├── .ci_support └── environment.yml ├── .github └── workflows │ ├── deploy.yml │ ├── pypicheck.yml │ └── unittests.yml ├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── architector ├── __init__.py ├── __main__.py ├── _version.py ├── arch_context_manage.py ├── ase_db_utilities.py ├── complex_construction.py ├── data │ ├── Geometry_stats_generation.ipynb │ ├── Ligtype_binding_site_selections.ipynb │ ├── all_ref_geo_inds_dict.pkl │ ├── angle_stats_datasource.csv │ ├── avg_m_oxo_dists_csd.csv │ └── ligtype_angle_reference.csv ├── geometries.py ├── io_align_mol.py ├── io_calc.py ├── io_core.py ├── io_crest.py ├── io_lig.py ├── io_molecule.py ├── io_obabel.py ├── io_process_input.py ├── io_ptable.py ├── io_symmetry.py ├── io_xtb_calc.py ├── vibrations_free_energy.py └── visualization.py ├── development ├── .ipynb_checkpoints │ └── 7-Secondary_Solvation_Shell-checkpoint.ipynb ├── Secondary_Solvation_Shell.ipynb └── n_lig_combos.py ├── documentation ├── Debugging_Guide.ipynb ├── tutorials │ ├── 0-Quick_Start.ipynb │ ├── 1-Introduction.ipynb │ ├── 2-Specifying_Ligands.ipynb │ ├── 3-Core_Inputs.ipynb │ ├── 4-Ligand_Evaluations.ipynb │ ├── 5-Spin_Solvent_Free_Energy_Manifolds.ipynb │ ├── 6-Functionalizing_Ligands.ipynb │ ├── 7-Building_With_Reference_Ligands.ipynb │ └── 8-2D_Prepopulated_Construction.ipynb └── view_default_core_ligand_types.ipynb ├── environment.yml ├── setup.cfg ├── setup.py ├── tests ├── 01_import │ ├── __init__.py │ ├── fe_usercore_ref.mol2 │ └── test_build.py ├── 02_lig_conformations │ ├── __init__.py │ ├── io_lig_testing.ipynb │ └── test_lig_conformations.py ├── 03_full_build │ ├── TAWKAG_comp_0_ref.mol2 │ ├── __init__.py │ └── test_build.py ├── 04_simple_ligands │ ├── __init__.py │ └── test_simple_ligands.py └── __init__.py ├── utils └── ligand_viewing_coordinating_atom_selecting.ipynb └── versioneer.py /.ci_support/environment.yml: -------------------------------------------------------------------------------- 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