rdworks 0.43.1__tar.gz → 0.43.2__tar.gz

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Files changed (85) hide show
  1. {rdworks-0.43.1 → rdworks-0.43.2}/PKG-INFO +1 -1
  2. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/__init__.py +1 -1
  3. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/conf.py +13 -3
  4. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/PKG-INFO +1 -1
  5. {rdworks-0.43.1 → rdworks-0.43.2}/LICENSE +0 -0
  6. {rdworks-0.43.1 → rdworks-0.43.2}/README.md +0 -0
  7. {rdworks-0.43.1 → rdworks-0.43.2}/pyproject.toml +0 -0
  8. {rdworks-0.43.1 → rdworks-0.43.2}/setup.cfg +0 -0
  9. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/__init__.py +0 -0
  10. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/autograph.py +0 -0
  11. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/centroid.py +0 -0
  12. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/dynamictreecut.py +0 -0
  13. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/nmrclust.py +0 -0
  14. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/autograph/rckmeans.py +0 -0
  15. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/bitqt/__init__.py +0 -0
  16. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/bitqt/bitqt.py +0 -0
  17. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/descriptor.py +0 -0
  18. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/display.py +0 -0
  19. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/ionized.py +0 -0
  20. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/matchedseries.py +0 -0
  21. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/mol.py +0 -0
  22. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/mollibr.py +0 -0
  23. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/pka.py +0 -0
  24. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Asinex_fragment.xml +0 -0
  25. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Astex_RO3.xml +0 -0
  26. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/Baell2010A.xml +0 -0
  27. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/Baell2010B.xml +0 -0
  28. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/Baell2010C.xml +0 -0
  29. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/PAINS-less-than-015-hits.xml +0 -0
  30. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/PAINS-less-than-150-hits.xml +0 -0
  31. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/PAINS-more-than-150-hits.xml +0 -0
  32. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Baell2010_PAINS/makexml.py +0 -0
  33. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Brenk2008_Dundee/makexml.py +0 -0
  34. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/CNS.xml +0 -0
  35. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/BMS.xml +0 -0
  36. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/Dundee.xml +0 -0
  37. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/Glaxo.xml +0 -0
  38. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/Inpharmatica.xml +0 -0
  39. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/LINT.xml +0 -0
  40. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/MLSMR.xml +0 -0
  41. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/PAINS.xml +0 -0
  42. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/SureChEMBL.xml +0 -0
  43. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ChEMBL_Walters/makexml.py +0 -0
  44. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/Hann1999.xml +0 -0
  45. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/Hann1999Acid.xml +0 -0
  46. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/Hann1999Base.xml +0 -0
  47. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/Hann1999ElPh.xml +0 -0
  48. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/Hann1999NuPh.xml +0 -0
  49. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Hann1999_Glaxo/makexml.py +0 -0
  50. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Kazius2005/Kazius2005.xml +0 -0
  51. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/Kazius2005/makexml.py +0 -0
  52. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ZINC_druglike.xml +0 -0
  53. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ZINC_fragment.xml +0 -0
  54. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ZINC_leadlike.xml +0 -0
  55. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/fragment.xml +0 -0
  56. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ionized/simple_smarts_pattern.csv +0 -0
  57. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/ionized/smarts_pattern.csv +0 -0
  58. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/misc/makexml.py +0 -0
  59. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/misc/reactive-part-2.xml +0 -0
  60. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/misc/reactive-part-3.xml +0 -0
  61. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/predefined/misc/reactive.xml +0 -0
  62. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/readin.py +0 -0
  63. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/rgroup.py +0 -0
  64. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/scaffold.py +0 -0
  65. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/std.py +0 -0
  66. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/stereoisomers.py +0 -0
  67. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/tautomers.py +0 -0
  68. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/testdata.py +0 -0
  69. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/torsion.py +0 -0
  70. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/units.py +0 -0
  71. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/utils.py +0 -0
  72. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/xml.py +0 -0
  73. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/xtb/__init__.py +0 -0
  74. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/xtb/wrapper.py +0 -0
  75. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/SOURCES.txt +0 -0
  76. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/dependency_links.txt +0 -0
  77. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/requires.txt +0 -0
  78. {rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/top_level.txt +0 -0
  79. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_basics.py +0 -0
  80. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_decimals.py +0 -0
  81. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_gypsumdl.py +0 -0
  82. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_iupac_name.py +0 -0
  83. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_nn_xtb.py +0 -0
  84. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_web.py +0 -0
  85. {rdworks-0.43.1 → rdworks-0.43.2}/tests/test_xtb_wrapper.py +0 -0
{rdworks-0.43.1 → rdworks-0.43.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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1
  Metadata-Version: 2.4
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  Name: rdworks
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- Version: 0.43.1
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+ Version: 0.43.2
4
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  Summary: Routine tasks built on RDKit and other tools
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  Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
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  Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>
{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/__init__.py RENAMED
@@ -1,4 +1,4 @@
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- __version__ = '0.43.1'
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+ __version__ = '0.43.2'
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  from rdworks.conf import Conf
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  from rdworks.mol import Mol
{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/conf.py RENAMED
@@ -206,11 +206,20 @@ class Conf:
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  if isinstance(calculator, str) :
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  PE_start = self.potential_energy(calculator)
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+ PE_final = None
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210
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  if calculator.lower() == 'xTB'.lower():
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  water = kwargs.get('water', None)
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- PE_final, self.rdmol = GFN2xTB(self.rdmol).optimize(water=water)
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-
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+ result = GFN2xTB(self.rdmol).optimize(water=water)
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+ # SimpleNamespace(
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+ # PE = datadict['total energy'] * hartree2kcalpermol,
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+ # charges = datadict['partial charges'],
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+ # wbo = Wiberg_bond_orders,
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+ # geometry = rdmol_opt,
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+ # )
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+ self.rdmol = result.geometry
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+ PE_final = result.PE
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+
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  elif calculator.lower() == 'MMFF94'.lower() or calculator.lower() == 'MMFF'.lower():
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  retcode = Chem.rdForceFieldHelpers.MMFFOptimizeMolecule(self.rdmol,
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  mmffVariant='MMFF94',
@@ -226,7 +235,8 @@ class Conf:
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  maxIters=max_iter)
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  # returns 0 if the optimization converged
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- PE_final = self.potential_energy(calculator)
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+ if PE_final is None:
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+ PE_final = self.potential_energy(calculator)
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  self.props.update({
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  'E_tot_init(kcal/mol)': PE_start , # energy before optimization
{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: rdworks
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- Version: 0.43.1
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+ Version: 0.43.2
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  Summary: Routine tasks built on RDKit and other tools
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  Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
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  Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>
{rdworks-0.43.1 → rdworks-0.43.2}/LICENSE RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/README.md RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/pyproject.toml RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/setup.cfg RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/mol.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/pka.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/readin.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/rgroup.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/std.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/units.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/utils.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/src/rdworks/xml.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/tests/test_basics.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/tests/test_nn_xtb.py RENAMED
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{rdworks-0.43.1 → rdworks-0.43.2}/tests/test_web.py RENAMED
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