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 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 SMILES🧬⚛️:')
with c2:
  components.html(source_code, height = 400,width=400)

# Sedatives, Amphetamines, Opiods?  Also COVID anti-virals, Drugs to Reduce Side Effect via Bond Selection Compound Analysis for Refactoring
    
MakeMolecule("Nicotine", "CN1CCC[C@H]1c2cccnc2")
MakeMolecule("Ethanol", "CCO")

MakeMolecule("Peptides - BPC-157", "CC(C)CC(C(=O)NC(C(C)C)C(=O)O)NC(=O)CNC(=O)C(C)NC(=O)C(CC(=O)O)NC(=O)C(CC(=O)O)NC(=O)C(C)NC(=O)C1CCCN1C(=O)C(CCCCN)NC(=O)CNC(=O)C2CCCN2C(=O)C3CCCN3C(=O)C4CCCN4C(=O)C(CCC(=O)O)NC(=O)CN")

MakeMolecule("Caffeine", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C")

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("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("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")

MakeMolecule("Favipiravir", "C1=C(N=C(C(=O)N1)C(=O)N)F")
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")

st.write('Asthma Inhaler Medications:')
st.write('Option 1: Symbicort @ Budesonide 160 mcg with Formoterol Fumurate Dihydrate 4.5 mcg')
st.write('Option 2: Dulera @ Mometasone 200 mcg with Formoterol Fumurate Dihydrate 5 mcg')
st.write('Symbicort - https://pubchem.ncbi.nlm.nih.gov/#query=Symbicort - Isomeric SMILES: CCCC1O[C@@H]2C[C@H]3[C@@H]4CCC5=CC(=O)C=C[C@@]5([C@H]4[C@H](C[C@@]3([C@@]2(O1)C(=O)CO)C)O)C.C[C@@H](CC1=CC=C(C=C1)OC)NC[C@H](C2=CC(=C(C=C2)O)NC=O)O')
st.write('Dulera - https://pubchem.ncbi.nlm.nih.gov/#query=Dulera - Isomeric SMILES: C[C@@H]1C[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@@]4([C@]3([C@H](C[C@@]2([C@]1(C(=O)CCl)OC(=O)C5=CC=CO5)C)O)Cl)C.C[C@H](CC1=CC=C(C=C1)OC)NC[C@@H](C2=CC(=C(C=C2)O)NC=O)O.C[C@H](CC1=CC=C(C=C1)OC)NC[C@@H](C2=CC(=C(C=C2)O)NC=O)O.C(=C/C(=O)O)\C(=O)O.O.O')


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

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("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")

# Request list:
markDown = '''
# Opioids:
1. Fentanyl (Duragesic).  https://pubchem.ncbi.nlm.nih.gov/#query=Fentanyl - CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3
2. Hydrocodone (Vicodin).  https://pubchem.ncbi.nlm.nih.gov/#query=Hydrocodone - CN1CC[C@]23[C@@H]4[C@H]1CC5=C2C(=C(C=C5)OC)O[C@H]3C(=O)CC4
3. Oxycodone (OxyContin).  https://pubchem.ncbi.nlm.nih.gov/#query=Oxycodone - CN1CC[C@]23[C@@H]4C(=O)CC[C@]2([C@H]1CC5=C3C(=C(C=C5)OC)O4)O
4. Oxymorphone (Darvon).  https://pubchem.ncbi.nlm.nih.gov/#query=Oxymorphone - 
5. Hydromorphone (Dilaudid).  https://pubchem.ncbi.nlm.nih.gov/#query=Hydromorphone
6. Meperidine (Demerol).  https://pubchem.ncbi.nlm.nih.gov/#query=Meperidine
7. Diphenoxylate (Lomotil).  https://pubchem.ncbi.nlm.nih.gov/#query=Diphenoxylate
8. Morphine Sulfate.  https://pubchem.ncbi.nlm.nih.gov/#query=Morphine

# Central Nervous System (CNS) Depressants
1. Pentobarbital sodium (Nembutal).  https://pubchem.ncbi.nlm.nih.gov/#query=Pentobarbital - CCC(C)C1(C(=O)NC(=O)NC1=O)CC
2. Diazepam (Valium).  https://pubchem.ncbi.nlm.nih.gov/#query=Diazepam - CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3  
3. Alprazolam (Xanax).  https://pubchem.ncbi.nlm.nih.gov/#query=Alprazolam - CC1=NN=C2N1C3=C(C=C(C=C3)Cl)C(=NC2)C4=CC=CC=C4
4. Zolpidem Tartrate (Ambien).  https://pubchem.ncbi.nlm.nih.gov/#query=Zolpidem - CC1=CC=C(C=C1)C2=C(N3C=C(C=CC3=N2)C)CC(=O)N(C)C
5. Sertraline (Zoloft).  https://pubchem.ncbi.nlm.nih.gov/#query=Sertraline - CN[C@H]1CC[C@H](C2=CC=CC=C12)C3=CC(=C(C=C3)Cl)Cl

# Stimulants
1. Dextroamphetamine (Dexedrine).  https://pubchem.ncbi.nlm.nih.gov/#query=Dextroamphetamine - C[C@@H](CC1=CC=CC=C1)N  
2. Methylphenidate (Ritalin and Concerta).  https://pubchem.ncbi.nlm.nih.gov/#query=Methylphenidate - COC(=O)C(C1CCCCN1)C2=CC=CC=C2
3. Amphetamines (Adderall).  https://pubchem.ncbi.nlm.nih.gov/#query=Amphetamines - C[C@@H](CC1=CC=CC=C1)N.C[C@@H](CC1=CC=CC=C1)N.C[C@@H](CC1=CC=CC=C1)N.C[C@@H](CC1=CC=CC=C1)N.CC(CC1=CC=CC=C1)N.CC(CC1=CC=CC=C1)N.C([C@@H](C(=O)O)N)C(=O)O.[C@H]([C@@H]([C@@H](C(=O)O)O)O)([C@H](C(=O)O)O)O.OS(=O)(=O)O.OS(=O)(=O)O    

# More at PubChem: https://pubchem.ncbi.nlm.nih.gov/substance/135324815#section=Identity
'''


st.write(markDown)