Represent a single solution to a kinematic closure problem. More...

#include <ClosureSolution.hh>

Inheritance diagram for protocols::kinematic_closure::ClosureSolution:

Public Member Functions
void	apply (Pose &pose) const
	Apply this solution to the given pose. More...

bool	apply_if_reasonable (Pose &pose, bool rama_on=true, bool bump_on=true, bool be_lenient=false) const
	If this solution passes rama and bump checks, apply it to the given pose. Return whether or not the filters were passed. More...

Size	get_index () const
	Return a unique number identifying this solution. More...

Real	get_jacobian () const
	Return the Jacobian for this solution. More...

Real	get_distance (ClosureProblem const *problem) const

Private Member Functions
	ClosureSolution (ClosureProblem const *problem, Size const solution_index, ParameterList const &torsion_angles, ParameterList const &bond_angles, ParameterList const &bond_lengths)
	Constructor used internally to build a solution from the internal degrees of freedom returned by the closure algorithm. More...

bool	check_rama (Pose const &pose, Real const temperature) const
	Check for unlikely pivot torsions in this solution. More...

bool	check_overlap (Pose const &pose, Real const scale_factor) const
	Check for overlapping backbone atoms in this solution. More...

Private Attributes
ClosureProblem const *	problem_

Size const	index_

ParameterList const	bond_lengths_

ParameterList const	bond_angles_

ParameterList const	torsion_angles_

Real	jacobian_

Friends
class	ClosureProblem

Detailed Description

Represent a single solution to a kinematic closure problem.

The ClosureSolution class represents the solutions returned by ClosureProblem.solve(). The most important methods of this class are apply() and apply_if_reasonable(). The former unconditionally applies the solution to the given pose, while the latter does so only if the solution passes a rama and bump check.

Constructor & Destructor Documentation

protocols::kinematic_closure::ClosureSolution::ClosureSolution	(	ClosureProblem const *	problem,
		Size const	index,
		ParameterList const &	torsion_angles,
		ParameterList const &	bond_angles,
		ParameterList const &	bond_lengths
	)

private

Constructor used internally to build a solution from the internal degrees of freedom returned by the closure algorithm.

This constructor is called by ClosureProblem, which is a friend class. It is declared as private because it should only be called from code that has been specifically written to solve a closure problem.

Member Function Documentation

void protocols::kinematic_closure::ClosureSolution::apply ( Pose & pose ) const

Apply this solution to the given pose.

References protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), bond_angles_, bond_lengths_, problem_, and torsion_angles_.

Referenced by apply_if_reasonable().

bool protocols::kinematic_closure::ClosureSolution::apply_if_reasonable	(	Pose &	pose,
		bool	rama_on = `true`,
		bool	bump_on = `true`,
		bool	be_lenient = `false`
	)		const

If this solution passes rama and bump checks, apply it to the given pose. Return whether or not the filters were passed.

References apply(), check_overlap(), check_rama(), protocols::kinematic_closure::num_bump_filter_fails, protocols::kinematic_closure::num_rama_filter_fails, problem_, and protocols::kinematic_closure::ClosureProblem::restore().

bool protocols::kinematic_closure::ClosureSolution::check_overlap	(	Pose const &	pose,
		Real const	scale_factor
	)		const

private

Check for overlapping backbone atoms in this solution.

Apply the solution to the pose before calling this filter.

References protocols::kinematic_closure::ClosureProblem::first_residue(), protocols::kinematic_closure::ClosureProblem::last_residue(), problem_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by apply_if_reasonable().

bool protocols::kinematic_closure::ClosureSolution::check_rama	(	Pose const &	pose,
		Real const	temperature
	)		const

private

Check for unlikely pivot torsions in this solution.

References core::pose::Pose::aa(), protocols::kinematic_closure::ClosureProblem::pivot_atoms(), protocols::kinematic_closure::ClosureProblem::pivot_residues(), protocols::simple_moves::bb_sampler::probability, problem_, core::scoring::rama, torsion_angles_, and protocols::kinematic_closure::ClosureProblem::unperturbed_torsions_.

Referenced by apply_if_reasonable().

Real protocols::kinematic_closure::ClosureSolution::get_distance ( ClosureProblem const * problem ) const

@ brief Return a distance metric indicating how similar this solution is to the given problem.

Note that this is not a rigorous distance metric. It's just meant to distinguish one solution that's nearly identical to the given problem from several solutions that aren't.

References bond_angles_, bond_lengths_, core::kinematics::distance(), protocols::kinematic_closure::ClosureProblem::num_atoms(), torsion_angles_, protocols::kinematic_closure::ClosureProblem::unperturbed_angles_, protocols::kinematic_closure::ClosureProblem::unperturbed_lengths_, and protocols::kinematic_closure::ClosureProblem::unperturbed_torsions_.

Size protocols::kinematic_closure::ClosureSolution::get_index ( ) const

Return a unique number identifying this solution.

References index_.

Real protocols::kinematic_closure::ClosureSolution::get_jacobian ( ) const

Return the Jacobian for this solution.

This quantity indicates how much the dihedral space around the pivots was warped by the choice of controls and is used as a normalization factor when picking a move in such a way that obeys detailed balance. The return value is cached, so it's cheap to call this function multiple times.

References bond_angles_, bond_lengths_, jacobian_, protocols::kinematic_closure::ClosureProblem::num_atoms(), protocols::kinematic_closure::ClosureProblem::pivot_atoms(), problem_, protocols::hybridization::r1, protocols::hybridization::r2, and torsion_angles_.