Development Update for May 2019

[charlesdavid]

I have made a number of changes to JEDi and fixed a number of bugs:

• BUGS SQUASHED:
  • KPA now works as expected
  • No commas in raw text files... (only in the formatted file for eigenvalue + %var + cum var)
• CODE REVISION:
  • There is no longer a distinction between SINGLE and MULTI chain PDB files.
  • Single chain PDB files with no chain ids are fixed by adding a default chain id: "A"
  • Residue Lists formatted for Single use will still work for a single chain pdb.
  • Multi chain PDB files work as usual...
    • Multi chain PDB files still MUST have unique chain IDs!
  • Multi residue lists work as normal...
  • Down sampling of frames is now implemented
  • Frame range selection may be implemented soon ...
  • Messages to STD OUT now more clear and organized
  • Log file structure and clarity improved
  • The aligned coordinates (transformed) for each subset processed is written out to file.
  • The output from the Free Energy Surface method now included a 3-D Scatterplot
• Development:
  • Covariance shrinkage --> DONE!
  • Clustering of frames --> DONE!
  • Multi Threading --> DONE!
  • SPLOC --> IN PROGRESS