Package rdkit :: Package Chem :: Package Draw

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# Package Draw

source code

Submodules | [hide private]

- rdkit.Chem.Draw.IPythonConsole
- rdkit.Chem.Draw.MolDrawing
- rdkit.Chem.Draw.SimilarityMaps
- rdkit.Chem.Draw.aggCanvas
- rdkit.Chem.Draw.cairoCanvas
- rdkit.Chem.Draw.canvasbase
- rdkit.Chem.Draw.mplCanvas
- rdkit.Chem.Draw.qtCanvas
- rdkit.Chem.Draw.spingCanvas

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