Represent and solve a kinematic closure problem. More...

#include <ClosureProblem.hh>

Inheritance diagram for protocols::kinematic_closure::ClosureProblem:

Classes
class	Memento
	Save the current state of the closure problem. This is meant to facilitate undoing rejected perturbations when necessary. More...

Public Member Functions
	ClosureProblem ()
	Default constructor. More...

	~ClosureProblem () override
	Default destructor. More...

void	frame (Pose const &pose, Loop const &loop, pivot_pickers::PivotPickerOP pivot_picker)
	Choose pivots and copy coordinate information into the problem. More...

SolutionList	solve () const
	Return every possible solution to this problem. More...

void	restore (Pose &pose) const
	Undo any changes made to the pose during the last move. More...

void	perturb_phi (core::Size residue, Real value, AngleUnit unit)
	Perturb the given phi angle. More...

void	perturb_psi (core::Size residue, Real value, AngleUnit unit)
	Perturb the given psi angle. More...

void	perturb_omega (core::Size residue, Real value, AngleUnit unit)
	Perturb the given omega angle. More...

void	perturb_n_ca_c (core::Size residue, Real value, AngleUnit unit)
	Perturb the N-CA-C bond angle in the given residue. More...

void	perturb_ca_c_n (core::Size residue, Real value, AngleUnit unit)
	Perturb the CA-C-N bond angle in the given residue. More...

void	perturb_c_n_ca (core::Size residue, Real value, AngleUnit unit)
	Perturb the C-N-CA bond angle in the given residue. More...

void	perturb_n_ca (core::Size residue, Real value)
	Perturb the N-CA bond length in the given residue. More...

void	perturb_ca_c (core::Size residue, Real value)
	Perturb the CA-C bond length in the given residue. More...

void	perturb_c_n (core::Size residue, Real value)
	Perturb the C-N bond length in the given residue. More...

ParameterList &	perturb_torsions ()
	Provide non-const access to the raw torsion angle list. More...

ParameterList &	perturb_angles ()
	Provide non-const access to the raw bond angle list. More...

ParameterList &	perturb_lengths ()
	Provide non-const access to the raw bond length list. More...

core::Size	first_residue () const
	Return the index of the first pivot residue. More...

core::Size	cut_residue () const
	Return the index of the second pivot residue. More...

core::Size	last_residue () const
	Return the index of the third pivot residue. More...

core::Size	num_residues () const
	Return the number of residues in the loop. More...

core::Size	num_atoms () const
	Return the number of atoms in the loop. More...

Real	phi (core::Size residue, AngleUnit unit) const
	Return the current value of the given phi angle. More...

Real	psi (core::Size residue, AngleUnit unit) const
	Return the current value of the given psi angle. More...

Real	omega (core::Size residue, AngleUnit unit) const
	Return the current value of the given omega angle. More...

Real	n_ca_c (core::Size residue, AngleUnit unit) const
	Return the current value of the given N-CA-C bond angle. More...

Real	ca_c_n (core::Size residue, AngleUnit unit) const
	Return the current value of the given CA-C-N bond angle. More...

Real	c_n_ca (core::Size residue, AngleUnit unit) const
	Return the current value of the given C-N-CA bond angle. More...

Real	n_ca (core::Size residue) const
	Return the current value of the given N-CA bond length. More...

Real	ca_c (core::Size residue) const
	Return the current value of the given CA-C bond length. More...

Real	c_n (core::Size residue) const
	Return the current value of the given C-N bond length. More...

bool	is_pivot_residue (core::Size residue) const
	Return true if the given residue is a pivot. More...

bool	is_nonpivot_residue (core::Size residue) const
	Return true if the given residue is not a pivot. More...

Loop	pivot_loop () const
	Return a loop specifying the three pivot residues. More...

IndexList	residues () const
	Return the indices of every residue in the loop. More...

IndexList	pivot_residues () const
	Return the indices of all three pivot residues. More...

IndexList	nonpivot_residues () const
	Return the indices of every nonpivot residue in the loop. More...

IndexList	pivot_atoms () const
	Return the indices of all three pivot atoms. More...

void	perturbed_sequence (utility::vector1< std::string > const &values)
	Set AA sequence from left pivot to the right pivot (including the pivots) More...

utility::vector1< std::string >	perturbed_sequence () const
	Get perturbed AA sequence from left pivot to the right pivot (including the pivots) More...

utility::vector1< std::string >	unperturbed_sequence () const
	Get unperturbed AA sequence from left pivot to the right pivot (including the pivots) More...

bool	sequence_mutated () const
	Return if mutations have been made to the sequence. More...

Private Member Functions
void	extract_cartesian_coordinates (Pose const &pose, CoordinateList &atom_xyzs) const
	Extract cartesian coordinates for those backbone atoms which are relevant to the closure algorithm. This includes all atoms from within the loop and from the two residues on either side of the loop. More...

void	extract_internal_coordinates (CoordinateList const &atom_xyzs, ParameterList &bond_lengths, ParameterList &bond_angles, ParameterList &torsion_angles) const
	Extract torsion angles, bond angles, and bond lengths for those backbone atoms which are relevant to the closure algorithm. More...

void	extract_internal_coordinates (Pose const &pose, ParameterList &bond_lengths, ParameterList &bond_angles, ParameterList &torsion_angles) const

void	apply_internal_coordinates (ParameterList const &bond_lengths, ParameterList const &bond_angles, ParameterList const &torsion_angles, Pose &pose) const
	Apply the given internal coordinates to the given pose. More...

void	frame_lower_pivot (Pose const &pose, CoordinateList &atom_xyzs) const
	Extract coordinates for the residue just beyond the N-terminal pivot. These coordinates help anchor the closure problem. More...

void	frame_upper_pivot (Pose const &pose, CoordinateList &atom_xyzs) const
	Extract coordinates for the residue just beyond the C-terminal pivot. These coordinates help anchor the closure problem. More...

bool	ids_span_cut (core::id::AtomID left, core::id::AtomID right) const
	Return true if the two given atoms are on opposite sides of the cutpoint specified by the loop that was used to create this problem. More...

core::id::AtomID	id_from_index (core::Size index) const
	Return an AtomID referring to the atom at the given index relative to the start of the loop. More...

void	mutate_residues (core::pose::Pose &pose, utility::vector1< std::string > sequence) const
	Mutate the residues between pivots to the sequence_ (including pivots) More...

Private Attributes
Loop	pivots_

bool	frame_called_

ParameterList	perturbed_lengths_

ParameterList	perturbed_angles_

ParameterList	perturbed_torsions_

ParameterList	unperturbed_lengths_

ParameterList	unperturbed_angles_

ParameterList	unperturbed_torsions_

CoordinateList	unperturbed_xyzs_

utility::vector1< std::string >	unperturbed_sequence_

utility::vector1< std::string >	perturbed_sequence_

Friends
class	ClosureSolution

class	Memento

Detailed Description

Represent and solve a kinematic closure problem.

A number of parameters are needed to define a kinematic closure problem. These parameters include a region of the protein backbone, a set of pivot residues, and a new set of torsion angles for the nonpivot residues. All of this can be specified using the frame() and perturb_* methods. Once that has been done, the solve() method can be called to return the complete set of backbone conformations consistent with the given parameters. These conformations are represented by the ClosureSolution class. The restore() method can be used to undo a solution once it has been applied, which is useful in some Monte Carlo schemes.

Constructor & Destructor Documentation

◆ ClosureProblem()

protocols::kinematic_closure::ClosureProblem::ClosureProblem ( )

Default constructor.

◆ ~ClosureProblem()

protocols::kinematic_closure::ClosureProblem::~ClosureProblem ( )

overridedefault

Default destructor.

Member Function Documentation

◆ apply_internal_coordinates()

void protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates	(	ParameterList const &	bond_lengths,
		ParameterList const &	bond_angles,
		ParameterList const &	torsion_angles,
		Pose &	pose
	)		const

private

Apply the given internal coordinates to the given pose.

References protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::pose::Pose::conformation(), first_residue(), id_from_index(), last_residue(), num_atoms(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::kinematic_closure::ClosureSolution::apply().

◆ c_n()

Real protocols::kinematic_closure::ClosureProblem::c_n ( core::Size residue ) const

Return the current value of the given C-N bond length.

References first_residue(), and perturbed_lengths_.

◆ c_n_ca()

Real protocols::kinematic_closure::ClosureProblem::c_n_ca	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given C-N-CA bond angle.

References first_residue(), and perturbed_angles_.

◆ ca_c()

Real protocols::kinematic_closure::ClosureProblem::ca_c ( core::Size residue ) const

Return the current value of the given CA-C bond length.

References first_residue(), and perturbed_lengths_.

◆ ca_c_n()

Real protocols::kinematic_closure::ClosureProblem::ca_c_n	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given CA-C-N bond angle.

References first_residue(), and perturbed_angles_.

◆ cut_residue()

Size protocols::kinematic_closure::ClosureProblem::cut_residue ( ) const

Return the index of the second pivot residue.

References protocols::loops::Loop::cut(), frame_called_, and pivots_.

Referenced by ids_span_cut(), is_pivot_residue(), nonpivot_residues(), pivot_atoms(), and pivot_residues().

◆ extract_cartesian_coordinates()

void protocols::kinematic_closure::ClosureProblem::extract_cartesian_coordinates	(	Pose const &	pose,
		CoordinateList &	atom_xyzs
	)		const

private

Extract cartesian coordinates for those backbone atoms which are relevant to the closure algorithm. This includes all atoms from within the loop and from the two residues on either side of the loop.

This method does not change anything about the problem object itself. All changes are made to the given atom_xyzs pseudo-matrix.

References first_residue(), frame_lower_pivot(), frame_upper_pivot(), last_residue(), num_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

◆ extract_internal_coordinates() [1/2]

void protocols::kinematic_closure::ClosureProblem::extract_internal_coordinates	(	CoordinateList const &	atom_xyzs,
		ParameterList &	bond_lengths,
		ParameterList &	bond_angles,
		ParameterList &	torsion_angles
	)		const

private

Extract torsion angles, bond angles, and bond lengths for those backbone atoms which are relevant to the closure algorithm.

References protocols::environment::bond_angles(), protocols::environment::bond_lengths(), and num_atoms().

◆ extract_internal_coordinates() [2/2]

void protocols::kinematic_closure::ClosureProblem::extract_internal_coordinates	(	Pose const &	pose,
		ParameterList &	bond_lengths,
		ParameterList &	bond_angles,
		ParameterList &	torsion_angles
	)		const

private

◆ first_residue()

Size protocols::kinematic_closure::ClosureProblem::first_residue ( ) const

Return the index of the first pivot residue.

References frame_called_, pivots_, and protocols::loops::Loop::start().

Referenced by apply_internal_coordinates(), c_n(), c_n_ca(), ca_c(), ca_c_n(), protocols::kinematic_closure::ClosureSolution::check_overlap(), extract_cartesian_coordinates(), frame_lower_pivot(), id_from_index(), is_pivot_residue(), n_ca(), n_ca_c(), nonpivot_residues(), omega(), phi(), pivot_atoms(), pivot_residues(), psi(), and residues().

◆ frame()

void protocols::kinematic_closure::ClosureProblem::frame	(	Pose const &	pose,
		Loop const &	loop,
		pivot_pickers::PivotPickerOP	pivot_picker
	)

Choose pivots and copy coordinate information into the problem.

References core::conformation::Residue::name3(), and core::pose::Pose::residue().

◆ frame_lower_pivot()

void protocols::kinematic_closure::ClosureProblem::frame_lower_pivot	(	Pose const &	pose,
		CoordinateList &	atom_xyzs
	)		const

private

Extract coordinates for the residue just beyond the N-terminal pivot. These coordinates help anchor the closure problem.

References core::id::BB, core::conformation::Residue::clone(), core::pose::Pose::conformation(), first_residue(), core::conformation::Residue::is_lower_terminus(), core::id::omega_dihedral, core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by extract_cartesian_coordinates().

◆ frame_upper_pivot()

void protocols::kinematic_closure::ClosureProblem::frame_upper_pivot	(	Pose const &	pose,
		CoordinateList &	atom_xyzs
	)		const

private

Extract coordinates for the residue just beyond the C-terminal pivot. These coordinates help anchor the closure problem.

References core::id::BB, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::Residue::is_upper_terminus(), last_residue(), core::id::omega_dihedral, core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by extract_cartesian_coordinates().

◆ id_from_index()

AtomID protocols::kinematic_closure::ClosureProblem::id_from_index ( core::Size index ) const

private

Return an AtomID referring to the atom at the given index relative to the start of the loop.

More specifically, the first atom in the loop is taken to be the backbone nitrogen of the residue preceding the first pivot. Thus the index of the first pivot is 5 (pivots must be alpha carbons).

References first_residue().

Referenced by apply_internal_coordinates().

◆ ids_span_cut()

bool protocols::kinematic_closure::ClosureProblem::ids_span_cut	(	core::id::AtomID	left,
		core::id::AtomID	right
	)		const

private

Return true if the two given atoms are on opposite sides of the cutpoint specified by the loop that was used to create this problem.

References cut_residue(), core::sequence::left, and core::id::AtomID::rsd().

◆ is_nonpivot_residue()

bool protocols::kinematic_closure::ClosureProblem::is_nonpivot_residue ( core::Size residue ) const

Return true if the given residue is not a pivot.

References is_pivot_residue().

◆ is_pivot_residue()

bool protocols::kinematic_closure::ClosureProblem::is_pivot_residue ( core::Size residue ) const

Return true if the given residue is a pivot.

References cut_residue(), first_residue(), and last_residue().

Referenced by is_nonpivot_residue().

◆ last_residue()

Size protocols::kinematic_closure::ClosureProblem::last_residue ( ) const

Return the index of the third pivot residue.

References frame_called_, pivots_, and protocols::loops::Loop::stop().

Referenced by apply_internal_coordinates(), protocols::kinematic_closure::ClosureSolution::check_overlap(), extract_cartesian_coordinates(), frame_upper_pivot(), is_pivot_residue(), nonpivot_residues(), pivot_atoms(), pivot_residues(), and residues().

◆ mutate_residues()

void protocols::kinematic_closure::ClosureProblem::mutate_residues	(	core::pose::Pose &	pose,
		utility::vector1< std::string >	sequence
	)		const

private

Mutate the residues between pivots to the sequence_ (including pivots)

References protocols::loops::add_cutpoint_variants(), protocols::simple_moves::MutateResidue::apply(), core::pose::Pose::fold_tree(), frame_called_, core::conformation::Residue::name3(), pivots_, core::util::remove_cutpoint_variants(), core::pose::Pose::residue(), protocols::simple_moves::MutateResidue::set_res_name(), protocols::simple_moves::MutateResidue::set_target(), core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().

◆ n_ca()

Real protocols::kinematic_closure::ClosureProblem::n_ca ( core::Size residue ) const

Return the current value of the given N-CA bond length.

References first_residue(), and perturbed_lengths_.

◆ n_ca_c()

Real protocols::kinematic_closure::ClosureProblem::n_ca_c	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given N-CA-C bond angle.

References first_residue(), and perturbed_angles_.

◆ nonpivot_residues()

IndexList protocols::kinematic_closure::ClosureProblem::nonpivot_residues ( ) const

Return the indices of every nonpivot residue in the loop.

References cut_residue(), first_residue(), and last_residue().

◆ num_atoms()

Size protocols::kinematic_closure::ClosureProblem::num_atoms ( ) const

Return the number of atoms in the loop.

References num_residues().

Referenced by apply_internal_coordinates(), extract_cartesian_coordinates(), extract_internal_coordinates(), protocols::kinematic_closure::ClosureSolution::get_distance(), and protocols::kinematic_closure::ClosureSolution::get_jacobian().

◆ num_residues()

Size protocols::kinematic_closure::ClosureProblem::num_residues ( ) const

Return the number of residues in the loop.

References frame_called_, protocols::loops::Loop::length(), and pivots_.

Referenced by num_atoms().

◆ omega()

Real protocols::kinematic_closure::ClosureProblem::omega	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given omega angle.

References first_residue(), and perturbed_torsions_.

◆ perturb_angles()

ParameterList & protocols::kinematic_closure::ClosureProblem::perturb_angles ( )

Provide non-const access to the raw bond angle list.

◆ perturb_c_n()

void protocols::kinematic_closure::ClosureProblem::perturb_c_n	(	core::Size	residue,
		Real	value
	)

Perturb the C-N bond length in the given residue.

◆ perturb_c_n_ca()

void protocols::kinematic_closure::ClosureProblem::perturb_c_n_ca	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the C-N-CA bond angle in the given residue.

◆ perturb_ca_c()

void protocols::kinematic_closure::ClosureProblem::perturb_ca_c	(	core::Size	residue,
		Real	value
	)

Perturb the CA-C bond length in the given residue.

◆ perturb_ca_c_n()

void protocols::kinematic_closure::ClosureProblem::perturb_ca_c_n	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the CA-C-N bond angle in the given residue.

◆ perturb_lengths()

ParameterList & protocols::kinematic_closure::ClosureProblem::perturb_lengths ( )

Provide non-const access to the raw bond length list.

◆ perturb_n_ca()

void protocols::kinematic_closure::ClosureProblem::perturb_n_ca	(	core::Size	residue,
		Real	value
	)

Perturb the N-CA bond length in the given residue.

◆ perturb_n_ca_c()

void protocols::kinematic_closure::ClosureProblem::perturb_n_ca_c	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the N-CA-C bond angle in the given residue.

◆ perturb_omega()

void protocols::kinematic_closure::ClosureProblem::perturb_omega	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the given omega angle.

◆ perturb_phi()

void protocols::kinematic_closure::ClosureProblem::perturb_phi	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the given phi angle.

◆ perturb_psi()

void protocols::kinematic_closure::ClosureProblem::perturb_psi	(	core::Size	residue,
		Real	value,
		AngleUnit	unit
	)

Perturb the given psi angle.

◆ perturb_torsions()

ParameterList & protocols::kinematic_closure::ClosureProblem::perturb_torsions ( )

Provide non-const access to the raw torsion angle list.

◆ perturbed_sequence() [1/2]

utility::vector1< std::string > protocols::kinematic_closure::ClosureProblem::perturbed_sequence ( ) const

Get perturbed AA sequence from left pivot to the right pivot (including the pivots)

References perturbed_sequence_.

◆ perturbed_sequence() [2/2]

void protocols::kinematic_closure::ClosureProblem::perturbed_sequence ( utility::vector1< std::string > const & values )

Set AA sequence from left pivot to the right pivot (including the pivots)

References perturbed_sequence_.

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().

◆ phi()

Real protocols::kinematic_closure::ClosureProblem::phi	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given phi angle.

References first_residue(), and perturbed_torsions_.

◆ pivot_atoms()

IndexList protocols::kinematic_closure::ClosureProblem::pivot_atoms ( ) const

Return the indices of all three pivot atoms.

References cut_residue(), first_residue(), and last_residue().

Referenced by protocols::kinematic_closure::ClosureSolution::check_rama(), and protocols::kinematic_closure::ClosureSolution::get_jacobian().

◆ pivot_loop()

Loop protocols::kinematic_closure::ClosureProblem::pivot_loop ( ) const

Return a loop specifying the three pivot residues.

References pivots_.

◆ pivot_residues()

IndexList protocols::kinematic_closure::ClosureProblem::pivot_residues ( ) const

Return the indices of all three pivot residues.

References cut_residue(), first_residue(), and last_residue().

Referenced by protocols::kinematic_closure::ClosureSolution::check_rama().

◆ psi()

Real protocols::kinematic_closure::ClosureProblem::psi	(	core::Size	residue,
		AngleUnit	unit
	)		const

Return the current value of the given psi angle.

References first_residue(), and perturbed_torsions_.

◆ residues()

IndexList protocols::kinematic_closure::ClosureProblem::residues ( ) const

Return the indices of every residue in the loop.

References first_residue(), and last_residue().

◆ restore()

void protocols::kinematic_closure::ClosureProblem::restore ( Pose & pose ) const

Undo any changes made to the pose during the last move.

This method is typically used to restore the pose if no solutions to the closure problem could be found. It should only be called after frame() and solve().

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().

◆ sequence_mutated()

bool protocols::kinematic_closure::ClosureProblem::sequence_mutated ( ) const

Return if mutations have been made to the sequence.

References perturbed_sequence_, and unperturbed_sequence_.

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().

◆ solve()

SolutionList protocols::kinematic_closure::ClosureProblem::solve ( ) const

Return every possible solution to this problem.

References protocols::forge::methods::order().

◆ unperturbed_sequence()

utility::vector1< std::string > protocols::kinematic_closure::ClosureProblem::unperturbed_sequence ( ) const

Get unperturbed AA sequence from left pivot to the right pivot (including the pivots)

References unperturbed_sequence_.

Friends And Related Function Documentation

◆ ClosureSolution

friend class ClosureSolution

friend

◆ Memento

friend class Memento

friend

Member Data Documentation

◆ frame_called_

bool protocols::kinematic_closure::ClosureProblem::frame_called_

private

Referenced by cut_residue(), first_residue(), last_residue(), mutate_residues(), and num_residues().

◆ perturbed_angles_

ParameterList protocols::kinematic_closure::ClosureProblem::perturbed_angles_

private

Referenced by c_n_ca(), ca_c_n(), n_ca_c(), and protocols::kinematic_closure::ClosureProblem::Memento::restore().

◆ perturbed_lengths_

ParameterList protocols::kinematic_closure::ClosureProblem::perturbed_lengths_

private

Referenced by c_n(), ca_c(), n_ca(), and protocols::kinematic_closure::ClosureProblem::Memento::restore().

◆ perturbed_sequence_

utility::vector1<std::string> protocols::kinematic_closure::ClosureProblem::perturbed_sequence_

private

Referenced by perturbed_sequence(), and sequence_mutated().

◆ perturbed_torsions_

ParameterList protocols::kinematic_closure::ClosureProblem::perturbed_torsions_

private

Referenced by omega(), phi(), psi(), and protocols::kinematic_closure::ClosureProblem::Memento::restore().

◆ pivots_

Loop protocols::kinematic_closure::ClosureProblem::pivots_

private

Referenced by cut_residue(), first_residue(), last_residue(), mutate_residues(), num_residues(), and pivot_loop().

◆ unperturbed_angles_

ParameterList protocols::kinematic_closure::ClosureProblem::unperturbed_angles_

private

Referenced by protocols::kinematic_closure::ClosureSolution::get_distance().

◆ unperturbed_lengths_

ParameterList protocols::kinematic_closure::ClosureProblem::unperturbed_lengths_

private

Referenced by protocols::kinematic_closure::ClosureSolution::get_distance().

◆ unperturbed_sequence_

utility::vector1<std::string> protocols::kinematic_closure::ClosureProblem::unperturbed_sequence_

private

Referenced by sequence_mutated(), and unperturbed_sequence().

◆ unperturbed_torsions_

ParameterList protocols::kinematic_closure::ClosureProblem::unperturbed_torsions_

private

Referenced by protocols::kinematic_closure::ClosureSolution::check_rama(), and protocols::kinematic_closure::ClosureSolution::get_distance().

◆ unperturbed_xyzs_

CoordinateList protocols::kinematic_closure::ClosureProblem::unperturbed_xyzs_

private

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

src/protocols/kinematic_closure/ClosureProblem.hh
src/protocols/kinematic_closure/ClosureProblem.cc

Classes

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ClosureProblem()

◆ ~ClosureProblem()

Member Function Documentation

◆ apply_internal_coordinates()

◆ c_n()

◆ c_n_ca()

◆ ca_c()

◆ ca_c_n()

◆ cut_residue()

◆ extract_cartesian_coordinates()

◆ extract_internal_coordinates() [1/2]

◆ extract_internal_coordinates() [2/2]

◆ first_residue()

◆ frame()

◆ frame_lower_pivot()

◆ frame_upper_pivot()

◆ id_from_index()

◆ ids_span_cut()

◆ is_nonpivot_residue()

◆ is_pivot_residue()

◆ last_residue()

◆ mutate_residues()

◆ n_ca()

◆ n_ca_c()

◆ nonpivot_residues()

◆ num_atoms()

◆ num_residues()

◆ omega()

◆ perturb_angles()

◆ perturb_c_n()

◆ perturb_c_n_ca()

◆ perturb_ca_c()

◆ perturb_ca_c_n()

◆ perturb_lengths()

◆ perturb_n_ca()

◆ perturb_n_ca_c()

◆ perturb_omega()

◆ perturb_phi()

◆ perturb_psi()

◆ perturb_torsions()

◆ perturbed_sequence() [1/2]

◆ perturbed_sequence() [2/2]

◆ phi()

◆ pivot_atoms()

◆ pivot_loop()

◆ pivot_residues()

◆ psi()

◆ residues()

◆ restore()

◆ sequence_mutated()

◆ solve()

◆ unperturbed_sequence()

Friends And Related Function Documentation

◆ ClosureSolution

◆ Memento

Member Data Documentation

◆ frame_called_

◆ perturbed_angles_

◆ perturbed_lengths_

◆ perturbed_sequence_

◆ perturbed_torsions_

◆ pivots_

◆ unperturbed_angles_

◆ unperturbed_lengths_

◆ unperturbed_sequence_

◆ unperturbed_torsions_

◆ unperturbed_xyzs_