You want to depict a molecule as a peptide i.e. a series of amino acid components. See example in Figure 1.
Requires OpenEye toolkits version 2017.Feb or later.
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 3-letter code.
prompt > python3 peptide2img.py oxytocin.ism oxytocin.png
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.