SciToolAgent
SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration
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최종 버전 다운로드 (.zip)- profiles_settings.xml
- Project_Default.xml
- .gitignore
- deployment.xml
- misc.xml
- modules.xml
- SciToolAgent.iml
- vcs.xml
- launch.json
- settings.json
- __init__.cpython-39.pyc
- __init__.cpython-39.pyc
- __init__.cpython-39.pyc
- config.cpython-39.pyc
- __init__.py
- config.py
- __init__.cpython-39.pyc
- openai_api.cpython-39.pyc
- __init__.py
- openai_api.py
- __init__.cpython-39.pyc
- extract_tool.cpython-39.pyc
- __init__.py
- extract_answer.py
- extract_tool.py
- __init__.cpython-39.pyc
- prompt_templates.cpython-39.pyc
- tool_plan_executor.cpython-39.pyc
- __init__.py
- prompt_templates.py
- tool_plan_executor.py
- __init__.cpython-39.pyc
- tool_runner.cpython-39.pyc
- __init__.cpython-39.pyc
- toxicity_checker.cpython-39.pyc
- utils.cpython-39.pyc
- __init__.py
- toxicity_checker.py
- utils.py
- __init__.py
- tool_runner.py
- __init__.py
- README.md
- tool_example.xlsx
- toxin_compound.csv
- toxin_protein.csv
- overview.png
- result.png
- default__vector_store.json
- docstore.json
- graph_store.json
- image__vector_store.json
- index_store.json
- example_standard_answer.jsonl
- example_standard_toolpath.jsonl
- level1_correct_answer.jsonl
- level1_question.jsonl
- level2_correct_answer.jsonl
- level2_question.jsonl
- eval_accuracy.py
- eval_tool_path.py
- README.md
- __init__.cpython-39.pyc
- custom_kg_retrievers.cpython-39.pyc
- retrieve_tool_info.cpython-39.pyc
- utils.cpython-39.pyc
- __init__.py
- custom_kg_retrievers.py
- generate_kg_index.py
- retrieve_tool_info.py
- utils.py
- __init__.cpython-39.pyc
- test_run_SciToolAgent.cpython-39-pytest-8.3.3.pyc
- __init__.py
- test_embedding.py
- test_openai.py
- test_run_SciToolAgent.py
- alpha_protein.pdb
- IJCAI_2023__Graph_Sampling_based_Meta_Learning_for_Molecular_Property_Prediction.pdf
- Knowledge graph‐enhanced molecular contrastive learning with functional prompt.pdf
- 3cc49684h3_av.txt
- 3cc49684h3_pd.txt
- 3cc49684h3_pov.txt
- 3cc49684h3_sa.txt
- HKUST-1_av.txt
- HKUST-1_pd.txt
- HKUST-1_pov.txt
- HKUST-1_sa.txt
- KAJZIH_freeONLY_av.txt
- KAJZIH_freeONLY_pd.txt
- KAJZIH_freeONLY_pov.txt
- KAJZIH_freeONLY_sa.txt
- LASYOU_av.txt
- LASYOU_pd.txt
- LASYOU_pov.txt
- LASYOU_sa.txt
- LISZOE_av.txt
- LISZOE_pd.txt
- LISZOE_pov.txt
- LISZOE_sa.txt
- mof-5_cellopt_av.txt
- mof-5_cellopt_pd.txt
- mof-5_cellopt_pov.txt
- mof-5_cellopt_sa.txt
- RSM3434_av.txt
- RSM3434_pd.txt
- RSM3434_pov.txt
- RSM3434_sa.txt
- RUSWOT_av.txt
- RUSWOT_clean_av.txt
- RUSWOT_clean_pd.txt
- RUSWOT_clean_pov.txt
- RUSWOT_clean_sa.txt
- RUSWOT_pd.txt
- RUSWOT_pov.txt
- RUSWOT_sa.txt
- TBAPy_Ti_Andres_av.txt
- TBAPy_Ti_Andres_pd.txt
- TBAPy_Ti_Andres_pov.txt
- TBAPy_Ti_Andres_sa.txt
- ambiguous.txt
- HKUST-1_connection_indices_linker_0.txt
- HKUST-1_connection_indices_linker_1.txt
- HKUST-1_connection_indices_linker_2.txt
- HKUST-1_connection_indices_linker_3.txt
- HKUST-1_connection_indices_linker_4.txt
- HKUST-1_connection_indices_linker_5.txt
- HKUST-1_connection_indices_linker_6.txt
- HKUST-1_connection_indices_linker_7.txt
- HKUST-1_linker_0.net
- HKUST-1_linker_0.xyz
- HKUST-1_linker_1.net
- HKUST-1_linker_1.xyz
- HKUST-1_linker_2.net
- HKUST-1_linker_2.xyz
- HKUST-1_linker_3.net
- HKUST-1_linker_3.xyz
- HKUST-1_linker_4.net
- HKUST-1_linker_4.xyz
- HKUST-1_linker_5.net
- HKUST-1_linker_5.xyz
- HKUST-1_linker_6.net
- HKUST-1_linker_6.xyz
- HKUST-1_linker_7.net
- HKUST-1_linker_7.xyz
- hMOF-3000336-(id_58248)_connection_indices_linker_0.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_1.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_10.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_11.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_12.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_13.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_14.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_15.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_16.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_17.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_2.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_3.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_4.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_5.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_6.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_7.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_8.txt
- hMOF-3000336-(id_58248)_connection_indices_linker_9.txt
- hMOF-3000336-(id_58248)_linker_0.net
- hMOF-3000336-(id_58248)_linker_0.xyz
- hMOF-3000336-(id_58248)_linker_1.net
- hMOF-3000336-(id_58248)_linker_1.xyz
- hMOF-3000336-(id_58248)_linker_10.net
- hMOF-3000336-(id_58248)_linker_10.xyz
- hMOF-3000336-(id_58248)_linker_11.net
- hMOF-3000336-(id_58248)_linker_11.xyz
- hMOF-3000336-(id_58248)_linker_12.net
- hMOF-3000336-(id_58248)_linker_12.xyz
- hMOF-3000336-(id_58248)_linker_13.net
- hMOF-3000336-(id_58248)_linker_13.xyz
- hMOF-3000336-(id_58248)_linker_14.net
- hMOF-3000336-(id_58248)_linker_14.xyz
- hMOF-3000336-(id_58248)_linker_15.net
- hMOF-3000336-(id_58248)_linker_15.xyz
- hMOF-3000336-(id_58248)_linker_16.net
- hMOF-3000336-(id_58248)_linker_16.xyz
- hMOF-3000336-(id_58248)_linker_17.net
- hMOF-3000336-(id_58248)_linker_17.xyz
- hMOF-3000336-(id_58248)_linker_2.net
- hMOF-3000336-(id_58248)_linker_2.xyz
- hMOF-3000336-(id_58248)_linker_3.net
- hMOF-3000336-(id_58248)_linker_3.xyz
- hMOF-3000336-(id_58248)_linker_4.net
- hMOF-3000336-(id_58248)_linker_4.xyz
- hMOF-3000336-(id_58248)_linker_5.net
- hMOF-3000336-(id_58248)_linker_5.xyz
- hMOF-3000336-(id_58248)_linker_6.net
- hMOF-3000336-(id_58248)_linker_6.xyz
- hMOF-3000336-(id_58248)_linker_7.net
- hMOF-3000336-(id_58248)_linker_7.xyz
- hMOF-3000336-(id_58248)_linker_8.net
- hMOF-3000336-(id_58248)_linker_8.xyz
- hMOF-3000336-(id_58248)_linker_9.net
- hMOF-3000336-(id_58248)_linker_9.xyz
- hMOF-5030024-(id_89850)_connection_indices_linker_0.txt
- hMOF-5030024-(id_89850)_connection_indices_linker_1.txt
- hMOF-5030024-(id_89850)_connection_indices_linker_2.txt
- hMOF-5030024-(id_89850)_linker_0.net
- hMOF-5030024-(id_89850)_linker_0.xyz
- hMOF-5030024-(id_89850)_linker_1.net
- hMOF-5030024-(id_89850)_linker_1.xyz
- hMOF-5030024-(id_89850)_linker_2.net
- hMOF-5030024-(id_89850)_linker_2.xyz
- KAJZIH_freeONLY_connection_indices_linker_0.txt
- KAJZIH_freeONLY_connection_indices_linker_1.txt
- KAJZIH_freeONLY_connection_indices_linker_2.txt
- KAJZIH_freeONLY_connection_indices_linker_3.txt
- KAJZIH_freeONLY_connection_indices_linker_4.txt
- KAJZIH_freeONLY_connection_indices_linker_5.txt
- KAJZIH_freeONLY_connection_indices_linker_6.txt
- KAJZIH_freeONLY_connection_indices_linker_7.txt
- KAJZIH_freeONLY_linker_0.net
- KAJZIH_freeONLY_linker_0.xyz
- KAJZIH_freeONLY_linker_1.net
- KAJZIH_freeONLY_linker_1.xyz
- KAJZIH_freeONLY_linker_2.net
- KAJZIH_freeONLY_linker_2.xyz
- KAJZIH_freeONLY_linker_3.net
- KAJZIH_freeONLY_linker_3.xyz
- KAJZIH_freeONLY_linker_4.net
- KAJZIH_freeONLY_linker_4.xyz
- KAJZIH_freeONLY_linker_5.net
- KAJZIH_freeONLY_linker_5.xyz
- KAJZIH_freeONLY_linker_6.net
- KAJZIH_freeONLY_linker_6.xyz
- KAJZIH_freeONLY_linker_7.net
- KAJZIH_freeONLY_linker_7.xyz
- LASYOU_connection_indices_linker_0.txt
- LASYOU_connection_indices_linker_1.txt
- LASYOU_connection_indices_linker_2.txt
- LASYOU_linker_0.net
- LASYOU_linker_0.xyz
- LASYOU_linker_1.net
- LASYOU_linker_1.xyz
- LASYOU_linker_2.net
- LASYOU_linker_2.xyz
- mof-5_cellopt_connection_indices_linker_0.txt
- mof-5_cellopt_connection_indices_linker_1.txt
- mof-5_cellopt_connection_indices_linker_2.txt
- mof-5_cellopt_connection_indices_linker_3.txt
- mof-5_cellopt_connection_indices_linker_4.txt
- mof-5_cellopt_connection_indices_linker_5.txt
- mof-5_cellopt_linker_0.net
- mof-5_cellopt_linker_0.xyz
- mof-5_cellopt_linker_1.net
- mof-5_cellopt_linker_1.xyz
- mof-5_cellopt_linker_2.net
- mof-5_cellopt_linker_2.xyz
- mof-5_cellopt_linker_3.net
- mof-5_cellopt_linker_3.xyz
- mof-5_cellopt_linker_4.net
- mof-5_cellopt_linker_4.xyz
- mof-5_cellopt_linker_5.net
- mof-5_cellopt_linker_5.xyz
- RSM3434_connection_indices_linker_0.txt
- RSM3434_connection_indices_linker_1.txt
- RSM3434_connection_indices_linker_2.txt
- RSM3434_connection_indices_linker_3.txt
- RSM3434_linker_0.net
- RSM3434_linker_0.xyz
- RSM3434_linker_1.net
- RSM3434_linker_1.xyz
- RSM3434_linker_2.net
- RSM3434_linker_2.xyz
- RSM3434_linker_3.net
- RSM3434_linker_3.xyz
- RUSWOT_clean_connection_indices_linker_0.txt
- RUSWOT_clean_connection_indices_linker_1.txt
- RUSWOT_clean_connection_indices_linker_2.txt
- RUSWOT_clean_linker_0.net
- RUSWOT_clean_linker_0.xyz
- RUSWOT_clean_linker_1.net
- RUSWOT_clean_linker_1.xyz
- RUSWOT_clean_linker_2.net
- RUSWOT_clean_linker_2.xyz
- RUSWOT_connection_indices_linker_0.txt
- RUSWOT_connection_indices_linker_1.txt
- RUSWOT_connection_indices_linker_2.txt
- RUSWOT_linker_0.net
- RUSWOT_linker_0.xyz
- RUSWOT_linker_1.net
- RUSWOT_linker_1.xyz
- RUSWOT_linker_2.net
- RUSWOT_linker_2.xyz
- short_ligands.txt
- TBAPy_Ti_Andres_connection_indices_linker_0.txt
- TBAPy_Ti_Andres_connection_indices_linker_1.txt
- TBAPy_Ti_Andres_connection_indices_linker_2.txt
- TBAPy_Ti_Andres_connection_indices_linker_3.txt
- TBAPy_Ti_Andres_linker_0.net
- TBAPy_Ti_Andres_linker_0.xyz
- TBAPy_Ti_Andres_linker_1.net
- TBAPy_Ti_Andres_linker_1.xyz
- TBAPy_Ti_Andres_linker_2.net
- TBAPy_Ti_Andres_linker_2.xyz
- TBAPy_Ti_Andres_linker_3.net
- TBAPy_Ti_Andres_linker_3.xyz
- uneven.txt
- HKUST-1.log
- hMOF-3000336-(id_58248).log
- hMOF-5030024-(id_89850).log
- KAJZIH_freeONLY.log
- LASYOU.log
- mof-5_cellopt.log
- RSM3434.log
- RUSWOT.log
- RUSWOT_clean.log
- TBAPy_Ti_Andres.log
- c3cc49684h3.cif
- HKUST-1.cif
- hMOF-3000336-(id_58248).cif
- hMOF-5030024-(id_89850).cif
- KAJZIH_freeONLY.cif
- LASYOU.cif
- LISZOE.cif
- mof-5_cellopt.cif
- RSM3434.cif
- RUSWOT.cif
- RUSWOT_clean.cif
- TBAPy_Ti_Andres.cif
- HKUST-1_connection_indices_sbu_0.txt
- HKUST-1_connection_indices_sbu_1.txt
- HKUST-1_connection_indices_sbu_2.txt
- HKUST-1_connection_indices_sbu_3.txt
- HKUST-1_connection_indices_sbu_4.txt
- HKUST-1_connection_indices_sbu_5.txt
- HKUST-1_sbu_0.net
- HKUST-1_sbu_0.xyz
- HKUST-1_sbu_1.net
- HKUST-1_sbu_1.xyz
- HKUST-1_sbu_2.net
- HKUST-1_sbu_2.xyz
- HKUST-1_sbu_3.net
- HKUST-1_sbu_3.xyz
- HKUST-1_sbu_4.net
- HKUST-1_sbu_4.xyz
- HKUST-1_sbu_5.net
- HKUST-1_sbu_5.xyz
- hMOF-3000336-(id_58248)_connection_indices_sbu_0.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_1.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_2.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_3.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_4.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_5.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_6.txt
- hMOF-3000336-(id_58248)_connection_indices_sbu_7.txt
- hMOF-3000336-(id_58248)_sbu_0.net
- hMOF-3000336-(id_58248)_sbu_0.xyz
- hMOF-3000336-(id_58248)_sbu_1.net
- hMOF-3000336-(id_58248)_sbu_1.xyz
- hMOF-3000336-(id_58248)_sbu_2.net
- hMOF-3000336-(id_58248)_sbu_2.xyz
- hMOF-3000336-(id_58248)_sbu_3.net
- hMOF-3000336-(id_58248)_sbu_3.xyz
- hMOF-3000336-(id_58248)_sbu_4.net
- hMOF-3000336-(id_58248)_sbu_4.xyz
- hMOF-3000336-(id_58248)_sbu_5.net
- hMOF-3000336-(id_58248)_sbu_5.xyz
- hMOF-3000336-(id_58248)_sbu_6.net
- hMOF-3000336-(id_58248)_sbu_6.xyz
- hMOF-3000336-(id_58248)_sbu_7.net
- hMOF-3000336-(id_58248)_sbu_7.xyz
- hMOF-5030024-(id_89850)_connection_indices_sbu_0.txt
- hMOF-5030024-(id_89850)_sbu_0.net
- hMOF-5030024-(id_89850)_sbu_0.xyz
- KAJZIH_freeONLY_connection_indices_sbu_0.txt
- KAJZIH_freeONLY_connection_indices_sbu_1.txt
- KAJZIH_freeONLY_connection_indices_sbu_2.txt
- KAJZIH_freeONLY_connection_indices_sbu_3.txt
- KAJZIH_freeONLY_connection_indices_sbu_4.txt
- KAJZIH_freeONLY_connection_indices_sbu_5.txt
- KAJZIH_freeONLY_sbu_0.net
- KAJZIH_freeONLY_sbu_0.xyz
- KAJZIH_freeONLY_sbu_1.net
- KAJZIH_freeONLY_sbu_1.xyz
- KAJZIH_freeONLY_sbu_2.net
- KAJZIH_freeONLY_sbu_2.xyz
- KAJZIH_freeONLY_sbu_3.net
- KAJZIH_freeONLY_sbu_3.xyz
- KAJZIH_freeONLY_sbu_4.net
- KAJZIH_freeONLY_sbu_4.xyz
- KAJZIH_freeONLY_sbu_5.net
- KAJZIH_freeONLY_sbu_5.xyz
- LASYOU_connection_indices_sbu_0.txt
- LASYOU_connection_indices_sbu_1.txt
- LASYOU_connection_indices_sbu_2.txt
- LASYOU_sbu_0.net
- LASYOU_sbu_0.xyz
- LASYOU_sbu_1.net
- LASYOU_sbu_1.xyz
- LASYOU_sbu_2.net
- LASYOU_sbu_2.xyz
- mof-5_cellopt_connection_indices_sbu_0.txt
- mof-5_cellopt_connection_indices_sbu_1.txt
- mof-5_cellopt_sbu_0.net
- mof-5_cellopt_sbu_0.xyz
- mof-5_cellopt_sbu_1.net
- mof-5_cellopt_sbu_1.xyz
- RSM3434_connection_indices_sbu_0.txt
- RSM3434_connection_indices_sbu_1.txt
- RSM3434_sbu_0.net
- RSM3434_sbu_0.xyz
- RSM3434_sbu_1.net
- RSM3434_sbu_1.xyz
- RUSWOT_clean_connection_indices_sbu_0.txt
- RUSWOT_clean_sbu_0.net
- RUSWOT_clean_sbu_0.xyz
- RUSWOT_connection_indices_sbu_0.txt
- RUSWOT_sbu_0.net
- RUSWOT_sbu_0.xyz
- TBAPy_Ti_Andres_connection_indices_sbu_0.txt
- TBAPy_Ti_Andres_connection_indices_sbu_1.txt
- TBAPy_Ti_Andres_sbu_0.net
- TBAPy_Ti_Andres_sbu_0.xyz
- TBAPy_Ti_Andres_sbu_1.net
- TBAPy_Ti_Andres_sbu_1.xyz
- c3cc49684h3.net
- c3cc49684h3.xyz
- HKUST-1.net
- HKUST-1.xyz
- hMOF-3000336-(id_58248).net
- hMOF-3000336-(id_58248).xyz
- hMOF-5030024-(id_89850).net
- hMOF-5030024-(id_89850).xyz
- KAJZIH_freeONLY.net
- KAJZIH_freeONLY.xyz
- LASYOU.net
- LASYOU.xyz
- LISZOE.net
- LISZOE.xyz
- mof-5_cellopt.net
- mof-5_cellopt.xyz
- RSM3434.net
- RSM3434.xyz
- RUSWOT.net
- RUSWOT.xyz
- RUSWOT_clean.net
- RUSWOT_clean.xyz
- TBAPy_Ti_Andres.net
- TBAPy_Ti_Andres.xyz
- FailedStructures.log
- full_featurization_frame.csv
- lc_descriptors.csv
- linker_descriptors.csv
- sbu_descriptors.csv
- demo_test.csv
- demo_test_electrical_descriptors.csv
- demo_test_Morgan_fingerprints.csv
- demo_test_RDK_fingerprints.csv
- demo_train.csv
- demo_train_electrical_descriptors.csv
- demo_train_Morgan_fingerprints.csv
- demo_train_RDK_fingerprints.csv
- HKUST-1.cif
- LASYOU.cif
- LISZOE.cif
- mof-5_cellopt.cif
- RSM3434.cif
- RUSWOT.cif
- TBAPy_Ti_Andres.cif
- WIHSUD.cif
- alpha_protein.pdb
- beta_protein.pdb
- HKUST-1.cif
- nwchem.nwi
- nwchem.nwo
- __init__.py
- test_biology_tools.py
- test_chemical_tools.py
- test_general_tools.py
- test_material_tools.py
- test_openai.py
- __init__.py
- processFun.py
- utils.py
- __init__.py
- biologyCommon.py
- extensionsTools.py
- ForceGPT.py
- novoproToolsBio.py
- protAgentTools.py
- qizhipeiTools.py
- tool_name_dict.py
- __init__.py
- MLChemTools.py
- novoproToolsChem.py
- rdkitToolsPartOne.py
- rdkitToolsPartThree.py
- rdkitToolsPartTwo.py
- rxn4chem_ncbi.py
- tool_name_dict.py
- utils.py
- __init__.py
- generalCommon.py
- tool_name_dict.py
- __init__.py
- config.ini
- MOF_descriptors.py
- mof_func.py
- prompt.py
- simulation_template.input
- __init__.py
- adsorbStabilityTools copy.py
- adsorbStabilityTools.py
- chatmofTools.py
- extensionsTools.py
- materialCommon.py
- MPtools.py
- tool_name_dict.py
- __init__.py
- common.py
- sendRequest.py
- __init__.py
- tools_dict.py
- .gitignore
- __init__.py
- config.py
- example.env
- main.py
- README.md
- requirements.txt
- run.sh
- struct.md
- tool_runner.py
- .gitattributes
- __init__.py
- app.py
- Cases.ipynb
- example.env
- gitignore
- LICENSE
- README.md
- requirements.txt
- requirements_agent.txt
- struct.md
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/HICAI-ZJU/SciToolAgent
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd SciToolAgent
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. 공식 설치 스크립트
쉬움 추천사전 준비물
- Python 3 pip 명령어를 쓰려면 Python이 필요합니다.
pip install --no-deps -e .
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
3. Python
쉬움사전 준비물
pip install -r requirements.txt
requirements.txt 등에 명시된 파이썬 라이브러리를 설치합니다.
pip install -r requirement_agent.txt
requirements.txt 등에 명시된 파이썬 라이브러리를 설치합니다.
pip install --no-deps -e .
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
// repository documentation
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