def MolToImage(mol, size=(300, 300), kekulize=True, wedgeBonds=True, **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 [])
"""
from MolDrawing import MolDrawing
if not mol:
raise ValueError, 'Null molecule provided'
img, canvas = _createCanvas(size)
drawer = MolDrawing(canvas)
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.wedgeDashedBonds = wedgeBonds
if kwargs.has_key('legend'):
legend = kwargs['legend']
del kwargs['legend']
else:
legend = ''
drawer.AddMol(mol, **kwargs)
if legend:
from rdkit.Chem.Draw.MolDrawing import Font
bbox = drawer.boundingBoxes[mol]
pos = size[0] / 2, int(.94 *
size[1]) # 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 drawmol(s):
bsize = 200
tsize = 80
size = (bsize, bsize + tsize)
m = Chem.MolFromSmiles(s)
#print("wt", MolWt(m))
img, canvas, drawer = Draw.MolToImage(m, size=size, returnCanvas=True)
# centerIt=False, drawingTrans=(bsize/2+1,bsize/2+tsize))
font = Font(face='sans', size=12)
pos = bsize / 2, bsize, 0
canvas.addCanvasText('%s\r\nMolWt: %g\tTPSA: %g' % (s, MolWt(m), TPSA(m)),
pos, font)
with open('xx' + s + '.png', 'w') as f:
canvas.flush()
img.save(f)
def _CairoDrawer(self, rdmol):
"""Render an svg using cairo or agg renderer."""
# Some drawing options
options = Draw.DrawingOptions()
options.bondLineWidth = 1
# Prepare drawing
useAGG, useCairo, Canvas = Draw._getCanvas()
canvas = Canvas(size=(self.width, self.height),
imageType='svg',
fileName=self.svgfile)
drawer = Draw.MolDrawing(canvas=canvas, drawingOptions=options)
drawer.AddMol(rdmol)
if self.legend is not None:
from rdkit.Chem.Draw.MolDrawing import Font
pos = (self.width / 2, int(.1 * self.height), 0)
font = Font(face='serif', size=18)
canvas.addCanvasText(self.legend, pos, font)
canvas.flush()
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
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 [])
- highlightColor: RGB color as tuple (default [1, 0, 0])
NOTE:
use 'matplotlib.colors.to_rgb()' to convert string and
HTML color codes into the RGB tuple representation, eg.
from matplotlib.colors import ColorConverter
img = Draw.MolToImage(m, highlightAtoms=[1,2], highlightColor=ColorConverter().to_rgb('aqua'))
img.save("molecule.png")
RETURNS:
a PIL Image object
"""
if not mol:
raise ValueError('Null molecule provided')
if canvas is None:
img, canvas = _createCanvas(size)
else:
img = None
options = options or DrawingOptions()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
if 'highlightColor' in kwargs:
color = kwargs.pop('highlightColor', (1, 0, 0))
options.selectColor = color
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
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)
if 'legend' in kwargs:
legend = kwargs['legend']
del kwargs['legend']
else:
legend = ''
drawer.AddMol(mol, **kwargs)
if legend:
from rdkit.Chem.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