Depicting Peptides

Problem

You want to depict a molecule as a peptide, that is, a series of amino acid components. See the example in Figure 1.

../_images/OEDrawPeptide-Oxytocin.png — **Figure 1.** Depictions of oxytocin as a molecule (on the left) and as a peptide (on the right).

Ingredients

OEChem TK - Cheminformatics toolkit
OEDepict TK - Molecule depiction toolkit
Grapheme TK - Molecule and property visualization toolkit

Difficulty Level

Solution

GraphSim TK provides a function called OEDrawPeptide that depicts a molecule as a peptide. It identifies standard amino acid components in the molecule and substitutes them with circular glyphs and their corresponding codes, either three letters or a single letter.

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

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

    # read a molecules

    mol = oechem.OEGraphMol()

Download code

peptide2img.py and supporting data oxytocin.ism

Usage:

prompt > python3 peptide2img.py oxytocin.ism oxytocin.png

Discussion

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

prompt > python3 peptide2img.py -in oxytocin.ism -out oxytocin.svg -labelstyle threeletters
prompt > python3 peptide2img.py -in oxytocin.ism -out oxytocin.svg -labelstyle singleletter

**Table 1.** Oxytocin depicted in three- and one-letter codes.

Note

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

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

The amino acids that appear 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.** Depictions of L- and D-Serine.

Depicting Peptides

Problem

Ingredients

Difficulty Level

Solution

Discussion

See also in OEDepict TK Manual

See also in Grapheme^TM TK Manual

Depicting Peptides

Problem

Ingredients

Difficulty Level

Solution

Discussion

See also in OEDepict TK Manual

See also in GraphemeTM TK Manual

See also in Grapheme^TM TK Manual