def MolToMPL(mol,size=(300,300),kekulize=True, wedgeBonds=True,
imageType=None,**kwargs):
""" Generates a drawing of a molecule on a matplotlib canvas
"""
if not mol:
raise ValueError,'Null molecule provided'
from MolDrawing import MolDrawing
from mplCanvas import Canvas
canvas = Canvas(size)
drawer = MolDrawing(canvas)
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.wedgeDashedBonds=wedgeBonds
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 MolToMPL(mol,
size=(300, 300),
kekulize=True,
wedgeBonds=True,
imageType=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)
drawer = MolDrawing(canvas)
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.wedgeDashedBonds = wedgeBonds
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 _createCanvas(size):
useAGG, useCairo, Canvas = _getCanvas()
if useAGG or useCairo:
import Image
img = Image.new("RGBA", size, "white")
canvas = Canvas(img)
else:
MolDrawing.radicalSymbol = '.' #<- the sping canvas doesn't support unicode well
from spingCanvas import Canvas
canvas = Canvas(size=size, name='MolToImageFile')
img = canvas._image
return img, canvas
def _createCanvas(size):
useAGG, useCairo, Canvas = _getCanvas()
if useAGG or useCairo:
try:
import Image
except ImportError:
from PIL import Image
img = Image.new("RGBA", size, (0, 0, 0, 0))
canvas = Canvas(img)
else:
from spingCanvas import Canvas
canvas = Canvas(size=size, name='MolToImageFile')
img = canvas._image
return img, canvas
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()
