def MolToQPixmap(mol, size=(300, 300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, **kwargs): """ Generates a drawing of a molecule on a Qt QPixmap """ if not mol: raise ValueError('Null molecule provided') from rdkit.Chem.Draw.qtCanvas import Canvas canvas = Canvas(size) if options is None: options = DrawingOptions() options.bgColor = None if fitImage: options.dotsPerAngstrom = int(min(size) / 10) options.wedgeDashedBonds = wedgeBonds 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 = MolDrawing(canvas=canvas, drawingOptions=options) drawer.AddMol(mol, **kwargs) canvas.flush() return canvas.pixmap
def MolToQPixmap(mol, size=(300,300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, **kwargs): """ Generates a drawing of a molecule on a Qt QPixmap """ if not mol: raise ValueError('Null molecule provided') from rdkit.Chem.Draw.qtCanvas import Canvas canvas = Canvas(size) if options is None: options = DrawingOptions() options.bgColor = None if fitImage: options.dotsPerAngstrom = int(min(size) / 10) options.wedgeDashedBonds=wedgeBonds 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 = MolDrawing(canvas=canvas, drawingOptions=options) drawer.AddMol(mol, **kwargs) canvas.flush() return canvas.pixmap
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 rdkit.Chem.Draw.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 iteritems(omol._atomPs): 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: from PIL import Image img = Image.new("RGBA", size, (0, 0, 0, 0)) canvas = Canvas(img) else: from rdkit.Chem.Draw.spingCanvas import Canvas canvas = Canvas(size=size, name='MolToImageFile') img = canvas._image return img, canvas
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()