ravenswing / mdsaps Goto Github PK

Current reweight implementation is very slapdash...

• Add 2D functionality.
• Extract auxiliary script to its own module.
• Improve implementation in run_reweight.
• Test reweighting of 1D and 2D FES.
• [EXTRA] Add other methods of reweight (i.e. PLUMED or KDE) to module.
• [EXTRA] Improve code and resolution?

Collection of stretch goals from previous issues:

• From #1 : Add parallelisation for reweighting.

• Add axis input and/or output to existing plotting
• Make multiplot function
• Test multiplot function

• Update base README.
• Find the best way to document/auto-document the code.
• [EXTRA] Add buttons/images to README.

• unify running with apo vs. holo
• make sure naming and argument ordering is consistent
• better group selection (e.g. Protein_LIG throughout)
• --> auto-renaming Protein -> Protein_LIG in .mdp and .sh files
• new function: auto-run prep
• fix: fix_itp_includes interaction with chains and numbers
• fix: step 04 POSRES Ca renaming
• ??? put input files into lib
• [EXTRA] create a pipeline for more automatic running over many systems

ALL external scripts that are copied or used:

• PLUMED template files
• local_dirs .sh & .mdp files for system prep.
• GMX forcefields

Ensure that the ordering and name of input variables are consistent

• traj_path
• top_path
• out_path
• select
  etc...

Add logging initialisation to all scripts.
Add logging and debugging messages to all scripts.
Check logging works and improve output messages.

• Ensure loading PDB works.
• Ensure PDB formatting works.
• [EXTRA] Convert load pdb to using read_fwf from Pandas

• Work out the best method for reweighting
• Implement reweighting in 1D
• Add to convergence sumhills and/or plots
• Implement reweighting in 2D
• Test reweighting
• [EXTRA] Add parallelisation for reweighting

• Make sure load.fes works with fun-metaD FES
• Make sure plot.fes2D works with fun-metaD FES

• Check required dependencies.
• Add list of dependencies/installation instructions.
• Is Parmed needed?
• Is pytraj needed?
• Seperate code?

• Combine com_dist_per_frame and dist_per_frame
• Combine measure_com_dist and measure_dist
• Combine save_com_dist and save_dist