Merge pull request #3581 from RosettaCommons/JackMaguire/MoveMRSToPublic
Moving Multistage Rosetta Scripts From Pilot To Public
Thanks to Steven for the review!
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3571 from CyrusBiotechnology/davela/add_H3_to_outlier_list_commons
From @d8vela :
This is a follow-up to the previous PR (#3551) which provides additions of orientation lines to the outlier_list file.
Now, we are also adding H3 lines to the outlier list, which are all set to false for neutrality. These are necessary for proper function of the antibody.cc app.
(The test failures are the usual junk)
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3573 from RosettaCommons/jkleman/sci_bench_template
Jkleman/sci bench template:
* updating relax scientific tests (fast_relax, fast_relax 5 iterations, cart_relax) to include cutoffs
* added a readme to each of these directories
* added a template directory as a starting point for adding scientific tests, these should be reasonably well commented
- [x] DONE: I have documentation for it, but:
- [x] TODO: it needs to be added to the wiki in some place. There are old pages about scientific tests, need to ask Rocco where to put or move pages
latest run:
http://benchmark.graylab.jhu.edu/revision?branch=&id=11038
documentation:
https://www.rosettacommons.org/docs/wiki/development_documentation/test/Scientific-Benchmarks
find the template in:
`/Rosetta/main/tests/scientific/tests/_template_`
notify author
notify list [rosetta-logs@googlegroups.com]
Pass new scorefxn along to lowres and highres movers when set (PR #3565)
Previously, if you called set_lowres_scorefxn or set_highres_scorefxn,
DockingProtocol would store your new scorefxn in a pointer, but wouldn't
alter the docking loweres mover or the docking highres mover. Your changes
were effectively ignored! This also affected rosetta_scripts, as
parse_my_tag invoked these functions.
Now, when you invoke any of these functions (there are four, as the
set_highres_scorefxn function is overloaded), the change is passed
along to the mover that's going to actually perform the docking.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3551 from CyrusBiotechnology/davela/add_orientation_to_outlier_list
On @d8vela 's behalf:
Add required PDB entries for the current outlier_list to reinforce the abililty to black-list templates during modeling of antibody Fv heavy to light chain orientations. This fixes antibody.cc (provides the correct input to what it expects to see) so that it will run correctly with recent addition of the filtering feature for orientation. Note that the outlier status for all existing PDB entries in the outlier list are set to "false" meaning they will not be black-listed by default. So, these additions to the outlier_list are neutral changes and will not alter the default behavior of antibody.cc.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3566 from RosettaCommons/roccomoretti/fix_metal_gasteiger
Add fixes for Gasteiger typing of coordinated metals.
This PR does two things. First, it provides better support for "pseudobonds" in input params files, such that it works appropriately with the Gasteiger typing machinery. (Such that we can avoid treating coordinating bonds to metals as regular single bonds when Gasteiger typing.) Secondly, it adds a few ad hoc Gasteiger types for metals which aren't present. (More may need to be added, depending on the full suite of metal ions being used.)
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3564 from RosettaCommons/vmullig/fix_signed_char_issue
Fixing an issue with assignment of -1 to a char
According to the C++ standard, the `char` type can be signed or unsigned -- it's up to the implementation. We have a spot in the Rosetta code where -1 is assigned to a `char`, and although that's fine for compilation on most systems, it breaks the Blue Gene/Q build. (It also likely breaks Android builds -- they also tend to default to `char == unsigned char`.) The simple fix is to declare this `char` to be `signed` explicitly.
In general, if you assign numeric values to a `char` or do math other than just incrementing or decrementing, it's a good idea to make it explicit whether you're working with a signed or unsigned `char`.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3560 from RosettaCommons/roccmoretti/utracer_tab_fix
Fix issue with tabs in UTracer.
UTracer had an issue where it used delta-based comparisons for numbers separated by spaces, but didn't for tab-separated values.
Update the parsing such that the delta-based comparison also applies to tab-separated values.
notify author
notify list [rosetta-logs@googlegroups.com]