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
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  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
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  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
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  466. molSimplify/tf_nn/homolumo/homo_test_y.csv +176 -0
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  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
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  476. molSimplify/tf_nn/oxoandhomo/homo_empty_test_y.csv +144 -0
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  478. molSimplify/tf_nn/oxoandhomo/homo_empty_train_x.csv +514 -0
  479. molSimplify/tf_nn/oxoandhomo/homo_empty_train_y.csv +514 -0
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  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
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  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
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  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
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  574. molSimplify/tf_nn/sc_static_clf/sc_static_clf_train_y.csv +1592 -0
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  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/Data/ML_FSR_for_inter2.dat ADDED
@@ -0,0 +1,110 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are sym1_valency, sym2_valency, ox state, spin multiplicity, fsr
3
+ # usually, fsr_bondl_m3D and fsr_bondl_sub
4
+ C0 H0 - - 1.14
5
+ N0 H0 - - 1.1
6
+ O0 H0 - - 1.26
7
+ C0 C0 - - 1.1
8
+ N0 C0 - - 1.1
9
+ O0 C0 - - 1.27
10
+ N0 N0 - - 1.1
11
+ O0 N0 - - 1.27
12
+ O0 O0 - - 1.27
13
+ C1 H0 - - 1.14
14
+ N1 H0 - - 1.1
15
+ O1 H0 - - 1.26
16
+ C1 C0 - - 1.1
17
+ N1 C0 - - 1.1
18
+ O1 C0 - - 1.27
19
+ N1 N0 - - 1.1
20
+ O1 N0 - - 1.27
21
+ O1 O0 - - 1.27
22
+ C1 C1 - - 0.90
23
+ C1 O1 - - 1.8 1.8
24
+ N1 C1 - - 1.1
25
+ O1 C1 - - 1.27 1.8
26
+ N1 N1 - - 0.80
27
+ O1 N1 - - 1.27
28
+ O1 O1 - - 1.27
29
+ C2 H0 - - 1.14
30
+ N2 H0 - - 1.1
31
+ O2 H0 - - 1.26
32
+ C2 C0 - - 1.1
33
+ N2 C0 - - 1.1
34
+ O2 C0 - - 1.27
35
+ N2 N0 - - 1.1
36
+ O2 N0 - - 1.27
37
+ O2 O0 - - 1.27
38
+ C2 C1 - - 1.1
39
+ N2 C1 - - 1.1
40
+ O2 C1 - - 1.27
41
+ N2 N1 - - 0.80
42
+ O2 N1 - - 1.27
43
+ O2 O1 - - 1.27
44
+ C2 C2 - - 0.82
45
+ N2 C2 - - 1.1
46
+ O2 C2 - - 1.27
47
+ N2 N2 - - 0.85
48
+ O2 N2 - - 1.27
49
+ O2 O2 - - 1.27
50
+ C3 H0 - - 1.14
51
+ N3 H0 - - 1.1
52
+ C3 C0 - - 1.1
53
+ C3 N0 - - 1.1
54
+ C3 O0 - - 1.1
55
+ N3 C0 - - 1.1
56
+ N3 N0 - - 1.1
57
+ N3 O0 - - 1.1
58
+ C3 C1 - - 1.1
59
+ C3 N1 - - 1.1
60
+ C3 O1 - - 1.1
61
+ N3 C1 - - 1.1
62
+ N3 N1 - - 1.1
63
+ N3 O1 - - 1.1
64
+ C3 C2 - - 1.1
65
+ C3 N2 - - 1.1
66
+ C3 O2 - - 1.1
67
+ N3 C2 - - 1.1
68
+ N3 N2 - - 1.1
69
+ N3 O2 - - 1.1
70
+ C3 C3 - - 1.1
71
+ C3 N3 - - 1.1
72
+ N3 N3 - - 1.1
73
+ C4 H0 - - 1.14
74
+ C4 C0 - - 1.1
75
+ C4 N0 - - 1.1
76
+ C4 O0 - - 1.1
77
+ C4 C1 - - 1.1
78
+ C4 N1 - - 1.1
79
+ C4 O1 - - 1.1
80
+ C4 C2 - - 1.1
81
+ C4 N2 - - 1.1
82
+ C4 O2 - - 1.1
83
+ C4 C3 - - 1.1
84
+ C4 N3 - - 1.1
85
+ C4 C4 - - 1.1
86
+ # usually, fsr_bondl_core3D
87
+ Ti O1 - - 1.1
88
+ V O1 - - 1.1
89
+ Cr O1 - - 1.1
90
+ Mn O1 - - 1.1
91
+ Fe O1 - - 0.85
92
+ Co O1 - - 1.1
93
+ Ni O1 - - 1.1
94
+ Cu O1 - - 1.1
95
+ Ti N1 - - 1.1
96
+ V N1 - - 1.1
97
+ Cr N1 - - 1.1
98
+ Mn N1 - - 1.1
99
+ Fe N1 - - 1.1
100
+ Co N1 - - 1.1
101
+ Ni N1 - - 1.1
102
+ Cu N1 - - 1.1
103
+ Ti C1 - - 1.1
104
+ V C1 - - 1.1
105
+ Cr C1 - - 1.1
106
+ Mn C1 - - 1.1
107
+ Fe C1 - - 1.1
108
+ Co C1 - - 1.1
109
+ Ni C1 - - 1.1
110
+ Cu C1 - - 1.1
molSimplify/Data/ML_bond_for_cat.dat ADDED
@@ -0,0 +1,8 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, C-H BL, H-O BL,O-M BL
3
+ ## Default
4
+ Pd - - - 1.10 2.20
5
+ ## amidates
6
+ # DOI = 10.1021/om700573h
7
+ Pd - - N-quinolinylbutyramidate 1.10 2.20
8
+ Pd 1 1 N-quinolinylbutyramidate 1.10 2.20
molSimplify/Data/ML_bond_for_click.dat ADDED
@@ -0,0 +1,8 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, C-X BL (bondl_sub), X-M BL (bondl_m3D),C-M BL (bondl_core3D)
3
+ ## Default
4
+ Cu - - - 1.19 1.88 3
5
+ ## triazoles
6
+ # DOI = 10.1021/ja0471525
7
+ Cu - - methylazide 1.19 1.88 3
8
+ Cu 1 1 methylazide 1.19 1.88 3
molSimplify/Data/ML_bond_for_inter.dat ADDED
@@ -0,0 +1,48 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, reacting atom, bondl_m3D, bondl_sub, bondl_core3D
3
+ # hat, reacting atom = H
4
+ Co - - H 1.30 1.20 1.80
5
+ Co 4 2 H 1.32 1.19 1.82
6
+ Co 4 4 H 1.25 1.25 1.77
7
+ Cr - - H 1.30 1.20 1.80
8
+ Cr 4 3 H 1.32 1.21 1.81
9
+ Fe - - H 1.30 1.20 1.80
10
+ Fe 4 3 H 1.36 1.17 1.78
11
+ Fe 4 5 H 1.28 1.24 1.81
12
+ Fe 5 2 H 1.27 1.24 1.74
13
+ Fe 5 4 H 1.25 1.27 1.78
14
+ Mn - - H 1.30 1.25 1.75
15
+ Mn 4 2 H 1.32 1.21 1.75
16
+ Mn 4 4 H 1.30 1.24 1.77
17
+ Mn 5 3 H 1.27 1.26 1.76
18
+ # oat, reacting atom = N
19
+ Co - - N 1.14 1.55 1.87
20
+ Co 4 2 N 1.15 1.50 1.90
21
+ Co 4 4 N 1.13 1.60 1.85
22
+ Cr - - N 1.14 1.61 1.96
23
+ Cr 4 3 N 1.14 1.61 1.96
24
+ Fe - - N 1.16 1.60 1.83
25
+ Fe 4 3 N 1.14 1.52 1.90
26
+ Fe 4 5 N 1.25 1.60 1.88
27
+ Fe 5 2 N 1.11 1.62 1.77
28
+ Fe 5 4 N 1.13 1.65 1.88
29
+ Mn - - N 1.13 1.50 1.87
30
+ Mn 4 4 N 1.11 1.55 1.80
31
+ Mn 5 3 N 1.15 1.45 1.94
32
+ Cu - - N 1.90 1.20 1.26
33
+ # cat, reacting atom = C
34
+ Co - - C 1.37 2.10 1.70
35
+ Co 4 2 C 1.37 2.10 1.70
36
+ Co 4 4 C 1.37 2.10 1.70
37
+ Cr - - C 1.37 2.10 1.70
38
+ Cr 4 3 C 1.37 2.10 1.70
39
+ Cr 5 2 C 1.37 2.10 1.70
40
+ Fe - - C 1.37 2.10 1.70
41
+ Fe 4 3 C 1.37 2.10 1.70
42
+ Fe 4 5 C 1.37 2.10 1.70
43
+ Fe 5 2 C 1.37 2.10 1.70
44
+ Fe 5 4 C 1.37 2.10 1.70
45
+ Mn - - C 1.37 2.10 1.70
46
+ Mn 4 2 C 1.37 2.10 1.70
47
+ Mn 4 4 C 1.37 2.10 1.70
48
+ Mn 5 3 C 1.37 2.10 1.70
molSimplify/Data/ML_bond_for_inter2.dat ADDED
@@ -0,0 +1,48 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, reacting atom, bondl_m3D, bondl_sub, bondl_core3D
3
+ # hat, reacting atom = H
4
+ Co - - H 1.30 1.20 1.80
5
+ Co 4 2 H 1.32 1.19 1.82
6
+ Co 4 4 H 1.25 1.25 1.77
7
+ Cr - - H 1.30 1.20 1.80
8
+ Cr 4 3 H 1.32 1.21 1.81
9
+ Fe - - H 1.30 1.20 1.80
10
+ Fe 4 3 H 1.36 1.17 1.78
11
+ Fe 4 5 H 1.28 1.24 1.81
12
+ Fe 5 2 H 1.27 1.24 1.74
13
+ Fe 5 4 H 1.25 1.27 1.78
14
+ Mn - - H 1.30 1.25 1.75
15
+ Mn 4 2 H 1.32 1.21 1.75
16
+ Mn 4 4 H 1.30 1.24 1.77
17
+ Mn 5 3 H 1.27 1.26 1.76
18
+ # oat, reacting atom = N
19
+ Co - - N 1.14 1.55 1.87
20
+ Co 4 2 N 1.15 1.50 1.90
21
+ Co 4 4 N 1.13 1.60 1.85
22
+ Cr - - N 1.14 1.61 1.96
23
+ Cr 4 3 N 1.14 1.61 1.96
24
+ Fe - - N 1.16 1.60 1.83
25
+ Fe 4 3 N 1.14 1.52 1.90
26
+ Fe 4 5 N 1.25 1.60 1.88
27
+ Fe 5 2 N 1.11 1.62 1.77
28
+ Fe 5 4 N 1.13 1.65 1.88
29
+ Mn - - N 1.13 1.50 1.87
30
+ Mn 4 4 N 1.11 1.55 1.80
31
+ Mn 5 3 N 1.15 1.45 1.94
32
+ Cu - - N 1.90 1.20 1.26
33
+ # cat, reacting atom = C
34
+ Co - - C 1.37 2.10 1.70
35
+ Co 4 2 C 1.37 2.10 1.70
36
+ Co 4 4 C 1.37 2.10 1.70
37
+ Cr - - C 1.37 2.10 1.70
38
+ Cr 4 3 C 1.37 2.10 1.70
39
+ Cr 5 2 C 1.37 2.10 1.70
40
+ Fe - - C 1.37 2.10 1.70
41
+ Fe 4 3 C 1.37 2.10 1.70
42
+ Fe 4 5 C 1.37 2.10 1.70
43
+ Fe 5 2 C 1.37 2.10 1.70
44
+ Fe 5 4 C 1.37 2.10 1.70
45
+ Mn - - C 1.37 2.10 1.70
46
+ Mn 4 2 C 1.37 2.10 1.70
47
+ Mn 4 4 C 1.37 2.10 1.70
48
+ Mn 5 3 C 1.37 2.10 1.70
molSimplify/Data/ML_bond_for_intra.dat ADDED
@@ -0,0 +1,10 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, C-X BL (bondl_sub), X-M BL (bondl_m3D),C-M BL (bondl_core3D)
3
+ # hat, reacting atom = H
4
+ # DOI = 10.1021/om700573h
5
+ Pd - - H 1.52 1.28 2.84
6
+ Pd 1 1 H 1.52 1.28 2.84
7
+ # cat, reacting atom = C
8
+ Pd - - C 2.09 1.94 2.09
9
+ # DOI = 10.1021/ja0471525
10
+ Cu - - N 1.20 1.90 2.95
molSimplify/Data/ML_bond_for_intra2.dat ADDED
@@ -0,0 +1,6 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, C-X BL (bondl_sub), X-M BL (bondl_m3D),C-M BL (bondl_core3D)
3
+ # cat, reacting atom = C
4
+ # DOI = 10.1021/om700573h
5
+ Pd - - C 1.104 2.202 2.202
6
+ Pd 1 1 C 1.104 2.202 2.202
molSimplify/Data/ML_bond_for_oa.dat ADDED
@@ -0,0 +1,18 @@
1
+ # Default data for bond lengths (in A) between metal, connection atom and ligand
2
+ # keys are metal, ox state, spin multiplicity, C-X BL (bondl_sub), X-M BL (bondl_m3D),C-M BL (bondl_core3D)
3
+ ## Default
4
+ Cu - - - 2.04 1.96 1.96
5
+ ## aryl halides
6
+ # DOI = 10.1021/om700573h
7
+ Cu - - bromobenzene 2.04 1.96 1.96
8
+ Cu 1 1 bromobenzene 2.04 1.96 1.96
9
+ ## triazoles
10
+ # DOI = 10.1021/ja0471525
11
+ Cu - - triazole 2.35 1.78 1.96
12
+ Cu 1 1 triazole 2.35 1.78 1.96
13
+ ## Default
14
+ Pd - - - 2.17 2.18 1.96
15
+ ## aryl halides
16
+ # DOI = 10.1021/om060784a
17
+ Pd - - bromobenzene 2.17 2.18 1.96
18
+ Pd 1 1 bromobenzene 2.17 2.18 1.96
molSimplify/Data/bp1.dat ADDED
@@ -0,0 +1,21 @@
1
+ 0.000000 0.000000 0.000000
2
+ -0.012626 2.095331 0.005794
3
+ -2.026225 0.632505 0.973013
4
+ 1.048325 2.765351 -0.474221
5
+ 1.868812 2.157373 -0.842142
6
+ 1.114247 4.155290 -0.509034
7
+ 1.994085 4.651235 -0.904156
8
+ 0.026501 4.877440 -0.021170
9
+ 0.033482 5.963060 -0.027052
10
+ -1.075986 4.188729 0.481709
11
+ -1.920983 4.745324 0.868231
12
+ -3.384882 2.535241 1.505617
13
+ -3.525388 3.608868 1.530463
14
+ -4.394150 1.699197 1.979881
15
+ -5.312892 2.122817 2.373472
16
+ -4.204420 0.319344 1.941992
17
+ -4.961194 -0.368843 2.302784
18
+ -3.004398 -0.165542 1.428332
19
+ -2.809898 -1.232315 1.379045
20
+ -1.073577 2.789878 0.485810
21
+ -2.204299 1.974417 1.005392
molSimplify/Data/li.dat ADDED
@@ -0,0 +1,3 @@
1
+ 0.0 0.0 0.0
2
+ 2.0000 0.0 0.0
3
+ -2.000 0.0 0.0
molSimplify/Data/no.dat ADDED
@@ -0,0 +1,2 @@
1
+ 0.0 0.0 0.0
2
+ 2.00 0.0 0.0
molSimplify/Data/oct.dat ADDED
@@ -0,0 +1,7 @@
1
+ 0.0 0.0 0.0
2
+ 0.0 2.077 0.0
3
+ 2.077 0.0 0.0
4
+ 0.0 -2.077 0.0
5
+ -2.077 0.0 0.0
6
+ 0.0 0.0 2.077
7
+ 0.0 0.0 -2.077
molSimplify/Data/pbp.dat ADDED
@@ -0,0 +1,8 @@
1
+ 0.0000 0.0000 0.0000
2
+ 2.0000 0.0000 0.0000
3
+ 0.6180 1.9021 0.0000
4
+ -1.6180 1.1755 0.0000
5
+ -1.6180 -1.1755 0.0000
6
+ 0.6180 -1.9021 0.0000
7
+ 0.0000 0.0000 2.0000
8
+ 0.0000 0.0000 -2.0000
molSimplify/Data/spy.dat ADDED
@@ -0,0 +1,6 @@
1
+ 0.00000 0.00000 0.00000
2
+ -2.00000 2.00000 0.00000
3
+ -2.00000 -2.00000 0.00000
4
+ 2.00000 -2.00000 0.00000
5
+ 2.00000 2.00000 0.00000
6
+ 0.00000 0.00000 2.00000
molSimplify/Data/sqap.dat ADDED
@@ -0,0 +1,9 @@
1
+ 0.00000 0.00000 0.00000
2
+ -1.61492 -1.61492 -0.43036
3
+ -1.61492 1.61492 0.43036
4
+ -0.93422 -0.93422 2.15616
5
+ -0.93422 0.93422 -2.15616
6
+ 1.61492 -1.61492 0.43036
7
+ 1.61492 1.61492 -0.43036
8
+ 0.93422 -0.93422 -2.15616
9
+ 0.93422 0.93422 2.15616
molSimplify/Data/sqp.dat ADDED
@@ -0,0 +1,5 @@
1
+ 0.00000 0.00000 0.00000
2
+ -1.40000 1.40000 0.00000
3
+ -1.40000 -1.40000 0.00000
4
+ 1.40000 -1.40000 0.00000
5
+ 1.40000 1.40000 0.00000
molSimplify/Data/tbp.dat ADDED
@@ -0,0 +1,6 @@
1
+ 0.0 0.0 0.0
2
+ -1.7865930597 -0.0003546225 -0.0007425232
3
+ 1.7865967124 -0.0003546332 -0.0007425118
4
+ 2.86499999724e-07 1.382576768 -1.1498771629
5
+ 2.92799999801e-07 0.2985354596 1.7728580026
6
+ 4.09099999654e-07 -1.6828658296 -0.6318871017
molSimplify/Data/tdhd.dat ADDED
@@ -0,0 +1,9 @@
1
+ 0.00000 0.00000 0.00000
2
+ -1.61492 -1.61492 -0.43036
3
+ -1.61492 1.61492 0.43036
4
+ -0.93422 -0.93422 2.15616
5
+ -0.93422 0.93422 -2.15616
6
+ 1.61492 -1.61492 0.43036
7
+ 1.61492 1.61492 -0.43036
8
+ 0.93422 -0.93422 -2.15616
9
+ 0.93422 0.93422 2.15616
molSimplify/Data/thd.dat ADDED
@@ -0,0 +1,5 @@
1
+ 0.00000 0.00000 0.00000
2
+ 2.07654 0.00000 0.00000
3
+ -0.69222 1.95776 0.00000
4
+ -0.69222 -0.97887 1.69548
5
+ -0.69222 -0.97887 -1.69548
molSimplify/Data/tpl.dat ADDED
@@ -0,0 +1,4 @@
1
+ 0.00000 0.00000 0.00000
2
+ -1.58487 0.39844 0.52472
3
+ 0.77037 -1.41380 0.59470
4
+ 0.78682 0.99734 -1.17123
molSimplify/Data/tpr.dat ADDED
@@ -0,0 +1,7 @@
1
+ 0.000000 0.0000 0.000
2
+ -1.73205 -1.000 1.200
3
+ 1.732050 -1.000 1.200
4
+ 0.00000 2.0000 1.200
5
+ -1.5000 -1.0000 -1.80
6
+ 1.50000 -1.0000 -1.80
7
+ 0.00000 1.8027 -1.80
molSimplify/Informatics/HFXsensitivity/__init__.py ADDED
File without changes