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
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molSimplify/tf_nn/oxoandhomo/oxo20_val_names.csv ADDED
@@ -0,0 +1,143 @@
1
+ co_5_eq_chloride_ax1_chloride_ax2_oxo_s_1
2
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3
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4
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5
+ co_5_eq_water_ax1_isothiocyanate_ax2_oxo_s_1
6
+ co_5_eq_water_ax1_pisc_ax2_oxo_s_1
7
+ cr_4_eq_carbonyl_ax1_carbonyl_ax2_oxo_s_1
8
+ cr_4_eq_cyanide_ax1_cyanide_ax2_oxo_s_1
9
+ cr_4_eq_pisc_ax1_pisc_ax2_oxo_s_1
10
+ cr_4_eq_pyridine_ax1_ammonia_ax2_oxo_s_1
11
+ cr_4_eq_water_ax1_ammonia_ax2_oxo_s_1
12
+ cr_4_eq_water_ax1_chloride_ax2_oxo_s_1
13
+ cr_4_eq_water_ax1_nme3_ax2_oxo_s_1
14
+ cr_4_eq_water_ax1_pisc_ax2_oxo_s_1
15
+ fe_4_eq_acac_ax1_ammonia_ax2_oxo_s_1
16
+ fe_4_eq_acac_ax1_isothiocyanate_ax2_oxo_s_1
17
+ fe_4_eq_ammonia_ax1_water_ax2_oxo_s_1
18
+ fe_4_eq_bifuran_ax1_nme3_ax2_oxo_s_1
19
+ fe_4_eq_isothiocyanate_ax1_isothiocyanate_ax2_oxo_s_1
20
+ fe_4_eq_pme3_ax1_pme3_ax2_oxo_s_1
21
+ fe_4_eq_porphyrin_ax1_water_ax2_oxo_s_1
22
+ fe_4_eq_water_ax1_ammonia_ax2_oxo_s_1
23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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58
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59
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60
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61
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62
+ fe_4_eq_acac_ax1_cyanide_ax2_oxo_s_3
63
+ fe_4_eq_ammonia_ax1_cyanide_ax2_oxo_s_3
64
+ cr_4_eq_isothiocyanate_ax1_isothiocyanate_ax2_oxo_s_3
65
+ co_5_eq_pyridine_ax1_pyridine_ax2_oxo_s_3
66
+ mn_5_eq_ome2_ax1_tetrahydrofuran_ax2_oxo_s_3
67
+ fe_4_eq_acac_ax1_isothiocyanate_ax2_oxo_s_3
68
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69
+ cr_4_eq_cyanide_ax1_isothiocyanate_ax2_oxo_s_3
70
+ fe_4_eq_pyridine_ax1_pyridine_ax2_oxo_s_3
71
+ cr_4_eq_porphyrin_ax1_water_ax2_oxo_s_3
72
+ fe_4_eq_ammonia_ax1_carbonyl_ax2_oxo_s_3
73
+ fe_4_eq_pyrrole_ax1_water_ax2_oxo_s_3
74
+ cr_4_eq_cyanopyridine_ax1_ammonia_ax2_oxo_s_3
75
+ fe_4_eq_en_ax1_carbonyl_ax2_oxo_s_3
76
+ mn_5_eq_bipy_ax1_water_ax2_oxo_s_3
77
+ cr_4_eq_en_ax1_carbonyl_ax2_oxo_s_3
78
+ cr_4_eq_chloride_ax1_chloride_ax2_oxo_s_3
79
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80
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81
+ co_5_eq_ammonia_ax1_water_ax2_oxo_s_3
82
+ fe_4_eq_cyanide_ax1_isothiocyanate_ax2_oxo_s_3
83
+ fe_4_eq_phosphine_ax1_pph3_ax2_oxo_s_3
84
+ cr_4_eq_ammonia_ax1_nme3_ax2_oxo_s_3
85
+ cr_4_eq_acac_ax1_isothiocyanate_ax2_oxo_s_3
86
+ cr_4_eq_phen_ax1_ammonia_ax2_oxo_s_3
87
+ mn_5_eq_en_ax1_carbonyl_ax2_oxo_s_3
88
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89
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90
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91
+ fe_5_eq_carbonyl_ax1_cyanide_ax2_oxo_s_4
92
+ mn_5_eq_pyridine_ax1_nme3_ax2_oxo_s_3
93
+ mn_5_eq_carbonyl_ax1_ammonia_ax2_oxo_s_3
94
+ fe_5_eq_pisc_ax1_chloride_ax2_oxo_s_4
95
+ co_5_eq_tbuc_ax1_carbonyl_ax2_oxo_s_5
96
+ co_5_eq_porphyrin_ax1_cyanide_ax2_oxo_s_5
97
+ co_4_eq_carbonyl_ax1_ammonia_ax2_oxo_s_4
98
+ co_4_eq_acac_ax1_cyanide_ax2_oxo_s_4
99
+ co_4_eq_isothiocyanate_ax1_cyanide_ax2_oxo_s_4
100
+ co_4_eq_water_ax1_chloride_ax2_oxo_s_4
101
+ co_4_eq_ammonia_ax1_cyanide_ax2_oxo_s_4
102
+ co_5_eq_bipy_ax1_nme3_ax2_oxo_s_5
103
+ co_4_eq_porphyrin_ax1_ammonia_ax2_oxo_s_4
104
+ co_4_eq_en_ax1_carbonyl_ax2_oxo_s_4
105
+ fe_5_eq_bipyrrole_ax1_pyridine_ax2_oxo_s_4
106
+ co_4_eq_cyanopyridine_ax1_ammonia_ax2_oxo_s_4
107
+ co_4_eq_pyrrole_ax1_cyanopyridine_ax2_oxo_s_4
108
+ co_4_eq_pyridine_ax1_ammonia_ax2_oxo_s_4
109
+ co_5_eq_cyanopyridine_ax1_ammonia_ax2_oxo_s_5
110
+ co_4_eq_pyridine_ax1_pyridine_ax2_oxo_s_4
111
+ co_4_eq_water_ax1_cyanopyridine_ax2_oxo_s_4
112
+ co_4_eq_ammonia_ax1_ammonia_ax2_oxo_s_4
113
+ fe_5_eq_ammonia_ax1_nme3_ax2_oxo_s_4
114
+ co_4_eq_ome2_ax1_water_ax2_oxo_s_4
115
+ co_5_eq_bipyrrole_ax1_acetonitrile_ax2_oxo_s_5
116
+ fe_5_eq_ox_ax1_pisc_ax2_oxo_s_4
117
+ fe_5_eq_porphyrin_ax1_ammonia_ax2_oxo_s_4
118
+ fe_5_eq_acac_ax1_ammonia_ax2_oxo_s_4
119
+ fe_5_eq_porphyrin_ax1_water_ax2_oxo_s_4
120
+ mn_4_eq_tbuc_ax1_ammonia_ax2_oxo_s_4
121
+ mn_4_eq_water_ax1_ome2_ax2_oxo_s_4
122
+ fe_5_eq_pyridine_ax1_pyridine_ax2_oxo_s_4
123
+ co_5_eq_carbonyl_ax1_carbonyl_ax2_oxo_s_5
124
+ co_5_eq_ammonia_ax1_ammonia_ax2_oxo_s_5
125
+ mn_4_eq_phen_ax1_ammonia_ax2_oxo_s_4
126
+ mn_4_eq_ome2_ax1_furan_ax2_oxo_s_4
127
+ fe_5_eq_acac_ax1_isothiocyanate_ax2_oxo_s_4
128
+ mn_4_eq_pyridine_ax1_pyridine_ax2_oxo_s_4
129
+ fe_5_eq_en_ax1_ammonia_ax2_oxo_s_4
130
+ fe_5_eq_ammonia_ax1_carbonyl_ax2_oxo_s_4
131
+ fe_5_eq_ammonia_ax1_water_ax2_oxo_s_4
132
+ fe_5_eq_phosphine_ax1_phosphine_ax2_oxo_s_4
133
+ fe_5_eq_ome2_ax1_pyridine_ax2_oxo_s_4
134
+ mn_4_eq_ox_ax1_pisc_ax2_oxo_s_4
135
+ fe_4_eq_bipyrrole_ax1_pyridine_ax2_oxo_s_5
136
+ fe_4_eq_acac_ax1_cyanide_ax2_oxo_s_5
137
+ fe_4_eq_acac_ax1_chloride_ax2_oxo_s_5
138
+ fe_4_eq_tbuc_ax1_ammonia_ax2_oxo_s_5
139
+ fe_4_eq_en_ax1_pisc_ax2_oxo_s_5
140
+ fe_4_eq_carbonyl_ax1_carbonyl_ax2_oxo_s_5
141
+ fe_4_eq_en_ax1_ammonia_ax2_oxo_s_5
142
+ fe_4_eq_ome2_ax1_ome2_ax2_oxo_s_5
143
+ fe_4_eq_pyrrole_ax1_cyanopyridine_ax2_oxo_s_5