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:

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

LocalInserter_SimpleMin()

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

inline

References set_default_score_functions().

Member Function Documentation

make_local_bb_change()

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().

make_local_bb_change_close_gaps()

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

Similar to make_local_bb_change(), but before the torsions from the given backbone segment are inserted, the bond lengths and angles for those residues are idealized, so that if there was a chainbreak, it would be fixed.

Note

This whole function, with the exception of the "idx" for-loop, is duplicated from make_local_bb_change(). This could be easily refactored.

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(), core::pose::Pose::conformation(), protocols::relax::delete_virtual_residues(), core::conformation::insert_ideal_bonds_at_polymer_junction(), protocols::loophash::BackboneSegment::length(), core::kinematics::MoveMap::set_bb(), core::pose::set_ss_from_phipsi(), core::pose::setPoseExtraScore(), core::pose::Pose::size(), core::pose::TR(), and core::pose::transfer_phi_psi().

make_local_bb_change_include_cut()

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

It looks to me like this method applies coordinate constraints and inserts the given backbone segment, but never does any minimization.

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::pose::set_ss_from_phipsi(), core::pose::setPoseExtraScore(), core::pose::TR(), and core::pose::transfer_phi_psi().

scorefxn_cen_cst()

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().

scorefxn_rama_cst()

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().

set_default_score_functions()

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

private

Define hard-coded default scorefunctions for the minimization steps.

References core::scoring::cbeta, core::scoring::cenpack, core::scoring::coordinate_constraint, core::scoring::env, core::scoring::hs_pair, core::scoring::pair, core::scoring::rama, core::scoring::rg, core::scoring::rsigma, core::scoring::sheet, core::scoring::ss_pair, and core::scoring::vdw.

Referenced by LocalInserter_SimpleMin().

Member Data Documentation

options2_

core::optimization::MinimizerOptions protocols::loophash::LocalInserter_SimpleMin::options2_

private

options_

core::optimization::MinimizerOptions protocols::loophash::LocalInserter_SimpleMin::options_

private

scorefxn_cen_cst_

core::scoring::ScoreFunctionOP protocols::loophash::LocalInserter_SimpleMin::scorefxn_cen_cst_

private

scorefxn_rama_cst_

core::scoring::ScoreFunctionOP protocols::loophash::LocalInserter_SimpleMin::scorefxn_rama_cst_

private

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

• src/protocols/loophash/LocalInserter.hh
• src/protocols/loophash/LocalInserter.cc