Source code for scopy.ScoVisualize.highlight

# -*- coding: utf-8 -*-

#Created on Mon Sep 16 09:56:26 2019
#@Author: Zhi-Jiang Yang, Dong-Sheng Cao
#@Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China

import re
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
from rdkit import Chem
from rdkit.Chem import rdDepictor

[docs]def HighlightAtoms(mol,highlightAtoms,figsize=[400,200],kekulize=True): """This function is used for showing which part of fragment matched the SMARTS by the id of atoms. :param mol: The molecule to be visualized :type mol: rdkit.Chem.rdchem.Mol :param highlightAtoms: The atoms to be highlighted :type highlightAtoms: tuple :param figsize: The resolution ratio of figure :type figsize: list :return: a figure with highlighted molecule :rtype: IPython.core.display.SVG """ def _revised(svg_words): """ """ svg_words = svg_words.replace( 'stroke-width:2px','stroke-width:1.5px').replace( 'font-size:17px','font-size:15px').replace( 'stroke-linecap:butt','stroke-linecap:square').replace( 'fill:#FFFFFF','fill:none').replace( 'svg:','') return svg_words mc = Chem.Mol(mol.ToBinary()) if kekulize: try: Chem.Kekulize(mc) except: mc = Chem.Mol(mol.ToBinary()) if not mc.GetNumConformers(): rdDepictor.Compute2DCoords(mc) drawer = rdMolDraw2D.MolDraw2DSVG(*figsize) drawer.DrawMolecule(mc,highlightAtoms=highlightAtoms) drawer.FinishDrawing() svg = drawer.GetDrawingText() # It seems that the svg renderer used doesn't quite hit the spec. # Here are some fixes to make it work in the notebook, although I think # the underlying issue needs to be resolved at the generation step return SVG(_revised(svg))
if '__main__' == __name__: mol = Chem.MolFromSmiles('C1=CC=C2C(=O)CC(=O)C2=C1') svg = HighlightAtoms(mol, highlightAtoms=(0, 1, 2, 6, 8,10))