Merge pull request #2171 from RosettaCommons/guffysl/hbond_residue_selector
This commit adds two new residue selectors, BondedResidueSelector and HBondSelector.
BondedResidueSelector requires either an input residue selector or list of residue numbers and selects all residues with chemical bonds to the input set. HBondSelector optionally takes an input residue selector or list of residue numbers. If provided, it selects all residues that form hydrogen bonds with residues in the input set given that those hydrogen bonds meet a specified energy requirement (default -0.5 REU). If no selector is provided, all residues in the pose that form hydrogen bonds are selected. By default, backbone-backbone hydrogen bonds are ignored.
Merge pull request #2143 from RosettaCommons/vmullig/tweak_genkic
Decrease verbosity of GenKIC backbone_bin filter
The backbone_bin GeneralizedKICFilter is a bit too verbose. Switching its output to the debug tracer.
Cosmetic changes expected to the genkic_bin_setting integration test.
Merge pull request #2118 from RosettaCommons/dimaio/beta16_fix_tors_corr
Fixing a few errors with -beta_nov16. Since these are bugfixes, I am making this change the behavior of beta_nov16 rather than add a new flag. This will trigger rebuilding of Dunbrack binaries.
Merge pull request #2106 from RosettaCommons/vmullig/fix_aib_patching
Fixing NtermProteinFull patch case for AIB (which still said MAL).
This is a pretty small change. No unit or integration test changes expected.
Merge pull request #2079 from RosettaCommons/roccomoretti/with_message
Adjust output printing for utility_exit()
Just utility_exit()-ing without a message is very user unfriendly. Fix a few instances of that, and also bump tracer priority for other locations.
Merge pull request #2044 from RosettaCommons/jadolfbr/fix_ignore_termini_residue
Fix a long-standing bug in PoseFromSFRBuilder where an ignored unrecognized residue at the N terminus, such as PCA, would make the next residue not start a new chain or have the proper terminus variant.
Merge pull request #1797 from RosettaCommons/roccomoretti/select_columns
Add columns selection script.
Add a simple script that obviates the need to write ad-hoc awk scripts to select out particular columns from Rosetta score files.
Merge pull request #1978 from RosettaCommons/vmullig/tweak_peppred
Adding a final symmetry filtering step to simple_cycpep_predict
When sampling with quasi-symmetry, sometimes the final relaxation step would break symmetry. This adds one more filtration step based on symmetry after that relaxation, so that asymmetric poses are thrown out.
Tasks:
- Add extra filtering step.
- Double-check that BOINC build is still happy.
- I think it is, but I have an older version of the Linux BOINC libraries built. Will check on Ralph the next time that Rosetta is deployed.
- Also, add filtering to bettercluster.cc.
- Add threshold option to bettercluster.cc.
- Beauty.
Merge pull request #1954 from RosettaCommons/Cyrus/mergetarget
From Steven Lewis:
three items:
1) @yfsong -sourced bugfixes and updates to Hybridize. This is mostly an update to add a more powerful constructor (previously the class was dependent on parse_my_tag being called). This code is marked as smlewis code because it's a squash-cherrypick from an abandoned poisoned branch.
2) read_topology_file, the function that converts params files into ResidueTypes, previously assumed that the file was coming in from disk (string filename, or izstream from file). The interface has been rearranged to allow a std::istream, for params files not coming from disk (coming in over network communication from some non-Rosetta black box in my case). There has been discussion of unifying the function name read_topology_file and the file names "*.params" to match better - that's been put off to the winter meeting.
3) @roccomoretti pointed out a bug in my last ACTCCMover updates; fixed.
Tests all look fine from my end. There is an added unit test to support read_topology_file.
Merge pull request #1924 from RosettaCommons/rhiju/minor_stepwise_fixes_rna_puzzle18_movie
Rhiju/minor stepwise fixes rna puzzle18 movie
one integration test changes (align_pdb no longer being treated as 'pseudo-native')