Merge pull request #1485 from RosettaCommons/jadolfbr/singleton_code_template
Add code_template for Singletons
Thanks to @JWLabonte for some great singleton examples and tips.
Now, we have almost full coverage of common Rosetta classes!!!
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Merge pull request #1486 from RosettaCommons/jadolfbr/jadolfbr/h3_camelid
Fix H3 model camelid integration test
It turns out that camelid antibodies NEVER actually worked in AntibodyModelerProtocol. So my simple addition of an integration test and simple fixes for what I thought I had broken while working on antibody design, was not enough.
Adding the integration test caused a failure, which I thought was due to adding the test.
This fixes that.
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Merge pull request #1488 from RosettaCommons/yhsia/sym_residue_selector
ResidueSelector: Selects input residues + all of its symmetrical cloned residues
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Merge pull request #1481 from RosettaCommons/tlinsky/stream_util
Add std::set operator<< in stream_util.hh
Cosmetic integration test changes expected for symm_disulfidize and dcys_disulfidize, due to disulfidize mover now using std::pair operator<< found in stream_util.hh
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Merge pull request #1475 from RosettaCommons/vmullig/aspartimide
Add a score term to penalize sequences that are likely to result in aspartimide during peptide synthesis
In designing peptides, we're having to throw away or redesign a heck of a lot of designs because of DN, DS, DT, Dx, DG, dn, ds, dt, dX, or dG sequences, which often result in the unwanted aspartimide side-product during peptide synthesis. My Thursday night project will be to add a score term to penalize these two-residue sequences during design, so that the packer simply doesn't put them in. (There are several other things that we're also having to filter for, and each one cuts down our viable designs by an order of magnitude, greatly increasing the number of designs that we have to do in order to get one that we can synthesize. This is the easiest and quickest thing for me to fix with a non-filter-based solution, increasing our good design rate by an order of magnitude or so.)
Tasks:
- Add the score term.
- Have it only apply itself to pairs of residues that are conventionally connected (i.e. residue i is connected to residue j at residue i's C-terminus and residue j's N-terminus).
- Have it penalize the sequences in question.
X Double-check which sequences should be penalized. (Some also say DC, DD, and DR [and their mirrors]. DP and Dx', where x' is N-methylated, should be immune to aspartimide formation, though.) @gbhardwaj --> If there's a need to tweak what's penalized in the future, or to add general user controls, we can do this when we need it.
- Unit test.
- Beauty.
- Documentation.
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Merge pull request #1372 from RosettaCommons/jadolfbr/antibodies/fix_h3_ab_protocol
Camelid and antibody protocol fix
This PR enables camelid antibodies for the antibody protocol, specifically, antibody_H3. I don't think this ever actually worked as the test for camelids was never being checked. This also adds an integration test for camelid antibodies and antibody_H3.
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