Iterative loop closure mover, based on a linearization of the kinematics, which adjusts all free backbone torsion angles simultaneously in each iteration. More...

#include <JacobiLoopClosureMover.hh>

Inheritance diagram for protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover:

[legend]

Public Member Functions
	JacobiLoopClosureMover ()
	Constructors ///. More...

	JacobiLoopClosureMover (JacobiLoopClosureMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	JacobiLoopClosureMover (protocols::loops::Loop const &loop)
	Constructor based on a loop. More...

	JacobiLoopClosureMover (protocols::loops::Loop const &loop, core::kinematics::MoveMapCOP const &mm)
	Constructor based on a loop and a MoveMap. More...

	JacobiLoopClosureMover (core::kinematics::jacobian::SeriesJacobiansOP const jacobian_chain)
	Constructor based on a Jacobian serial chain. More...

	~JacobiLoopClosureMover () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	set_loop (protocols::loops::Loop const &new_loop)
	Mover Methods ///. More...

protocols::loops::Loop	get_loop ()

void	set_movemap (core::kinematics::MoveMapOP const new_mm)
	Set the MoveMap. More...

void	apply (core::pose::Pose &pose) override
	Execute the loop closure. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

bool	last_closure_success ()
	Get boolean indicating whether last closure was successfully completed. More...

core::Size	last_closure_cycles ()
	Returns the number of cycles that were needed for the last closure. More...

void	set_max_cycles (core::Size max_cycles)
	Set maximum number of iterations to find a loop closure solution. More...

core::Size	get_max_cycles ()
	Get value for maximum number of iterations to find a loop closure solution. More...

void	set_error_norms (core::Real error_norm_rot, core::Real error_norm_lin)
	Set norm-values of allowed rotational [deg] and linear error vectors [Ang] that define successful closure. More...

core::Real	get_allowed_norm_rot ()
	Get value for norm of allowed rotational error vector [deg] that defines successful closure. More...

core::Real	get_allowed_norm_lin ()
	Get value for norm of allowed linear error vector [Ang] that defines successful closure. More...

void	set_dq_max_allowed (core::Real dq_max_allowed)
	Set maximum change in dihedral angle in each cycle. More...

core::Real	get_dq_max_allowed ()
	Get value for maximum change applied to a torsion angle during a single cycle [rad]. More...

void	set_verbose (bool setting)
	Set whether or not to output non-critical information. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
core::kinematics::MoveMapOP	create_default_movemap (protocols::loops::Loop loop)
	Create default MoveMap. More...

void	init_constructor (protocols::loops::Loop const &loop, core::kinematics::MoveMapCOP const &mm)
	Initializes data members from constructor input arguments. More...

void	init_apply (core::pose::Pose &pose)
	Initializes private parameters of the Jacobi mover that depend on the pose and are only set when apply() is called. More...

void	prepare_foldtree (core::pose::Pose &pose)
	Function that checks and adjusts the fold tree as part of the init_apply method. More...

void	store_target_icoors (core::pose::Pose const &pose)
	extract internal coordinates of the upper loop connection (between the final residue of the loop and the first residue that follows) More...

std::pair< numeric::xyzVector < core::Real > , numeric::xyzVector < core::Real > >	update_target (core::pose::Pose const &pose)
	Calculate the target position and Euler angles of the final C-atom in the loop w.r.t the reference frame connected to ref_bb_atom_id_. More...

std::pair< numeric::xyzVector < core::Real > , numeric::xyzVector < core::Real > >	update_current (core::pose::Pose const &pose)
	Calculate the current position and Euler angles of the final C-atom in the loop w.r.t the reference frame connected to ref_bb_atom_id_. More...

std::pair< numeric::xyzVector < core::Real > , numeric::xyzVector < core::Real > >	calculate_error_twist (std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > > target, std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > > current)
	Extract the error twist (linearized rotations) from the current and target position and orientation (in Euler angles) More...

numeric::MathMatrix< core::Real >	weigh_columns_inversely_squared (numeric::MathMatrix< core::Real > const &)
	method that gives weights to different columns (that all represent that same error twist in their respective torsion space), inversely proptional to the norm of the required torsion changes More...

Private Attributes
core::Size	max_cycles_ = 200
	number of iterations before closure is aborted More...

core::Real	err_rot_allowed_ = 5 * numeric::constants::d::degrees_to_radians
	Maximum norms of rotational [rad] and linear error [Ang] for closure to be accepted as successful. More...

core::Real	err_lin_allowed_ = 0.1

core::Real	delta_euler_angle_max_ = numeric::constants::d::pi / 4
	maximum Euler angle error that is projected onto torsion angles during each cycle [rad] More...

core::Real	dq_max_allowed_ = 45 * numeric::constants::d::degrees_to_radians
	maximum change applied to a torsion angle during an individual cycle [rad] More...

bool	verbose_ = false
	setting that determines whether non-critical information is printed to tracer. Errors/warnings are always printed More...

protocols::loops::Loop	loop_
	copy of the input loop More...

core::kinematics::MoveMapCOP	movemap_
	copy of the pointer to the movemap More...

utility::vector1< core::Size >	free_residues_
	vector1 with the numbers of the residues whose phi and psi angles are allowed to be adjusted by the mover More...

core::kinematics::jacobian::SeriesJacobiansOP	jacobian_chain_ {nullptr}
	pointer to vector with Jacobian objects More...

core::Size	closure_cycles_ {0}
	counter of number of cycles in the loop closure while-loop More...

bool	closure_success_ {false}
	BOOl to communicate with user about success/failure of closure. More...

core::id::AtomID	ref_bb_atom_id_ {0,0}
	atom id of the first CA atom in the loop, which is fixed to the preceding backbone residue and whose stub is the reference frame for all vectors and matrices More...

utility::vector1 < core::id::AtomID >	target_bb_atom_ids_ {6}
	atom ids of the backbone atoms of the last residue of the loop and the first residue following More...

utility::vector1 < core::chemical::AtomICoor >	icoor_targets_ {3}
	internal coordinates of the target residue, which determine how the loop must be connected to the backbone. Stored in this form, and not as homogeneous matrix, because maybe a user in the future would like to change individual values manually More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Iterative loop closure mover, based on a linearization of the kinematics, which adjusts all free backbone torsion angles simultaneously in each iteration.

Constructor & Destructor Documentation

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::JacobiLoopClosureMover ( )

Constructors ///.

Default constructor

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::JacobiLoopClosureMover ( JacobiLoopClosureMover const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::JacobiLoopClosureMover ( protocols::loops::Loop const & loop )

Constructor based on a loop.

References create_default_movemap(), init_constructor(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::JacobiLoopClosureMover	(	protocols::loops::Loop const &	loop,
		core::kinematics::MoveMapCOP const &	mm
	)

Constructor based on a loop and a MoveMap.

References init_constructor(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::TR(), and verbose_.

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::JacobiLoopClosureMover ( core::kinematics::jacobian::SeriesJacobiansOP const jacobian_chain )

Constructor based on a Jacobian serial chain.

Constructor based on a pointer to a Jacobian serial chain.

References core::id::BB, init_constructor(), and jacobian_chain_.

protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::~JacobiLoopClosureMover ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply ( core::pose::Pose & pose )

overridevirtual

Execute the loop closure.

Apply the mover.

Implements protocols::moves::Mover.

References calculate_error_twist(), closure_cycles_, closure_success_, core::pose::Pose::conformation(), dq_max_allowed_, err_lin_allowed_, err_rot_allowed_, init_apply(), jacobian_chain_, protocols::mean_field::max(), max_cycles_, protocols::loops::TR(), update_current(), update_target(), verbose_, and weigh_columns_inversely_squared().

core::kinematics::jacobian::ModuleType1::Screw protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::calculate_error_twist	(	std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > >	target,
		std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > >	current
	)

private

Extract the error twist (linearized rotations) from the current and target position and orientation (in Euler angles)

References delta_euler_angle_max_.

Referenced by apply().

protocols::moves::MoverOP protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::kinematics::MoveMapOP protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::create_default_movemap ( protocols::loops::Loop loop )

private

Create default MoveMap.

References core::id::BB, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by JacobiLoopClosureMover(), and parse_my_tag().

protocols::moves::MoverOP protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_allowed_norm_lin ( )

inline

Get value for norm of allowed linear error vector [Ang] that defines successful closure.

References err_lin_allowed_.

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_allowed_norm_rot ( )

inline

Get value for norm of allowed rotational error vector [deg] that defines successful closure.

References err_rot_allowed_.

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_dq_max_allowed ( )

inline

Get value for maximum change applied to a torsion angle during a single cycle [rad].

References dq_max_allowed_.

protocols::loops::Loop protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_loop ( )

inline

References loop_.

core::Size protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_max_cycles ( )

inline

Get value for maximum number of iterations to find a loop closure solution.

References max_cycles_.

std::string protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::init_apply ( core::pose::Pose & pose )

private

Initializes private parameters of the Jacobi mover that depend on the pose and are only set when apply() is called.

Initializes private parameters of the Jacobi mover that depend on the pose and are only set when apply() is called. This function also checks and - if necessary - adjusts the FoldTree in preparation for Jacobi loop closure.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), free_residues_, jacobian_chain_, loop_, prepare_foldtree(), ref_bb_atom_id_, core::pose::Pose::residue(), protocols::loops::Loop::start(), store_target_icoors(), and protocols::loops::TR().

Referenced by apply().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::init_constructor	(	protocols::loops::Loop const &	loop,
		core::kinematics::MoveMapCOP const &	mm
	)

private

Initializes data members from constructor input arguments.

References free_residues_, loop_, movemap_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by JacobiLoopClosureMover(), parse_my_tag(), set_loop(), and set_movemap().

core::Size protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::last_closure_cycles ( )

inline

Returns the number of cycles that were needed for the last closure.

References closure_cycles_.

bool protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::last_closure_success ( )

inline

Get boolean indicating whether last closure was successfully completed.

References closure_success_.

std::string protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::mover_name ( )

static

Referenced by get_name(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::keyname(), and provide_xml_schema().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References create_default_movemap(), err_lin_allowed_, err_rot_allowed_, init_constructor(), max_cycles_, protocols::loop_modeling::utilities::parse_loops_from_tag(), and verbose_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree ( core::pose::Pose & pose )

private

Function that checks and adjusts the fold tree as part of the init_apply method.

References core::conformation::Residue::connected_residue_at_upper(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::id::D, core::pose::Pose::fold_tree(), core::chemical::ResidueType::get_base_type_cop(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::is_root(), loop_, protocols::mean_field::min(), core::pose::Pose::omega(), core::id::PHI, core::pose::Pose::psi(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_dof(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), core::id::THETA, protocols::loops::TR(), and verbose_.

Referenced by init_apply().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::loop_modeling::utilities::append_subelement_and_attributes_for_parse_loops_from_tag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::provide_xml_schema().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_dq_max_allowed ( core::Real dq_max_allowed )

inline

Set maximum change in dihedral angle in each cycle.

References dq_max_allowed_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_error_norms	(	core::Real	error_norm_rot,
		core::Real	error_norm_lin
	)

Set norm-values of allowed rotational [deg] and linear error vectors [Ang] that define successful closure.

error_norm_rot should be supplied in degrees.

References err_lin_allowed_, err_rot_allowed_, and protocols::loops::TR().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_loop ( protocols::loops::Loop const & new_loop )

Mover Methods ///.

Set the loop to be closed

References init_constructor(), and movemap_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_max_cycles ( core::Size max_cycles )

inline

Set maximum number of iterations to find a loop closure solution.

References max_cycles_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_movemap ( core::kinematics::MoveMapOP const new_mm )

Set the MoveMap.

References init_constructor(), and loop_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_verbose ( bool setting )

inline

Set whether or not to output non-critical information.

Default is false

References verbose_.

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::loops::loop_closure::jacobi::operator<<().

void protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors ( core::pose::Pose const & pose )

private

extract internal coordinates of the upper loop connection (between the final residue of the loop and the first residue that follows)

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::D, core::kinematics::tree::Atom::distance(), core::kinematics::tree::Atom::dof(), core::pose::Pose::dof(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), icoor_targets_, core::kinematics::FoldTree::is_jump_point(), loop_, core::conformation::Residue::mainchain_atom(), core::pose::Pose::omega(), core::id::PHI, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::loops::start, protocols::loops::Loop::stop(), target_bb_atom_ids_, core::id::THETA, and protocols::loops::TR().

Referenced by init_apply().

std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > > protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_current ( core::pose::Pose const & pose )

private

Calculate the current position and Euler angles of the final C-atom in the loop w.r.t the reference frame connected to ref_bb_atom_id_.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::BB, core::kinematics::tree::Atom::get_stub(), icoor_targets_, loop_, ref_bb_atom_id_, protocols::loops::Loop::stop(), target_bb_atom_ids_, and core::pose::Pose::torsion().

Referenced by apply().

std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > > protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_target ( core::pose::Pose const & pose )

private

Calculate the target position and Euler angles of the final C-atom in the loop w.r.t the reference frame connected to ref_bb_atom_id_.

This function calculates the pose (position and orientation) of the last backbone atom of the loop (C-atom [C] of the end residue [e] of the loop [l], 'Cle'). For that, the stored internal coordinates of the connection to the backbone are used to relate Cl to the first CA-atom of the backbone (CAbb) after the loop This CAbb atom in term is fixed w.r.t. the CA atom of the start residue of the loop (CA1).

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::kinematics::Stub::from_four_points(), core::kinematics::RT::get_rotation(), core::kinematics::tree::Atom::get_stub(), core::kinematics::RT::get_translation(), icoor_targets_, ref_bb_atom_id_, target_bb_atom_ids_, and core::kinematics::tree::Atom::xyz().

Referenced by apply().

numeric::MathMatrix< core::Real > protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::weigh_columns_inversely_squared ( numeric::MathMatrix< core::Real > const & input_cols )

private

method that gives weights to different columns (that all represent that same error twist in their respective torsion space), inversely proptional to the norm of the required torsion changes

method that gives weights to different columns (that all represent that same error twist in their respective torsion space), inversely proportional to the norm of the required torsion changes

References protocols::loops::TR(), and verbose_.

Referenced by apply().

Member Data Documentation

core::Size protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::closure_cycles_ {0}

private

counter of number of cycles in the loop closure while-loop

Referenced by apply(), and last_closure_cycles().

bool protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::closure_success_ {false}

private

BOOl to communicate with user about success/failure of closure.

Referenced by apply(), and last_closure_success().

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::delta_euler_angle_max_ = numeric::constants::d::pi / 4

private

maximum Euler angle error that is projected onto torsion angles during each cycle [rad]

Referenced by calculate_error_twist().

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::dq_max_allowed_ = 45 * numeric::constants::d::degrees_to_radians

private

maximum change applied to a torsion angle during an individual cycle [rad]

increasing this value potentially increases speed of closure (number of cycles needed), but also increases risk of erratic behavior. Decreasing will reduce erratic behavior, but slows down speed of closure

Referenced by apply(), get_dq_max_allowed(), and set_dq_max_allowed().

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::err_lin_allowed_ = 0.1

private

Referenced by apply(), get_allowed_norm_lin(), parse_my_tag(), and set_error_norms().

core::Real protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::err_rot_allowed_ = 5 * numeric::constants::d::degrees_to_radians

private

Maximum norms of rotational [rad] and linear error [Ang] for closure to be accepted as successful.

Referenced by apply(), get_allowed_norm_rot(), parse_my_tag(), and set_error_norms().

utility::vector1<core::Size> protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::free_residues_

private

vector1 with the numbers of the residues whose phi and psi angles are allowed to be adjusted by the mover

Referenced by init_apply(), and init_constructor().

utility::vector1< core::chemical::AtomICoor > protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::icoor_targets_ {3}

private

internal coordinates of the target residue, which determine how the loop must be connected to the backbone. Stored in this form, and not as homogeneous matrix, because maybe a user in the future would like to change individual values manually

this member variable is set when the apply() function is called because it relies on the conformation

Referenced by store_target_icoors(), update_current(), and update_target().

core::kinematics::jacobian::SeriesJacobiansOP protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::jacobian_chain_ {nullptr}

private

pointer to vector with Jacobian objects

Referenced by apply(), init_apply(), and JacobiLoopClosureMover().

protocols::loops::Loop protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::loop_

private

copy of the input loop

Referenced by get_loop(), init_apply(), init_constructor(), prepare_foldtree(), set_movemap(), store_target_icoors(), and update_current().

core::Size protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::max_cycles_ = 200

private

number of iterations before closure is aborted

Referenced by apply(), get_max_cycles(), parse_my_tag(), and set_max_cycles().

core::kinematics::MoveMapCOP protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::movemap_

private

copy of the pointer to the movemap

Referenced by init_constructor(), and set_loop().

core::id::AtomID protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::ref_bb_atom_id_ {0,0}

private

atom id of the first CA atom in the loop, which is fixed to the preceding backbone residue and whose stub is the reference frame for all vectors and matrices

this member variable is set when the apply() function is called because it relies on the conformation

Referenced by init_apply(), update_current(), and update_target().

utility::vector1<core::id::AtomID> protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::target_bb_atom_ids_ {6}

private

atom ids of the backbone atoms of the last residue of the loop and the first residue following

this member variable is set when the apply() function is called because it relies on the conformation

Referenced by store_target_icoors(), update_current(), and update_target().

bool protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::verbose_ = false

private

setting that determines whether non-critical information is printed to tracer. Errors/warnings are always printed

Referenced by apply(), JacobiLoopClosureMover(), parse_my_tag(), prepare_foldtree(), set_verbose(), and weigh_columns_inversely_squared().

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

src/protocols/loops/loop_closure/jacobi/JacobiLoopClosureMover.hh
src/protocols/loops/loop_closure/jacobi/JacobiLoopClosureMover.cc

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