mlmm-toolkit 0.2.3.dev0__tar.gz → 0.2.4.dev0__tar.gz

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Files changed (546) hide show
  1. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/release.yml +1 -0
  2. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/CHANGELOG.md +1 -1
  3. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/PKG-INFO +1 -1
  4. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/index.md +1 -1
  5. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/index.md +1 -1
  6. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/_version.py +3 -3
  7. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/PKG-INFO +1 -1
  8. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/docs.yml +0 -0
  9. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/docs_quality.yml +0 -0
  10. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/pytest.yml +0 -0
  11. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/smoke_test.yml +0 -0
  12. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.gitignore +0 -0
  13. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/CONTRIBUTING.md +0 -0
  14. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/LICENSE +0 -0
  15. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/MANIFEST.in +0 -0
  16. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/README.md +0 -0
  17. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/THIRD_PARTY_NOTICES.txt +0 -0
  18. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/Makefile +0 -0
  19. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/_static/custom.css +0 -0
  20. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/_templates/page.html +0 -0
  21. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/add_elem_info.md +0 -0
  22. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/all.md +0 -0
  23. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/cli_conventions.md +0 -0
  24. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/concepts.md +0 -0
  25. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/conf.py +0 -0
  26. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/define_layer.md +0 -0
  27. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/device_hpc.md +0 -0
  28. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/dft.md +0 -0
  29. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/energy_diagram.md +0 -0
  30. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/extract.md +0 -0
  31. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/fix_altloc.md +0 -0
  32. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/freq.md +0 -0
  33. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/getting_started.md +0 -0
  34. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/glossary.md +0 -0
  35. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/init.md +0 -0
  36. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/irc.md +0 -0
  37. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/add_elem_info.md +0 -0
  38. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/all.md +0 -0
  39. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/cli_conventions.md +0 -0
  40. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/concepts.md +0 -0
  41. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/define_layer.md +0 -0
  42. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/device_hpc.md +0 -0
  43. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/dft.md +0 -0
  44. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/energy_diagram.md +0 -0
  45. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/extract.md +0 -0
  46. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/fix_altloc.md +0 -0
  47. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/freq.md +0 -0
  48. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/getting_started.md +0 -0
  49. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/glossary.md +0 -0
  50. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/init.md +0 -0
  51. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/irc.md +0 -0
  52. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/mlmm_calc.md +0 -0
  53. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/mm_parm.md +0 -0
  54. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/oniom_export.md +0 -0
  55. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/oniom_gaussian.md +0 -0
  56. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/oniom_import.md +0 -0
  57. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/oniom_orca.md +0 -0
  58. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/opt.md +0 -0
  59. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/path_opt.md +0 -0
  60. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/path_search.md +0 -0
  61. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/pysis.md +0 -0
  62. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/python_api.md +0 -0
  63. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/quickstart_all.md +0 -0
  64. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/quickstart_scan_spec.md +0 -0
  65. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/quickstart_tsopt_freq.md +0 -0
  66. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/recipes_common_errors.md +0 -0
  67. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/scan.md +0 -0
  68. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/scan2d.md +0 -0
  69. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/scan3d.md +0 -0
  70. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/trj2fig.md +0 -0
  71. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/troubleshooting.md +0 -0
  72. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/tsopt.md +0 -0
  73. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/yaml_reference.md +0 -0
  74. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/make.bat +0 -0
  75. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/mlmm_calc.md +0 -0
  76. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/mlmm_toolkit_overview.png +0 -0
  77. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/mm_parm.md +0 -0
  78. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/oniom_export.md +0 -0
  79. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/oniom_gaussian.md +0 -0
  80. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/oniom_import.md +0 -0
  81. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/oniom_orca.md +0 -0
  82. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/opt.md +0 -0
  83. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/path_opt.md +0 -0
  84. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/path_search.md +0 -0
  85. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/pysis.md +0 -0
  86. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/python_api.md +0 -0
  87. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/quickstart_all.md +0 -0
  88. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/quickstart_scan_spec.md +0 -0
  89. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/quickstart_tsopt_freq.md +0 -0
  90. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/recipes_common_errors.md +0 -0
  91. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/add_elem_info.md +0 -0
  92. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/all.md +0 -0
  93. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/define_layer.md +0 -0
  94. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/dft.md +0 -0
  95. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/energy_diagram.md +0 -0
  96. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/extract.md +0 -0
  97. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/fix_altloc.md +0 -0
  98. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/freq.md +0 -0
  99. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/index.md +0 -0
  100. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/irc.md +0 -0
  101. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/mm_parm.md +0 -0
  102. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/oniom_export.md +0 -0
  103. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/oniom_import.md +0 -0
  104. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/opt.md +0 -0
  105. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/path_opt.md +0 -0
  106. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/path_search.md +0 -0
  107. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/pysis.md +0 -0
  108. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/scan.md +0 -0
  109. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/scan2d.md +0 -0
  110. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/scan3d.md +0 -0
  111. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/trj2fig.md +0 -0
  112. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/commands/tsopt.md +0 -0
  113. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/reference/yaml.md +0 -0
  114. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/requirements_docs.txt +0 -0
  115. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/scan.md +0 -0
  116. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/scan2d.md +0 -0
  117. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/scan3d.md +0 -0
  118. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/trj2fig.md +0 -0
  119. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/troubleshooting.md +0 -0
  120. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/tsopt.md +0 -0
  121. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/yaml_reference.md +0 -0
  122. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/complex.parm7 +0 -0
  123. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/complex.pdb +0 -0
  124. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/complex.rst7 +0 -0
  125. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/pocket.pdb +0 -0
  126. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/r_layered.pdb +0 -0
  127. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/run_all.sh +0 -0
  128. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/methyltransferase/run_stepwise.sh +0 -0
  129. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/ml_region_p.pdb +0 -0
  130. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/ml_region_r.pdb +0 -0
  131. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/opt_ase.py +0 -0
  132. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/p_complex.parm7 +0 -0
  133. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/p_complex.pdb +0 -0
  134. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/p_complex.rst7 +0 -0
  135. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/p_complex_layered.pdb +0 -0
  136. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/r_complex.pdb +0 -0
  137. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/r_complex_layered.pdb +0 -0
  138. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/run.sh +0 -0
  139. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/examples/toy_system/test_core.py +0 -0
  140. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/__init__.py +0 -0
  141. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/analytical_hessian.py +0 -0
  142. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/constants.py +0 -0
  143. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/forcefield.py +0 -0
  144. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/loaders.py +0 -0
  145. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/Makefile +0 -0
  146. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/__init__.py +0 -0
  147. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/analytical_hessian.py +0 -0
  148. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/analytical_hessian_ext.cpp +0 -0
  149. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/bonded.py +0 -0
  150. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/bonded_ext.cpp +0 -0
  151. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/loader.py +0 -0
  152. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/nonbonded.py +0 -0
  153. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/native/nonbonded_ext.cpp +0 -0
  154. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/prmtop_parmed.py +0 -0
  155. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/system.py +0 -0
  156. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/__init__.py +0 -0
  157. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/angle.py +0 -0
  158. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/bond.py +0 -0
  159. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/cmap.py +0 -0
  160. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/dihedral.py +0 -0
  161. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/terms/nonbonded.py +0 -0
  162. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/__init__.py +0 -0
  163. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/conftest.py +0 -0
  164. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/data/small/complex.parm7 +0 -0
  165. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/data/small/complex.pdb +0 -0
  166. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/data/small/complex.rst7 +0 -0
  167. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/test_coords_input.py +0 -0
  168. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/test_energy_force.py +0 -0
  169. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/test_hessian.py +0 -0
  170. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/test_smoke.py +0 -0
  171. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/tests/test_validation.py +0 -0
  172. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/hessian_ff/workflows.py +0 -0
  173. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/__init__.py +0 -0
  174. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/__main__.py +0 -0
  175. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/add_elem_info.py +0 -0
  176. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/advanced_help.py +0 -0
  177. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/align_freeze_atoms.py +0 -0
  178. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/all.py +0 -0
  179. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/bond_changes.py +0 -0
  180. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/bool_compat.py +0 -0
  181. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/cli.py +0 -0
  182. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/cli_utils.py +0 -0
  183. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/default_group.py +0 -0
  184. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/defaults.py +0 -0
  185. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/define_layer.py +0 -0
  186. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/dft.py +0 -0
  187. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/energy_diagram.py +0 -0
  188. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/extract.py +0 -0
  189. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/fix_altloc.py +0 -0
  190. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/freq.py +0 -0
  191. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/harmonic_constraints.py +0 -0
  192. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/hessian_cache.py +0 -0
  193. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/hessian_calc.py +0 -0
  194. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/irc.py +0 -0
  195. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/mlmm_calc.py +0 -0
  196. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/mm_parm.py +0 -0
  197. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/oniom_export.py +0 -0
  198. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/oniom_import.py +0 -0
  199. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/opt.py +0 -0
  200. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/path_opt.py +0 -0
  201. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/path_search.py +0 -0
  202. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/preflight.py +0 -0
  203. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/py.typed +0 -0
  204. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/pysis_runner.py +0 -0
  205. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/scan.py +0 -0
  206. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/scan2d.py +0 -0
  207. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/scan3d.py +0 -0
  208. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/scan_common.py +0 -0
  209. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/summary_log.py +0 -0
  210. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/trj2fig.py +0 -0
  211. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/tsopt.py +0 -0
  212. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/utils.py +0 -0
  213. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/xtb_embedcharge_correction.py +0 -0
  214. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/SOURCES.txt +0 -0
  215. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/dependency_links.txt +0 -0
  216. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/entry_points.txt +0 -0
  217. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/requires.txt +0 -0
  218. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/top_level.txt +0 -0
  219. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pyproject.toml +0 -0
  220. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/Geometry.py +0 -0
  221. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/LICENSE +0 -0
  222. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/TableFormatter.py +0 -0
  223. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/TablePrinter.py +0 -0
  224. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/__init__.py +0 -0
  225. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AFIR.py +0 -0
  226. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPot.py +0 -0
  227. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPot2.py +0 -0
  228. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPot3.py +0 -0
  229. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPot4.py +0 -0
  230. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPotBase.py +0 -0
  231. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AnaPotCBM.py +0 -0
  232. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/AtomAtomTransTorque.py +0 -0
  233. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/CFOUR.py +0 -0
  234. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Calculator.py +0 -0
  235. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/CerjanMiller.py +0 -0
  236. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Composite.py +0 -0
  237. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/ConicalIntersection.py +0 -0
  238. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/DFTBp.py +0 -0
  239. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/DFTD3.py +0 -0
  240. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/DFTD4.py +0 -0
  241. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Dalton.py +0 -0
  242. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Dimer.py +0 -0
  243. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Dummy.py +0 -0
  244. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/EGO.py +0 -0
  245. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/EnergyMin.py +0 -0
  246. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/ExternalPotential.py +0 -0
  247. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/FakeASE.py +0 -0
  248. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/FourWellAnaPot.py +0 -0
  249. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/FreeEndNEBPot.py +0 -0
  250. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Gaussian09.py +0 -0
  251. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Gaussian16.py +0 -0
  252. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/HardSphere.py +0 -0
  253. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/IDPPCalculator.py +0 -0
  254. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/IPIClient.py +0 -0
  255. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/IPIServer.py +0 -0
  256. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/LEPSBase.py +0 -0
  257. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/LEPSExpr.py +0 -0
  258. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/LennardJones.py +0 -0
  259. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/MOPAC.py +0 -0
  260. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/MullerBrownSympyPot.py +0 -0
  261. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/MultiCalc.py +0 -0
  262. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/NFK.py +0 -0
  263. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/OBabel.py +0 -0
  264. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/ONIOMv2.py +0 -0
  265. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/ORCA.py +0 -0
  266. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/ORCA5.py +0 -0
  267. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/OpenMM.py +0 -0
  268. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/OpenMolcas.py +0 -0
  269. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/OverlapCalculator.py +0 -0
  270. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Psi4.py +0 -0
  271. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/PyPsi4.py +0 -0
  272. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/PySCF.py +0 -0
  273. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/PyXTB.py +0 -0
  274. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/QCEngine.py +0 -0
  275. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Rastrigin.py +0 -0
  276. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Remote.py +0 -0
  277. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Rosenbrock.py +0 -0
  278. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/SocketCalc.py +0 -0
  279. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/TIP3P.py +0 -0
  280. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/TransTorque.py +0 -0
  281. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/Turbomole.py +0 -0
  282. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/VRIPot.py +0 -0
  283. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/WFOWrapper.py +0 -0
  284. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/WFOWrapper2.py +0 -0
  285. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/XTB.py +0 -0
  286. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/__init__.py +0 -0
  287. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/cosmo_data.py +0 -0
  288. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/calculators/parser.py +0 -0
  289. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/color.py +0 -0
  290. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/config.py +0 -0
  291. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/constants.py +0 -0
  292. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/AdaptiveNEB.py +0 -0
  293. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/ChainOfStates.py +0 -0
  294. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/FreeEndNEB.py +0 -0
  295. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/FreezingString.py +0 -0
  296. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/GrowingChainOfStates.py +0 -0
  297. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/GrowingNT.py +0 -0
  298. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/GrowingString.py +0 -0
  299. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/NEB.py +0 -0
  300. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/SimpleZTS.py +0 -0
  301. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/__init__.py +0 -0
  302. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/cos/stiffness.py +0 -0
  303. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/__init__.py +0 -0
  304. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/afir.py +0 -0
  305. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/barriers.py +0 -0
  306. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/birkholz.py +0 -0
  307. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/cluster.py +0 -0
  308. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/diabatization.py +0 -0
  309. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/merge.py +0 -0
  310. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/merge_mol2.py +0 -0
  311. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/opt.py +0 -0
  312. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/perf.py +0 -0
  313. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/pka.py +0 -0
  314. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/precon_pos_rot.py +0 -0
  315. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/rates.py +0 -0
  316. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/replace.py +0 -0
  317. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/scan.py +0 -0
  318. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/spectrum.py +0 -0
  319. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/drivers/thermo.py +0 -0
  320. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/Gaussian.py +0 -0
  321. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/__init__.py +0 -0
  322. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/colvars.py +0 -0
  323. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/driver.py +0 -0
  324. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/helpers.py +0 -0
  325. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/lincs.py +0 -0
  326. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/mdp.py +0 -0
  327. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/rattle.py +0 -0
  328. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/thermostats.py +0 -0
  329. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/dynamics/wigner.py +0 -0
  330. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/elem_data.py +0 -0
  331. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/exceptions.py +0 -0
  332. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/filtertrj.py +0 -0
  333. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/helpers.py +0 -0
  334. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/helpers_pure.py +0 -0
  335. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/init_logging.py +0 -0
  336. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Bend.py +0 -0
  337. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Bend2.py +0 -0
  338. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/BondedFragment.py +0 -0
  339. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Cartesian.py +0 -0
  340. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/CartesianCoords.py +0 -0
  341. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Coords.py +0 -0
  342. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/DLC.py +0 -0
  343. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/DistanceFunction.py +0 -0
  344. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/DummyImproper.py +0 -0
  345. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/DummyTorsion.py +0 -0
  346. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/LinearBend.py +0 -0
  347. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/LinearDisplacement.py +0 -0
  348. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/OutOfPlane.py +0 -0
  349. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/PrimTypes.py +0 -0
  350. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Primitive.py +0 -0
  351. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/RedundantCoords.py +0 -0
  352. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/RobustTorsion.py +0 -0
  353. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Rotation.py +0 -0
  354. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Stretch.py +0 -0
  355. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Torsion.py +0 -0
  356. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Torsion2.py +0 -0
  357. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/Translation.py +0 -0
  358. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/__init__.py +0 -0
  359. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/augment_bonds.py +0 -0
  360. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/derivatives.py +0 -0
  361. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/eval.py +0 -0
  362. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/exceptions.py +0 -0
  363. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/findiffs.py +0 -0
  364. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/generate_derivatives.py +0 -0
  365. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/helpers.py +0 -0
  366. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/logging_conf.py +0 -0
  367. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/mp_derivatives.py +0 -0
  368. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/setup.py +0 -0
  369. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/setup_fast.py +0 -0
  370. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/update.py +0 -0
  371. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/intcoords/valid.py +0 -0
  372. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/Geodesic.py +0 -0
  373. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/IDPP.py +0 -0
  374. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/Interpolator.py +0 -0
  375. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/LST.py +0 -0
  376. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/Redund.py +0 -0
  377. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/__init__.py +0 -0
  378. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/interpolate/helpers.py +0 -0
  379. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/__init__.py +0 -0
  380. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/aomix.py +0 -0
  381. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/cjson.py +0 -0
  382. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/crd.py +0 -0
  383. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/cube.py +0 -0
  384. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/fchk.py +0 -0
  385. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/hdf5.py +0 -0
  386. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/hessian.py +0 -0
  387. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/mol2.py +0 -0
  388. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/molden.py +0 -0
  389. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/orca.py +0 -0
  390. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/pdb.py +0 -0
  391. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/psf.py +0 -0
  392. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/pubchem.py +0 -0
  393. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/qcschema.py +0 -0
  394. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/sdf.py +0 -0
  395. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/xyz.py +0 -0
  396. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/io/zmat.py +0 -0
  397. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/DWI.py +0 -0
  398. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/DampedVelocityVerlet.py +0 -0
  399. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/Euler.py +0 -0
  400. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/EulerPC.py +0 -0
  401. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/GonzalezSchlegel.py +0 -0
  402. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/IMKMod.py +0 -0
  403. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/IRC.py +0 -0
  404. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/IRCDummy.py +0 -0
  405. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/Instanton.py +0 -0
  406. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/LQA.py +0 -0
  407. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/ModeKill.py +0 -0
  408. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/ParamPlot.py +0 -0
  409. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/RK4.py +0 -0
  410. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/__init__.py +0 -0
  411. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/irc/initial_displ.py +0 -0
  412. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/linalg.py +0 -0
  413. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/Backtracking.py +0 -0
  414. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/HagerZhang.py +0 -0
  415. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/LineSearch.py +0 -0
  416. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/StrongWolfe.py +0 -0
  417. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/__init__.py +0 -0
  418. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/line_searches/interpol.py +0 -0
  419. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/modefollow/NormalMode.py +0 -0
  420. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/modefollow/__init__.py +0 -0
  421. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/modefollow/davidson.py +0 -0
  422. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/modefollow/lanczos.py +0 -0
  423. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/BFGS.py +0 -0
  424. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/BacktrackingOptimizer.py +0 -0
  425. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/ConjugateGradient.py +0 -0
  426. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/CubicNewton.py +0 -0
  427. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/FIRE.py +0 -0
  428. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/HessianOptimizer.py +0 -0
  429. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/LBFGS.py +0 -0
  430. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/LayerOpt.py +0 -0
  431. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/MicroOptimizer.py +0 -0
  432. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/NCOptimizer.py +0 -0
  433. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/Optimizer.py +0 -0
  434. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/PreconLBFGS.py +0 -0
  435. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/PreconSteepestDescent.py +0 -0
  436. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/QuickMin.py +0 -0
  437. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/RFOptimizer.py +0 -0
  438. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/RSA.py +0 -0
  439. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/StabilizedQNMethod.py +0 -0
  440. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/SteepestDescent.py +0 -0
  441. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/StringOptimizer.py +0 -0
  442. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/__init__.py +0 -0
  443. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/closures.py +0 -0
  444. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/cls_map.py +0 -0
  445. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/exceptions.py +0 -0
  446. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/gdiis.py +0 -0
  447. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/guess_hessians.py +0 -0
  448. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/hessian_updates.py +0 -0
  449. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/poly_fit.py +0 -0
  450. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/precon.py +0 -0
  451. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/optimizers/restrict_step.py +0 -0
  452. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/pack.py +0 -0
  453. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/peakdetect.py +0 -0
  454. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/plot.py +0 -0
  455. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/run.py +0 -0
  456. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/socket_helper.py +0 -0
  457. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/stocastic/FragmentKick.py +0 -0
  458. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/stocastic/Kick.py +0 -0
  459. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/stocastic/Pipeline.py +0 -0
  460. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/stocastic/__init__.py +0 -0
  461. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/stocastic/align.py +0 -0
  462. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/testing.py +0 -0
  463. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/thermo.py +0 -0
  464. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/trj.py +0 -0
  465. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/tsoptimizers/RSIRFOptimizer.py +0 -0
  466. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/tsoptimizers/RSPRFOptimizer.py +0 -0
  467. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/tsoptimizers/TRIM.py +0 -0
  468. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/tsoptimizers/TSHessianOptimizer.py +0 -0
  469. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/tsoptimizers/__init__.py +0 -0
  470. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/Basis.py +0 -0
  471. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/DIIS.py +0 -0
  472. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/__init__.py +0 -0
  473. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/build_ext.py +0 -0
  474. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/cart2sph.py +0 -0
  475. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/diabatization.py +0 -0
  476. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/excited_states.py +0 -0
  477. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/gen_ints.py +0 -0
  478. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/helpers.py +0 -0
  479. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/__init__.py +0 -0
  480. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/boys.py +0 -0
  481. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/boys_table_N_64_xasym_27.1_step_0.01.npy +0 -0
  482. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/cart_gto3d.py +0 -0
  483. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/coulomb3d.py +0 -0
  484. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/diag_quadrupole3d.py +0 -0
  485. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/dipole3d.py +0 -0
  486. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/int2c2e3d.py +0 -0
  487. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/int3c2e3d_sph.py +0 -0
  488. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/kinetic3d.py +0 -0
  489. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/ovlp3d.py +0 -0
  490. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/quadrupole3d.py +0 -0
  491. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/ints/self_ovlp3d.py +0 -0
  492. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/localization.py +0 -0
  493. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/multipole.py +0 -0
  494. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/normalization.py +0 -0
  495. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/pop_analysis.py +0 -0
  496. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/shells.py +0 -0
  497. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wavefunction/wavefunction.py +0 -0
  498. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wrapper/__init__.py +0 -0
  499. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wrapper/exceptions.py +0 -0
  500. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wrapper/jmol.py +0 -0
  501. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wrapper/mwfn.py +0 -0
  502. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/wrapper/packmol.py +0 -0
  503. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/xyzloader.py +0 -0
  504. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/pysisyphus/yaml_mods.py +0 -0
  505. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/check_all_scan_contract.py +0 -0
  506. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/check_intro_template.py +0 -0
  507. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/check_markdown_links.py +0 -0
  508. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/generate_reference.py +0 -0
  509. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/run_docs_quality.py +0 -0
  510. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/smoke_docs_commands.py +0 -0
  511. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/scripts/smoke_dump_trajectories.py +0 -0
  512. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/setup.cfg +0 -0
  513. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/README.md +0 -0
  514. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/conftest.py +0 -0
  515. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/p_complex.parm7 +0 -0
  516. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/p_complex.pdb +0 -0
  517. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/p_complex.rst7 +0 -0
  518. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/p_complex_layered.pdb +0 -0
  519. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/pocket_p.pdb +0 -0
  520. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/pocket_r.pdb +0 -0
  521. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/r_complex.pdb +0 -0
  522. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/r_complex_layered.pdb +0 -0
  523. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/smoke/run.sh +0 -0
  524. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_all_multiplicity_option.py +0 -0
  525. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_bool_compat_cli.py +0 -0
  526. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_cli_feature_regressions.py +0 -0
  527. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_cli_help.py +0 -0
  528. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_cli_utils.py +0 -0
  529. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_default_group.py +0 -0
  530. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_defaults.py +0 -0
  531. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_e2e_minimal.py +0 -0
  532. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_error_handling.py +0 -0
  533. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_extract.py +0 -0
  534. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_imports.py +0 -0
  535. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_mm_parm_preflight.py +0 -0
  536. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_opt.py +0 -0
  537. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_preflight.py +0 -0
  538. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_scan_oniom_smoke.py +0 -0
  539. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_summary_log.py +0 -0
  540. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/tests/test_utils.py +0 -0
  541. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/LICENSE +0 -0
  542. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/QCData.py +0 -0
  543. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/__init__.py +0 -0
  544. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/config.py +0 -0
  545. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/constants.py +0 -0
  546. {mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/thermoanalysis/thermo.py +0 -0
{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/.github/workflows/release.yml RENAMED
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  with:
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  fetch-depth: 0
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  - name: Setup Python
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  uses: actions/setup-python@v5
{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/CHANGELOG.md RENAMED
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  The format follows [Keep a Changelog](https://keepachangelog.com/).
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- ## [0.2.2] — 2026-03-18
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+ ## [0.2.3] — 2026-03-18
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  ### Added
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  - GitHub Pages deployment and PyPI release workflows.
{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: mlmm-toolkit
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- Version: 0.2.3.dev0
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  Summary: mlmm - ML/MM toolkit for enzyme reaction analysis
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  Author-email: Takuto Ohmura <ohmura.takuto@gmail.com>
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  License: GNU GENERAL PUBLIC LICENSE
{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/index.md RENAMED
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  # mlmm-toolkit Documentation
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- *Version: v0.2.2*
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+ *Version: v0.2.3*
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  **mlmm-toolkit** is a Python CLI toolkit for automated enzymatic reaction-path modeling using ML/MM (machine-learning / molecular mechanics) methods.
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{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/docs/ja/index.md RENAMED
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  # mlmm-toolkit ドキュメント
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- *バージョン: v0.2.2*
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  **mlmm-toolkit** は、機械学習原子間ポテンシャル（Machine Learning Interatomic Potential）と分子力学（Molecular Mechanics）を ONIOM 的に結合した **ML/MM 法** を用いて、PDB 構造から酵素反応経路を自動モデリングする Python 製 CLI ツールキットです。
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{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm/_version.py RENAMED
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{mlmm_toolkit-0.2.3.dev0 → mlmm_toolkit-0.2.4.dev0}/mlmm_toolkit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mlmm-toolkit
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- Version: 0.2.3.dev0
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  Summary: mlmm - ML/MM toolkit for enzyme reaction analysis
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  Author-email: Takuto Ohmura <ohmura.takuto@gmail.com>
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  License: GNU GENERAL PUBLIC LICENSE