Update app.py

app.py

@@ -1,7 +1,26 @@
 import streamlit as st
+import py3Dmol
 from rdkit import Chem
 from rdkit.Chem import Draw
 from PIL import Image
+from rdkit import Chem
+from rdkit.Chem import AllChem
+
+def smi2conf(smiles):
+    '''Convert SMILES to rdkit.Mol with 3D coordinates'''
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is not None:
+        mol = Chem.AddHs(mol)
+        AllChem.EmbedMolecule(mol)
+        AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
+        return mol
+    else:
+        return None
+
+smi = 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br'
+conf = smi2conf(smi)
+viewer = MolTo3DView(conf, size=(600, 300), style='sphere')
+viewer.show()
 
 compound_smiles = 'c1cc(C(=O)O)c(OC(=O)C)cc1'
 m = Chem.MolFromSmiles(compound_smiles)
@@ -20,3 +39,83 @@ MakeMolecule("Acetic acid", "CC(=O)O")
 MakeMolecule("Cyclohexane", "C1CCCCC1")
 MakeMolecule("Pyridine", "c1cnccc1")
 
+
+def MolTo3DView(mol, size=(300, 300), style="stick", surface=False, opacity=0.5):
+    """Draw molecule in 3D
+    
+    Args:
+    ----
+        mol: rdMol, molecule to show
+        size: tuple(int, int), canvas size
+        style: str, type of drawing molecule
+               style can be 'line', 'stick', 'sphere', 'carton'
+        surface, bool, display SAS
+        opacity, float, opacity of surface, range 0.0-1.0
+    Return:
+    ----
+        viewer: py3Dmol.view, a class for constructing embedded 3Dmol.js views in ipython notebooks.
+    """
+    assert style in ('line', 'stick', 'sphere', 'carton')
+    mblock = Chem.MolToMolBlock(mol)
+    viewer = py3Dmol.view(width=size[0], height=size[1])
+    viewer.addModel(mblock, 'mol')
+    viewer.setStyle({style:{}})
+    if surface:
+        viewer.addSurface(py3Dmol.SAS, {'opacity': opacity})
+    viewer.zoomTo()
+    return viewer
+    
+viewer = MolTo3DView(conf, size=(600, 300), style='sphere')
+viewer.show()
+
+from ipywidgets import interact,fixed,IntSlider
+import ipywidgets
+
+smis = [ 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br',
+    'CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O',
+    'Cc1c(COc2cc(OCc3cccc(c3)C#N)c(CN3C[C@H](O)C[C@H]3C(O)=O)cc2Cl)cccc1-c1ccc2OCCOc2c1',
+    'CCCCC(=O)NCCCCC(=O)NCCCCCC(=O)[O-]',
+    "CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O"]
+    
+confs = [smi2conf(s) for s in smis]
+
+def conf_viewer(idx):
+    mol = confs[idx]
+    return MolTo3DView(mol).show()
+
+interact(conf_viewer, idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1))
+
+from ipywidgets import interact,fixed,IntSlider
+import ipywidgets
+
+smis = [ 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br',
+    'CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O',
+    'Cc1c(COc2cc(OCc3cccc(c3)C#N)c(CN3C[C@H](O)C[C@H]3C(O)=O)cc2Cl)cccc1-c1ccc2OCCOc2c1',
+    'CCCCC(=O)NCCCCC(=O)NCCCCCC(=O)[O-]',
+    "CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O"]
+
+confs = [smi2conf(s) for s in smis]
+
+def style_selector(idx, s):
+    conf = confs[idx]
+    return MolTo3DView(conf, style=s).show()
+
+interact(style_selector, 
+         idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1),
+         s=ipywidgets.Dropdown(
+            options=['line', 'stick', 'sphere'],
+            value='line',
+            description='Style:'))
+            
+            
+            
+@interact
+def smi2viewer(smi='CC=O'):
+    try:
+        conf = smi2conf(smi)
+        return MolTo3DView(conf).show()
+    except:
+        return None
+        
+        
+