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('⚛️🧬Chemical Graph 3D Molecule 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('⚛️🧬Chemical Graph 3D 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')
st.write('Learn about it at Wikipedia: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system')
st.write('Search for any compound on PubChem at National Library of Medicine: https://pubchem.ncbi.nlm.nih.gov/#query=vitamin%20e')


MakeMolecule("COVID-19 Antiviral Remdesivir GS5734", "CCC(CC)COC(=O)[C@H](C)N[P@](=O)(OC[C@@H]1[C@H]([C@H]([C@](O1)(C#N)C2=CC=C3N2N=CN=C3N)O)O)OC4=CC=CC=C4")
MakeMolecule("Ritonavir", "CC(C)C1=NC(=CS1)CN(C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CC2=CC=CC=C2)C[C@@H]([C@H](CC3=CC=CC=C3)NC(=O)OCC4=CN=CS4)O")
MakeMolecule("Chloroquine", "CCN(CC)CCCC(C)NC1=C2C=CC(=CC2=NC=C1)Cl")
MakeMolecule("Fingolimod", "CCCCCCCCC1=CC=C(C=C1)CCC(CO)(CO)N")
MakeMolecule("N4-Hydroxycytidine", "C1=CN(C(=O)N=C1NO)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O")
MakeMolecule("Favipiravir", "C1=C(N=C(C(=O)N1)C(=O)N)F")

MakeMolecule("DNA", "C1C(C(OC1N)COP(=O)(O)OC2CC(OC2COP(=O)(O)OC3CC(OC3CO)N)N)O")
MakeMolecule("Trecovirsen DNA", "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)OC3CC(OC3COP(=S)(O)OC4CC(OC4COP(=S)(O)OC5CC(OC5COP(=S)(O)OC6CC(OC6COP(=S)(O)OC7CC(OC7COP(=S)(O)OC8CC(OC8COP(=S)(O)OC9CC(OC9COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1CO)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=NC2=C1N=C(NC2=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C(N=CN=C21)N)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C(N=CN=C21)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)O")



MakeMolecule("Ibuprofen", "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O")
MakeMolecule("LSD", "CCN(CC)C(=O)[C@H]1CN([C@@H]2CC3=CNC4=CC=CC(=C34)C2=C1)C")

MakeMolecule("Ethanol", "CCO")
MakeMolecule("Acetic acid", "CC(=O)O")
MakeMolecule("Cyclohexane", "C1CCCCC1")
MakeMolecule("Pyridine", "c1cnccc1")
MakeMolecule("Nicotine", "CN1CCC[C@H]1c2cccnc2")


MakeMolecule("Helium", "[3He]")
MakeMolecule("Hydrogen", "[H]")
MakeMolecule("Caffeine", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
MakeMolecule("Sugar", "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@]2([C@H]([C@@H]([C@H](O2)CO)O)O)CO)O)O)O)O")
MakeMolecule("Dinitrogen", "N#N")
MakeMolecule("Methyl isocyanate (MIC)", "CN=C=O")
MakeMolecule("Copper(II) sulfate", "[Cu+2].[O-]S(=O)(=O)[O-]")
MakeMolecule("Flavopereirin (C17H15N2)", "CCc(c1)ccc2[n+]1ccc3c2[nH]c4c3cccc4 CCc1c[n+]2ccc3c4ccccc4[nH]c3c2cc1")
MakeMolecule("Glucose (β-D-glucopyranose) (C6H12O6)", "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)1")
MakeMolecule("Thiamine (vitamin B1, C12H17N4OS+)", "OCCc1c(C)[n+](cs1)Cc2cnc(C)nc2N")
MakeMolecule("cephalostatin-1", "CC(C)(O1)C[C@@H](O)[C@@]1(O2)[C@@H](C)[C@@H]3CC=C4[C@]3(C2)C(=O)C[C@H]5[C@H]4CC[C@@H](C6)[C@]5(C)Cc(n7)c6nc(C[C@@]89(C))c7C[C@@H]8CC[C@@H]%10[C@@H]9C[C@@H](O)[C@@]%11(C)C%10=C[C@H](O%12)[C@]%11(O)[C@H](C)[C@]%12(O%13)[C@H](O)C[C@@]%13(C)CO")
MakeMolecule("Vitamin E", "CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC [C@]1(C)CCc2c(C)c(O)c(C)c(C)c2O1")
MakeMolecule("Vitamin K2", "CC1=C(C(=O)C2=CC=CC=C2C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C")
MakeMolecule("Vitamin K1", "CC(C)CCCC(C)CCCC(C)CCCC(=CCC12C(=O)C3=CC=CC=C3C(=O)C1(O2)C)C")
MakeMolecule("Vitamin D3", "C[C@@H]([C@@H]1C2([C@H](/C(=C/C=C/3\C(=C)CCC(C3)O)/CCC2)CC1)C)CCCC(C)C.C[C@@H]([C@@H]1C2([C@H](/C(=C/C=C/3\C(=C)CCC(C3)O)/CCC2)CC1)C)CCCC(C)C")