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 from ipywidgets import interact,fixed,IntSlider import ipywidgets 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 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 def MakeMolecule(name, ingredients): st.write(name) m = Chem.MolFromSmiles(ingredients) im=Draw.MolToImage(m) st.image(im) def conf_viewer(idx): mol = confs[idx] return MolTo3DView(mol).show() @interact def smi2viewer(smi='CC=O'): try: conf = smi2conf(smi) return MolTo3DView(conf).show() except: 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) im=Draw.MolToImage(m) st.image(im) MakeMolecule("Ethanol", "CCO") MakeMolecule("Acetic acid", "CC(=O)O") MakeMolecule("Cyclohexane", "C1CCCCC1") MakeMolecule("Pyridine", "c1cnccc1") viewer = MolTo3DView(conf, size=(600, 300), style='sphere') viewer.show() 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] interact(conf_viewer, idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1)) 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:'))