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/imidazole.mol ADDED
@@ -0,0 +1,23 @@
1
+
2
+ OpenBabel11031515043D
3
+
4
+ 9 9 0 0 0 0 0 0 0 0999 V2000
5
+ -1.1886 -0.0056 -0.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
6
+ -0.3419 1.0812 0.0001 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 0.9709 0.6789 0.0004 N 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 0.9305 -0.6336 -0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ -0.3569 -1.0911 0.0026 N 0 0 0 0 0 0 0 0 0 0 0 0
10
+ -0.6369 -2.0606 0.0079 H 0 0 0 0 0 0 0 0 0 0 0 0
11
+ -2.2205 -0.0014 -0.0028 H 0 0 0 0 0 0 0 0 0 0 0 0
12
+ -0.6526 2.0653 0.0003 H 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 1.7643 -1.2416 -0.0024 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 1 2 2 0 0 0 0
15
+ 1 5 1 0 0 0 0
16
+ 1 7 1 0 0 0 0
17
+ 2 3 1 0 0 0 0
18
+ 2 8 1 0 0 0 0
19
+ 3 4 2 0 0 0 0
20
+ 4 5 1 0 0 0 0
21
+ 4 9 1 0 0 0 0
22
+ 5 6 1 0 0 0 0
23
+ M END
molSimplify/Ligands/imidazolidinone.mol ADDED
@@ -0,0 +1,29 @@
1
+
2
+ OpenBabel10091800053D
3
+
4
+ 12 12 0 0 0 0 0 0 0 0999 V2000
5
+ -0.7754 0.4951 0.5394 O 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 0.4025 0.5617 0.2244 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 1.0789 1.7037 0.1575 N 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 2.4441 1.4547 -0.2413 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.4859 -0.0981 -0.4130 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 1.1383 -0.5004 -0.0863 N 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 3.1393 1.7928 0.5567 H 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 2.6593 1.9741 -1.1996 H 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 3.2024 -0.5650 0.2963 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 2.7224 -0.3836 -1.4604 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 0.6831 2.6333 0.3616 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 0.7939 -1.4719 -0.0925 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 1 2 2 0 0 0 0
18
+ 2 3 1 0 0 0 0
19
+ 2 6 1 0 0 0 0
20
+ 3 4 1 0 0 0 0
21
+ 4 5 1 0 0 0 0
22
+ 4 7 1 0 0 0 0
23
+ 4 8 1 0 0 0 0
24
+ 5 6 1 0 0 0 0
25
+ 5 9 1 0 0 0 0
26
+ 5 10 1 0 0 0 0
27
+ 11 3 1 0 0 0 0
28
+ 12 6 1 0 0 0 0
29
+ M END
molSimplify/Ligands/imine.mol ADDED
@@ -0,0 +1,13 @@
1
+
2
+ OpenBabel07231507463D
3
+
4
+ 4 3 0 0 0 0 0 0 0 0999 V2000
5
+ -3.6406 2.5431 -0.0182 C 0 0 0 0 0 0 0 0 0 0 0 0
6
+ -2.4278 2.9594 -0.0121 N 0 0 0 0 0 0 0 0 0 0 0 0
7
+ -3.8595 1.4794 -0.0193 H 0 0 0 0 0 0 0 0 0 0 0 0
8
+ -1.6442 2.2906 -0.0082 H 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 1 2 2 0 0 0 0
10
+ 1 3 1 0 0 0 0
11
+ 2 4 1 0 0 0 0
12
+ M CHG 1 1 -1
13
+ M END
molSimplify/Ligands/iminodiacetic.mol ADDED
@@ -0,0 +1,33 @@
1
+
2
+ OpenBabel10261611433D
3
+
4
+ 14 13 0 0 0 0 0 0 0 0999 V2000
5
+ 1.8413 1.8120 -1.7583 O 0 0 0 0 0 0 0 0 0 0 0 0
6
+ -1.2403 1.7181 -2.1189 O 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 3.1456 0.0851 -1.0632 O 0 0 0 0 0 0 0 0 0 0 0 0
8
+ -2.5556 -0.0956 -1.7344 O 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 0.0918 -0.1067 0.3336 N 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 1.3186 0.7062 0.3378 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ -1.1488 0.6309 0.0484 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 2.1297 0.8405 -0.9918 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ -1.6356 0.7236 -1.4340 C 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 2.0007 0.2540 1.0670 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.1098 1.7049 0.7398 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ -1.9517 0.1313 0.6025 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ -1.0999 1.6371 0.4812 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 0.1385 -1.1078 0.1744 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 1 8 1 0 0 0 0
20
+ 2 9 1 0 0 0 0
21
+ 3 8 2 0 0 0 0
22
+ 4 9 2 0 0 0 0
23
+ 5 6 1 0 0 0 0
24
+ 5 7 1 0 0 0 0
25
+ 5 14 1 0 0 0 0
26
+ 6 8 1 0 0 0 0
27
+ 6 10 1 0 0 0 0
28
+ 6 11 1 0 0 0 0
29
+ 7 9 1 0 0 0 0
30
+ 7 12 1 0 0 0 0
31
+ 7 13 1 0 0 0 0
32
+ M CHG 2 1 -1 2 -1
33
+ M END
molSimplify/Ligands/iodide.mol ADDED
@@ -0,0 +1,7 @@
1
+
2
+ OpenBabel07231507383D
3
+
4
+ 1 0 0 0 0 0 0 0 0 0999 V2000
5
+ -0.6779 2.2548 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
6
+ M CHG 1 1 -1
7
+ M END
molSimplify/Ligands/iodobenzene.xyz ADDED
@@ -0,0 +1,14 @@
1
+ 12
2
+
3
+ C 0.00000000 0.00000000 0.00000000
4
+ C 0.96574672 1.04549042 -0.05901953
5
+ C 2.18984999 0.92577632 0.65961805
6
+ C 2.44820654 -0.23942821 1.43727515
7
+ C 1.48245982 -1.28491862 1.49629467
8
+ C 0.25835655 -1.16520452 0.77765710
9
+ H -0.48061426 -1.96519368 0.82281771
10
+ H 1.68014929 -2.17651071 2.09134293
11
+ H 3.38486682 -0.33103113 1.98716280
12
+ H 2.92882081 1.72576548 0.61445744
13
+ H 0.76805726 1.93708251 -0.65406778
14
+ I -1.80457485 0.17648271 -1.05941657
molSimplify/Ligands/isoleucine.mol ADDED
@@ -0,0 +1,48 @@
1
+
2
+ OpenBabel04201614333D
3
+
4
+ 22 21 0 0 1 0 0 0 0 0999 V2000
5
+ 0.1160 -0.2160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 1.5650 -0.0360 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7
+ 1.9280 1.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1.0650 2.3200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.2420 -0.8100 -1.2030 C 0 0 2 0 0 0 0 0 0 0 0 0
10
+ 1.8500 -2.3190 -1.3100 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 3.7990 -0.7150 -1.1850 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 2.2230 -3.0200 -2.6330 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ -0.3390 -1.1960 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ -0.5650 0.6220 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.9540 -0.4550 0.9460 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 1.5230 3.2430 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 1.8870 -0.3210 -2.1350 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 2.2590 -2.8840 -0.4500 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 0.7520 -2.4230 -1.2120 H 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 4.2610 -1.2090 -2.0580 H 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 4.1720 0.3240 -1.2290 H 0 0 0 0 0 0 0 0 0 0 0 0
22
+ 4.2340 -1.1820 -0.2810 H 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 1.8460 -4.0590 -2.6550 H 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 1.7910 -2.4990 -3.5090 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 3.3150 -3.0770 -2.7880 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 3.3260 1.7290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 1 10 1 0 0 0 0
28
+ 1 9 1 0 0 0 0
29
+ 1 2 1 0 0 0 0
30
+ 2 11 1 1 0 0 0
31
+ 3 2 1 0 0 0 0
32
+ 4 3 1 0 0 0 0
33
+ 5 13 1 6 0 0 0
34
+ 5 7 1 0 0 0 0
35
+ 5 2 1 0 0 0 0
36
+ 6 15 1 0 0 0 0
37
+ 6 5 1 0 0 0 0
38
+ 6 14 1 0 0 0 0
39
+ 7 18 1 0 0 0 0
40
+ 8 6 1 0 0 0 0
41
+ 12 4 1 0 0 0 0
42
+ 16 7 1 0 0 0 0
43
+ 17 7 1 0 0 0 0
44
+ 19 8 1 0 0 0 0
45
+ 20 8 1 0 0 0 0
46
+ 21 8 1 0 0 0 0
47
+ 22 3 2 0 0 0 0
48
+ M END
molSimplify/Ligands/isothiocyanate.mol ADDED
@@ -0,0 +1,11 @@
1
+
2
+ OpenBabel06131814033D
3
+
4
+ 3 2 0 0 0 0 0 0 0 0999 V2000
5
+ -6.5435 2.2988 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6
+ -5.3764 2.2927 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ -3.7569 2.2861 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1 2 2 0 0 0 0
9
+ 2 3 2 0 0 0 0
10
+ M CHG 1 1 -1
11
+ M END
molSimplify/Ligands/leucine.mol ADDED
@@ -0,0 +1,48 @@
1
+
2
+ OpenBabel04201614333D
3
+
4
+ 22 21 0 0 1 0 0 0 0 0999 V2000
5
+ 0.0020 0.0190 -0.1280 N 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 1.4870 -0.0030 -0.0090 C 0 0 2 0 0 0 0 0 0 0 0 0
7
+ 2.0860 1.4190 0.1550 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1.8390 2.2380 -0.9090 O 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.1090 -0.7860 -1.2010 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 1.8220 -2.3100 -1.2880 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 2.3090 -2.8640 -2.6370 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 2.4950 -3.1050 -0.1550 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ -0.5480 -0.7380 0.2950 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ -0.4370 0.7240 -0.7330 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.7460 -0.5320 0.9270 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 2.2520 3.0800 -0.7170 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 1.7840 -0.2980 -2.1420 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 3.2080 -0.6450 -1.1920 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 0.7270 -2.4710 -1.2310 H 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 2.0870 -3.9430 -2.7420 H 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 1.8190 -2.3570 -3.4880 H 0 0 0 0 0 0 0 0 0 0 0 0
22
+ 3.4010 -2.7420 -2.7690 H 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 2.2990 -4.1900 -0.2400 H 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 3.5930 -2.9710 -0.1470 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 2.1240 -2.7980 0.8400 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 2.7300 1.7790 1.1360 O 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 1 2 1 0 0 0 0
28
+ 1 9 1 0 0 0 0
29
+ 2 3 1 0 0 0 0
30
+ 2 11 1 1 0 0 0
31
+ 3 22 2 0 0 0 0
32
+ 4 12 1 0 0 0 0
33
+ 4 3 1 0 0 0 0
34
+ 5 14 1 0 0 0 0
35
+ 5 2 1 0 0 0 0
36
+ 6 15 1 0 0 0 0
37
+ 6 5 1 0 0 0 0
38
+ 6 8 1 0 0 0 0
39
+ 7 6 1 0 0 0 0
40
+ 8 20 1 0 0 0 0
41
+ 8 21 1 0 0 0 0
42
+ 10 1 1 0 0 0 0
43
+ 13 5 1 0 0 0 0
44
+ 16 7 1 0 0 0 0
45
+ 17 7 1 0 0 0 0
46
+ 18 7 1 0 0 0 0
47
+ 19 8 1 0 0 0 0
48
+ M END
molSimplify/Ligands/ligands.dict ADDED
@@ -0,0 +1,257 @@
1
+ # ligand name, ligand structure file, abbreviation (unique), connection atoms, groups, force field (BA:before and after,B:before only,A:after only,N:no), formal charge
2
+ # if connecting atoms
3
+ 12crown4:12crown4.mol,12crown4,6 9 0 3,build tetradentate,N,0
4
+ Hpyrrole:Hpyrrole.mol,Hpyrl,0,build organic,BA,-1
5
+ N-quinolinylbutyramidate:N-quinolinylbutyramidate.xyz,n-qnbuam,9 2,build small,BA,-1
6
+ N-quinolinylmethylmethinylacetamidate:N-quinolinylmethylmethinylacetamidate.xyz,n-qnbuam3-,9 2 20,build small,BA,-2
7
+ acac:acac.mol,acac,0 5,build functionalize bidentate,BA,-1
8
+ acacen:acacen.mol,acacen, 9 3 14 5,build tetradentate,N,0
9
+ acetate:acetate.xyz,acetate,2,build small,BA,-1
10
+ aceticacidbipyridine:aceticacidbipyridine.mol,aceticacidbip,0 1,build bidentate,BA,0
11
+ acetonitrile:acetonitrile.mol,actnt,1,build small,N,0
12
+ acetylacetone:acac.mol,acac,0 5,build functionalize bidentate,BA,-1
13
+ alanine:alanine.mol,Ala,3,build functionalize aminoacid,BA,0
14
+ alanineB:alanine.mol,Ala,3 11,build functionalize aminoacid,BA,0
15
+ amine:amine.mol,ami,0,functionalize small,N,-1
16
+ ammonia:ammonia.mol,ammo,0,build small,N,0
17
+ antipyrine:Antipyrine.mol,antipyrine,4,build bulky,BA,0
18
+ arginine:arginine.mol,Arg,3,build functionalize aminoacid,BA,0
19
+ arginineB:arginine.mol,Arg,3 25,build functionalize aminoacid,BA,0
20
+ asparagine:asparagine.mol,Asn,6,build functionalize aminoacid,BA,0
21
+ aspartic:aspartic_acid.mol,Asp,6,build functionalize aminoacid,BA,-1
22
+ asparticB:aspartic_acid.mol,Asp,6 7,build functionalize aminoacid,BA,-1
23
+ azide:azide.mol,azide,0,functionalize small,BA,-1
24
+ benzene:benzene.mol,bnz,4,build small organic,BA,-1
25
+ benzene_pi:benzene_pi.mol,bnp,0 1 2 3 4 5 pi,build small organometallic,N,-1
26
+ benzenedithiol:benzenedithiol.mol,benzenedithiol,0 11,build functionalize bidentate,BA,-2
27
+ benzenethiol:benzenethiol.mol,bthil,0,build functionalize small,N,-1
28
+ benzisc:benzylisocy.mol,benzisc,0,bulkymono build,N,0
29
+ bidiazine:bidiazine.mol,diazine,0 1,build bidentate,A,0
30
+ bidiazole:bidiazole.mol,bidiazole,4 9,build bidentate,A,0
31
+ bifuran:bifuran.mol,bifuran,0 9,build bidentate,N,0
32
+ bihydrodiazine:bihydrodiazine.mol,hydrodiazine,0 1,build bidentate,A,0
33
+ bihydrodiazole:bihydrodiazole.mol,bihydrodiazole,4 13,build bidentate,A,0
34
+ bihydrooxazine:bihydrooxazine.mol,hydrooxazine,0 1,build bidentate,A,0
35
+ bihydrooxazole:bihydrooxazole.mol,bihydrooxazole,4 13,build bidentate,A,0
36
+ bihydrothiazine:bihydrothiazine.mol,hydrothiazine,0 1,build bidentate,A,0
37
+ bihydrothiazole:bihydrothiazole.mol,bihydrothiazole,4 13,,build bidentate,A,0
38
+ biimidazole:biimidazole.mol,biimd,2 10,build bidentate,BA,0
39
+ bioxazole:bioxazole.mol,bioxazole,4 9,build bidentate,A,0
40
+ bipy:bipy.mol,bip,0 1,build bidentate,N,0
41
+ bipyrazine:bipyrazine.xyz,bpz,0 1,build bidentate,N,0
42
+ bipyrimidine:bipyrimidine.mol,bipyrimidine,0 1,build bidentate,N,0
43
+ bipyrrole:bipyrrole.mol,bipyrrole,4 11,build bidentate,A,0
44
+ bisnapthyridylpyridine:bisnapthyridylpyridine.mol,bisnp,5 13 36,build tridentate,BA,0
45
+ bithiazole:bithiazole.mol,bithiazole,4 9,build bidentate,A,0
46
+ bpabipy:BPAbipy.mol,bpabp,0 13 26 48 30,build core,BA,0
47
+ bromide:bromide.mol,brode,0,build functionalize small,N,-1
48
+ c2:c2.mol,c2,0,build functionalize small,N,0
49
+ caprolactone:caprolactone.mol,caprolactone,4,bulky mono,N,0
50
+ carbonyl:carbonyl.mol,crbn,0,build small,N,0
51
+ carboxyl:carboxyl.mol,crbx,1,functionalize small,N,-1
52
+ cat:cat.mol,cat,0 7,bulkybi build,BA,-2
53
+ chloride:chloride.mol,chlde,0,build functionalize small,N,-1
54
+ chloropyridine:chloropyridine.mol,chloropyrdine,3,build organic,BA,0
55
+ cl:chloride.mol,chlde,0,build functionalize small,N,-1
56
+ cn:cyanide.mol,cyan,0,build small,N,-1
57
+ co2:co2.mol,co2,0,all small,N,0
58
+ co:carbonyl.mol,crbn,0,build small,N,0
59
+ corrolazine:corrolazine.mol,corrolazine,21 19 17 16, build tetradentate, A,-2
60
+ cs:cs.mol,cs,0,build functionalize small,N,0
61
+ cyanate:cyanate.xyz,cyanate,0,build functionalize small,N,-1
62
+ cyanide:cyanide.mol,cyan,0,build small,N,-1
63
+ cyanoaceticporphyrin:cyanoaceticporphyrin.mol,caprph,0 1 3 2,build tetradentate,N,-2
64
+ cyanopyridine:cyanopyridine.mol,cyanopyrd,3,build organic,BA,0
65
+ cyclam:cyclam.mol,cyclam,17 34 36 15,build tetradentate,A,0
66
+ cyclen:cyclen.mol,cyclen,6 9 0 3,build tetradentate,A,0
67
+ cyclopentadienyl:cyclopentadienyl.mol,Cp,0 1 2 3 4 pi,build aromatic organometallic,N,-1
68
+ cysteine:cysteine.mol,Cys,5,build functionalize aminoacid,BA,0
69
+ diaminomethyl:diaminomethyl.mol,damthyl,3 1,build bidentate,N,-1
70
+ diazine:diazine.mol,diazine,0,build organic,BA,0
71
+ diazole:diazole.mol,diazole,4,build functionalize,A,0
72
+ dicyanamide:dicyanamide.mol,dicyanamide,0,build small,N,-1
73
+ dihydrofuran:dihydrofuran.mol,dihydrofuran,0,build bulkymono,A,0
74
+ dimethylamide:NMe2_-1.xyz,nme2,0,build small organic,BA,-1
75
+ dmap:dmap.xyz,dmap,10 3 22, build tridentate,N,0
76
+ dmf:dmf.mol,dmf,1, build monodentate,A,0
77
+ dmi:dmi.mol,dmi,0, build monodentate,A,0
78
+ dmpe:dmpe.mol,dmpe,1 3, build bidentate,A,0
79
+ dpmu:dpmu.mol,dpmu,0, build monodentate,A,0
80
+ dppe:dppe.mol,dppe,21 25, build bidentate,A,0
81
+ e2acetate:acetate.xyz,acetate,2 3,build small,BA,-1
82
+ e2o2:o2.xyz,e2o2,0 1 pi, build small inorganic,BA,0
83
+ e6benzene:benzene_pi.mol,bnp,0 1 2 3 4 5 pi,build small organometallic,N,-1
84
+ edta:edta.mol,edta,0 1 2 3 4 5,build big,A,-4
85
+ en:en.mol,en,0 1,build bidentate,N,0
86
+ ethanethiol:ethanethiol.mol,ethil,0,build functionalize small,N,-1
87
+ ethanolamine:ethanolamine.mol,ethanolamine,1 7,functionalize bidentate,BA,0
88
+ ethbipyridine:ethbipy.mol,ethbip,0 1,build bidentate,BA,0
89
+ ethyl:ethyl.mol,eth,1,functionalize organometallic small,N,-1
90
+ ethylamine:ethylamine.mol,ethylamine,1,functionalize small,N,0
91
+ ethylene:ethylene.mol,ethylene,0 1 pi,organometallic small,N,-1
92
+ ethylesteracac:ethylesteracac.mol,ethylesteracac,0 5,build functionalize bidentate,BA,-1
93
+ fluoride:fluoride.mol,fluo,0,build functionalize small,N,-1
94
+ formaldehyde:formaldehyde.mol,formaldehyde,1,functionalize small,N,0
95
+ formamidate:formamidate.xyz,hconh,1,build small,BA,-1
96
+ formate:formate.xyz,formate, 0, build mono,B,-1
97
+ furan:furan.mol,furan,0,build bulkymono,A,0
98
+ glutamic:glutamic_acid.mol,Glu,3,build functionalize aminoacid,BA,0
99
+ glutamicB:glutamic_acid.mol,Glu,3 18,build functionalize aminoacid,BA,0
100
+ glutamine:glutamine.mol,Gln,3,build functionalize aminoacid,BA,0
101
+ glutamineB:glutamine.mol,Gln,3 19,build functionalize aminoacid,BA,0
102
+ glycinate:glycinate.mol,glycinate,2 3,build custom custom,BA,-1
103
+ glycine:glycine.mol,Gly,8,build functionalize aminoacid,BA,0
104
+ glycineB:glycine.mol,Gly,8 3,build functionalize aminoacid,BA,0
105
+ h2o:water.mol,wat,0,build small,N,0
106
+ h2s:h2s.mol,h2s,0,build functionalize small,N,0
107
+ helium:helium.mol,he,0,build functionalize small,N,0
108
+ histidine:histidine.mol,His,9,build functionalize aminoacid,BA,0
109
+ hmpa:hmpa.mol,hmpa,0, build monodentate,A,0
110
+ hs-:hs-.mol,hs-,0,build functionalize small,N,-1
111
+ hydride:hydride.mol,hydride,0,build functionalize small,N,-1
112
+ hydrocarboxyacetylide:hydrocarboxyacetylide.xyz,cccooh,2,build small,BA,-1
113
+ hydrocyanide:hydrocyanide.mol,hydc,1,build small,N,-2
114
+ hydrodiazine:hydrodiazine.mol,hydrodiazine,0,build organic,BA,0
115
+ hydrodiazole:hydrodiazole.mol,hydrodiazole,4,build functionalize,A,0
116
+ hydrogensulfide:hydrogensulfide.mol, hydrogensulfide,0,build functionalize small,N,0
117
+ hydroisocyanide:hydroisocyanide.mol,hisc,0,build small,N,0
118
+ hydrooxazine:hydrooxazine.mol,hydrooxazine,0,build organic,BA,0
119
+ hydrooxazole:hydrooxazole.mol,hydrooxazole,4,build functionalize,A,0
120
+ hydrothiazine:hydrothiazine.mol,hydrothiazine,0,build organic,BA,0
121
+ hydrothiazole:hydrothiazole.mol,hydrothiazole,4,build functionalize,A,0
122
+ hydroxyl:hydroxyl.mol,hxl,0,build functionalize small,N,-1
123
+ imidazole:imidazole.mol,imd,2,build small,BA,0
124
+ imidazolidinone:imidazolidinone.mol,imidazolidinone,0, bulky monodentate,A,0
125
+ imine:imine.mol,imi,0,functionalize small,N,-1
126
+ iminodiacetic:iminodiacetic.mol,iminodiacetic,0 1,build bidentate, BA, -2
127
+ iodide:iodide.mol,i,0,build functionalize small,N,-1
128
+ iodobenzene:iodobenzene.xyz,phi,0 11 pi,build small,BA,0
129
+ isocyanide:cyanide.mol,isocyanide,1,build small,N,-1
130
+ isoleucine:isoleucine.mol,Ile,3,build functionalize aminoacid,BA,0
131
+ isoleucineB:isoleucine.mol,Ile,3 21,build functionalize aminoacid,BA,0
132
+ isothiocyanate:isothiocyanate.mol,ithcynt,0,build functionalize small,BA,-1
133
+ leucine:leucine.mol,Leu,21,build functionalize aminoacid,BA,0
134
+ leucineB:leucine.mol,Leu,3 21,build functionalize aminoacid,BA,0
135
+ lysine:lysine.mol,Lys,3,build functionalize aminoacid,BA,0
136
+ lysineB:lysine.mol,Lys,3 23,build functionalize aminoacid,BA,0
137
+ mebenzenedithiol:mebenzenedithiol.mol,mebenzenedithiol,0 11,build functionalize bidentate,BA,-2
138
+ mebim_py:mebim_py.xyz,mebim_py,0 11,build bidentate,N,0
139
+ mebim_pz:mebim_pz.xyz,mebim_pz,0 10,build bidentate,N,0
140
+ mebimpy:(1_methylbenzimidazol_2_yl)pyridine.xyz,mebimpy,10 4 15, build tridentate,N,0
141
+ mebipy:mebipy.mol,mebipy,0 1,build bidentate,BA,0
142
+ mec:mecat.mol,mec,0 7,build bidentate,BA,-2
143
+ methanal:methanal.mol,metha,0,functionalize small,N,-1
144
+ methanethiol:methanethiol.mol,mthil,0,build functionalize small,N,-1
145
+ methanol:methanol.mol,methanol,1,functionalize small,N,0
146
+ methionine:methionine.mol,Met,6,build functionalize aminoacid,BA,0
147
+ methyl:methyl.mol,meth,0,functionalize small organometallic,N,-1
148
+ methylacetylide:methylacetylide.xyz,mecc-,1,build small organic,N,-1
149
+ methylamine:methylamine.mol,methylamine,1,functionalize small,N,0
150
+ methylazide:methylazide.xyz,men3,1,build small organic,B,-1
151
+ methylpyridine:methylpyridine.mol,mpyrd,3,build organic,BA,0
152
+ misc:methylisocy.mol,misc,0,small,A,0
153
+ n2:n2.mol,n2,0,build functionalize small,N,0
154
+ n4py:n4py.xyz,n4py,5 15 25 35 41, build functionalize tetra dentate,BA,0
155
+ nch:nch.mol,nch,0,build functionalize small,N,0
156
+ nco-:nco-.mol,nco-,0,build functionalize small,N,-1
157
+ ncs:isothiocyanate.mol,ithcynt,0,build functionalize small,N,-1
158
+ nethanolamine:nethanolamine.mol,nethanolamine,1,functionalize small,N,0
159
+ nh3:ammonia.mol,ammo,0,build small,N,0
160
+ nitrate:nitrate.mol,nitrate,1,build mono, B, -1
161
+ nitrite:nitrite.mol,nitrite,1,build mono, B, -1
162
+ nitro:nitro.mol,nit,1,build functionalize small,N,-1
163
+ nitrobipyridine:nitrobipy.mol,nitrobip,0 1,build bidentate,BA,0
164
+ nitroso:nitroso.mol,nits,0,build functionalize small,N,0
165
+ nme2:NMe2_-1.xyz,nme2,0,build small organic,BA,-1
166
+ nme3:nme3.mol,nme3,0,build small,N,0
167
+ no-:no-.mol,no-,0,build functionalize small,N,-1
168
+ no2-:no2-.mol,no2-,0,build functionalize small,N,-1
169
+ noxygen:noxygen.mol,noxd,0,build small,N,0
170
+ ns-:ns-.mol,ns-,0,build functionalize small,N,-1
171
+ o-pyridylbenzene:o-pyridylbenzene.xyz,o-pyph,4,build small,BA,0
172
+ o-pyridylphenyl:o-pyridylphenylanion.xyz,o-pyphanion,4 12,build small,BA,-1
173
+ o2-:o2-.mol,o2-,0,build functionalize small,N,-2
174
+ o22-:o2.xyz,o22-,0 1,build functionalize small,N,-2
175
+ o2:o2.xyz,o2,0, build small inorganic,B,0
176
+ och2:och2.mol,och2,0,build functionalize small,N,0
177
+ oethanolamine:oethanolamine.mol,oethanolamine,7,functionalize small,N,0
178
+ ome2:ome2.mol,ome2,0,build small,N,0
179
+ ooh:ooh.xyz,ooh,0,all small,N,-1
180
+ opme3:pme3o.mol,opme3,13,build big,BA,0
181
+ opph3:pph3o.mol,opph,34,build bulky big,BA,0
182
+ ox:oxalate.mol,oxate,1 4,build bidentate,A,-2
183
+ oxo:oxygen.mol,oxo,0,build small,N,-2
184
+ pcy3:PCy3.mol,pcy3,0,build bulky big,BA,0
185
+ pentacyanopentadienide:pentacyanocyclopentadienide.mol,pcyanopent,1,build bulky,A,-1
186
+ pf3:phosphorustrifluoride.mol,pf3,1,build small,BA,0
187
+ ph2-:ph2-.mol,ph2-,0,build functionalize small,N,-1
188
+ ph3:ph3.mol,ph3,0,build functionalize small,N,0
189
+ phen:phen.mol,phen,9 12,build bidentate,BA,0
190
+ phenacac:phenacac.mol,phenacac,0 5,build functionalize bidentate,BA,-1
191
+ phenalalanine:phenalalanine.mol,Phe,3,build functionalize aminoacid,BA,0
192
+ phenalalanineB:phenalalanine.mol,Phe,3 21,build functionalize aminoacid,BA,0
193
+ phenanthroline:phen.mol,phen,9 12,build bidentate,BA,0
194
+ phendione:phendione.mol,phendione,9 12,build bidentate,BA,0
195
+ phenisc:phenylisocy.mol,phenisc,0,build mono,A,0
196
+ phenphen:phenphen.mol,phenphen,9 12 26,build,BA,0
197
+ phenyl:benzene.mol,ph,4,build small organic,BA,-1
198
+ phenylbenzoxazole:phenylbenzoxazole.mol,phenylbenzoxazole,8 14,build bidentate,BA,-1
199
+ phenylcyc:phenylcyc.mol,phenylcyc,27 11 13 26,build tetradentate,B,0
200
+ phenylenediamine:phenylenediamine.mol,phenylenediamine,0 7,build bidentate,N,0
201
+ phosacidbipyridine:phosacidbipy.mol,phosacidbip,0 1,build bidentate,BA,0
202
+ phosphine:phosphine.mol,phosphine,0,build small,N,0
203
+ phosphorine:phosphorine.mol,phob,3,build,BA,0
204
+ phthalocyanine:phthalocyanine.mol,phthalocyanine,30 29 0 2,build tetradentate,A,-2
205
+ pisc:tbuphisocy.mol,pisc,0,bulkymono build,N,0
206
+ pme3:PMe3.xyz,pme3,0,build small organic,BA,0
207
+ porphyrin:porphyrin.mol,prph,2 3 1 0,build tetradentate,A,-2
208
+ pph3:PPh3.mol,pph,2,build bulky big,BA,0
209
+ proline:proline.mol,Pro,3,build functionalize aminoacid,BA,0
210
+ prolineB:proline.mol,Pro,3 15,build functionalize aminoacid,BA,0
211
+ propdiol:propdiol.mol,propdiol,0 4,build functionalize bidentate,BA,-1
212
+ propylene:propylene.mol,propylene,0 1 pi, organometallic,N,-1
213
+ propyphenazone:Propyphenazone.mol,propyphenazone,0,build bulky,BA,0
214
+ pyr:pyridine.mol,pyrd,3,build organic,BA,0
215
+ pyridine:pyridine.mol,pyrd,3,build organic,BA,0
216
+ pyrimidone:pyrimidone.mol,pyrimidone,0, build monodentate,A,0
217
+ pyrrole:pyrrole.mol,pyrl,0,build organic,BA,-1
218
+ quinoxalinedithiol:quinoxalinedithiol.mol,quinoxaline,0 7,build functionalize bidentate,BA,-2
219
+ s2-:s2-.mol,s2-,0,build functionalize small,N,-2
220
+ salen:salen.mol,slph,7 10 18 24,build tetradentate,A,-2
221
+ salphen:salphen.mol,slph,7 10 18 24,build tetradentate,A,-2
222
+ scn:thiocyanate.mol,thcynt,0,build functionalize small,N,-1
223
+ serine:serine.mol,Ser,3,build functionalize aminoacid,BA,0
224
+ serineB:serine.mol,Ser,3 12,build functionalize aminoacid,BA,0
225
+ sulfacidbipyridine:sulfacidbipy.mol,sulfacidbip,0 1,build bidentate,BA,2
226
+ tbisc:tbutylisocy.mol,tbisc,0,build bulkymono,A,0
227
+ tbuc:tbucat.mol,tbuc,0 11,bulkybi build,BA,-2
228
+ tbutylcyclen:tbutylcyclen.mol,tbutylcyclen,3 0 9 6,build tetradentate,A,0
229
+ tbutylthiol:tbutylthiol.mol,tbthil,0,build functionalize small,N,-1
230
+ tcnoet:tcnoet.mol,tcnoet,7,build big,N,-2
231
+ tcnoetOH:tcnoetOH.mol,tcnoet,15,build big,BA,-1
232
+ terpy:terpy.mol,trpy,0 1 2,build tridentate,BA,0
233
+ terpyridine:terpy.mol,trpy,0 1 2,build tridentate,BA,0
234
+ tetrahydrofuran:tetrahydrofuran.mol,tetrahydrofuran,0,build bulkymono,A,0
235
+ thiane:thiane.mol,thiane,0,build functionalize small,N,0
236
+ thiazole:thiazole.mol,thiazole,4,build functionalize,A,0
237
+ thiocyanate:thiocyanate.mol,thcynt,0,build functionalize small,BA,-1
238
+ thiol:thiol.mol,thil,0,build functionalize small,N,-1
239
+ thiophene:thiophene.mol,thip,0,build,BA,0
240
+ thiopyridine:thiopyridine.mol,thiopyrd,3,build organic,BA,0
241
+ threonine:threonine.mol,Thr,3,build functionalize aminoacid,BA,0
242
+ threonineB:threonine.mol,Thr,3 15,build functionalize aminoacid,BA,0
243
+ tpp:tpp.mol,tpp,0 1 3 2,build bulky,A,0
244
+ triazole:1-4-dimethyl-1-2-3-triazole.xyz,triazole,0,build small organic,B,0
245
+ tricyanomethyl:tricyanomethyl.mol,tricyanomethyl,5,build,BA,-1
246
+ trifluoromethyl:trifluoromethyl.mol,trflume,0,functionalize small,BA,-1
247
+ trimethylphosphine:PMe3.xyz,pme3,0,build small organic,BA,0
248
+ tryptophan:tryptophan.mol,Trp,3,build functionalize aminoacid,BA,0
249
+ tryptophanB:tryptophan.mol,Trp,3 25,build functionalize aminoacid,BA,0
250
+ tyrosine:tyrosine.mol,Tyr,11,build functionalize aminoacid,BA,0
251
+ tyrosineB:tyrosine.mol,Tyr,3 22,build functionalize aminoacid,BA,0
252
+ uthiol:uthiol.mol,uthil,0,build functionalize small,N,0
253
+ uthiolme2:uthiolme2.mol,uthilme2,0,build functionalize small,N,0
254
+ valine:valine.mol,Val,3,build functionalize aminoacid,BA,0
255
+ valineB:valine.mol,Val,3 17,build functionalize aminoacid,BA,0
256
+ water:water.mol,wat,0,build small,BA,0
257
+ x:x.mol,x,0,all small,N,0
molSimplify/Ligands/lysine.mol ADDED
@@ -0,0 +1,54 @@
1
+
2
+ OpenBabel04201614333D
3
+
4
+ 25 24 0 0 1 0 0 0 0 0999 V2000
5
+ 1.2250 0.6260 1.3440 N 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 2.6800 0.7480 1.3440 C 0 0 2 0 0 0 0 0 0 0 0 0
7
+ 3.1010 2.1980 1.3440 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 2.2820 3.1140 1.3440 O 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 3.2950 0.0030 0.1220 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 4.8510 0.0290 0.0850 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 5.4890 -0.6100 -1.1560 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ 7.0190 -0.4260 -1.1030 C 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 7.6300 -1.0520 -2.3100 N 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 0.5780 1.4910 1.3440 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 0.7310 -0.3350 1.3440 H 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 3.0580 0.2980 2.2810 H 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 2.8810 0.4410 -0.8110 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 2.9390 -1.0460 0.1190 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 5.2050 1.0780 0.1100 H 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 5.2440 -0.4320 1.0150 H 0 0 0 0 0 0 0 0 0 0 0 0
21
+ 5.1990 -1.6800 -1.2070 H 0 0 0 0 0 0 0 0 0 0 0 0
22
+ 5.0620 -0.1350 -2.0650 H 0 0 0 0 0 0 0 0 0 0 0 0
23
+ 7.2780 0.6590 -1.0380 H 0 0 0 0 0 0 0 0 0 0 0 0
24
+ 7.4290 -0.8660 -0.1630 H 0 0 0 0 0 0 0 0 0 0 0 0
25
+ 8.6560 -0.9870 -2.3370 H 0 0 0 0 0 0 0 0 0 0 0 0
26
+ 7.4060 -2.0530 -2.3890 H 0 0 0 0 0 0 0 0 0 0 0 0
27
+ 7.2960 -0.6270 -3.1860 H 0 0 0 0 0 0 0 0 0 0 0 0
28
+ 4.5100 2.4410 1.3440 O 0 0 0 0 0 0 0 0 0 0 0 0
29
+ 5.0140 1.5430 1.3440 H 0 0 0 0 0 0 0 0 0 0 0 0
30
+ 1 11 1 0 0 0 0
31
+ 1 10 1 0 0 0 0
32
+ 1 2 1 0 0 0 0
33
+ 2 12 1 1 0 0 0
34
+ 3 2 1 0 0 0 0
35
+ 4 3 2 0 0 0 0
36
+ 5 2 1 0 0 0 0
37
+ 6 15 1 0 0 0 0
38
+ 6 5 1 0 0 0 0
39
+ 6 16 1 0 0 0 0
40
+ 7 8 1 0 0 0 0
41
+ 7 6 1 0 0 0 0
42
+ 8 19 1 0 0 0 0
43
+ 8 20 1 0 0 0 0
44
+ 9 8 1 0 0 0 0
45
+ 13 5 1 0 0 0 0
46
+ 14 5 1 0 0 0 0
47
+ 17 7 1 0 0 0 0
48
+ 18 7 1 0 0 0 0
49
+ 21 9 1 0 0 0 0
50
+ 22 9 1 0 0 0 0
51
+ 23 9 1 0 0 0 0
52
+ 24 25 1 0 0 0 0
53
+ 24 3 1 0 0 0 0
54
+ M END
molSimplify/Ligands/mebenzenedithiol.mol ADDED
@@ -0,0 +1,36 @@
1
+
2
+ OpenBabel11161612223D
3
+
4
+ 15 15 0 0 0 0 0 0 0 0999 V2000
5
+ -1.5042 1.1446 0.2643 S 0 5 0 0 0 0 0 0 0 0 0 0
6
+ 0.1925 0.6902 -0.1041 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 1.2753 1.4528 0.3729 C 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 0.4362 -0.4549 -0.8763 C 0 0 0 0 0 0 0 0 0 0 0 0
9
+ 2.5854 1.0605 0.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
10
+ 2.8245 -0.0933 -0.6745 C 0 0 0 0 0 0 0 0 0 0 0 0
11
+ 1.7510 -0.8530 -1.1574 C 0 0 0 0 0 0 0 0 0 0 0 0
12
+ -0.3992 -1.0418 -1.2375 H 0 0 0 0 0 0 0 0 0 0 0 0
13
+ 3.4223 1.6451 0.4396 H 0 0 0 0 0 0 0 0 0 0 0 0
14
+ 3.8437 -0.3865 -0.8908 H 0 0 0 0 0 0 0 0 0 0 0 0
15
+ 1.0107 2.9280 1.3634 S 0 0 0 0 0 0 0 0 0 0 0 0
16
+ 2.0166 -2.0936 -1.9608 C 0 0 0 0 0 0 0 0 0 0 0 0
17
+ 2.4453 -2.8725 -1.2961 H 0 0 0 0 0 0 0 0 0 0 0 0
18
+ 2.7373 -1.8758 -2.7769 H 0 0 0 0 0 0 0 0 0 0 0 0
19
+ 1.0843 -2.4916 -2.4151 H 0 0 0 0 0 0 0 0 0 0 0 0
20
+ 2 1 1 0 0 0 0
21
+ 2 3 1 0 0 0 0
22
+ 2 4 2 0 0 0 0
23
+ 3 5 2 0 0 0 0
24
+ 4 8 1 0 0 0 0
25
+ 5 6 1 0 0 0 0
26
+ 5 9 1 0 0 0 0
27
+ 6 7 2 0 0 0 0
28
+ 6 10 1 0 0 0 0
29
+ 7 4 1 0 0 0 0
30
+ 11 3 1 0 0 0 0
31
+ 12 7 1 0 0 0 0
32
+ 12 13 1 0 0 0 0
33
+ 12 14 1 0 0 0 0
34
+ 12 15 1 0 0 0 0
35
+ M CHG 2 1 -1 12 -1
36
+ M END
molSimplify/Ligands/mebim_py.xyz ADDED
@@ -0,0 +1,29 @@
1
+ 27
2
+ Energy: -3.5188140
3
+ N 0.30889 7.58351 18.06621
4
+ C 1.42295 7.69076 17.30755
5
+ H 1.25547 7.89591 16.25238
6
+ C 2.70634 7.55658 17.80808
7
+ H 3.56961 7.65586 17.15620
8
+ C 2.85872 7.30553 19.16732
9
+ H 3.85525 7.21601 19.59549
10
+ C 1.72917 7.18429 19.97557
11
+ H 1.86294 7.04000 21.03519
12
+ C 0.49113 7.31311 19.37533
13
+ N -0.72710 7.21224 20.14429
14
+ C -1.84760 7.63825 19.55552
15
+ N -2.86054 7.59328 20.42259
16
+ C -2.41047 7.02017 21.60001
17
+ C -1.04118 6.73758 21.41472
18
+ C -4.20413 8.04139 20.11335
19
+ H -4.23215 8.46704 19.10641
20
+ H -4.50477 8.80603 20.83463
21
+ H -4.88873 7.19049 20.16401
22
+ C -0.30756 6.07960 22.40372
23
+ C -0.98918 5.76775 23.58982
24
+ C -2.34612 6.08429 23.77533
25
+ C -3.09188 6.71536 22.77531
26
+ H -2.82969 5.81802 24.71610
27
+ H -4.14235 6.94585 22.90340
28
+ H 0.72659 5.78970 22.27840
29
+ H -0.45398 5.25553 24.39124
molSimplify/Ligands/mebim_pz.xyz ADDED
@@ -0,0 +1,28 @@
1
+ 26
2
+ Energy: 56.3012172
3
+ N 0.30052 7.62615 18.05073
4
+ C 1.44043 7.72531 17.31949
5
+ H 1.31671 7.96376 16.26734
6
+ C 2.69774 7.53611 17.86803
7
+ H 3.60169 7.61705 17.27236
8
+ N 2.86735 7.24672 19.17797
9
+ C 1.72944 7.14511 19.91186
10
+ H 1.90161 6.96210 20.95987
11
+ C 0.47295 7.31478 19.35445
12
+ N -0.74304 7.21533 20.12972
13
+ C -1.86729 7.64374 19.54957
14
+ N -2.87510 7.58925 20.42138
15
+ C -2.41634 7.01889 21.59693
16
+ C -1.04599 6.74461 21.40514
17
+ C -4.22362 8.03189 20.12172
18
+ H -4.26009 8.45881 19.11560
19
+ H -4.52276 8.79413 20.84615
20
+ H -4.90380 7.17766 20.17571
21
+ C -0.30110 6.10048 22.39498
22
+ C -0.97517 5.78902 23.58578
23
+ C -2.33415 6.09350 23.77580
24
+ C -3.08980 6.71351 22.77654
25
+ H -2.81069 5.82800 24.72048
26
+ H -4.14136 6.93663 22.90949
27
+ H 0.73633 5.82038 22.27321
28
+ H -0.43144 5.28730 24.38843