MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000160Rosetta[All Projects] Bad Codingpublic2012-12-10 09:542012-12-10 13:18
Reportersmlewis 
Assigned To 
PrioritylowSeverityminorReproducibilityalways
StatusnewResolutionopen 
PlatformAll platformsOSAnyOS VersionAny
Product VersionAll 
Fixed in Version 
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
Summary0000160: Generalize "favor native residue" support
Descriptionwww.rosettacommons.org/content/favor-native-residue-fixbb-design

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.
Steps To Reproduce
Additional Information
TagsNo tags attached.
Relationships
child of 0000161new  Fixbb really should have a protocol-level mover 
Attached Files
Issue History
Date ModifiedUsernameFieldChange
2012-12-10 09:54smlewisNew Issue
2012-12-10 13:18smlewisNote Added: 0000132
2012-12-10 13:18smlewisRelationship addedrelated to 0000161
2012-12-10 13:18smlewisRelationship replacedchild of 0000161

Notes
(0000132)
smlewis   
2012-12-10 13:18   
Here is a code snippet that would work if we fixed 0000161 first:

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


//body
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 );

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