app.py

import streamlit as st
import ipywidgets
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 streamlit as st
import streamlit.components.v1 as components
import py3Dmol
from rdkit import Chem
from rdkit.Chem import Draw
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

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, ":    ", ingredients)
  m = Chem.MolFromSmiles(ingredients)
  im=Draw.MolToImage(m)
  st.image(im)    

def conf_viewer(idx):
    mol = confs[idx]
    return MolTo3DView(mol).show()

def style_selector(idx, s):
    conf = confs[idx]
    return MolTo3DView(conf, style=s).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)

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]


st.title('⚛️🧬Molecule 3D Modeler🧬⚛️')
def show(smi, style='stick'):
    mol = Chem.MolFromSmiles(smi)
    mol = Chem.AddHs(mol)
    AllChem.EmbedMolecule(mol)
    AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
    mblock = Chem.MolToMolBlock(mol)

    view = py3Dmol.view(width=400, height=400)
    view.addModel(mblock, 'mol')
    view.setStyle({style:{}})
    view.zoomTo()
    view.show()
    view.render()
    t =view.js()
    f = open('viz.html', 'w')
    f.write(t.startjs)
    f.write(t.endjs)
    f.close()

compound_smiles=st.text_input('SMILES please','CCCCC(=O)NCCCCC(=O)NCCCCCC(=O)[O-]')
m = Chem.MolFromSmiles(compound_smiles)

#Draw.MolToFile(m,'mol.png')

show(compound_smiles)
HtmlFile = open("viz.html", 'r', encoding='utf-8')
source_code = HtmlFile.read() 
c1,c2=st.columns(2)
with c1:
  st.write('⚛️🧬Molecule🧬⚛️:')
with c2:
  components.html(source_code, height = 400,width=400)

st.write('Info about SMILES: https://archive.epa.gov/med/med_archive_03/web/html/smiles.html')


MakeMolecule("Ethanol", "CCO")
MakeMolecule("Acetic acid", "CC(=O)O")
MakeMolecule("Cyclohexane", "C1CCCCC1")
MakeMolecule("Pyridine", "c1cnccc1")