Closed rafwiewiora closed 8 years ago
We have to be a bit careful here: We should ideally also generate a reference PDB file in the root of the munged directory with all of the appropriate atoms in it, since we will need this for automated MSM construction (for @maxentile).
Ah, very good point. Let me add that!
Ok, added generation of the no-solvent PDBs for every RUN (in the same dir as the output h5's, i.e.. munged-with-time/11705/no-solvent/run0.pdb
and munged-with-time/11705/no-solvent/run1.pdb
.
Had to do these inside the strip_water()
not the wrapper, so that we don't have all Workers checking for existence of these files and maybe there would be problem if multiple ones at start saw it wasn't there and all tried to write it.
Also some memory saving stuff in the wrapper - cut down the loaded trajectory to first frame only and del
it before the stripping is done.
Looks good?
Btw tested on 2 trajectories - all ok.
Should fix https://github.com/choderalab/FAHMunge/issues/23 - only remove water and neutralizing ions for no-solvent trajs. I've only included
NA
andCL
ions for removal - add others if need be.Please review @jchodera