0000160: Generalize "favor native residue" support

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0000160

Rosetta

[All Projects] Bad Coding

public

2012-12-10 09:54

2012-12-10 13:18

Reporter

smlewis

Assigned To

Priority

low

Severity

minor

Reproducibility

always

Status

new

Resolution

open

Platform

All platforms

Any

OS Version

Any

Product Version

All

Fixed in Version

Summary

0000160: Generalize "favor native residue" support

Description

www.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.

Tags

No tags attached.

Application(s) Affected

fixbb in particular, but packing in general; enzdes and RosettaScripts are exempt

Command Line Used

fixbb -favor_native_res is legal but useless

Developer Options

Feature Request

Fixed in SVN Version

Attached Files

Relationships

child of

0000161

new

Fixbb really should have a protocol-level mover

Notes
(0000132) smlewis (Administrator) 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);

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