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/Ligands/BPAbipy.mol ADDED
@@ -0,0 +1,106 @@
1
+
2
+ OpenBabel03211612003D
3
+
4
+ 49 52 0 0 0 0 0 0 0 0999 V2000
5
+ 0.7466 17.4328 1.9016 N 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 0.9437 17.9312 0.6834 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 0.5924 17.4597 -0.0616 H 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1.6318 19.0979 0.4523 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 1.7717 19.4191 -0.4303 H 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 2.1110 19.7884 1.5494 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 2.5857 20.6009 1.4295 H 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 1.8998 19.2950 2.8095 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 2.2097 19.7728 3.5699 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 1.2267 18.0918 2.9679 C 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.0355 17.4363 4.2687 C 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 0.9381 18.1283 4.9697 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 1.8400 16.8998 4.4822 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ -0.1550 16.5558 4.2874 N 0 0 0 0 0 0 0 0 0 0 0 0
19
+ -0.0494 15.4804 5.2932 C 0 0 0 0 0 0 0 0 0 0 0 0
20
+ -0.3582 15.8152 6.1714 H 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 0.8972 15.2048 5.3845 H 0 0 0 0 0 0 0 0 0 0 0 0
22
+ -0.8809 14.3005 4.8838 C 0 0 0 0 0 0 0 0 0 0 0 0
23
+ -1.2838 13.3445 5.7906 C 0 0 0 0 0 0 0 0 0 0 0 0
24
+ -1.1157 13.4631 6.7183 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ -1.9311 12.2171 5.3438 C 0 0 0 0 0 0 0 0 0 0 0 0
26
+ -2.1873 11.5348 5.9557 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ -2.2048 12.0845 3.9991 C 0 0 0 0 0 0 0 0 0 0 0 0
28
+ -2.6689 11.3249 3.6689 H 0 0 0 0 0 0 0 0 0 0 0 0
29
+ -1.7898 13.0809 3.1484 C 0 0 0 0 0 0 0 0 0 0 0 0
30
+ -1.9790 12.9966 2.2207 H 0 0 0 0 0 0 0 0 0 0 0 0
31
+ -1.1280 14.1687 3.5743 N 0 0 0 0 0 0 0 0 0 0 0 0
32
+ -1.4224 17.3586 4.5185 C 0 0 0 0 0 0 0 0 0 0 0 0
33
+ -1.9407 16.9387 5.2492 H 0 0 0 0 0 0 0 0 0 0 0 0
34
+ -1.1754 18.2722 4.8101 H 0 0 0 0 0 0 0 0 0 0 0 0
35
+ -2.0039 16.6607 2.2934 N 0 0 0 0 0 0 0 0 0 0 0 0
36
+ -2.2833 17.4527 3.3025 C 0 0 0 0 0 0 0 0 0 0 0 0
37
+ -3.3879 18.3157 3.2529 C 0 0 0 0 0 0 0 0 0 0 0 0
38
+ -3.6008 18.8942 3.9760 H 0 0 0 0 0 0 0 0 0 0 0 0
39
+ -4.1530 18.2858 2.1041 C 0 0 0 0 0 0 0 0 0 0 0 0
40
+ -4.8998 18.8670 2.0292 H 0 0 0 0 0 0 0 0 0 0 0 0
41
+ -3.8603 17.4406 1.0762 C 0 0 0 0 0 0 0 0 0 0 0 0
42
+ -4.4019 17.4247 0.2960 H 0 0 0 0 0 0 0 0 0 0 0 0
43
+ -2.7689 16.6129 1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0
44
+ -2.2985 15.6488 0.1882 C 0 0 0 0 0 0 0 0 0 0 0 0
45
+ -2.9941 15.3381 -0.9706 C 0 0 0 0 0 0 0 0 0 0 0 0
46
+ -3.8257 15.7569 -1.1577 H 0 0 0 0 0 0 0 0 0 0 0 0
47
+ -2.4674 14.4140 -1.8455 C 0 0 0 0 0 0 0 0 0 0 0 0
48
+ -2.9401 14.1823 -2.6367 H 0 0 0 0 0 0 0 0 0 0 0 0
49
+ -1.2598 13.8321 -1.5693 C 0 0 0 0 0 0 0 0 0 0 0 0
50
+ -0.8647 13.2143 -2.1712 H 0 0 0 0 0 0 0 0 0 0 0 0
51
+ -0.6386 14.1714 -0.3962 C 0 0 0 0 0 0 0 0 0 0 0 0
52
+ 0.1794 13.7391 -0.1849 H 0 0 0 0 0 0 0 0 0 0 0 0
53
+ -1.1031 15.0602 0.4567 N 0 0 0 0 0 0 0 0 0 0 0 0
54
+ 1 10 2 0 0 0 0
55
+ 2 1 1 0 0 0 0
56
+ 3 2 1 0 0 0 0
57
+ 4 2 2 0 0 0 0
58
+ 4 6 1 0 0 0 0
59
+ 5 4 1 0 0 0 0
60
+ 6 8 2 0 0 0 0
61
+ 7 6 1 0 0 0 0
62
+ 8 10 1 0 0 0 0
63
+ 8 9 1 0 0 0 0
64
+ 10 11 1 0 0 0 0
65
+ 11 14 1 0 0 0 0
66
+ 11 13 1 0 0 0 0
67
+ 11 12 1 0 0 0 0
68
+ 14 28 1 0 0 0 0
69
+ 14 15 1 0 0 0 0
70
+ 15 17 1 0 0 0 0
71
+ 15 16 1 0 0 0 0
72
+ 18 15 1 0 0 0 0
73
+ 18 19 2 0 0 0 0
74
+ 19 20 1 0 0 0 0
75
+ 21 19 1 0 0 0 0
76
+ 21 22 1 0 0 0 0
77
+ 23 21 2 0 0 0 0
78
+ 24 23 1 0 0 0 0
79
+ 25 27 2 0 0 0 0
80
+ 25 23 1 0 0 0 0
81
+ 26 25 1 0 0 0 0
82
+ 27 18 1 0 0 0 0
83
+ 28 30 1 0 0 0 0
84
+ 28 29 1 0 0 0 0
85
+ 31 32 2 0 0 0 0
86
+ 32 28 1 0 0 0 0
87
+ 33 32 1 0 0 0 0
88
+ 33 34 1 0 0 0 0
89
+ 35 33 2 0 0 0 0
90
+ 36 35 1 0 0 0 0
91
+ 37 39 2 0 0 0 0
92
+ 37 35 1 0 0 0 0
93
+ 38 37 1 0 0 0 0
94
+ 39 31 1 0 0 0 0
95
+ 40 49 1 0 0 0 0
96
+ 40 39 1 0 0 0 0
97
+ 41 40 2 0 0 0 0
98
+ 42 41 1 0 0 0 0
99
+ 43 45 2 0 0 0 0
100
+ 43 41 1 0 0 0 0
101
+ 44 43 1 0 0 0 0
102
+ 45 47 1 0 0 0 0
103
+ 46 45 1 0 0 0 0
104
+ 47 48 1 0 0 0 0
105
+ 47 49 2 0 0 0 0
106
+ M END
molSimplify/Ligands/Hpyrrole.mol ADDED
@@ -0,0 +1,26 @@
1
+
2
+ OpenBabel10061815053D
3
+
4
+ 10 10 0 0 0 0 0 0 0 0999 V2000
5
+ -1.6228 0.6210 0.0044 N 0 5 0 0 0 0 0 0 0 0 0 0
6
+ -0.8165 1.6837 0.0026 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 0.5048 1.3113 -0.0038 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 0.5047 -0.0694 -0.0065 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ -0.8165 -0.4418 0.0041 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ -1.1446 2.6622 0.0056 H 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 1.3276 1.9342 -0.0061 H 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 1.3274 -0.6924 -0.0148 H 0 0 0 0 0 0 0 0 0 0 0 0
13
+ -1.0187 -1.0317 -0.8654 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ -1.0004 -1.0037 0.8960 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1 2 2 0 0 0 0
16
+ 1 5 1 0 0 0 0
17
+ 2 3 1 0 0 0 0
18
+ 2 6 1 0 0 0 0
19
+ 3 4 2 0 0 0 0
20
+ 3 7 1 0 0 0 0
21
+ 4 5 1 0 0 0 0
22
+ 4 8 1 0 0 0 0
23
+ 5 9 1 0 0 0 0
24
+ 5 10 1 0 0 0 0
25
+ M CHG 1 1 -1
26
+ M END
molSimplify/Ligands/N-quinolinylbutyramidate.xyz ADDED
@@ -0,0 +1,31 @@
1
+ 29
2
+
3
+ C 0.00000000 0.00000000 0.00000000
4
+ C -0.95538641 0.44246362 1.12386064
5
+ N -1.56699250 -0.59329749 2.05312751
6
+ C -2.50997130 -0.15658016 3.16239256
7
+ C -3.08315082 -1.12726549 4.03327457
8
+ C -3.96688326 -0.71798664 5.07284567
9
+ C -5.15962505 -1.45486480 5.32499211
10
+ C -5.46863444 -2.60102179 4.53756743
11
+ C -4.58490199 -3.01030064 3.49799635
12
+ N -3.39216019 -2.27342249 3.24584992
13
+ H -4.82135003 -3.88731792 2.89547414
14
+ H -6.38129752 -3.16486678 4.73050504
15
+ H -5.83584012 -1.14169250 6.12045191
16
+ C -4.27743617 0.66197753 5.24153476
17
+ C -3.70425665 1.63266286 4.37065274
18
+ C -2.82052422 1.22338402 3.33108165
19
+ H -2.38193829 1.96613376 2.66469947
20
+ H -3.94188578 2.68858491 4.49973038
21
+ H -4.95365122 0.97514984 6.03699457
22
+ O -1.23334709 1.67760179 1.27484595
23
+ C 0.16391531 -1.53076520 0.03859645
24
+ C 1.11930172 -1.97322881 -1.08526420
25
+ H 1.23531970 -3.05669249 -1.05794593
26
+ H 0.70784550 -1.67608454 -2.04989317
27
+ H 2.09095502 -1.50008171 -0.94341329
28
+ H 0.57537153 -1.82790947 1.00322543
29
+ H -0.80773799 -2.00391230 -0.10325446
30
+ H -0.41145622 0.29714427 -0.96462898
31
+ H 0.97165330 0.47314711 0.14185090
molSimplify/Ligands/N-quinolinylmethylmethinylacetamidate.xyz ADDED
@@ -0,0 +1,30 @@
1
+ 28
2
+
3
+ C 0.00000000 0.00000000 0.00000000
4
+ C 1.28846900 -0.32827600 0.73327800
5
+ N 2.14684600 0.64084200 1.16625500
6
+ C 3.35337300 0.44611100 1.91340800
7
+ C 4.32104000 1.46306000 1.88996700
8
+ C 5.53046900 1.32612700 2.61006100
9
+ C 6.47490900 2.35914600 2.55699600
10
+ C 6.21224300 3.50102600 1.79879400
11
+ C 5.00579800 3.60010500 1.10328600
12
+ N 4.09684800 2.59084200 1.16625500
13
+ H 4.80223600 4.47465300 0.50432700
14
+ H 6.93841400 4.30187100 1.74754300
15
+ H 7.41185600 2.28301500 3.09618800
16
+ C 5.76631900 0.16802400 3.35897500
17
+ C 4.80632300 -0.84248600 3.39598300
18
+ C 3.60978800 -0.71033700 2.68522100
19
+ H 2.90018700 -1.51771100 2.76700300
20
+ H 4.98820400 -1.73414400 3.98195400
21
+ H 6.68753000 0.04654200 3.91636700
22
+ O 1.54949100 -1.51043800 0.89082500
23
+ C -0.28466300 1.49492400 -0.18992600
24
+ C -1.59329700 1.73865700 -0.93094200
25
+ H -1.75256700 2.83379200 -1.04018000
26
+ H -1.55598500 1.28346700 -1.94263200
27
+ H -2.44592500 1.31195800 -0.36239900
28
+ H 0.53399100 1.95422200 -0.78452700
29
+ H 0.04195100 -0.48305700 -1.00099600
30
+ H -0.84204000 -0.44924700 0.57127200
molSimplify/Ligands/NMe2_-1.xyz ADDED
@@ -0,0 +1,11 @@
1
+ 9
2
+ 3
3
+ N 1.06998 -0.05138 -0.07525
4
+ C 0.56219 -0.64580 -1.30296
5
+ C 2.52529 -0.04088 -0.05357
6
+ H -0.53358 -0.64937 -1.31033
7
+ H 0.87871 -1.68797 -1.42650
8
+ H 0.87871 -0.09638 -2.19711
9
+ H 2.89826 0.40814 0.87382
10
+ H 2.95280 0.54275 -0.87708
11
+ H 2.95280 -1.04884 -0.10648
molSimplify/Ligands/PCy3.mol ADDED
@@ -0,0 +1,111 @@
1
+
2
+ OpenBabel10261611303D
3
+
4
+ 52 54 0 0 0 0 0 0 0 0999 V2000
5
+ -0.1966 -0.0874 -1.1223 P 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 0.5231 1.5340 -0.5602 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ -1.7967 -0.0455 -0.1732 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 0.7983 -1.2406 -0.0501 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 0.7131 1.5736 0.9576 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 1.8419 1.8342 -1.2940 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ -2.6493 1.1669 -0.5537 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ -2.5804 -1.3568 -0.3581 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 0.4020 -2.6995 -0.3104 C 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 2.3008 -1.0282 -0.2744 C 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.1765 2.9545 1.4330 C 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 2.7666 2.7818 -0.5222 C 0 0 0 0 0 0 0 0 0 0 0 0
17
+ -3.9009 1.2750 0.3234 C 0 0 0 0 0 0 0 0 0 0 0 0
18
+ -4.0879 -1.2032 -0.1294 C 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 1.2392 -3.6635 0.5289 C 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 3.1331 -1.9965 0.5647 C 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 1.9910 3.7210 0.3899 C 0 0 0 0 0 0 0 0 0 0 0 0
22
+ -4.4076 -0.0731 0.8383 C 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 2.7337 -3.4469 0.3120 C 0 0 0 0 0 0 0 0 0 0 0 0
24
+ -0.1674 2.3314 -0.8505 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ -1.5732 0.0242 0.8956 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 0.5679 -1.0449 1.0033 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 1.4558 0.8673 1.3303 H 0 0 0 0 0 0 0 0 0 0 0 0
28
+ -0.2051 1.3548 1.5079 H 0 0 0 0 0 0 0 0 0 0 0 0
29
+ 1.5559 2.3616 -2.2182 H 0 0 0 0 0 0 0 0 0 0 0 0
30
+ 2.4046 0.9862 -1.6846 H 0 0 0 0 0 0 0 0 0 0 0 0
31
+ -2.9563 1.0868 -1.6056 H 0 0 0 0 0 0 0 0 0 0 0 0
32
+ -2.1210 2.1183 -0.4645 H 0 0 0 0 0 0 0 0 0 0 0 0
33
+ -2.2534 -2.0595 0.4142 H 0 0 0 0 0 0 0 0 0 0 0 0
34
+ -2.4153 -1.8277 -1.3341 H 0 0 0 0 0 0 0 0 0 0 0 0
35
+ 0.5469 -2.9428 -1.3721 H 0 0 0 0 0 0 0 0 0 0 0 0
36
+ -0.6352 -2.9227 -0.0906 H 0 0 0 0 0 0 0 0 0 0 0 0
37
+ 2.6639 -0.0502 0.0233 H 0 0 0 0 0 0 0 0 0 0 0 0
38
+ 2.5565 -1.1810 -1.3311 H 0 0 0 0 0 0 0 0 0 0 0 0
39
+ 1.7687 2.8337 2.3487 H 0 0 0 0 0 0 0 0 0 0 0 0
40
+ 0.3072 3.5626 1.7124 H 0 0 0 0 0 0 0 0 0 0 0 0
41
+ 3.3724 3.3598 -1.2296 H 0 0 0 0 0 0 0 0 0 0 0 0
42
+ 3.4686 2.1945 0.0821 H 0 0 0 0 0 0 0 0 0 0 0 0
43
+ -4.6907 1.7724 -0.2528 H 0 0 0 0 0 0 0 0 0 0 0 0
44
+ -3.6969 1.9234 1.1844 H 0 0 0 0 0 0 0 0 0 0 0 0
45
+ -4.5056 -2.1479 0.2375 H 0 0 0 0 0 0 0 0 0 0 0 0
46
+ -4.5774 -0.9991 -1.0902 H 0 0 0 0 0 0 0 0 0 0 0 0
47
+ 0.9786 -4.6968 0.2730 H 0 0 0 0 0 0 0 0 0 0 0 0
48
+ 0.9995 -3.5270 1.5907 H 0 0 0 0 0 0 0 0 0 0 0 0
49
+ 3.0043 -1.7627 1.6290 H 0 0 0 0 0 0 0 0 0 0 0 0
50
+ 4.1968 -1.8643 0.3353 H 0 0 0 0 0 0 0 0 0 0 0 0
51
+ 1.3166 4.3376 -0.2177 H 0 0 0 0 0 0 0 0 0 0 0 0
52
+ 2.6751 4.4130 0.8938 H 0 0 0 0 0 0 0 0 0 0 0 0
53
+ -3.9457 -0.2894 1.8100 H 0 0 0 0 0 0 0 0 0 0 0 0
54
+ -5.4878 -0.0165 1.0135 H 0 0 0 0 0 0 0 0 0 0 0 0
55
+ 3.3023 -4.1071 0.9764 H 0 0 0 0 0 0 0 0 0 0 0 0
56
+ 2.9971 -3.7240 -0.7161 H 0 0 0 0 0 0 0 0 0 0 0 0
57
+ 1 2 1 0 0 0 0
58
+ 1 3 1 0 0 0 0
59
+ 1 4 1 0 0 0 0
60
+ 2 5 1 0 0 0 0
61
+ 2 6 1 0 0 0 0
62
+ 2 20 1 0 0 0 0
63
+ 3 7 1 0 0 0 0
64
+ 3 8 1 0 0 0 0
65
+ 3 21 1 0 0 0 0
66
+ 4 9 1 0 0 0 0
67
+ 4 10 1 0 0 0 0
68
+ 4 22 1 0 0 0 0
69
+ 5 11 1 0 0 0 0
70
+ 5 23 1 0 0 0 0
71
+ 5 24 1 0 0 0 0
72
+ 6 12 1 0 0 0 0
73
+ 6 25 1 0 0 0 0
74
+ 6 26 1 0 0 0 0
75
+ 7 13 1 0 0 0 0
76
+ 7 27 1 0 0 0 0
77
+ 7 28 1 0 0 0 0
78
+ 8 14 1 0 0 0 0
79
+ 8 29 1 0 0 0 0
80
+ 8 30 1 0 0 0 0
81
+ 9 15 1 0 0 0 0
82
+ 9 31 1 0 0 0 0
83
+ 9 32 1 0 0 0 0
84
+ 10 16 1 0 0 0 0
85
+ 10 33 1 0 0 0 0
86
+ 10 34 1 0 0 0 0
87
+ 11 17 1 0 0 0 0
88
+ 11 35 1 0 0 0 0
89
+ 11 36 1 0 0 0 0
90
+ 12 17 1 0 0 0 0
91
+ 12 37 1 0 0 0 0
92
+ 12 38 1 0 0 0 0
93
+ 13 18 1 0 0 0 0
94
+ 13 39 1 0 0 0 0
95
+ 13 40 1 0 0 0 0
96
+ 14 18 1 0 0 0 0
97
+ 14 41 1 0 0 0 0
98
+ 14 42 1 0 0 0 0
99
+ 15 19 1 0 0 0 0
100
+ 15 43 1 0 0 0 0
101
+ 15 44 1 0 0 0 0
102
+ 16 19 1 0 0 0 0
103
+ 16 45 1 0 0 0 0
104
+ 16 46 1 0 0 0 0
105
+ 17 47 1 0 0 0 0
106
+ 17 48 1 0 0 0 0
107
+ 18 49 1 0 0 0 0
108
+ 18 50 1 0 0 0 0
109
+ 19 51 1 0 0 0 0
110
+ 19 52 1 0 0 0 0
111
+ M END
molSimplify/Ligands/PMe3.xyz ADDED
@@ -0,0 +1,15 @@
1
+ 13
2
+ 3
3
+ P 0.92577 0.17336 -0.21146
4
+ C 0.44599 -1.45530 -0.90542
5
+ C 0.44599 -0.07321 1.54162
6
+ C 2.74065 -0.05786 -0.08087
7
+ H -0.64300 -1.55944 -0.91389
8
+ H 0.86255 -2.28330 -0.32412
9
+ H 0.80193 -1.54977 -1.93556
10
+ H -0.64300 -0.11973 1.63519
11
+ H 0.80193 0.76023 2.15440
12
+ H 0.86256 -0.99855 1.95061
13
+ H 3.19227 -0.09406 -1.07664
14
+ H 2.99562 -0.98427 0.44236
15
+ H 3.19227 0.77623 0.46425
molSimplify/Ligands/PPh3.mol ADDED
@@ -0,0 +1,76 @@
1
+
2
+ OpenBabel04301517493D
3
+
4
+ 34 36 0 0 0 0 0 0 0 0999 V2000
5
+ 0.2699 0.0251 -0.1454 C 0 0 0 0 0 0 0 0 0 0 0 0
6
+ -0.1350 0.7811 -1.2562 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 0.4801 2.4931 -1.4172 P 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1.3006 2.3671 -3.0455 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.6538 1.9795 -3.0556 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 3.3579 1.8310 -4.2536 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 2.7220 2.0708 -5.4670 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 1.3828 2.4518 -5.4804 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 0.6766 2.5927 -4.2801 C 0 0 0 0 0 0 0 0 0 0 0 0
14
+ -1.0311 3.4853 -1.6617 C 0 0 0 0 0 0 0 0 0 0 0 0
15
+ -0.9797 4.7233 -2.3249 C 0 0 0 0 0 0 0 0 0 0 0 0
16
+ -2.1250 5.5109 -2.4809 C 0 0 0 0 0 0 0 0 0 0 0 0
17
+ -3.3414 5.0893 -1.9528 C 0 0 0 0 0 0 0 0 0 0 0 0
18
+ -3.4087 3.8886 -1.2553 C 0 0 0 0 0 0 0 0 0 0 0 0
19
+ -2.2624 3.1031 -1.1011 C 0 0 0 0 0 0 0 0 0 0 0 0
20
+ -0.9979 0.1844 -2.1884 C 0 0 0 0 0 0 0 0 0 0 0 0
21
+ -1.4546 -1.1237 -2.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
22
+ -1.0463 -1.8573 -0.8963 C 0 0 0 0 0 0 0 0 0 0 0 0
23
+ -0.1813 -1.2846 0.0330 C 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 0.9444 0.4510 0.5958 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 3.1751 1.7759 -2.1217 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 4.3997 1.5220 -4.2349 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 3.2665 1.9540 -6.4001 H 0 0 0 0 0 0 0 0 0 0 0 0
28
+ 0.8807 2.6325 -6.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
29
+ -0.3731 2.8681 -4.3351 H 0 0 0 0 0 0 0 0 0 0 0 0
30
+ -0.0386 5.0929 -2.7292 H 0 0 0 0 0 0 0 0 0 0 0 0
31
+ -2.0620 6.4592 -3.0083 H 0 0 0 0 0 0 0 0 0 0 0 0
32
+ -4.2311 5.7020 -2.0696 H 0 0 0 0 0 0 0 0 0 0 0 0
33
+ -4.3496 3.5615 -0.8192 H 0 0 0 0 0 0 0 0 0 0 0 0
34
+ -2.3516 2.1860 -0.5223 H 0 0 0 0 0 0 0 0 0 0 0 0
35
+ -1.3361 0.7353 -3.0622 H 0 0 0 0 0 0 0 0 0 0 0 0
36
+ -2.1293 -1.5664 -2.7346 H 0 0 0 0 0 0 0 0 0 0 0 0
37
+ -1.4005 -2.8748 -0.7559 H 0 0 0 0 0 0 0 0 0 0 0 0
38
+ 0.1425 -1.8563 0.8994 H 0 0 0 0 0 0 0 0 0 0 0 0
39
+ 1 2 2 0 0 0 0
40
+ 1 19 1 0 0 0 0
41
+ 1 20 1 0 0 0 0
42
+ 2 3 1 0 0 0 0
43
+ 2 16 1 0 0 0 0
44
+ 3 4 1 0 0 0 0
45
+ 3 10 1 0 0 0 0
46
+ 4 5 2 0 0 0 0
47
+ 4 9 1 0 0 0 0
48
+ 5 6 1 0 0 0 0
49
+ 5 21 1 0 0 0 0
50
+ 6 7 2 0 0 0 0
51
+ 6 22 1 0 0 0 0
52
+ 7 8 1 0 0 0 0
53
+ 7 23 1 0 0 0 0
54
+ 8 9 2 0 0 0 0
55
+ 8 24 1 0 0 0 0
56
+ 9 25 1 0 0 0 0
57
+ 10 11 2 0 0 0 0
58
+ 10 15 1 0 0 0 0
59
+ 11 12 1 0 0 0 0
60
+ 11 26 1 0 0 0 0
61
+ 12 13 2 0 0 0 0
62
+ 12 27 1 0 0 0 0
63
+ 13 14 1 0 0 0 0
64
+ 13 28 1 0 0 0 0
65
+ 14 15 2 0 0 0 0
66
+ 14 29 1 0 0 0 0
67
+ 15 30 1 0 0 0 0
68
+ 16 17 2 0 0 0 0
69
+ 16 31 1 0 0 0 0
70
+ 17 18 1 0 0 0 0
71
+ 17 32 1 0 0 0 0
72
+ 18 19 2 0 0 0 0
73
+ 18 33 1 0 0 0 0
74
+ 19 34 1 0 0 0 0
75
+ M CHG 1 1 0
76
+ M END
molSimplify/Ligands/Propyphenazone.mol ADDED
@@ -0,0 +1,77 @@
1
+
2
+ OpenBabel03301714483D
3
+
4
+ 35 36 0 0 0 0 0 0 0 0999 V2000
5
+ 0.3364 0.5466 -0.0302 O 0 3 0 0 0 0 0 0 0 0 0 0
6
+ 1.6937 0.5151 -0.0663 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 2.8831 1.5476 -0.2667 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 4.0424 0.6914 -0.3495 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 3.7229 -0.5590 -0.1152 N 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 2.4102 -0.7165 0.0462 N 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 2.0902 -2.1006 0.1994 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 2.0603 -2.6879 1.4766 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 2.1256 -4.0866 1.6042 C 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 2.2429 -4.9004 0.4683 C 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 2.3063 -4.3237 -0.7984 C 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 2.2526 -2.9384 -0.9287 C 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 4.7833 -1.6180 -0.0698 C 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 5.5472 0.9880 -0.6680 C 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 3.4822 3.0805 -0.5015 C 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 3.5873 3.3539 -2.0082 C 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 3.8558 4.4506 0.2835 C 0 0 0 0 0 0 0 0 0 0 0 0
22
+ 2.0540 -2.0677 2.3616 H 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 2.1237 -4.5431 2.5834 H 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 2.3129 -5.9759 0.5660 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 2.4364 -4.9429 -1.6787 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 2.4013 -2.5017 -1.9102 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 5.5281 -1.3707 0.7141 H 0 0 0 0 0 0 0 0 0 0 0 0
28
+ 5.2894 -1.6998 -1.0550 H 0 0 0 0 0 0 0 0 0 0 0 0
29
+ 4.4560 -2.6363 0.1878 H 0 0 0 0 0 0 0 0 0 0 0 0
30
+ 5.9012 1.9802 -1.0093 H 0 0 0 0 0 0 0 0 0 0 0 0
31
+ 5.8683 0.3685 -1.5259 H 0 0 0 0 0 0 0 0 0 0 0 0
32
+ 6.1653 0.7433 0.2212 H 0 0 0 0 0 0 0 0 0 0 0 0
33
+ 4.4634 2.9159 -0.1170 H 0 0 0 0 0 0 0 0 0 0 0 0
34
+ 2.5992 3.6377 -2.4125 H 0 0 0 0 0 0 0 0 0 0 0 0
35
+ 3.9681 2.4589 -2.5426 H 0 0 0 0 0 0 0 0 0 0 0 0
36
+ 4.3125 4.1698 -2.2296 H 0 0 0 0 0 0 0 0 0 0 0 0
37
+ 3.2396 5.3620 0.2394 H 0 0 0 0 0 0 0 0 0 0 0 0
38
+ 4.7668 4.9259 -0.1669 H 0 0 0 0 0 0 0 0 0 0 0 0
39
+ 4.1823 4.3396 1.3463 H 0 0 0 0 0 0 0 0 0 0 0 0
40
+ 1 2 2 0 0 0 0
41
+ 2 3 1 0 0 0 0
42
+ 2 6 1 0 0 0 0
43
+ 3 4 2 0 0 0 0
44
+ 3 15 1 0 0 0 0
45
+ 4 5 1 0 0 0 0
46
+ 4 14 1 0 0 0 0
47
+ 5 6 1 0 0 0 0
48
+ 5 13 1 0 0 0 0
49
+ 6 7 1 0 0 0 0
50
+ 7 8 2 0 0 0 0
51
+ 7 12 1 0 0 0 0
52
+ 8 9 1 0 0 0 0
53
+ 8 18 1 0 0 0 0
54
+ 9 10 2 0 0 0 0
55
+ 9 19 1 0 0 0 0
56
+ 10 11 1 0 0 0 0
57
+ 10 20 1 0 0 0 0
58
+ 11 12 2 0 0 0 0
59
+ 11 21 1 0 0 0 0
60
+ 12 22 1 0 0 0 0
61
+ 13 23 1 0 0 0 0
62
+ 13 24 1 0 0 0 0
63
+ 13 25 1 0 0 0 0
64
+ 14 26 1 0 0 0 0
65
+ 14 27 1 0 0 0 0
66
+ 14 28 1 0 0 0 0
67
+ 15 16 1 0 0 0 0
68
+ 15 17 1 0 0 0 0
69
+ 15 29 1 0 0 0 0
70
+ 16 30 1 0 0 0 0
71
+ 16 31 1 0 0 0 0
72
+ 16 32 1 0 0 0 0
73
+ 17 33 1 0 0 0 0
74
+ 17 34 1 0 0 0 0
75
+ 17 35 1 0 0 0 0
76
+ M CHG 1 1 0
77
+ M END
molSimplify/Ligands/acac.mol ADDED
@@ -0,0 +1,33 @@
1
+
2
+ OpenBabel03142421563D
3
+
4
+ 14 13 0 0 0 0 0 0 0 0999 V2000
5
+ 3.1144 0.8372 -1.4020 O 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 2.5505 0.2219 -0.5095 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 1.0576 0.0909 -0.5564 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 3.3222 -0.3885 0.6057 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 4.6639 -0.3188 0.7249 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 5.4090 0.3313 -0.1923 O 0 5 0 0 0 0 0 0 0 0 0 0
11
+ 5.3707 -0.9629 1.8831 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 0.5953 1.1001 -0.5394 H 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 0.6737 -0.4886 0.3095 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 0.7595 -0.4299 -1.4905 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 2.7584 -0.9218 1.3662 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 4.6658 -1.4697 2.5767 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 5.9265 -0.1881 2.4512 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 6.0904 -1.7166 1.5010 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 1 2 2 0 0 0 0
20
+ 2 3 1 0 0 0 0
21
+ 2 4 1 0 0 0 0
22
+ 3 8 1 0 0 0 0
23
+ 3 9 1 0 0 0 0
24
+ 3 10 1 0 0 0 0
25
+ 4 5 2 0 0 0 0
26
+ 4 11 1 0 0 0 0
27
+ 5 6 1 0 0 0 0
28
+ 5 7 1 0 0 0 0
29
+ 7 12 1 0 0 0 0
30
+ 7 13 1 0 0 0 0
31
+ 7 14 1 0 0 0 0
32
+ M CHG 1 6 -1
33
+ M END
molSimplify/Ligands/acacen.mol ADDED
@@ -0,0 +1,76 @@
1
+
2
+ OpenBabel07181817433D
3
+
4
+ 36 35 0 0 0 0 0 0 0 0999 V2000
5
+ 2.0145 -3.7977 -2.0701 C 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 1.3272 -3.0553 -0.9407 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 1.4079 -1.7579 -0.8232 N 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 2.2073 -0.9477 -1.7122 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.4824 0.4173 -1.0725 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 1.5108 0.7409 -0.0385 N 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 1.4525 1.9392 0.4827 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 0.4616 2.3633 1.5312 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ -0.5310 1.3658 2.0196 C 0 0 0 0 0 0 0 0 0 0 0 0
14
+ -0.5869 0.2123 1.6334 O 0 0 0 0 0 0 0 0 0 0 0 0
15
+ -1.5229 1.7959 3.0602 C 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 2.3841 3.0711 0.0673 C 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 0.6289 -3.8782 0.1057 C 0 0 0 0 0 0 0 0 0 0 0 0
18
+ -0.6495 -3.3006 0.5990 C 0 0 0 0 0 0 0 0 0 0 0 0
19
+ -0.7631 -2.1043 0.8195 O 0 0 0 0 0 0 0 0 0 0 0 0
20
+ -1.8110 -4.2030 0.8887 C 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 1.8401 -4.8921 -2.0135 H 0 0 0 0 0 0 0 0 0 0 0 0
22
+ 1.6177 -3.4421 -3.0447 H 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 3.1110 -3.6368 -2.0349 H 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 3.2074 -1.3923 -1.9111 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 1.6606 -0.8541 -2.6743 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 2.4669 1.1485 -1.9106 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 3.4870 0.4251 -0.5933 H 0 0 0 0 0 0 0 0 0 0 0 0
28
+ -0.1177 3.2172 1.1173 H 0 0 0 0 0 0 0 0 0 0 0 0
29
+ 1.0333 2.7215 2.4145 H 0 0 0 0 0 0 0 0 0 0 0 0
30
+ -1.3829 2.8627 3.3367 H 0 0 0 0 0 0 0 0 0 0 0 0
31
+ -1.3958 1.1758 3.9727 H 0 0 0 0 0 0 0 0 0 0 0 0
32
+ -2.5536 1.6626 2.6703 H 0 0 0 0 0 0 0 0 0 0 0 0
33
+ 3.1487 2.8158 -0.6881 H 0 0 0 0 0 0 0 0 0 0 0 0
34
+ 2.9329 3.4411 0.9581 H 0 0 0 0 0 0 0 0 0 0 0 0
35
+ 1.7802 3.9065 -0.3471 H 0 0 0 0 0 0 0 0 0 0 0 0
36
+ 0.5270 -4.9522 -0.1631 H 0 0 0 0 0 0 0 0 0 0 0 0
37
+ 1.3072 -3.8559 0.9804 H 0 0 0 0 0 0 0 0 0 0 0 0
38
+ -2.1273 -4.7205 -0.0405 H 0 0 0 0 0 0 0 0 0 0 0 0
39
+ -2.6716 -3.6206 1.2835 H 0 0 0 0 0 0 0 0 0 0 0 0
40
+ -1.5167 -4.9574 1.6482 H 0 0 0 0 0 0 0 0 0 0 0 0
41
+ 1 2 1 0 0 0 0
42
+ 1 17 1 0 0 0 0
43
+ 1 18 1 0 0 0 0
44
+ 1 19 1 0 0 0 0
45
+ 2 3 2 0 0 0 0
46
+ 2 13 1 0 0 0 0
47
+ 3 4 1 0 0 0 0
48
+ 4 5 1 0 0 0 0
49
+ 4 20 1 0 0 0 0
50
+ 4 21 1 0 0 0 0
51
+ 5 6 1 0 0 0 0
52
+ 5 22 1 0 0 0 0
53
+ 5 23 1 0 0 0 0
54
+ 6 7 2 0 0 0 0
55
+ 7 8 1 0 0 0 0
56
+ 7 12 1 0 0 0 0
57
+ 8 9 1 0 0 0 0
58
+ 8 24 1 0 0 0 0
59
+ 8 25 1 0 0 0 0
60
+ 9 10 2 0 0 0 0
61
+ 9 11 1 0 0 0 0
62
+ 11 26 1 0 0 0 0
63
+ 11 27 1 0 0 0 0
64
+ 11 28 1 0 0 0 0
65
+ 12 29 1 0 0 0 0
66
+ 12 30 1 0 0 0 0
67
+ 12 31 1 0 0 0 0
68
+ 13 14 1 0 0 0 0
69
+ 13 32 1 0 0 0 0
70
+ 13 33 1 0 0 0 0
71
+ 14 15 2 0 0 0 0
72
+ 14 16 1 0 0 0 0
73
+ 16 34 1 0 0 0 0
74
+ 16 35 1 0 0 0 0
75
+ 16 36 1 0 0 0 0
76
+ M END
molSimplify/Ligands/acetate.smi ADDED
@@ -0,0 +1 @@
1
+ CC(=O)[O-]
molSimplify/Ligands/acetate.xyz ADDED
@@ -0,0 +1,9 @@
1
+ 7
2
+
3
+ C 0.00000000 0.00000000 0.00000000
4
+ C 0.98785513 -0.86371329 -0.80606550
5
+ O 0.47513941 -1.82611565 -1.83606759
6
+ O 2.24153056 -0.76075860 -0.59792314
7
+ H 0.55313536 0.63236204 0.69444908
8
+ H -0.57550908 0.62600028 -0.68191857
9
+ H -0.67682244 -0.64703279 0.55799637