Create app.py

app.py

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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()
+              
+@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")