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| 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() | |
| 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") |