def MolToMPL(mol,size=(300,300),kekulize=True, wedgeBonds=True,
imageType=None, fitImage=False, options=None, **kwargs):
""" Generates a drawing of a molecule on a matplotlib canvas
"""
if not mol:
raise ValueError,'Null molecule provided'
from mplCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor=None
if fitImage:
drawingOptions.dotsPerAngstrom = int(min(size) / 10)
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.iteritems():
omol._atomPs[k]=canvas.rescalePt(v)
canvas._figure.set_size_inches(float(size[0])/100,float(size[1])/100)
return canvas._figure
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
if options is None:
options = DrawingOptions()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
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 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]),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 MolToFile(mol,
fileName,
size=(300, 300),
kekulize=True,
wedgeBonds=True,
imageType=None,
fitImage=False,
options=None,
**kwargs):
""" Generates a drawing of a molecule and writes it to a file
"""
# original contribution from Uwe Hoffmann
if not fileName:
raise ValueError, 'no fileName provided'
if not mol:
raise ValueError, 'Null molecule provided'
if imageType is None:
imageType = os.path.splitext(fileName)[1][1:]
if options is None:
options = DrawingOptions()
useAGG, useCairo, Canvas = _getCanvas()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
if useCairo or useAGG:
canvas = Canvas(size=size, imageType=imageType, fileName=fileName)
else:
options.radicalSymbol = '.' #<- the sping canvas doesn't support unicode well
canvas = Canvas(size=size, name=fileName, imageType=imageType)
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)
drawer.AddMol(mol, **kwargs)
if useCairo or useAGG:
canvas.flush()
else:
canvas.save()
def MolToFile(mol,fileName,size=(300,300),kekulize=True, wedgeBonds=True,
imageType=None, fitImage=False, options=None, **kwargs):
""" Generates a drawing of a molecule and writes it to a file
"""
# original contribution from Uwe Hoffmann
if not fileName:
raise ValueError,'no fileName provided'
if not mol:
raise ValueError,'Null molecule provided'
if imageType is None:
imageType=os.path.splitext(fileName)[1][1:]
if options is None:
options = DrawingOptions()
useAGG,useCairo,Canvas = _getCanvas()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
if useCairo or useAGG:
canvas = Canvas(size=size,imageType=imageType,
fileName=fileName)
else:
options.radicalSymbol = '.' #<- the sping canvas doesn't support unicode well
canvas = Canvas(size=size,name=fileName,imageType=imageType)
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)
drawer.AddMol(mol,**kwargs)
if useCairo or useAGG:
canvas.flush()
else:
canvas.save()
def MolToMPL(mol,
size=(300, 300),
kekulize=True,
wedgeBonds=True,
imageType=None,
fitImage=False,
options=None,
**kwargs):
""" Generates a drawing of a molecule on a matplotlib canvas
"""
if not mol:
raise ValueError, 'Null molecule provided'
from mplCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor = None
if fitImage:
drawingOptions.dotsPerAngstrom = int(min(size) / 10)
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.iteritems():
omol._atomPs[k] = canvas.rescalePt(v)
canvas._figure.set_size_inches(float(size[0]) / 100, float(size[1]) / 100)
return canvas._figure
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
if options is None:
options = DrawingOptions()
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
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 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]), 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
