rdkit.Chem.Draw package — The RDKit 2016.09.1 documentation

# rdkit.Chem.Draw package

## Submodules

- rdkit.Chem.Draw.IPythonConsole module
- rdkit.Chem.Draw.MolDrawing module
- rdkit.Chem.Draw.SimilarityMaps module
- rdkit.Chem.Draw.UnitTestDraw module
- rdkit.Chem.Draw.UnitTestIPython module
- rdkit.Chem.Draw.UnitTestSimilarityMaps module
- rdkit.Chem.Draw.aggCanvas module
- rdkit.Chem.Draw.cairoCanvas module
- rdkit.Chem.Draw.canvasbase module
- rdkit.Chem.Draw.mplCanvas module
- rdkit.Chem.Draw.qtCanvas module
- rdkit.Chem.Draw.spingCanvas module
- rdkit.Chem.Draw.test_list module

## Module contents

`rdkit.Chem.Draw.` `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

`rdkit.Chem.Draw.` `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

`rdkit.Chem.Draw.` `MolToImageFile`(mol, filename, size=(300, 300), kekulize=True, wedgeBonds=True, **kwargs)

  DEPRECATED: please use MolToFile instead

`rdkit.Chem.Draw.` `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

`rdkit.Chem.Draw.` `MolToQPixmap`(mol, size=(300, 300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, **kwargs)

  Generates a drawing of a molecule on a Qt QPixmap

`rdkit.Chem.Draw.` `MolsToGridImage`(mols, molsPerRow=3, subImgSize=(200, 200), legends=None, highlightAtomLists=None, useSVG=False, **kwargs)

`rdkit.Chem.Draw.` `MolsToImage`(mols, subImgSize=(200, 200), legends=None, **kwargs)

`rdkit.Chem.Draw.` `ReactionToImage`(rxn, subImgSize=(200, 200), **kwargs)

`rdkit.Chem.Draw.` `ShowMol`(mol, size=(300, 300), kekulize=True, wedgeBonds=True, title='RDKit Molecule', **kwargs)

  Generates a picture of a molecule and displays it in a Tkinter window

`rdkit.Chem.Draw.` `calcAtomGaussians`(mol, a=0.03, step=0.02, weights=None)

  useful things to do with these: fig.axes[0].imshow(z,cmap=cm.gray,interpolation=’bilinear’,origin=’lower’,extent=(0,1,0,1)) fig.axes[0].contour(x,y,z,20,colors=’k’)

  fig=Draw.MolToMPL(m); contribs=Crippen.rdMolDescriptors._CalcCrippenContribs(m) logps,mrs=zip(*contribs) x,y,z=Draw.calcAtomGaussians(m,0.03,step=0.01,weights=logps) fig.axes[0].imshow(z,cmap=cm.jet,interpolation=’bilinear’,origin=’lower’,extent=(0,1,0,1)) fig.axes[0].contour(x,y,z,20,colors=’k’,alpha=0.5) fig.savefig(‘coumlogps.colored.png’,bbox_inches=’tight’)