Created submodules. Working on logic for the continuation option
Working on the 'check' and 'continue' options. Finished: write_info_file for Model and System
Coded the 'check' option to check if the previously run temperatures finished.
New definition of contacts (heavy atoms<5.5A) incorporated. New option to select first T_array.
Removed some print statements
Added --R_CD option for new to set contact over dihedral ratio. Testing. Works
Refactoring to further compartamentalize the Model and System objects from main flow. Started HetGo code.
Created models.py options checker and smarter Model loading. Moved system to submodule. Preparing to refactor.
Added contact_energies option for HetGo. Starting to code HetGo details.
Started mutations/phi_values.py. Uses mdtraj to calculate deltaH_k for MC2004 HetGo.
continue options now loaded from file in updated style.
Working on new modular System style reads/generates options in new style:done. Working on new prepare_system.
Working on bonded itp file generation in modelbase. Moving nonbonded file generation to subclasses.
Finished new style of file preparation. Next to switch modelbuilder.py logical flow.
Prepares new and loaded Model & System correctly. Moving to refactor main logical flow.
Dry run of new project works with new setup. Going to do short sh3 walkthrough.
Cleaned up unused code in modelbuilder, models/. Deleted free_energy_analysis
Working on aggregating equilibrium sims. Next is to do equilibrium PMFS and mutations.
Starting to code mutations. Also debugging HetGo option.
Started implementing MC2004.