├── Biphenyl Example.ipynb ├── Figures.ipynb ├── README.md ├── code ├── BO.py ├── confab_no_evaluations.py ├── energy_diff.py ├── get_rmsd.py ├── get_rmsd_5_rotor.py ├── get_tfd.py ├── get_tfd_5_rotor.py ├── ref_point.py └── uniform_search.py ├── molecules ├── JP_set.smi ├── biphenyl.cml ├── biphenyl.sdf ├── omegacsd_CDBMPI10.pdf ├── omegacsd_CDBMPI10_BO_lowest.sdf ├── omegacsd_CDBMPI10_confab_lowest.sdf ├── omegacsd_FUPFIF.pdf ├── omegacsd_FUPFIF_BO_lowest.sdf ├── omegacsd_FUPFIF_confab_lowest.sdf ├── omegapdb_1sn5.pdf ├── omegapdb_1sn5_BO_lowest.sdf ├── omegapdb_1sn5_confab_lowest.sdf ├── step_1.pdf ├── step_15.pdf ├── step_2.pdf ├── step_3.pdf └── step_4.pdf ├── parameter_file ├── five_rotatable_bond.txt ├── four_rotatable_bond.txt ├── platinum_1.txt ├── platinum_2.txt ├── rdkit_list.txt ├── six_rotatable_bond.txt └── three_rotatable_bond.txt └── result ├── confab_no_evaluation ├── five_confab_no.txt ├── four_confab_no.txt ├── one_confab_no.txt ├── six_confab_no.txt ├── three_confab_no.txt └── two_confab_no.txt ├── energy ├── five_123.txt ├── five_200_123.txt ├── five_200_234.txt ├── five_200_345.txt ├── five_200_456.txt ├── five_234.txt ├── five_321.txt ├── five_345.txt ├── five_456.txt ├── four_1234.txt ├── four_2345.txt ├── four_321.txt ├── four_3456.txt ├── four_4567.txt ├── one_123.txt ├── one_1234.txt ├── one_234.txt ├── one_2345.txt ├── one_321.txt ├── one_345.txt ├── one_3456.txt ├── one_456.txt ├── one_4567.txt ├── six_123.txt ├── six_234.txt ├── six_321.txt ├── six_345.txt ├── six_456.txt ├── three_123.txt ├── three_234.txt ├── three_321.txt ├── three_345.txt ├── three_456.txt ├── two_123.txt ├── two_234.txt ├── two_321.txt ├── two_345.txt └── two_456.txt ├── rmsd ├── five_bo_rmsd_ref.txt ├── five_confab_rmsd_ref.txt ├── four_bo_rmsd_ref.txt ├── four_confab_rmsd_ref.txt ├── one_bo_rmsd_ref.txt ├── one_confab_rmsd_ref.txt ├── six_bo_rmsd_ref.txt ├── six_confab_rmsd_ref.txt ├── three_bo_rmsd_ref.txt ├── three_confab_rmsd_ref.txt ├── two_bo_rmsd_ref.txt └── two_confab_rmsd_ref.txt ├── summary ├── five_200_iter_summary.txt ├── five_200_lowest_point.txt ├── five_iter_summary.txt ├── five_lowest_point.txt ├── five_lowest_point_include_200_iterations.txt ├── four_iter_summary.txt ├── four_lowest_point.txt ├── one_iter_summary.txt ├── one_lowest_point.txt ├── six_iter_summary.txt ├── six_lowest_point.txt ├── three_iter_summary.txt ├── three_lowest_point.txt ├── two_iter_summary.txt └── two_lowest_point.txt └── tfd ├── five_bo_tfd_ref.txt ├── five_confab_tfd_ref.txt ├── four_bo_tfd_ref.txt ├── four_confab_tfd_ref.txt ├── one_bo_tfd_ref.txt ├── one_confab_tfd_ref.txt ├── six_bo_tfd_ref.txt ├── six_confab_tfd_ref.txt ├── three_bo_tfd_ref.txt ├── three_confab_tfd_ref.txt ├── two_bo_tfd_ref.txt └── two_confab_tfd_ref.txt /Biphenyl Example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucianlschan/Conformer-Geometry/HEAD/Biphenyl Example.ipynb 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