plot molecule

Author: korakot

kora/viz/chem.py

@@ -0,0 +1,25 @@
+import os
+os.system('pip install py3Dmol')
+import kora.install.rdkit
+
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import py3Dmol
+
+
+def plot(smiles, size=(200,200), style='stick'):
+    """ 
+    Visualize a molecule from its formula (smiles)
+    Adapted from https://birdlet.github.io/2019/10/02/py3dmol_example 
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    mol = Chem.AddHs(mol)
+    AllChem.EmbedMolecule(mol)
+    AllChem.MMFFOptimizeMolecule(mol)
+    block = Chem.MolToMolBlock(mol)
+
+    viewer = py3Dmol.view(width=size[0], height=size[1])
+    viewer.addModel(block, 'mol')
+    viewer.setStyle({style:{}})
+    viewer.zoomTo()
+    viewer.show()

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="kora", 
-    version="0.6.9",
+    version="0.6.10",
     author="Korakot Chaovavanich",
     author_email="korakot@gmail.com",
     description="Convenient tools for Colab",