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protocols::loophash::LocalInserter_SimpleMin Class Reference

Insert a backbone segment and use minimization with coordinate constraints to keep the insertion local. More...

#include <LocalInserter.hh>

Inheritance diagram for protocols::loophash::LocalInserter_SimpleMin:
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Public Member Functions

 LocalInserter_SimpleMin ()
 
void scorefxn_rama_cst (core::scoring::ScoreFunction const &scorefxn)
 Set the score function for the first round of minimization during a loophash insert. More...
 
void scorefxn_cen_cst (core::scoring::ScoreFunction const &scorefxn)
 Set the score function for the second round of minimization during a loophash insert. More...
 
core::Real make_local_bb_change (core::pose::Pose &start_pose, const core::pose::Pose &original_pose, const protocols::loophash::BackboneSegment &new_bs, core::Size res_pos) override
 
core::Real make_local_bb_change_close_gaps (core::pose::Pose &start_pose, const core::pose::Pose &original_pose, const protocols::loophash::BackboneSegment &new_bs, core::Size res_pos) override
 
core::Real make_local_bb_change_include_cut (core::pose::Pose &start_pose, const core::pose::Pose &original_pose, const protocols::loophash::BackboneSegment &new_bs, core::Size res_pos) override
 
- Public Member Functions inherited from protocols::loophash::LocalInserter
 ~LocalInserter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 LocalInserter ()
 

Private Member Functions

void set_default_score_functions ()
 Define hard-coded default scorefunctions for the minimization steps. More...
 

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_rama_cst_
 
core::optimization::MinimizerOptions options_
 
core::scoring::ScoreFunctionOP scorefxn_cen_cst_
 
core::optimization::MinimizerOptions options2_
 

Detailed Description

Insert a backbone segment and use minimization with coordinate constraints to keep the insertion local.

Constructor & Destructor Documentation

protocols::loophash::LocalInserter_SimpleMin::LocalInserter_SimpleMin ( )
inline

Member Function Documentation

core::Real protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change ( core::pose::Pose start_pose,
const core::pose::Pose original_pose,
const protocols::loophash::BackboneSegment new_bs,
core::Size  res_pos 
)
overridevirtual

This method uses the following algorithm:

  • Constrain atoms outside the region where the insertion will occur to their initial coordinates.
  • Apply the torsions from the given backbone segment.
  • Minimize first with only the rama term
  • Minimize again with a hard-coded centroid-like score function (see LocalInserter_SimpleMin::set_default_score_functions() for details) and a stricter convergence tolerance.

Implements protocols::loophash::LocalInserter.

References protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::Loops::add_loop(), protocols::loophash::BackboneSegment::apply_to_pose(), core::scoring::CA_rmsd(), protocols::loophash::BackboneSegment::length(), core::kinematics::MoveMap::set_bb(), core::pose::set_ss_from_phipsi(), core::pose::setPoseExtraScore(), core::pose::TR(), and core::pose::transfer_phi_psi().

core::Real protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps ( core::pose::Pose start_pose,
const core::pose::Pose original_pose,
const protocols::loophash::BackboneSegment new_bs,
core::Size  res_pos 
)
overridevirtual
core::Real protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut ( core::pose::Pose start_pose,
const core::pose::Pose original_pose,
const protocols::loophash::BackboneSegment new_bs,
core::Size  res_pos 
)
overridevirtual
void protocols::loophash::LocalInserter_SimpleMin::scorefxn_cen_cst ( core::scoring::ScoreFunction const &  scorefxn)

Set the score function for the second round of minimization during a loophash insert.

References core::scoring::ScoreFunction::clone().

void protocols::loophash::LocalInserter_SimpleMin::scorefxn_rama_cst ( core::scoring::ScoreFunction const &  scorefxn)

Set the score function for the first round of minimization during a loophash insert.

References core::scoring::ScoreFunction::clone().

void protocols::loophash::LocalInserter_SimpleMin::set_default_score_functions ( )
private

Member Data Documentation

core::optimization::MinimizerOptions protocols::loophash::LocalInserter_SimpleMin::options2_
private
core::optimization::MinimizerOptions protocols::loophash::LocalInserter_SimpleMin::options_
private
core::scoring::ScoreFunctionOP protocols::loophash::LocalInserter_SimpleMin::scorefxn_cen_cst_
private
core::scoring::ScoreFunctionOP protocols::loophash::LocalInserter_SimpleMin::scorefxn_rama_cst_
private

The documentation for this class was generated from the following files: