Depicting Molecule in JPG

Problem

You want to generate an image of your molecule in JPG format.

Ingredients

Pillow (Python 3 compatible PIL fork)
OEDepict TK - molecule depiction toolkit

Difficulty level

Download

Download code

mol2img.py

Solution

The following table lists the image file formats natively supported in OEDepict TK and their associated file extensions.

Graphics File Format	Format Type	File Extension
PNG (Portable Network Graphics)	raster image	`.png`
SVG (Scalable Vector Graphics)	vector image	`.svg`
bare SVG (with no header)	vector image	`.bsvg`
Postscript	vector image	`.ps`
Encapsulated PostScript	vector image	`.eps`
PDF (Portable Document Format)	vector image	`.pdf`

Unfortunately, the jpg image format is not supported by OEDepict TK. However you can render your molecule into a png image file and then convert it to jpg, gif or tiff image types using the Pillow image library.

def RenderMolecule(mol, opts, ofilename):

    disp = oedepict.OE2DMolDisplay(mol, opts)

    ext = oechem.OEGetFileExtension(ofilename)
    if oedepict.OEIsRegisteredImageFile(ext):

        ofs = oechem.oeofstream()
        if not ofs.open(ofilename):
            oechem.OEThrow.Fatal("Cannot open output file!")
        oedepict.OERenderMolecule(ofs, ext, disp)

    elif ext in ['jpg', 'tiff', 'gif']:

        imagestr = oedepict.OERenderMoleculeToString('png', disp)
        imagefile = io.BytesIO(imagestr)
        image = Image.open(imagefile)
        image.save(ofilename)

Usage

Usage

mol2img.py

prompt > python3 mol2img.py molecule.ism molecule.jpg
prompt > python3 mol2img.py molecule.sdf molecule.png

To install Pillow in a Python 3 conda environment:

prompt > conda create -n oecookbook python=3
prompt > source activate oecookbook
(oecookbook) prompt > pip install Pillow

Depicting Molecule in JPG

Problem

Ingredients

Difficulty level

Download

Solution

Usage

See also in OEChem manual

See also in OEDepict manual