def _legacyMolToFile(mol, fileName, size, kekulize, wedgeBonds, imageType,
fitImage, options, **kwargs):
""" Generates a drawing of a molecule and writes it to a file
"""
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 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:
# <- the sping canvas doesn't support unicode well
options.radicalSymbol = '.'
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()