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IDProjectCategoryView StatusDate SubmittedLast Update
0000160Rosetta[All Projects] Bad Codingpublic2012-12-10 09:542012-12-10 13:18
Assigned To 
PlatformAll platformsOSAnyOS VersionAny
Product VersionAll 
Fixed in Version 
Summary0000160: Generalize "favor native residue" support

It would be nice if we had a generalized favor_native_residue support, or at least a version that works for fixbb. The existing Mover for the purpose, FavorNativeResiduePreCycle, works _only_ with RosettaScripts and not in isolation. There is a FavorNativeResidue class, and the ResidueTypeConstraint is easy to use in isolation, but it is moderately nontrivial to synchronize these with the fixbb/JD2 paradigm of "no pose until apply" and the necessary scorefunction sharing.

What would be really nice would be if this worked from resfile. That would require the packer to add/remove constraints (PackerTask can't because it doesn't see the pose at its application time), which might be breaking encapsulation.
TagsNo tags attached.
Application(s) Affectedfixbb in particular, but packing in general; enzdes and RosettaScripts are exempt
Command Line Usedfixbb -favor_native_res is legal but useless
Developer OptionsFeature Request
Fixed in SVN Version
Attached Files

- Relationships
child of 0000161new Fixbb really should have a protocol-level mover 

-  Notes
smlewis (Administrator)
2012-12-10 13:18

Here is a code snippet that would work if we fixed 0000161 first:

#include <core/scoring/constraints/ResidueTypeConstraint.hh>
basic::options::RealOptionKey const fav_nat_bonus("fav_nat_bonus");

for ( Size i=1; i<= pose.total_residue(); ++i ) {
        pose.add_constraint( new ResidueTypeConstraint( pose, i,
basic::options::option[fav_nat_bonus].value()) );
//might want to check is_protein
scorefxn->set_weight( res_type_constraint, 1.0 );

option.add( fav_nat_bonus, "favor native residue" ).def(1.5);

- Issue History
Date Modified Username Field Change
2012-12-10 09:54 smlewis New Issue
2012-12-10 13:18 smlewis Note Added: 0000132
2012-12-10 13:18 smlewis Relationship added related to 0000161
2012-12-10 13:18 smlewis Relationship replaced child of 0000161

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