├── .env.example ├── .github └── workflows │ ├── build.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .secrets.baseline ├── LICENSE ├── README.md ├── dev-requirements.txt ├── environment.yaml ├── mdcrow ├── __init__.py ├── agent │ ├── __init__.py │ ├── agent.py │ ├── memory.py │ └── prompt.py ├── tools │ ├── __init__.py │ ├── base_tools │ │ ├── __init__.py │ │ ├── analysis_tools │ │ │ ├── __init__.py │ │ │ ├── bond_angles_dihedrals_tool.py │ │ │ ├── distance_tools.py │ │ │ ├── hydrogen_bonding_tools.py │ │ │ ├── inertia.py │ │ │ ├── pca_tools.py │ │ │ ├── plot_tools.py │ │ │ ├── ppi_tools.py │ │ │ ├── rdf_tool.py │ │ │ ├── rgy.py │ │ │ ├── rmsd_tools.py │ │ │ ├── salt_bridge_tool.py │ │ │ ├── sasa.py │ │ │ ├── secondary_structure.py │ │ │ └── vis_tools.py │ │ ├── preprocess_tools │ │ │ ├── __init__.py │ │ │ ├── clean_tools.py │ │ │ ├── elements.py │ │ │ ├── packing.py │ │ │ ├── pdb_fix.py │ │ │ ├── pdb_get.py │ │ │ └── uniprot.py │ │ ├── simulation_tools │ │ │ ├── __init__.py │ │ │ ├── create_simulation.py │ │ │ └── setup_and_run.py │ │ └── util_tools │ │ │ ├── __init__.py │ │ │ ├── registry_tools.py │ │ │ └── search_tools.py │ └── maketools.py ├── utils │ ├── __init__.py │ ├── data_handling.py │ ├── makellm.py │ ├── path_registry.py │ └── set_ckpt.py └── version.py ├── notebooks ├── chat_examples.ipynb ├── experiments │ ├── Robustness │ │ ├── claude-3-5-sonnet-20240620 │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ ├── claude-3-5-sonnet-20241022 │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ ├── claude-3-opus │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ ├── gpt-4o-2024-08-06 │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ ├── llama-v3p1-405b-instruct │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ ├── robustness_prompts.py │ │ └── with_claude_pressure_fix │ │ │ ├── claude-3-5-sonnet-20240620 │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ │ ├── claude-3-5-sonnet-20241022 │ │ │ ├── prompt1.ipynb │ │ │ ├── prompt10.ipynb │ │ │ ├── prompt2.ipynb │ │ │ ├── prompt3.ipynb │ │ │ ├── prompt4.ipynb │ │ │ ├── prompt5.ipynb │ │ │ ├── prompt6.ipynb │ │ │ ├── prompt7.ipynb │ │ │ ├── prompt8.ipynb │ │ │ └── prompt9.ipynb │ │ │ └── claude-3-opus │ │ │ └── prompt7.ipynb │ ├── compare_python_code │ │ ├── llm_only │ │ │ ├── exp_1.ipynb │ │ │ ├── exp_10.ipynb │ │ │ ├── exp_11.ipynb │ │ │ ├── exp_12.ipynb │ │ │ ├── exp_13.ipynb │ │ │ ├── exp_13_test_code.ipynb │ │ │ ├── exp_14.ipynb │ │ │ ├── exp_15.ipynb │ │ │ ├── exp_16.ipynb │ │ │ ├── exp_17.ipynb │ │ │ ├── exp_18.ipynb │ │ │ ├── exp_19.ipynb │ │ │ ├── exp_2.ipynb │ │ │ ├── exp_20.ipynb │ │ │ ├── exp_21.ipynb │ │ │ ├── exp_22.ipynb │ │ │ ├── exp_23.ipynb │ │ │ ├── exp_24.ipynb │ │ │ ├── exp_25.ipynb │ │ │ ├── exp_3.ipynb │ │ │ ├── exp_4.ipynb │ │ │ ├── exp_5.ipynb │ │ │ ├── exp_5_test_code.ipynb │ │ │ ├── exp_6.ipynb │ │ │ ├── exp_7.ipynb │ │ │ ├── exp_8.ipynb │ │ │ └── exp_9.ipynb │ │ └── react_agent │ │ │ ├── exp_1.ipynb │ │ │ ├── exp_10.ipynb │ │ │ ├── exp_11.ipynb │ │ │ ├── exp_12.ipynb │ │ │ ├── exp_13.ipynb │ │ │ ├── exp_14.ipynb │ │ │ ├── exp_15.ipynb │ │ │ ├── exp_16.ipynb │ │ │ ├── exp_17.ipynb │ │ │ ├── exp_18.ipynb │ │ │ ├── exp_19.ipynb │ │ │ ├── exp_2.ipynb │ │ │ ├── exp_20.ipynb │ │ │ ├── exp_21.ipynb │ │ │ ├── exp_22.ipynb │ │ │ ├── exp_23.ipynb │ │ │ ├── exp_24.ipynb │ │ │ ├── exp_25.ipynb │ │ │ ├── exp_3.ipynb │ │ │ ├── exp_4.ipynb │ │ │ ├── exp_5.ipynb │ │ │ ├── exp_6.ipynb │ │ │ ├── exp_7.ipynb │ │ │ ├── exp_8.ipynb │ │ │ └── exp_9.ipynb │ └── main_experiments │ │ ├── claude-3-5-sonnet │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_11.ipynb │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_17.ipynb │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_21.ipynb │ │ ├── exp_22.ipynb │ │ ├── exp_23.ipynb │ │ ├── exp_24.ipynb │ │ ├── exp_25.ipynb │ │ ├── exp_3.ipynb │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_6.ipynb │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ └── exp_9.ipynb │ │ ├── claude-3-opus │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_11.ipynb │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_17.ipynb │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_21.ipynb │ │ ├── exp_22.ipynb │ │ ├── exp_23.ipynb │ │ ├── exp_24.ipynb │ │ ├── exp_25.ipynb │ │ ├── exp_3.ipynb │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_6.ipynb │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ └── exp_9.ipynb │ │ ├── gpt-3.5-turbo-0125 │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_10_gpt-35-turbo-0125.out │ │ ├── exp_11.ipynb │ │ ├── exp_11_gpt-35-turbo-0125.out │ │ ├── exp_12.ipynb │ │ ├── exp_12_gpt-35-turbo-0125.out │ │ ├── exp_13.ipynb │ │ ├── exp_13_gpt-35-turbo-0125.out │ │ ├── exp_14.ipynb │ │ ├── exp_14_gpt-35-turbo-0125.out │ │ ├── exp_15.ipynb │ │ ├── exp_15_gpt-35-turbo-0125.out │ │ ├── exp_16.ipynb │ │ ├── exp_16_gpt-35-turbo-0125.out │ │ ├── exp_17.ipynb │ │ ├── exp_17_gpt-35-turbo-0125.out │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_19_gpt-35-turbo-0125.out │ │ ├── exp_1_gpt-35-turbo-0125.out │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_20_gpt-35-turbo-0125.out │ │ ├── exp_21.ipynb │ │ ├── exp_21_gpt-35-turbo-0125.out │ │ ├── exp_22.ipynb │ │ ├── exp_22_gpt-35-turbo-0125.out │ │ ├── exp_23.ipynb │ │ ├── exp_23_gpt-35-turbo-0125.out │ │ ├── exp_24.ipynb │ │ ├── exp_24_gpt-35-turbo-0125.out │ │ ├── exp_25.ipynb │ │ ├── exp_2_gpt-35-turbo-0125.out │ │ ├── exp_3.ipynb │ │ ├── exp_3_gpt-35-turbo-0125.out │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_5_gpt-35-turbo-0125.out │ │ ├── exp_6.ipynb │ │ ├── exp_6_gpt-35-turbo-0125.out │ │ ├── exp_7.ipynb │ │ ├── exp_7_gpt-35-turbo-0125.out │ │ ├── exp_8.ipynb │ │ ├── exp_8_gpt-35-turbo-0125.out │ │ ├── exp_9.ipynb │ │ └── exp_9_gpt-35-turbo-0125.out │ │ ├── gpt-4-1106-preview │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_10_gpt41106preview.out │ │ ├── exp_11.ipynb │ │ ├── exp_11_gpt41106preview.out │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_13_gpt41106preview.out │ │ ├── exp_14.ipynb │ │ ├── exp_14_gpt41106preview.out │ │ ├── exp_15.ipynb │ │ ├── exp_15_gpt41106preview.out │ │ ├── exp_16.ipynb │ │ ├── exp_16_gpt41106preview.out │ │ ├── exp_17.ipynb │ │ ├── exp_17_gpt41106preview.out │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_19_gpt41106preview.out │ │ ├── exp_1_gpt41106preview.out │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_20_gpt41106preview.out │ │ ├── exp_21.ipynb │ │ ├── exp_21_gpt41106preview.out │ │ ├── exp_22.ipynb │ │ ├── exp_22_gpt41106preview.out │ │ ├── exp_23.ipynb │ │ ├── exp_23_gpt41106preview.out │ │ ├── exp_24_gpt41106preview.out │ │ ├── exp_25.ipynb │ │ ├── exp_2_gpt41106preview.out │ │ ├── exp_3.ipynb │ │ ├── exp_3_gpt41106preview.out │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_5_gpt41106preview.out │ │ ├── exp_6.ipynb │ │ ├── exp_6_gpt41106preview.out │ │ ├── exp_7.ipynb │ │ ├── exp_7_gpt41106preview.out │ │ ├── exp_8.ipynb │ │ ├── exp_8_gpt41106preview.out │ │ ├── exp_9.ipynb │ │ └── exp_9_gpt41106preview.out │ │ ├── gpt-4-turbo-2024-04-09 │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_11.ipynb │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_16_gpt-4-turbo-2024-04-09.out │ │ ├── exp_17.ipynb │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_21.ipynb │ │ ├── exp_22.ipynb │ │ ├── exp_23.ipynb │ │ ├── exp_23_gpt-4-turbo-2024-04-09.out │ │ ├── exp_24.ipynb │ │ ├── exp_24_gpt-4-turbo-2024-04-09.out │ │ ├── exp_25.ipynb │ │ ├── exp_2_gpt-4-turbo-2024-04-09 1.out │ │ ├── exp_2_gpt-4-turbo-2024-04-09.out │ │ ├── exp_3.ipynb │ │ ├── exp_3_gpt-4-turbo-2024-04-09.out │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_5_gpt-4-turbo-2024-04-09.out │ │ ├── exp_6.ipynb │ │ ├── exp_6_gpt-4-turbo-2024-04-09.out │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ └── exp_9.ipynb │ │ ├── gpt-4o-2024-08-06 │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_10_gpt4o20240806.out │ │ ├── exp_11.ipynb │ │ ├── exp_11_gpt4o20240806.out │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_13_gpt4o20240806.out │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_16_gpt4o20240806.out │ │ ├── exp_17.ipynb │ │ ├── exp_17_gpt4o20240806.out │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_19_gpt4o20240806.out │ │ ├── exp_1_gpt4o20240806.out │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_20_gpt4o20240806.out │ │ ├── exp_21.ipynb │ │ ├── exp_21_gpt4o20240806.out │ │ ├── exp_22.ipynb │ │ ├── exp_22_gpt4o20240806.out │ │ ├── exp_23.ipynb │ │ ├── exp_23_gp4o20240806.out │ │ ├── exp_24.ipynb │ │ ├── exp_24_gpt4o20240806.out │ │ ├── exp_25.ipynb │ │ ├── exp_3.ipynb │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_6.ipynb │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ ├── exp_8_gpt4o20240806.out │ │ ├── exp_9.ipynb │ │ └── exp_9_gpt4o20240806.out │ │ ├── llama-v3p1-405b-instruct │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_11.ipynb │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_17.ipynb │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_21.ipynb │ │ ├── exp_22.ipynb │ │ ├── exp_23.ipynb │ │ ├── exp_24.ipynb │ │ ├── exp_25.ipynb │ │ ├── exp_3.ipynb │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_6.ipynb │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ └── exp_9.ipynb │ │ └── llama-v3p1-70b-instruct │ │ ├── exp_1.ipynb │ │ ├── exp_10.ipynb │ │ ├── exp_11.ipynb │ │ ├── exp_12.ipynb │ │ ├── exp_13.ipynb │ │ ├── exp_14.ipynb │ │ ├── exp_15.ipynb │ │ ├── exp_16.ipynb │ │ ├── exp_17.ipynb │ │ ├── exp_18.ipynb │ │ ├── exp_19.ipynb │ │ ├── exp_2.ipynb │ │ ├── exp_20.ipynb │ │ ├── exp_21.ipynb │ │ ├── exp_22.ipynb │ │ ├── exp_23.ipynb │ │ ├── exp_24.ipynb │ │ ├── exp_25.ipynb │ │ ├── exp_3.ipynb │ │ ├── exp_4.ipynb │ │ ├── exp_5.ipynb │ │ ├── exp_6.ipynb │ │ ├── exp_7.ipynb │ │ ├── exp_8.ipynb │ │ └── exp_9.ipynb ├── lit_search.ipynb ├── mdcrow_extrapolation │ ├── modifying_sims.ipynb │ └── simulated_annealing.ipynb ├── memory_demo.ipynb └── paper_figures │ └── main_plots.ipynb ├── setup.py └── tests ├── 3pqr.cif ├── conftest.py ├── test_analysis ├── test_bond_angles_dihedrals.py ├── test_distance_tools.py ├── test_hydrogen_bonding.py ├── test_inertia.py ├── test_misc.py ├── test_pca_tool.py ├── test_rdftool.py ├── test_rgy_tool.py ├── test_rmsd_ppi.py ├── test_saltbridge.py ├── test_sasa.py └── test_secondary_structure.py ├── test_general_tools ├── test_search_tools.py └── test_util_tools.py ├── test_preprocess ├── test_cleaning.py ├── test_packing.py ├── test_pdb_tools.py └── test_uniprot.py ├── test_sim ├── test_setup.py ├── test_setupandrun.py └── test_write_script.py └── test_utils ├── test_datahandling.py ├── test_memory.py ├── test_pathregistry.py └── test_top_k_tools.py /.env.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ur-whitelab/MDCrow/HEAD/.env.example -------------------------------------------------------------------------------- /.github/workflows/build.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ur-whitelab/MDCrow/HEAD/.github/workflows/build.yml -------------------------------------------------------------------------------- /.github/workflows/tests.yml: -------------------------------------------------------------------------------- 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