├── .gitignore ├── .idea ├── .gitignore ├── CageCavityCalc.iml ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── CageCavityCalc ├── CageCavityCalc.py ├── __init__.py ├── __main__.py ├── calculations.py ├── data.py ├── electrostatics.py ├── examples │ ├── 10_mdanalysis_hydrophobicity │ │ ├── cage.gro │ │ ├── cage_cavity.pdb │ │ └── example_10.py │ ├── 11_errors │ │ └── example_11.py │ ├── 12_test_cage │ │ ├── fig_1.png │ │ ├── fig_2.png │ │ ├── fig_3.png │ │ ├── fig_4.png │ │ ├── fig_5.png │ │ ├── fig_6.png │ │ ├── test.mol2 │ │ ├── test.pdb │ │ ├── test.spartan │ │ ├── test_box_cavity.pdb │ │ ├── test_cavity.pdb │ │ ├── test_cavity.pml │ │ ├── test_cavity.pse │ │ ├── test_cavity_vol_calc.txt │ │ ├── test_extra_data.txt │ │ └── test_hydrophobicity_cavity_dummy_atoms.txt │ ├── 13_cages_review │ │ ├── 1148701.pdb │ │ ├── 1148701_cavity.pdb │ │ ├── 1148701_cavity.pml │ │ ├── 210396.pdb │ │ ├── 210396_cavity.pdb │ │ ├── 210396_cavity.pml │ │ ├── 218828.pdb │ │ ├── 218828_cavity.pdb │ │ ├── 218828_cavity.pml │ │ ├── 41586_2016_BFnature20771_MOESM527_ESM.pdb │ │ ├── 41586_2016_BFnature20771_MOESM527_ESM_cavity.pdb │ │ ├── 41586_2016_BFnature20771_MOESM527_ESM_cavity.pml │ │ ├── 41586_2016_BFnature20771_MOESM528_ESM.pdb │ │ ├── 41586_2016_BFnature20771_MOESM528_ESM_cavity.pdb │ │ ├── 41586_2016_BFnature20771_MOESM528_ESM_cavity.pml │ │ ├── 646911.pdb │ │ ├── 646911_cavity.pdb │ │ ├── 646911_cavity.pml │ │ ├── 664973.pdb │ │ ├── 664973_cavity.pdb │ │ ├── 664973_cavity.pml │ │ ├── 759106.pdb │ │ ├── 759106_cavity.pdb │ │ ├── 759106_cavity.pml │ │ ├── 794242.pdb │ │ ├── 794242_cavity.pdb │ │ ├── 794242_cavity.pml │ │ ├── CageOTf_Pentacenedione_ACIE_2016-CCDC_1492902.xyz │ │ ├── CageOTf_Pentacenedione_removed_ACIE_2016-CCDC_1492902.pdb │ │ ├── CageOTf_Pentacenedione_removed_ACIE_2016-CCDC_1492902_cavity.pdb │ │ ├── CageOTf_Pentacenedione_removed_ACIE_2016-CCDC_1492902_cavity.pml │ │ ├── Figure_113_ChemEurJ_2014_20_16707_cage1.mol2 │ │ ├── Figure_113_ChemEurJ_2014_20_16707_cage1_cavity.pdb │ │ ├── Figure_113_ChemEurJ_2014_20_16707_cage1_cavity.pml │ │ ├── Figure_130_ChemCommun_1997_118_497_cage_cram.pdb │ │ ├── Figure_130_ChemCommun_1997_118_497_cage_cram_cavity.pdb │ │ ├── Figure_130_ChemCommun_1997_118_497_cage_cram_cavity.pml │ │ ├── Figure_132_ChemEurJ_2019_25_3091_cage_x-ray.pdb │ │ ├── Figure_132_ChemEurJ_2019_25_3091_cage_x-ray_no_guest.pdb │ │ ├── Figure_132_ChemEurJ_2019_25_3091_cage_x-ray_no_guest_cavity.pdb │ │ ├── Figure_132_ChemEurJ_2019_25_3091_cage_x-ray_no_guest_cavity.pml │ │ ├── Figure_24_OrgLett_2010_12_1740_cage_ol.xyz │ │ ├── Figure_31_JPhysChemC_2014_118_12734_CC3_869701.pdb │ │ ├── Figure_31_JPhysChemC_2014_118_12734_CC3_869701_cavity.pdb │ │ ├── Figure_55_JACS_2020_142_18060.pdb │ │ ├── Figure_55_JACS_2020_142_18060_cavity.pdb │ │ ├── Figure_55_JACS_2020_142_18060_cavity.pml │ │ ├── Figure_73_ChemEurJ_2020_26_1558.pdb │ │ ├── Figure_73_ChemEurJ_2020_26_1558_cavity.pdb │ │ ├── Figure_73_ChemEurJ_2020_26_1558_cavity.pml │ │ ├── Figure_76_PNAS_2002_99_4962.pdb │ │ ├── Figure_76_PNAS_2002_99_4962_cavity.pdb │ │ ├── Figure_76_PNAS_2002_99_4962_cavity.pml │ │ ├── Figure_87_ChemEurJ_202005046_cage.mol2 │ │ ├── Figure_87_ChemEurJ_202005046_cage_cavity.pdb │ │ ├── Figure_87_ChemEurJ_202005046_cage_cavity.pml │ │ ├── Figure_93_ChemSci2011_2_1719_cage1_coronene.pdb │ │ ├── Figure_93_ChemSci2011_2_1719_cage1_coronene_removed_cavity.pdb │ │ ├── Figure_93_ChemSci2011_2_1719_cage1_coronene_removed_cavity.pml │ │ ├── Figure_96_AngewChemIntEd_2021.pdb │ │ ├── Figure_96_AngewChemIntEd_2021.xyz │ │ ├── Figure_96_AngewChemIntEd_2021_cavity.pdb │ │ ├── Figure_96_AngewChemIntEd_2021_cavity.pml │ │ ├── anie202211304-sup-0001-badjic_lzq-8-38.pdb │ │ ├── anie202211304-sup-0001-badjic_lzq-8-38_cavity.pdb │ │ ├── anie202211304-sup-0001-badjic_lzq-8-38_cavity.pml │ │ ├── anie202211304-sup-0001-compound-8.pdb │ │ ├── anie202211304-sup-0001-compound-8_cavity.pdb │ │ ├── anie202211304-sup-0001-compound-8_cavity.pml │ │ ├── ja4043609_si_002.pdb │ │ ├── ja4043609_si_002_cavity.pdb │ │ ├── ja4043609_si_002_cavity.pml │ │ ├── ja4043609_si_003.pdb │ │ ├── ja4043609_si_003_cavity.pdb │ │ ├── ja4043609_si_003_cavity.pml │ │ ├── ja4043609_si_004.pdb │ │ ├── ja4043609_si_004_cavity.pdb │ │ └── ja4043609_si_004_cavity.pml │ ├── 14_esp │ │ ├── example_14.py │ │ ├── ncage.pdb │ │ └── ncage.xyz │ ├── 15_from_table │ │ └── example_15.py │ ├── 16_save_trajectory │ │ ├── example_16.py │ │ ├── short.gro │ │ └── short.xtc │ ├── 1_mol2 │ │ ├── cage_1_JACS_2006_128_14120.mol2 │ │ ├── cage_1_JACS_2006_128_14120_cavity.pdb │ │ ├── cage_1_JACS_2006_128_14120_cavity.pse │ │ ├── cage_1_JACS_2006_128_14120_cavity_vol_calc.txt │ │ ├── cage_cavity.pdb │ │ ├── cage_cavity.pml │ │ ├── example_1.py │ │ ├── file.pdb │ │ └── file.xyz │ ├── 2_pdb │ │ ├── cage_ACIE_2006_45_901.cavity.pdb │ │ ├── cage_ACIE_2006_45_901.cavity.pse │ │ ├── cage_ACIE_2006_45_901.mol2 │ │ ├── cage_ACIE_2006_45_901.pdb │ │ ├── cage_ACIE_2006_45_901_box_cavity.pdb │ │ ├── cage_ACIE_2006_45_901_cavity.pdb │ │ ├── cage_ACIE_2006_45_901_cavity.pse │ │ ├── cage_ACIE_2006_45_901_cavity_vol_calc.txt │ │ ├── example_2.py │ │ ├── file.pdb │ │ └── test │ │ │ └── cage_ACIE_2006_45_901.pdb │ ├── 3_cgbind │ │ ├── cage_cavity.pdb │ │ ├── example_3.py │ │ └── file.pdb │ ├── 4_mdanalysis │ │ ├── cage.gro │ │ └── example_4.py │ ├── 5_other_formats │ │ ├── cage.gro │ │ ├── cage_cavity.gro │ │ └── example_5.py │ ├── 6_trajectory │ │ ├── .short.xtc_offsets.npz │ │ ├── example_6.py │ │ ├── short.gro │ │ └── short.xtc │ ├── 7_bash │ │ ├── cage.pdb │ │ ├── cage_cavity.pdb │ │ └── run.sh │ ├── 8_hydrophobicity │ │ ├── .cage_cavity_hydrophobicity.pdb.swp │ │ ├── cage_1_JACS_2006_128_14120.mol2 │ │ ├── cage_cavity_aromatic_contact.pdb │ │ ├── cage_cavity_esp.pdb │ │ ├── cage_cavity_hydrophobicity.pdb │ │ ├── cage_cavity_hydrophobicity.pml │ │ ├── cage_cavity_solvent_accessibility.pdb │ │ └── example_8.py │ ├── 9_large │ │ ├── cage.pdb │ │ └── example_9.py │ └── more_tests │ │ ├── 646911_exported_spartan_gives_error_Pd.pdb │ │ ├── 646911_exported_spartan_gives_error_Pd_cavity.pdb │ │ ├── 646911_exported_spartan_replace_spaces_before_after_Pd.pdb │ │ ├── Cage6_opt.xyz │ │ ├── Cage6_opt_cavity.pdb │ │ ├── Cage6_opt_cavity_cluster.pdb │ │ ├── cage_pdb.pdb │ │ └── cage_pdb_cavity.pdb ├── grid_classes.py ├── hydrophobicity.py ├── input_output.py ├── log.py ├── pic │ ├── C3_PyMol_Plugin.png │ ├── cage.png │ ├── cavity.png │ ├── graphical_abstract_CageCavityCalc.png │ ├── hydrophobicity.png │ ├── principle │ ├── principle.png │ └── principle.svg ├── pymol_plugin │ ├── __init__.py │ ├── cavecav_widget.ui │ └── simple.py └── window_size.py ├── LICENSE ├── README.md ├── Windows_Installer.md ├── pyproject.toml ├── readme_testing.txt ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | *.pyc 3 | 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