def MolToMPL(mol, size=(300, 300), kekulize=True, wedgeBonds=True, imageType=None, fitImage=False,
options=None, **kwargs):
if not mol:
raise ValueError('Null molecule provided')
from rdkit.Chem.Draw.mplCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor = None
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.atomLabelFontSize = 7
options.bondLineWidth = 2
options.coordScale = 1
options.wedgeDashedBonds = wedgeBonds
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
omol = mol
if kekulize:
from rdkit import Chem
mol = Chem.Mol(mol.ToBinary())
Chem.Kekulize(mol)
if not mol.GetNumConformers():
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
drawer.AddMol(mol, **kwargs)
omol._atomPs = drawer.atomPs[mol]
for k, v in omol._atomPs.items():
omol._atomPs[k] = canvas.rescalePt(v)
canvas._figure.set_size_inches(float(size[0]) / 100, float(size[1]) / 100)
return canvas._figure
def draw_molecule_with_highlights(filename, smiles, highlight_atoms):
drawoptions = DrawingOptions()
drawoptions.selectColor = (255.0/255.0, 0.0/255.0, 0.0/255.0) # A nice light blue.
drawoptions.elemDict = {} # Don't color nodes based on their element.
drawoptions.bgColor=None
mol = Chem.MolFromSmiles(smiles)
fig = Draw.MolToImage(mol, highlightAtoms=highlight_atoms, size=(500, 500), options=drawoptions)
fig.save(filename, bbox_inches='tight')
def draw_molecule_with_highlights(filename, smiles, highlight_atoms):
drawoptions = DrawingOptions()
drawoptions.selectColor = highlight_color
drawoptions.elemDict = {} # Don't color nodes based on their element.
drawoptions.bgColor=None
mol = Chem.MolFromSmiles(smiles)
fig = Draw.MolToMPL(mol, highlightAtoms=highlight_atoms, size=figsize, options=drawoptions,fitImage=False)
fig.gca().set_axis_off()
fig.savefig(filename, bbox_inches='tight')
plt.close(fig)