rdkit.Chem.Draw

Package rdkit :: Package Chem :: Package Draw |
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[frames] | no frames]

# Package Draw

source code

Submodules | [hide private]
rdkit.Chem.Draw.IPythonConsole rdkit.Chem.Draw.MolDrawing 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.rdMolDraw2D: Module containing a C++ implementation of 2D molecule drawing 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
_moltoimg(mol, sz, highlights, legend, **kwargs) | source code
_MolsToGridImage(mols, molsPerRow=3, subImgSize=`(`200`,` 200`)`, legends=None, highlightAtomLists=None, **kwargs) returns a PIL Image of the grid... | source code
_MolsToGridSVG(mols, molsPerRow=3, subImgSize=`(`200`,` 200`)`, legends=None, highlightAtomLists=None, stripSVGNamespace=True, **kwargs) returns an SVG of the grid... | source code
MolsToGridImage(mols, molsPerRow=3, subImgSize=`(`200`,` 200`)`, legends=None, highlightAtomLists=None, useSVG=False, **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)
| __package__ = ``'``rdkit.Chem.Draw``'``

Imports: os, re, iteritems, MolDrawing, DrawingOptions, IntStringMap, MolDraw2D, MolDraw2DSVG, MolDrawOptions, PrepareMolForDrawing, map_indexing_suite_IntStringMap_entry, rdMolDraw2D

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')

### _MolsToGridImage(mols, molsPerRow=3, subImgSize=`(`200`,` 200`)`, legends=None, highlightAtomLists=None, **kwargs) | source code
    returns a PIL Image of the grid

### _MolsToGridSVG(mols, molsPerRow=3, subImgSize=`(`200`,` 200`)`, legends=None, highlightAtomLists=None, stripSVGNamespace=True, **kwargs) | source code
    returns an SVG of the grid

### 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