Depicting Peptides


You want to depict a molecule as a peptide i.e. a series of amino acid components. See example in Figure 1.


Figure 1. Example of depicting oxytocin as a molecule (on the left) and as a peptide (on the right)


Difficulty Level



The GraphSim TK provides a function called OEDrawPeptide that depicts a molecule as a peptide. It identifies standard amino acids components in the molecule and substitute them with circular glyphs and their corresponding code either 3-letter or single letter.

        oechem.OEThrow.Fatal("Unknown image type!")

    ofs = oechem.oeofstream()
    if not
        oechem.OEThrow.Fatal("Cannot open output file!")

    # read a molecules

    mol = oechem.OEGraphMol()

Download code and supporting data oxytocin.ism


prompt > python3 oxytocin.ism oxytocin.png


If svg image file format, the peptide can be depicted in interactive mode. When the mouse is hovered over any glyph the corresponding amino acid is depicted.

prompt > python3 -in oxytocin.ism -out oxytocin.svg -labelstyle threeletters
prompt > python3 -in oxytocin.ism -out oxytocin.svg -labelstyle singleletter
Table 2. Example of depicting L- and D- Serine
../_images/peptide2img-oxytocin-threeletters.svg ../_images/peptide2img-oxytocin-singleletter.svg


The generated interactive svg images should be included into and HTML page with the SVG MIME type.

<object data="<imagename>.svg" type="image/svg+xml"></object>

The amino acids that are appears naturally in proteins are the L-stereoisomers. These are labeled with corresponding 3-letter codes: such as Ser for L-Serine. Their enantiomers are distinguished by adding the “D-” prefix to their 3-letter code: such as D-Ser for D-Serine.

Table 2. Example of depicting L- and D- Serine
../_images/peptide2img-peptide-L.svg ../_images/peptide2img-peptide-D.svg

See also in OEDepict TK manual



See also in GraphemeTM TK manual