Merge pull request #2040 from RosettaCommons/aleaverfay/ax_apbs
Removing the APBS software package from the external/ directory
I'm merging this; it's already been through the testing server:
http://benchmark.graylab.jhu.edu/revision?id=5689&branch=
External packages need a better review process so this doesn't happen again.
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Merge pull request #2030 from RosettaCommons/rhiju/6D_loop_close
implicit treatment of RNA loops via precalculated 6D tensors
• tests were run (except icc build, which is stuck; was run in a previous test, though) -- integration test changes are all expected (the ones that fluctuate; and a few are effected by new score term `rna_stub_coord_hack`): http://benchmark.graylab.jhu.edu/revision?id=5686&branch=
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Merge pull request #2034 from RosettaCommons/chnorn/evolution_debug
New stopping condition for GenericMonteCarloMover (max accepts), and a new flag to keep filters despite having a score function defined for GenericMonteCarloMover
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Merge pull request #2013 from RosettaCommons/GerardDaniel/scoreTermValueBasedSelector
This is a new residue selector that selects residues that score within the threshold limits of a score term of choice.
A subset of residues can be given as input by specifying residue number, selector sub tag or previously defined selector. By default it works on ALL residues
If a score function is not given, the default score function will be used. In apply() a copy of the pose is scored.
If "total" is given as the score term to be used, all weighted per residue scores are summed up and the value compared to the threshold.
A few regression test seem to fail due to insignificant changes in atom coordinates reported.
Soon, integration test will be added by Jason Klima and Benjamin Basanta.
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Merge pull request #1981 from RosettaCommons/kylebarlow/ddg_backrub
Enables use of our backrub ensemble sampling interface ddG protocol in RosettaScripts.
Integration test for the backrub ensemble sampling interface ddG protocol, implemented as a script
BackrubProtocol changes: ability to use residue selector to select pivot residues, option for apply() function to keep last sampled structure (instead of always recovering lowest energy sampled structure), trajectory options.
UseMultiCoolAnnealer task operation: allows use of MultiCoolAnnealer in RosettaScripts
ScoreFunction tags can now set fa_max_dis option in RosettaScripts.
Option to use harmonic function atom pairwise constraints in AddConstraintsToCurrentConformationMover. This functionality is used in the minimize_with_cst application, and is now available here in the protocols level (and is RosettaScripts accessible)
Option in MinMover to minimize to convergence, as measured by an absolute score convergence threshold. For example, if the maximum number of cycles is exceeded, and the score after minimization has changed by more than the threshold amount, minimization will be run again. This functionality is used in the minimize_with_cst command line application, and is now available here in the protocols level (and is RosettaScripts accessible).
Created InterfaceDdGMover to calculate change in binding ddGs, post mutation. Uses a saved reference Pose for either the wildtype or mutant state.
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Merge pull request #1998 from RosettaCommons/vmullig/helix_end_sequence_constraints_mover
Add a mover that will set up sequence constraints to require charges at helix termini
**The Problem**
It has been observed that designs with charged residues at the ends of helices that complement the helix macrodipole are often more successful than designs without this feature. Specifically, we want an easy way of imposing the following knowledge-based rule:
- Every helix should have at least one positively-charged residue among its C-terminal 3 residues.
- Every helix should have at least one negatively-charged residue among its N-terminal 3 residues.
Task operations cannot solve this problem: there is no way to set the identity of _at least one_ residue among a group of more than one residue to a desired identity with task operations. One can only force _all_ members of a group to have the desired identity, or risk that, after design, _no_ members of the group might have the desired identity.
**The Solution**
This pull request aims to create a mover that will set up **sequence constraints** imposing the rules above. Analogous to geometric constraints, sequence constraints work with the **aa\_composition** score term to impose a nonlinear penalty for devaition from a desired amino acid composition, and can be applied to sub-regions of a pose (like the N-terminal or C-terminal three residues in a particular helix).
Specifically, the new mover will do the following:
1. Apply DSSP to the pose to detect the secondary structure.
2. For every helix, add two new composition constraints:
2a. A composition constraint requiring at least one negatively-charged residue among the three N-terminal residues of the helix.
2b. A composition constraint requiring at least one positively-charged residue among the three N-terminal residues of the helix.
After applying the mover, the user should be able to design using any design tool that calls the packer (_e.g._ PackRotamersMover, FastDesign, _etc._). So long as the **aa\_composition** score term is turned on in the score function, the rule should be imposed. Note that this turns the packer's optimization problem ("give me the lowest-energy combination of rotamers that you can find") into a constrained optimization problem ("give me the lowest-energy combination of rotamers that you can find, subject to the rules that every helix has at least one negatively-charged residue at its N-terminus and at least one positively-charged residue at its C-terminus").
**Tasks**
- [x] Add the mover using Jared's code template scripts.
- [x] Add options for the N-terminal N residues (with N defaulting to 3) and C-terminal M residues (with M defaulting to 3).
- [x] Add options for disabling the N-terminal or C-terminal constraints
- [x] Add an optional residue selector for restricting the imposition of the rules above to a subset of the overall pose, if the user so wishes.
- [x] XSD information.
- [x] Have the mover call DSSP to identify helices.
- [x] Have it create two residue selectors for each helix, selecting the N-terminal N residues and the C-terminal M residues.
- [x] Have it set up composition constraints requiring at least one negatively-charged residue at the N-terminus and at least one positively-charged residue at the C-terminus of each helix.
- [x] Additional features requested by @grocklin (see comment below).
- [x] Penalize helix-disfavouring residue types.
- [x] User configurable charge counts at helix termini.
- [x] Penalize too many or too few alanines, weakly.
- [x] Penalize too few hydrophobic residues, weakly.
- [x] Unit tests.
- [x] Integration tests.
- [x] Basic setup with default settings only.
- [x] Advanced setup with RosettaScripts-accessible options.
- [x] Beauty.
- [x] Documentation.
- [x] Remove TEMPORARY_NOTE.txt.
**Note**
Frank and Hahnbeom are working on a physics-based solution to this problem that will actually consider the helix macrodipole. The mover that this pull request aims to implement, on the other hand, is a quick and dirty way of imposing prior knowledge, until such time as the physics-based solution is up and running; it is _not_ intended as a permanent solution. Note also that this mover is _only_ for the design step, while Frank and Hahnbeom's solution will ultimately be useful for both design and structure prediction-based validation.
@grocklin @dabaker @hahnbeom @fdimaio
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