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")