一般情况更新，文件注释等

pyproject.toml

@@ -0,0 +1,48 @@
+[project]
+name = "SIME"
+version = "1.0.0"
+description = "Structure-Informed Macrolide Expansion with MolE antimicrobial prediction"
+readme = "README.md"
+requires-python = ">=3.7"
+license = {text = "MIT"}
+
+dependencies = [
+    "certifi>=2019.11.28",
+    "Click>=8.0.0",
+    "Flask>=1.1.1",
+    "itsdangerous>=1.1.0",
+    "Jinja2>=2.10.3",
+    "MarkupSafe>=1.1.1",
+    "MolVS>=0.1.1",
+    "numpy>=1.20.0",
+    "olefile>=0.46",
+    "pandas>=1.3.0",
+    "Pillow>=7.0.0",
+    "pycairo>=1.19.0",
+    "python-dateutil>=2.8.1",
+    "pytz>=2019.3",
+    "six>=1.14.0",
+    "Werkzeug>=0.16.0",
+]
+
+[project.optional-dependencies]
+mole = [
+    "torch>=1.9.0",
+    "torch-geometric>=2.0.0",
+    "scipy>=1.7.0",
+    "scikit-learn>=1.0.0",
+    "xgboost>=1.5.0",
+    "rdkit>=2022.03.1",
+    "openpyxl>=3.0.0",
+    "pyyaml>=5.4.0",
+]
+
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.uv]
+dev-dependencies = []
+
+[tool.uv.sources]
+