protocols::kinematic_closure::solution_pickers::FilteredSolutions Class Reference

Apply rama and bump checks to quickly filter out bad solutions. More...

#include <FilteredSolutions.hh>

Public Member Functions
	FilteredSolutions (bool check_rama=true, bool check_overlap=true, bool be_lenient=false)
	Constructor which can enable or disable any of the filters used by this algorithm. More...
bool	pick_and_apply (Pose &pose, SolutionList const &solutions)
	Pick a solution from the given list, and if apply it to the given pose. If no solution is satisfactory, don't do anything. More...
void	check_rama ()
	Enable the rama check. More...
void	check_overlap ()
	Enable the bump check. More...
void	be_lenient ()
	Make the bump check more lenient. More...
void	dont_check_rama ()
	Disable the rama check. More...
void	dont_check_overlap ()
	Disable the bump check. More...
void	dont_be_lenient ()
	Make the bump check more lenient. More...

Private Attributes
bool	check_rama_
bool	check_overlap_
bool	be_lenient_

Detailed Description

Apply rama and bump checks to quickly filter out bad solutions.

The rama check only considers the pivot torsions, since it is assumed that the non-pivot torsions were set as desired. This check employs a Monte Carlo acceptance step, which means that the pivot torsions will really be sampled from a rama distribution (ignoring the inherent geometric biases in the closure algorithm) when this check is enabled. However, note that the rama distribution will be double-counted if the score function also contains a rama term, which it usually does.

The bump check checks for clashes between the N, CA, C, O, and CB atoms of every residue in the loop versus every other residue in the protein. This filter is O(n^2) and is much slower than the constant time rama check. The rama check is also very selective; it usually filters out more than 90% of proposed solutions. For these reasons, it is important that the rama check be run before the bump check. You can disable the rama check, but this would probably lead to a noticeable drop in performance.

Constructor & Destructor Documentation

protocols::kinematic_closure::solution_pickers::FilteredSolutions::FilteredSolutions	(	bool	check_rama = true,
		bool	check_overlap = true,
		bool	be_lenient = false
	)

Constructor which can enable or disable any of the filters used by this algorithm.

Member Function Documentation

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::be_lenient ( )

inline

Make the bump check more lenient.

References be_lenient_.

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_overlap ( )

inline

Enable the bump check.

References check_overlap_.

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_rama ( )

inline

Enable the rama check.

References check_rama_.

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_be_lenient ( )

inline

Make the bump check more lenient.

References be_lenient_.

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_check_overlap ( )

inline

Disable the bump check.

References check_overlap_.

void protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_check_rama ( )

inline

Disable the rama check.

References check_rama_.

bool protocols::kinematic_closure::solution_pickers::FilteredSolutions::pick_and_apply ( Pose &  pose, SolutionList const &  solutions  )

virtual

Pick a solution from the given list, and if apply it to the given pose. If no solution is satisfactory, don't do anything.

Implements protocols::kinematic_closure::solution_pickers::SolutionPicker.

Member Data Documentation

bool protocols::kinematic_closure::solution_pickers::FilteredSolutions::be_lenient_

private

Referenced by be_lenient(), and dont_be_lenient().

bool protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_overlap_

private

Referenced by check_overlap(), and dont_check_overlap().

bool protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_rama_

private

Referenced by check_rama(), and dont_check_rama().

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

• src/protocols/kinematic_closure/solution_pickers/FilteredSolutions.hh
• src/protocols/kinematic_closure/solution_pickers/FilteredSolutions.cc