Fig. 1

Summary of pyPept architecture and interfaces. Each monomer is mapped to chemical structure through a monomer dictionary, and monomers are connected by bonds defined for each monomer’s R-groups to yield a sanitized Sequence object. Information from the Sequence is used to create a Molecule object, and two options for 2D depictions are provided. Further, one can predict Conformer objects using additional secondary structure restraints. An executable driver program (run_pyPept.py) encapsulates the sequence-to-structure conversion, offering a non-programmatic way to obtain conformers directly from line notations. The solid lines indicate the default run_pyPept.py execution, with supported options shown by dotted arrows