New feature and major bug fix

1. New Feature: Adding your own cyclization moiety
   Users can now input their own custom cyclization moiety other than the default provided ones (DFBP, disulfide and amide). The user must enter the molecular weight of this CUSTOM moiety.

2. Bug fixes
   A major bug was found where any connection index input other than the first amino acid would case a stack overflow error. The recursive backtracking step in the program has been fixed where a more general base case was added to prevent infinite cycles.

Bug fixes: invalid branched fragments

The program was erroneously suggesting invalid branched fragments. Extra checks have been implemented when building the branched peptides.

Peptide Serum Stability (Cyclic and Linear)

This new release includes major updates to the program. Most notably, this program can now analyze cyclic peptides. Specifically, it can analyze disulfide, amide and DFBP cyclized peptides.

Furthermore, a new mode in the program called "input" has been included. This allows the user to bypass the interactive mode of the program and obtain a CSV file with the desired fragment results.

Peptide Serum Stability (Linear)

This first release is a functional linear peptide fragment analyzer.

Notable Features

• User interaction is mainly handled through the command line.
• Prints all the possible fragments of a linear peptide.
• Compares mass spectrometry data to possible fragment.

Comments

This is the first runnable JAR file of the program that handles the most basic problems of the project. A major framework re-design is on the way.