Merge pull request #1257 from RosettaCommons/tlinsky/store_residue_subset
Add StoreResidueSubset mover/StoredResidueSubset res selector
Store_residue_subset is a new integration test
Merge pull request #1217 from RosettaCommons/aleaverfay/fix_cloud_pdb_output_in_matcher_postXRW
Aleaverfay/fix cloud pdb output in matcher post xrw
Fixing a bug from the ChemXRW that broke cloud PDB writing.
This patch activats the "skip_connect_info" in the StructFileRepOptions
object in the CloudPDBWriter's call to dump_pdb_residue helping to
avoid assertion failures stemming from non-polymeric inter-residue
connections being seen as asymmetric (residue i's connection to residue
j isn't mirrored in residue j -- because residue j isn't being output).
It's not clear that dump_pdb_residue can function properly without
the skip_connect_info flag. This should be looked at more closely.
Merge pull request #1136 from RosettaCommons/jadolfbr/remove_extra_pdb_reader_tracers
Remove some extra output on pdb reading
Right now, each unknown record is printing to std::cout on PDB reading if -pdb_comments is passed. I'm not sure I agree with reading pdb_comments or other things at all, but this simple PR will change the cout printing to a TR.Debug.
Merge pull request #1120 from RosettaCommons/vmullig/tweak_etable
Splitting some of the changes from pull request #1093
Pull request #1093 (which aims to make RamaPrePro work with cyclic geometry and noncanonicals) revealed problems with cyclic geometry and the etable energies which I also fixed in that branch. It also produces a few more integration test changes than I had anticipated. I'm cherry-picking some of the changes from that pull request into a separate pull request so that I can pinpoint which changes are causing which integration test changes.
This pull request:
Tweaks the logic for the etable energies to ensure that cyclic geometry is handled properly.
If I've done things properly, the only integration tests that change should be the ones that involve cyclic geometry.
Test changes look good (only cyclic geometry and noncanonical connections show changes). Merging.
Merge pull request #1051 from RosettaCommons/vmullig/carbohydrate_issue
Fixing an issue with the CarbohydratePoseIOTests, which were randomly failing for me.
I tracked it down to the use of the atoi() function in core::io::carbohydrates::sugar_modifications_from_suffix(). The atoi() function expects a pointer to the first element of a null-terminated char array, but was being passed the address of a single char. As such, it was progressively reading from that memory location. In most cases, it would interpret the next byte as something other than a number, and would therefore only return the number associated with the input char. Sometimes, though, the next byte would correspond to the ASCII for a number, which would result in misinterpretation of the char passed in (e.g. 68 or 687 for '6', or whatnot).
The solution was to implement a simple utility function to convert a single-byte char to the integer that it represents.
All integration test changes seen are the switching behaviour seen in the unstable ones.
Merge pull request #1026 from RosettaCommons/roccomoretti/graphviz
Graphviz output for ResidueTypes
Just a little utility function I had lying around which allows you to create a Graphviz DOT file from the connectivity of a ResidueType.
New, unused functionality (aside from unit test) -- no test changes expected.
Merge pull request #1004 from RosettaCommons/aleaverfay/remove_multithread_jd2_job_dist
Scrapping attempted multithreaded job distributor for JD2
JD2 cannot accommodate a multithreaded job distributor. This feature will
come online with JD3. Hopefully, this fixes the multithreaded unit tests.
Merge pull request #969 from RosettaCommons/JWLabonte/sugars/input
Bug Fix: I was stupidly accessing map data before checking if they existed.
All unit tests pass.
carbohydrates integration test changes expected, because I had also added output of pdbs to the tests on this branch
Merge pull request #949 from RosettaCommons/rfalford12/fix_multi_mem_bug
Rfalford12/fix multi mem bug
This pull request fixes a 'once feature now bug.' Initially, I wanted to prevent the user from incorporating multiple membrane residues due to ambiguity in tracking. Now, since a single MEM can be easily tracked and changed, it makes sense to allow multiple MEM residues.
This change revises IO case 2 (AddMembraneMover lines 544-605) which deals with multiple MEM residues detected in AddMembraneMover:
- Old Behavior: throw an exception as a result of multiple membrane residues
- New Behavior:
- If the user doesn't point to a MEM, accept the first MEM in sequence by default
- If the user does point to a MEM, accept that MEM
I also added two new unit tests to the AddMembraneMover test suite to cover these test cases