Task to be done for paper release

[pcm32]

• Produce new cladiifications HMMER models and setup directories (expected 0.5 days)
  • Details on Produce new cladiifications HMMER models and setup directories #5 (spent so far 2 days)
  • We have a first version, but there are some issues with the cladification annotation files that need to be sorted out by Eric.
• Python refactoring to new annotation scheme (0.5 - 1 day)
  • Details on Python refactoring to new annotation scheme #4 (spent so far 2 day, but touches upon other parts as well, like domain verifications, includes DH/PS)
• Adapt Java code to Python refactoring (1 - 2 days) (spent so far 3 days, includes DH/PS)
• Cheminformatics work (all refer to working document):
  • P1. DH/PS resolution, including testing (1 to 2 days)
    - Done through domain verification, parts implemented in both Java and python. DH/PS domains that don't pass required verfications are dropped for the sake of molecule building. (1 day spent so far)
  • P1b. Use KR based stereo, including testing, might require some code re-design (how classes interact) (1 to 3 days)
  • P7. Work on termination rules implementation, using termination definition file (2 days)
    • P8. Work on sub features PK molecule changes (1 to 3 days)
    • P5. Add TE domains given to other domains models (0.5 days, surely less)
    • P6. Status of NRPS usage, write tests (1 day)
• Other new issues that came up:
  • Fit case where starter monomer is found in the middle of the molecule within the new annotation scheme. This introduces some combination aspects in the domain-based verification steps.
  • Fix stereochemistry CDK exception seen on certain cases when moving to latest CDK 2.0