def MolToImage(mol, size=(300,300), kekulize=True, wedgeBonds=True,
fitImage=False, options=None, canvas=None, **kwargs):
""" returns a PIL image containing a drawing of the molecule
Keyword arguments:
kekulize -- run kekulization routine on input `mol` (default True)
size -- final image size, in pixel (default (300,300))
wedgeBonds -- draw wedge (stereo) bonds (default True)
highlightAtoms -- list of atoms to highlight (default [])
highlightMap -- dictionary of (atom, color) pairs (default None)
highlightBonds -- list of bonds to highlight (default [])
"""
if not mol:
raise ValueError('Null molecule provided')
if canvas is None:
img,canvas=_createCanvas(size)
else:
img=None
fontSize = int(min(size) / 20)
if min(size) < 200:
fontSize = 1
if options is None:
options = DrawingOptions()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
options.atomLabelFontSize = fontSize
drawer = MolDrawing(canvas=canvas,drawingOptions=options)
if kekulize:
from rdkit import Chem
Chem.Kekulize(mol)
if not mol.GetNumConformers() or CoordsAreAllZero(mol):
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
if 'legend' in kwargs:
legend = kwargs['legend']
del kwargs['legend']
else:
legend=''
drawer.AddMol(mol,**kwargs)
if legend:
from chembl_beaker.beaker.draw.molDrawing import Font
bbox = drawer.boundingBoxes[mol]
pos = size[0]/2,int(.94*size[1]),0 # the 0.94 is extremely empirical
# canvas.addCanvasPolygon(((bbox[0],bbox[1]),(bbox[2],bbox[1]),(bbox[2],bbox[3]),(bbox[0],bbox[3])),
# color=(1,0,0),fill=False,stroke=True)
# canvas.addCanvasPolygon(((0,0),(0,size[1]),(size[0],size[1]),(size[0],0) ),
# color=(0,0,1),fill=False,stroke=True)
font=Font(face='sans',size=12)
canvas.addCanvasText(legend,pos,font)
if kwargs.get('returnCanvas',False):
return img,canvas,drawer
else:
canvas.flush()
return img
def MolToImage(mol,
size=(300, 300),
kekulize=True,
wedgeBonds=True,
fitImage=False,
options=None,
canvas=None,
**kwargs):
""" returns a PIL image containing a drawing of the molecule
Keyword arguments:
kekulize -- run kekulization routine on input `mol` (default True)
size -- final image size, in pixel (default (300,300))
wedgeBonds -- draw wedge (stereo) bonds (default True)
highlightAtoms -- list of atoms to highlight (default [])
highlightMap -- dictionary of (atom, color) pairs (default None)
highlightBonds -- list of bonds to highlight (default [])
"""
if not mol:
raise ValueError('Null molecule provided')
if canvas is None:
img, canvas = _createCanvas(size)
else:
img = None
fontSize = int(min(size) / 20)
if min(size) < 200:
fontSize = 1
if options is None:
options = DrawingOptions()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
options.atomLabelFontSize = fontSize
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
if kekulize:
from rdkit import Chem
Chem.Kekulize(mol)
if not mol.GetNumConformers() or CoordsAreAllZero(mol):
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
if 'legend' in kwargs:
legend = kwargs['legend']
del kwargs['legend']
else:
legend = ''
drawer.AddMol(mol, **kwargs)
if legend:
from chembl_beaker.beaker.draw.molDrawing import Font
bbox = drawer.boundingBoxes[mol]
pos = size[0] / 2, int(.94 *
size[1]), 0 # the 0.94 is extremely empirical
# canvas.addCanvasPolygon(((bbox[0],bbox[1]),(bbox[2],bbox[1]),(bbox[2],bbox[3]),(bbox[0],bbox[3])),
# color=(1,0,0),fill=False,stroke=True)
# canvas.addCanvasPolygon(((0,0),(0,size[1]),(size[0],size[1]),(size[0],0) ),
# color=(0,0,1),fill=False,stroke=True)
font = Font(face='sans', size=12)
canvas.addCanvasText(legend, pos, font)
if kwargs.get('returnCanvas', False):
return img, canvas, drawer
else:
canvas.flush()
return img
