smiles extra and decorator for rdkit functions

README.md

@@ -97,6 +97,11 @@ be compatible with:
 pip install "alphabase[stable]"
 ```
 
+If you want to use strucutural information of aminoacids, you can install the dependencies by including the `smiles` extra:
+``` bash
+pip install "alphabase[smiles]"
+```
+
 NOTE: You might need to run `pip install -U pip` before installing
 AlphaBase like this. Also note the double quotes `"`.
 

alphabase/__init__.py

@@ -40,4 +40,5 @@
 }
 __extra_requirements__ = {
     "development": "extra_requirements/development.txt",
+    "smiles": "extra_requirements/smiles.txt",
 }

alphabase/peptide/smiles.py

@@ -0,0 +1,25 @@
+import functools
+
+
+def requires_rdkit(func):
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        try:
+            from rdkit import Chem  # noqa
+        except ImportError:
+            raise ImportError(
+                f"RDKit is required for the function '{func.__name__}'. "
+                "Please install it with 'pip install alphabase[smiles]'"
+            )
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
+@requires_rdkit
+def rdkit_dependent_function(smiles):
+    from rdkit import Chem
+
+    # Your implementation using RDKit
+    mol = Chem.MolFromSmiles(smiles)
+    return mol

extra_requirements/smiles.txt

@@ -0,0 +1 @@
+rdkit>=2024.3.3