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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 | |
| 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 = MolTo3DView(conf, size=(600, 300), style='sphere') | |
| viewer.show() | |
| from ipywidgets import interact,fixed,IntSlider | |
| import ipywidgets | |
| 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 MolTo3DView(mol).show() | |
| interact(conf_viewer, idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1)) | |
| from ipywidgets import interact,fixed,IntSlider | |
| import ipywidgets | |
| 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 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:')) | |
| def smi2viewer(smi='CC=O'): | |
| try: | |
| conf = smi2conf(smi) | |
| return MolTo3DView(conf).show() | |
| except: | |
| return None | |