [ 47.13016529]
50
+ [ 44.96280992]
51
+ [ 33.79907025]
52
+ [ 1.44266529]
53
+ [ 1.20196281]
54
+ [ 1.37809917]
55
+ [ 2.75258264]
56
+ [ 4.87396694]
57
+ [ 4.62809917]
58
+ [ 3.84400826]
59
+ [ 0.6297359]
60
+ [ 0.68328698]
61
+ [ 0.60026131]
62
+ [ 0.57553388]
63
+ [ 9.36142769]
64
+ [ 11.49184329]
65
+ [ 12.52016064]
66
+ [ 16.56700868]
67
+ [ 71.25826446]
68
+ [ 50.05991736]
69
+ [ 63.50154959]
70
+ [ 55.92923554]
71
+ [ 1.5]
72
+ [ 1.5981405]
73
+ [ 2.11931818]
74
+ [ 2.86983471]
75
+ [ 5.66942149]
76
+ [ 6.54338843]
77
+ [ 5.7035124]
78
+ [ 0.60154473]
79
+ [ 0.71840888]
80
+ [ 0.8166314]
81
+ [ 0.86465573]
82
+ [ 3.10855269]
83
+ [ 31.62343275]
84
+ [ 39.67484205]
85
+ [ 31.71122304]
86
+ [ 660.00516529]
87
+ [ 1233.08780992]
88
+ [ 1034.68801653]
89
+ [ 913.82541322]
90
+ [ 8.88533058]
91
+ [ 7.16012397]
92
+ [ 89.31198347]
93
+ [ 106.09090909]
94
+ [ 95.8946281]
95
+ [ 1.64282355]
96
+ [ 5.9731093]
97
+ [ 7.12206198]
98
+ [ 5.9084156]
99
+ [ 253.18258926]
100
+ [ 527.06455227]
101
+ [ 991.37597149]
102
+ [ 1377.35547293]
103
+ [ 1827.67458678]
104
+ [ 4230.80165289]
105
+ [ 6185.83884298]
106
+ [ 6293.17561983]
107
+ [ 39.96177686]
108
+ [ 83.28305785]
109
+ [ 151.8677686]
110
+ [ 209.75826446]
111
+ [ 235.15082645]
112
+ [ 616.62396694]
113
+ [ 944.85950413]
114
+ [ 1118.22727273]
115
+ [ 17.17495723]
116
+ [ 43.71806136]
117
+ [ 72.22940289]
118
+ [ 90.71062934]
119
+ [ 0.54965909]
120
+ [ 0.64318182]
121
+ [ 0.76535124]
122
+ [ 4.11725207]
123
+ [ 3.45661157]
124
+ [ 5.02117769]
125
+ [ 0.10795455]
126
+ [-0.64307851]
127
+ [-0.36570248]
128
+ [ 0.21478822]
129
+ [ 0.14627066]
130
+ [ 0.28099174]
131
+ [ 0.79466942]
132
+ [ 0.95990186]
133
+ [ 1.43529959]
134
+ [ 4.42975207]
135
+ [ 3.8321281]
136
+ [ 8.04338843]
137
+ [-0.22830579]
138
+ [-1.15030992]
139
+ [-0.29855372]
140
+ [ 0.19256198]
141
+ [ 0.12753099]
142
+ [ 0.41803719]
143
+ [-7.42484504]
144
+ [-7.03252066]
145
+ [-5.07856405]
146
+ [ 105.91528926]
147
+ [ 187.53202479]
148
+ [ 150.22004132]
149
+ [ 21.11466942]
150
+ [ 35.63016529]
151
+ [ 26.97830579]
152
+ [ 3.02021694]
153
+ [ 5.8365186]
154
+ [ 4.52054752]
molSimplify/tf_nn/rescaling_data/ls_iii_mean_y.csv ADDED
@@ -0,0 +1,3 @@
1
+ [ 2.06664213]
2
+ [ 2.06305678]
3
+ [ 2.04413336]
molSimplify/tf_nn/rescaling_data/ls_iii_var_x.csv ADDED
@@ -0,0 +1,154 @@
1
+ [ 0.00816858]
2
+ [ 0.12149849]
3
+ [ 0.46478105]
4
+ [ 2146.10909022]
5
+ [ 10870.93737304]
6
+ [ 31425.50790114]
7
+ [ 51061.60848245]
8
+ [ 33869.5347942]
9
+ [ 192241.67448326]
10
+ [ 377601.0096465]
11
+ [ 408440.0915142]
12
+ [ 60.63550533]
13
+ [ 275.16125948]
14
+ [ 822.47825349]
15
+ [ 1362.35140615]
16
+ [ 2046.16877156]
17
+ [ 12922.10581479]
18
+ [ 26410.47361861]
19
+ [ 31922.54583767]
20
+ [ 8.44938362]
21
+ [ 57.53018655]
22
+ [ 136.06277891]
23
+ [ 192.17518452]
24
+ [ 3122.54267033]
25
+ [ 16714.31594367]
26
+ [ 46852.62316748]
27
+ [ 72647.95939762]
28
+ [ 45695.9153821]
29
+ [ 287657.81502288]
30
+ [ 663750.01063793]
31
+ [ 679763.49900963]
32
+ [ 84.76631975]
33
+ [ 413.34952787]
34
+ [ 1180.99972679]
35
+ [ 1878.77084472]
36
+ [ 2987.18236032]
37
+ [ 19313.17203401]
38
+ [ 40937.08173964]
39
+ [ 45428.02479339]
40
+ [ 13.87694074]
41
+ [ 94.81458923]
42
+ [ 229.82553796]
43
+ [ 290.56169089]
44
+ [ 3.49572257]
45
+ [ 29.74011311]
46
+ [ 105.82278769]
47
+ [ 165.66113805]
48
+ [ 5937.44851359]
49
+ [ 701.53161072]
50
+ [ 2259.41029045]
51
+ [ 2464.72744748]
52
+ [ 0.63178504]
53
+ [ 1.90316763]
54
+ [ 2.86737159]
55
+ [ 7.42458011]
56
+ [ 22.32502476]
57
+ [ 40.35084267]
58
+ [ 31.87132774]
59
+ [ 0.02168229]
60
+ [ 0.08656655]
61
+ [ 0.39974375]
62
+ [ 0.52392818]
63
+ [ 4.28523542]
64
+ [ 28.21169191]
65
+ [ 133.1089074]
66
+ [ 284.03606151]
67
+ [ 4170.53815484]
68
+ [ 778.67409586]
69
+ [ 2860.67380958]
70
+ [ 4237.08306057]
71
+ [ 0.61931818]
72
+ [ 2.34780646]
73
+ [ 4.63374871]
74
+ [ 7.79452394]
75
+ [ 30.36954016]
76
+ [ 59.24811744]
77
+ [ 51.57428518]
78
+ [ 0.01802694]
79
+ [ 0.09665664]
80
+ [ 0.51799151]
81
+ [ 0.7733229]
82
+ [ 0.18499781]
83
+ [ 13.3893815]
84
+ [ 211.06266698]
85
+ [ 737.48262477]
86
+ [ 3518.47208076]
87
+ [ 149011.92100843]
88
+ [ 197311.64646797]
89
+ [ 537133.71228805]
90
+ [ 13.91556993]
91
+ [ 40.48779007]
92
+ [ 500.96051755]
93
+ [ 3108.57024793]
94
+ [ 7894.29054966]
95
+ [ 0.01652897]
96
+ [ 0.28913575]
97
+ [ 6.26063943]
98
+ [ 22.98588054]
99
+ [ 21884.44828913]
100
+ [ 121881.97432684]
101
+ [ 379459.76663806]
102
+ [ 716907.07218308]
103
+ [ 361214.71332111]
104
+ [ 2013581.97718735]
105
+ [ 6627073.07320197]
106
+ [ 14171578.92783537]
107
+ [ 689.70205139]
108
+ [ 3222.35789478]
109
+ [ 10254.72631651]
110
+ [ 19909.78040691]
111
+ [ 24917.01030923]
112
+ [ 171118.17264873]
113
+ [ 456629.24472372]
114
+ [ 797791.28719008]
115
+ [ 89.07556449]
116
+ [ 637.10274101]
117
+ [ 1712.1509138]
118
+ [ 3430.63514697]
119
+ [ 1.27039534]
120
+ [ 1.08834421]
121
+ [ 1.70997596]
122
+ [ 43.84911352]
123
+ [ 55.39326207]
124
+ [ 73.41148332]
125
+ [ 4.95296358]
126
+ [ 2.76284465]
127
+ [ 2.853865]
128
+ [ 0.14090287]
129
+ [ 0.11547834]
130
+ [ 0.20802469]
131
+ [ 1.15202525]
132
+ [ 1.29938323]
133
+ [ 4.19597589]
134
+ [ 45.00539581]
135
+ [ 83.56763514]
136
+ [ 120.61536951]
137
+ [ 5.14105829]
138
+ [ 6.17394618]
139
+ [ 3.64898551]
140
+ [ 0.14945397]
141
+ [ 0.2011688]
142
+ [ 0.33096805]
143
+ [ 3.05329378]
144
+ [ 7.37035398]
145
+ [ 17.26623399]
146
+ [ 279.92051004]
147
+ [ 8304.61467689]
148
+ [ 21262.06005289]
149
+ [ 13.91556993]
150
+ [ 319.96652807]
151
+ [ 662.39105829]
152
+ [ 0.25939592]
153
+ [ 12.73017311]
154
+ [ 22.22719154]
molSimplify/tf_nn/rescaling_data/ls_iii_var_y.csv ADDED
@@ -0,0 +1,3 @@
1
+ [ 0.0271106]
2
+ [ 0.02565385]
3
+ [ 0.02027508]