You want to depict a molecule as a peptide i.e. a series of amino acid components. See example in Figure 1.
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 ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") # read a molecules mol = oechem.OEGraphMol()
prompt > python3 peptide2img.py 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 peptide2img.py -in oxytocin.ism -out oxytocin.svg -labelstyle threeletters prompt > python3 peptide2img.py -in oxytocin.ism -out oxytocin.svg -labelstyle singleletter
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.
See also in OEDepict TK manual¶