├── .github └── workflows │ └── deploy.yml ├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── data ├── chem_wep_smi.csv └── chem_wep_smi_canonicalized.csv ├── pyproject.toml ├── requirements.txt ├── scripts ├── __init__.py ├── generate_tool_envs.py ├── generate_tools_doc.py └── modules_utils.py ├── site ├── .nojekyll ├── archetypes │ └── default.md ├── assets │ ├── img │ │ ├── background.svg │ │ ├── bubble_background.svg │ │ ├── icon_logo.svg │ │ ├── icon_logo_white.svg │ │ ├── icon_text_logo.png │ │ ├── icon_text_logo.svg │ │ ├── osunlp_logo.jpg │ │ └── text_logo.svg │ └── js │ │ └── home.js ├── config │ └── _default │ │ ├── hugo.toml │ │ ├── languages.en.toml │ │ ├── markup.toml │ │ ├── menus.en.toml │ │ ├── module.toml │ │ └── params.toml ├── content │ ├── _index.md │ ├── dev-guide.md │ ├── get-started.md │ ├── quick-config.md │ └── tools │ │ └── _index.md ├── hugo.toml ├── layouts │ ├── partials │ │ ├── extend-footer.html │ │ ├── footer.html │ │ ├── header │ │ │ └── basic.html │ │ ├── home │ │ │ └── custom.html │ │ ├── quick-config │ │ │ └── custom.html │ │ └── recent-articles-demo.html │ ├── quick-config │ │ └── single.html │ ├── shortcodes │ │ └── tools-directory.html │ └── tools │ │ └── list.html └── static │ ├── ChemMCP-video.mp4 │ ├── android-chrome-192x192.png │ ├── android-chrome-512x512.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ └── site.webmanifest ├── src └── chemmcp │ ├── __init__.py │ ├── __main__.py │ ├── _version.py │ ├── tool_utils │ ├── __init__.py │ ├── canonicalization.py │ ├── chemspace.py │ ├── download.py │ ├── llm.py │ ├── names.py │ ├── property_prediction │ │ ├── __init__.py │ │ ├── data │ │ │ └── dict.txt │ │ ├── property_prediction.py │ │ ├── unimol │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ │ ├── __init__.py │ │ │ │ ├── add_2d_conformer_dataset.py │ │ │ │ ├── atom_type_dataset.py │ │ │ │ ├── conformer_sample_dataset.py │ │ │ │ ├── coord_pad_dataset.py │ │ │ │ ├── cropping_dataset.py │ │ │ │ ├── data_utils.py │ │ │ │ ├── distance_dataset.py │ │ │ │ ├── from_str_dataset.py │ │ │ │ ├── key_dataset.py │ │ │ │ ├── lmdb_dataset.py │ │ │ │ ├── mask_points_dataset.py │ │ │ │ ├── normalize_dataset.py │ │ │ │ ├── prepend_and_append_2d_dataset.py │ │ │ │ ├── remove_hydrogen_dataset.py │ │ │ │ └── tta_dataset.py │ │ │ ├── infer.py │ │ │ ├── losses │ │ │ │ ├── __init__.py │ │ │ │ ├── conf_gen.py │ │ │ │ ├── cross_entropy.py │ │ │ │ ├── docking_pose.py │ │ │ │ ├── reg_loss.py │ │ │ │ └── unimol.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── conf_gen.py │ │ │ │ ├── docking_pose.py │ │ │ │ ├── transformer_encoder_with_pair.py │ │ │ │ └── unimol.py │ │ │ ├── tasks │ │ │ │ ├── __init__.py │ │ │ │ ├── docking_pose.py │ │ │ │ ├── unimol.py │ │ │ │ ├── unimol_conf_gen.py │ │ │ │ ├── unimol_finetune.py │ │ │ │ ├── unimol_pocket.py │ │ │ │ └── unimol_pocket_finetune.py │ │ │ └── utils │ │ │ │ ├── __init__.py │ │ │ │ ├── conf_gen_cal_metrics.py │ │ │ │ ├── conformer_model.py │ │ │ │ ├── coordinate_model.py │ │ │ │ ├── docking.py │ │ │ │ └── docking_utils.py │ │ └── utils.py │ ├── pubchem.py │ ├── rxn4chem.py │ └── smiles.py │ ├── tools │ ├── __init__.py │ ├── bbbp_predictor.py │ ├── forward_synthesis.py │ ├── functional_groups.py │ ├── hiv_inhibitor_predictor.py │ ├── iupac2smiles.py │ ├── logd_predictor.py │ ├── molecule_atom_count.py │ ├── molecule_captioner.py │ ├── molecule_generator.py │ ├── molecule_modifier.py │ ├── molecule_price.py │ ├── molecule_similarity.py │ ├── molecule_smiles_check.py │ ├── molecule_visualizer.py │ ├── molecule_weight.py │ ├── name2smiles.py │ ├── patent_check.py │ ├── pubchem_search.py │ ├── pubchem_search_qa.py │ ├── python_executor │ │ ├── __init__.py │ │ ├── jupyter_backbone.py │ │ └── python_executor.py │ ├── reaction_smiles_check.py │ ├── retrosynthesis.py │ ├── safety_check.py │ ├── selfies2smiles.py │ ├── side_effect_predictor.py │ ├── smiles2cas.py │ ├── smiles2formula.py │ ├── smiles2iupac.py │ 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