Merge pull request #4942 from RosettaCommons/roccomoretti/header_fixups
Some header/namespace fixups.
There's some forward headers we didn't have that we probably should have. (Most notably, core/chemical/rings/RingConfomer.fwd.hh which was called out specifically by the code in places.)
Also, there was some "AUTO USING NS" stuff that is mostly pointless at this point -- we should either include the header or delete the using that was requiring it.
I also deleted a editor temporary file.
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Merge pull request #4939 from RosettaCommons/roccomoretti/filenotfoundfix
Fix bug in FileNotFound error.
We were putting the source file name in the error message, not the name of the missing data file.
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Merge pull request #4940 from RosettaCommons/vmullig/fix_hbond_counting_in_simple_cycpep_predict
Fix hydrogen bond reporting at the end of simple_cycpep_predict. I managed to break this in pull request #4702 by forgetting that my hydrogen bond counts were no longer negative numbers. This also adds a unit test confirming that another piece of needed functionality functions (though it turned out not to be the culprit).
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Merge pull request #4938 from RosettaCommons/roccomoretti/grid_cache_size
Fix issue with memory usage in ligand docking.
There's been a number of reports of ligand docking eating up memory. Most of these can be fixed by setting -max_grid_cache_size
I don't think there's a reason not to have this set to a finite value, so I'm making that change to the default.
Additionally, I think the memory growth is in part due to a fix I added a while back which adds the grid center to the lookup hash string. Because the ligand center moves during docking, when the InterfaceCalculator goes to calculate final grid scores, it creates a new (used-only-once) grid set. What we can do is allow the GridManager to pull out a grid which is "close enough", which should pick up the original grid in many cases and thus not cause a grid regeneration and associate memory bloat/cache churn.
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Merge pull request #4929 from RosettaCommons/roccomoretti/no_ascii_options
Try to give better feedback with non-ASCII options.
An error that comes up semi-regularly is where someone uses an en-dash instead of a hyphen in Rosetta options. (Certain Word processors like autoconverting things.)
Adjust option parsing to try to better highlight cases where this may be happening.
Additionally, we can handle dos/unix file ending issues in option files by broadening the meaning of 'whitespace'.
Vikram K. Mulligan 4 years Note: tests peptide_pnear_vs_ic50.beta.debug and peptide_pnear_vs_ic50.beta are known failures at this time. They should not fail to *run*, but on analysis, they do fail. Tests simple_cycpep_predict, simple_cycpep_predict.debug, peptide_pnear_vs_ic50, and peptide_pnear_vs_ic50.debug should all run and pass.
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reduce nbr_radius to something reasonable for DNA params (#4933)
It would appear dna has had its NBR_RADIUS set to 1000 for a very long time.
This isn't super scientific (I just used the calculated radius of GUA from molfile_to_params.py) for all of them (+0.1)
Perhaps in the future it might be smart to remake them in-case something else is wrong, but frank says that he has some DNA fixes #4871 and that these params seem to work well for him in that branch so its likely that only the NBR_RADIUS needs to be updated
danpf 2020-08-26 NBR WAS set to 1000.0, I set it to the value molfile_to_params.py set for GUA on a single PDB + 0.1 it is possible this could be improved, but this seems good enough for now as it is no longer 1000.0.
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