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import streamlit as st
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 ipywidgets
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
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)
def MakeMolecule(name, ingredients):
st.write(name)
m = Chem.MolFromSmiles(ingredients)
im=Draw.MolToImage(m)
st.image(im)
MakeMolecule("Ethanol", "CCO")
MakeMolecule("Acetic acid", "CC(=O)O")
MakeMolecule("Cyclohexane", "C1CCCCC1")
MakeMolecule("Pyridine", "c1cnccc1")
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
viewer = Chem.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]
def conf_viewer(idx):
mol = confs[idx]
return Chem.MolTo3DView(mol).show()
interact(conf_viewer, idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1))
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]
def style_selector(idx, s):
conf = confs[idx]
return Chem.MolTo3DView(conf, style=s).show()
interact(style_selector,
idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1),
s=ipywidgets.Dropdown(
options=['line', 'stick', 'sphere'],
value='line',
description='Style:'))
@interact
def smi2viewer(smi='CC=O'):
try:
conf = smi2conf(smi)
return Chem.MolTo3DView(conf).show()
except:
return None
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