Package Draw

source code

Submodules

[hide private]

Functions

[hide private]

_getCanvas()

source code

_createCanvas(size)

source code

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

source code

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...

source code

MolToImageFile(mol, filename, size=(300,300), kekulize=True, wedgeBonds=True, **kwargs)
DEPRECATED: please use MolToFile instead

source code

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...

source code

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...

source code

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')

source code

MolsToImage(mols, subImgSize=(200,200), legends=None, **kwargs)

source code

MolsToGridImage(mols, molsPerRow=3, subImgSize=(200,200), legends=None, highlightAtomLists=None, **kwargs)

source code

ReactionToImage(rxn, subImgSize=(200,200), **kwargs)

source code

MolToQPixmap(mol, size=(300,300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, **kwargs)
Generates a drawing of a molecule on a Qt QPixmap...

source code

Variables

[hide private]

tkRoot = None
hash(x)

tkLabel = None
hash(x)

tkPI = None
hash(x)

Imports: os, iteritems, MolDrawing, DrawingOptions

Function Details

[hide private]

MolToImage(mol, size=(300,300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, canvas=None, **kwargs)

source code

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

MolToFile(mol, fileName, size=(300,300), kekulize=True, wedgeBonds=True, imageType=None, fitImage=False, options=None, **kwargs)

source code

Generates a drawing of a molecule and writes it to a file

ShowMol(mol, size=(300,300), kekulize=True, wedgeBonds=True, title='RDKit Molecule', **kwargs)

source code

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

MolToMPL(mol, size=(300,300), kekulize=True, wedgeBonds=True, imageType=None, fitImage=False, options=None, **kwargs)

source code

Generates a drawing of a molecule on a matplotlib canvas

calcAtomGaussians(mol, a=0.03, step=0.02, weights=None)

source code


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')

MolToQPixmap(mol, size=(300,300), kekulize=True, wedgeBonds=True, fitImage=False, options=None, **kwargs)

source code

Generates a drawing of a molecule on a Qt QPixmap