v2.3.1

Fixes a minor bug in code that parses DSSP output.

v2.3.0

• Adds packing density evaluation function.

Version 2.2.0

Adds pacc module for parametric analysis of coiled coils.

v2.0.1

This release brings a new major version of ISAMBARD, and brings a number of breaking changes compared to previous versions. The aim of these changes is to make the processes that ISAMBARD is performing much more explicit, and removes a lot of the magic that hid the implementation. This might make ISAMBARD slightly harder to use initially, but make it much more obvious how you would extend the functionality in the future. For example, there are no longer any helper methods to set up the optimisers using "default" options, such as the standard build function with BUDE internal as the force field. You now need to be explicit about which build and scoring function you're using, but these means it's much clearer how to tweak the optimisation. All documentation has been update to reflect these changes.

Breaking changes

• ISAMBARD functionality has been split into 4 modules:
  • Specifications
  • Modelling
  • Optimisation
  • Evaluation
• All ISAMBARD functionality is no longer automatically imported by default, and each submodule needs to be
  imported specifically.
• Removal of the AMPAL module into its own separate module
• Removal of BUFF properties buff_internal_energy and buff_interaction_energy from AMPAL objects
  • BUFF has also been moved into a separate module called
    BUDEFF.
• The pack_new_sequences, pack_new_sequence and repack_all methods, which provided an interface
  to SCWRL4, have been removed. All SCRWL4 interop has been moved into its own module
  (isambard.modelling.scwrl)
• ampal_parent renamed to parent
• Class methods for optimisers that use the BUDE forcefield have been removed.