├── .flake8 ├── .github ├── dependabot.yml └── workflows │ ├── common_ccdc_status_checks.yml │ ├── lint-dockerfiles.yml │ ├── lint-markdown.yml │ ├── lint-python.yml │ └── lint-yaml.yml ├── .gitignore ├── .markdownlint.yml ├── .yamllint.yml ├── LICENSE ├── README.md ├── api_paper_2024 ├── example_1 │ ├── ReadMe.md │ ├── data_files │ │ └── demo_subset_of_pubchem.sdf │ ├── isovflavone_search.py │ └── process_pubchem_structures.py ├── example_2 │ ├── ReadMe.md │ ├── about_entry.py │ ├── crossref.py │ ├── language_processing.py │ ├── openalex.py │ ├── opencitations.py │ ├── references.py │ └── url_requesting.py ├── example_3 │ ├── Example │ │ ├── 1FM9_protein.mol2 │ │ ├── a_ligand.mol2 │ │ ├── cavity.atoms │ │ └── unconstrained.conf │ ├── ReadMe.md │ └── similarity_docking.py ├── example_4 │ ├── ReadMe.md │ ├── atom_weighting.json │ ├── mercury_metal_voronoi.py │ ├── mercury_molecular_voronoi.py │ └── voronoi.py └── example_5 │ ├── ReadMe.md │ ├── particle_shape.py │ ├── shape_classification.py │ └── visualiser.py ├── assets ├── csd-python-api-logo.png ├── download_zip.gif ├── search.gif └── single_download.gif ├── notebooks ├── API_Training_Exercises │ └── 01_Simple_Report.ipynb ├── CoRE-MOF │ ├── README.md │ ├── download_unmodified_MOFs_from_CSD.ipynb │ ├── list_coremof_csd_unmodified_20250227.json │ └── structures │ │ ├── CR │ │ ├── ASR │ │ │ ├── 2004[Co][rtl]3[ASR]2.cif │ │ │ ├── ABAVOP.cif │ │ │ ├── ABUXUT.cif │ │ │ ├── ACENIF.cif │ │ │ ├── ACODAA.cif │ │ │ ├── ACODED.cif │ │ │ ├── ACODIH.cif │ │ │ ├── ACOLUB.cif │ │ │ ├── ADABAK.cif │ │ │ ├── AFADAN.cif │ │ │ └── AFITIT.cif │ │ ├── FSR │ │ │ ├── ABAVOP.cif │ │ │ ├── ABUXUT.cif │ │ │ ├── ACENIF.cif │ │ │ ├── ACODED.cif │ │ │ ├── ACODIH.cif │ │ │ ├── ACOLUB.cif │ │ │ ├── ADABAK.cif │ │ │ ├── ADAQAA.cif │ │ │ ├── ADOGUZ.cif │ │ │ └── AFADAN.cif │ │ └── Ion │ │ │ ├── ADOBEB.cif │ │ │ ├── ADOCAY.cif │ │ │ ├── ADOCIG.cif │ │ │ ├── ANAGOO.cif │ │ │ ├── AVAGIP.cif │ │ │ ├── AVIVIK.cif │ │ │ ├── AVIVUW.cif │ │ │ ├── BAMKIM.cif │ │ │ ├── BELVAR.cif │ │ │ └── BOPHIZ.cif │ │ └── NCR │ │ ├── ABECIX.cif │ │ ├── ABECOD.cif │ │ ├── ABECUJ.cif │ │ ├── ABEDEU.cif │ │ ├── ABEDIY.cif │ │ ├── ABEMIF.cif │ │ ├── ABETIN.cif │ │ ├── ABINIM.cif │ │ └── ACATAA.cif ├── Discovery │ ├── .gitignore │ ├── 00_Background │ │ └── 00_Background.ipynb │ ├── 01_CSD_Search │ │ ├── 01_Substructure_searching_the_CSD.ipynb │ │ ├── 02_Similarity_searching_the_CSD.ipynb │ │ ├── 03_MCS_searching_the_CSD.ipynb │ │ ├── Lapatinib.mol │ │ ├── aryl_sulphonamide.con │ │ └── aryl_sulphonamide.qry │ ├── 02_Protein_Ligand │ │ ├── 01_Protein_Ligand_Searching.ipynb │ │ └── 02_API_Protein-Ligand_search_for_FAD.ipynb │ ├── 03_Molecular_geometries │ │ ├── 1ett.mol2 │ │ └── Molecular_geometries.ipynb │ ├── 04_Conformer_generation │ │ ├── Conformer_generation.ipynb │ │ ├── input.sdf │ │ └── lapatinib.mol2 │ ├── 05_Molecular_interactions │ │ └── Molecular_interactions.ipynb │ ├── 06_Interaction_maps │ │ ├── Interaction_maps.ipynb │ │ └── pdb2uw7.ent │ ├── 07_Cavities │ │ ├── Cavities.ipynb │ │ ├── pdb1fax.ent │ │ ├── pdbe_get.ps1 │ │ └── proteins │ │ │ ├── pdb1ett.ent │ │ │ ├── pdb1fax.ent │ │ │ ├── pdb2amq.ent │ │ │ ├── pdb4px6.ent │ │ │ ├── pdb4xg8.ent │ │ │ ├── pdb4yjp.ent │ │ │ ├── pdb5af9.ent │ │ │ ├── pdb5lma.ent │ │ │ └── pdb6lu7.ent │ ├── 08_Docking │ │ ├── 00a_Input_for_GOLD.ipynb │ │ ├── 00b_Input_for_GOLD-RDKit.ipynb │ │ ├── 01_Docking_foreground.ipynb │ │ ├── 02_Docking_background_conf.ipynb │ │ ├── 03_Docking_interactive.ipynb │ │ ├── 04_Docking_interactive_conf.ipynb │ │ ├── 05_Parameter_tests.ipynb │ │ ├── Basic_CLI_useage │ │ │ ├── gold.conf │ │ │ └── run.ps1 │ │ ├── Protein-ligand_descriptors.txt │ │ ├── ReadMe.txt │ │ └── input_files │ │ │ ├── ReadMe.txt │ │ │ ├── gold.conf │ │ │ ├── input.csv │ │ │ └── target │ │ │ ├── ligand.mol2 │ │ │ └── protein.mol2 │ ├── 09_Covalent_Docking │ │ ├── 01_Ligand_Preparation_for_Covalent_Docking.ipynb │ │ ├── 02a_Covalent_Complexes-atom.ipynb │ │ ├── 02b_Covalent_Complexes-substructure.ipynb │ │ ├── 10_Prochiral_Michael_Acceptors.ipynb │ │ ├── ReadMe.txt │ │ ├── cleanup.ps1 │ │ ├── gold_atom.conf │ │ ├── gold_substructure.conf │ │ ├── input.csv │ │ └── substructure.mol2 │ ├── 10_Editing_molecules │ │ └── Editing_molecules.ipynb │ ├── 11_Working_With_Proteins │ │ ├── 11_Working_With_Proteins.ipynb │ │ ├── 3kk6.cif │ │ ├── 3kk6.pdb │ │ └── tiny.pdb │ ├── 12_Ensemble_docking │ │ └── ensemble_docking.ipynb │ └── ReadMe.md ├── README.md └── ccdc_notebook_utilities │ ├── README.md │ ├── __init__.py │ ├── create_logger.py │ └── run_hermes.py └── scripts ├── ReadMe.md ├── concat_mol2 ├── ReadMe.md └── concat_mol2.py ├── conformer_demo ├── AZD9291.mol2 ├── conformer_demo.py └── description.md ├── create_castep_input ├── ReadMe.md ├── assets │ ├── add_script_location.png │ ├── file_output.png │ └── select_script.png └── create_castep_input.py ├── create_gaussian_input ├── ReadMe.md └── create_gaussian_input.py ├── find_binding_conformation ├── ReadMe.md ├── find_binding_conformation.py └── pdb_example.txt ├── gold_multi ├── .gitignore ├── ReadMe.md ├── gold.conf ├── gold_multi.py ├── input.sdf └── target │ ├── ligand.mol2 │ └── protein.mol2 ├── hydrogen_bond_propensity ├── ReadMe.md ├── assets │ ├── HXACAN_Report_Screenshot_1.png │ ├── HXACAN_Report_Screenshot_2.png │ ├── HXACAN_Report_Screenshot_3.png │ └── HXACAN_Report_Screenshot_4.png ├── hydrogen_bond_propensity_report.docx └── hydrogen_bond_propensity_report.py ├── mof_solvent_removal_2017_chem_mater_publication ├── Command_prompt_MOF_solvent_removal.py ├── Mercury_MOF_solvent_removal.py └── ReadMe.md ├── multi_component_hydrogen_bond_propensity ├── ReadMe.md ├── mol2smiles.py ├── multi_component_hydrogen_bond_propensity_report.docx ├── multi_component_hydrogen_bond_propensity_report.py └── multi_component_pair_hbp_report.docx ├── new_script_readme_template ├── ReadMe.md └── script_example.py ├── november_2023_morphology_webinar ├── ReadMe.md ├── calculate_morphologies_tabulate_output.py ├── exploring_surface_properties.py └── morphology_plot.py ├── packing_similarity_dendrogram ├── ReadMe.md ├── assets │ ├── dendogram_figure_1.png │ ├── dendogram_figure_2.png │ └── dendogram_figure_3.png └── packing_similarity_dendogram.py ├── particle_rugosity ├── ReadMe.md └── particle_rugosity.py ├── refcodes_with_properties ├── ReadMe.md ├── entry_property_calculator.py ├── example_control_file.txt ├── more_elaborate_control.txt ├── refcodes_with_properties.py └── test_entry_property_calculator.py ├── show_semiconductor_properties ├── ReadMe.md ├── hist_data.json ├── semiconductor_template.html ├── semiconductors.gcd └── show_semiconductor_properties.py ├── surface_charge ├── ReadMe.md ├── assets │ ├── adding_location.png │ ├── csd-python-api-logo.png │ ├── example_input.png │ ├── example_output_hxacan28.png │ └── selecting_script.png ├── surface_charge.py └── surface_charge_calculator.py 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