Briefly, the package works as follows:
The pyPept Sequence class converts the input line notation into a Sequence object, which is an ordered list of monomers together with all of the connectivity information necessary to accurately build the molecule. The Molecule class takes this Sequence object and creates a molecule object with a sanitized 2D representation. The Conformer class leverages distance geometry functionality to generate a 3D conformer.
Here we found it necessary to provide secondary structure constraints in the 3D generation to obtain conformations that can be close to a bioactive one. Therefore, we developed a method to predict peptide secondary structure elements, which we packaged into the SecStructPredictor class. In addition, we developed a helper class Converter which can be used to translate from HELM to BILN and back, or to convert a FASTA string into BILN.
A wrapper script (run_pyPept.py) is also provided that automates the sequence-to-structure/conformer conversion of a general peptide, thus demonstrating how to connect the individual components, and providing a non-programmatic way to use pyPept by simple command line execution.