class for applying backrub moves to arbitrary protein segments More...

#include <BackrubMover.hh>

Inheritance diagram for protocols::backrub::BackrubMover:

[legend]

Public Member Functions
	BackrubMover ()

	BackrubMover (BackrubMover const &mover)

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	init_with_options ()

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	parse_movemap_factory (utility::tag::TagCOP tag, basic::datacache::DataMap &data)

void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) override
	Callback executed before any Monte Carlo trials are attempted. More...

void	apply (Pose &pose) override
	Main Method. More...

core::Size	segment_id (core::id::AtomID start_atomid, core::id::AtomID end_atomid)
	get the segment ID for a given starting and ending atom More...

bool	has_segment (core::id::AtomID start_atomid, core::id::AtomID end_atomid)
	determine whether a given segment exists More...

BackrubSegment const &	segment (core::Size segment_id)
	get a particular segment More...

void	clear_segments ()
	remove all segements More...

core::Size	num_segments ()
	get the number of segments More...

core::Size	add_segment (core::id::AtomID start_atomid, core::id::AtomID end_atomid, core::Real max_angle_disp=0)
	add a segment to the mover More...

core::Size	add_mainchain_segments (utility::vector1< core::id::AtomID > atomids, core::Size min_atoms, core::Size max_atoms)
	add segments between a list of mainchain atomids More...

core::Size	add_mainchain_segments (utility::vector1< core::Size > resnums, utility::vector1< std::string > atomnames, core::Size min_atoms, core::Size max_atoms)
	add segments between mainchain atoms in contiguous stretches of residues More...

core::Size	add_mainchain_segments (Pose const &pose)
	add segments between mainchain atoms for the given pose, using stored parameters More...

core::Size	add_mainchain_segments_from_options (Pose const &pose)
	add segments between mainchain atoms for the given pose, using command line options More...

void	optimize_branch_angles (Pose &pose)
	optimize branching atoms for all segment pivot atoms More...

utility::vector1< core::Size >	pivot_residues (Pose const &pose) const
	get residues to pivot if no segments manually defined More...

void	set_pivot_residues (utility::vector1< core::Size > const &pivot_residues)
	set residues to pivot if no segments manually defined More...

void	set_pivot_residue_selector (core::select::residue_selector::ResidueSelectorCOP pivot_residues)

virtual void	set_movemap_factory (core::select::movemap::MoveMapFactoryCOP mmf)
	Sets up movemap from the movemap factory inputs. More...

void	set_movemap (core::kinematics::MoveMapCOP movemap)
	Sets Pivot Residues from the Movemap. Each contiguous set of residues with BB enabled will be used as a segment. More...

utility::vector1< std::string > const &	pivot_atoms () const
	get atom names to pivot if no segments manually defined More...

void	set_pivot_atoms (utility::vector1< std::string > const &pivot_atoms)
	set atom names to pivot if no segments manually defined More...

core::Size	min_atoms () const
	get minimum segment length if no segments manually defined More...

void	set_min_atoms (core::Size min_atoms)
	set minimum segment length if no segments manually defined More...

core::Size	max_atoms () const
	get maximum segment length if no segments manually defined More...

void	set_max_atoms (core::Size max_atoms)
	set maximum segment length if no segments manually defined More...

core::Real	max_angle_disp_4 () const
	get maximum angular displacement for 4 atom segments More...

void	set_max_angle_disp_4 (core::Real max_angle_disp_4)
	set maximum angular displacement for 4 atom segments More...

core::Real	max_angle_disp_7 () const
	get maximum angular displacement for 7 atom segments More...

void	set_max_angle_disp_7 (core::Real max_angle_disp_7)
	set maximum angular displacement for 7 atom segments More...

core::Real	max_angle_disp_slope () const
	get maximum angular displacement slope for other atom segments More...

void	set_max_angle_disp_slope (core::Real max_angle_disp_slope)
	set maximum angular displacement slope for other atom segments More...

virtual bool	custom_angle () const
	get whether rotation angle is customized More...

virtual void	set_custom_angle (bool custom_angle)
	set whether rotation angle is customized More...

bool	preserve_detailed_balance () const override
	get whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

void	set_preserve_detailed_balance (bool preserve_detailed_balance) override
	set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

bool	require_mm_bend () const
	get whether to exit during initialize_simulation if the mm_bend term isn't turned on More...

void	set_require_mm_bend (bool require_mm_bend)
	set whether to exit during initialize_simulation if the mm_bend term isn't turned on More...

utility::vector1< core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose) override
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

utility::vector1< core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose) override
	get the DOF_IDs perturbed by the mover during moves, along with their ranges More...

void	rotate_segment (Pose &pose, core::Size segment_id, core::Real angle, utility::vector0< core::Real > &start_constants, utility::vector0< core::Real > &end_constants)
	do a manual rotation about the given segment More...

core::Real	random_angle (Pose &pose, core::Size segment_id, utility::vector0< core::Real > &start_constants, utility::vector0< core::Real > &end_constants)
	get a random angle for a segment subject to bond angle and rotation constraints More...

protocols::branch_angle::BranchAngleOptimizer &	branchopt ()
	get the branch angle optimizer stored in the mover More...

core::Size	next_segment_id () const
	set the id for the next move (i.e. nonrandom) More...

void	set_next_segment_id (core::Size next_segment_id)
	set the id for the next move (i.e. nonrandom) More...

core::Size	last_segment_id () const
	get id the last backrub segment moved More...

std::string	last_start_atom_name () const
	get the name of the atom at the start of the last segment More...

std::string	last_end_atom_name () const
	get the name of the atom at the end of the last segment More...

void	set_next_angle (core::Real next_angle)
	set the rotation angle for the next move More...

core::Real	next_angle () const
	get the rotation angle for the next move More...

core::Real	last_angle () const
	get the last rotation angle More...

void	update_type ()
	update string describing the move type More...

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

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()
	Default constructor. More...

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

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

core::Real	last_proposal_density_ratio () override
	Return the proposal density ratio for last apply method. More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after all Monte Carlo trials are completed. More...

virtual bool	is_multi_trial ()
	Return true if the move performs multiple trials on each apply. More...

virtual core::Real	last_inner_score_delta_over_temperature ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. 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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

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 utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_backrub_mover (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 Attributes
utility::vector1< protocols::backrub::BackrubSegment >	segments_

protocols::branch_angle::BranchAngleOptimizer	branchopt_

std::map< protocols::backrub::BackrubSegment::BondAngleKey, core::Size >	bond_angle_map_

core::select::residue_selector::ResidueSelectorCOP	pivot_residue_selector_

utility::vector1< core::Size >	pivot_residues_

utility::vector1< std::string >	pivot_atoms_

core::Size	min_atoms_

core::Size	max_atoms_

core::Real	max_angle_disp_4_

core::Real	max_angle_disp_7_

core::Real	max_angle_disp_slope_

core::Size	next_segment_id_

core::Size	last_segment_id_

std::string	last_start_atom_name_

std::string	last_end_atom_name_

core::Real	next_angle_

core::Real	last_angle_

core::kinematics::MoveMapOP	movemap_

core::select::movemap::MoveMapFactoryCOP	movemap_factory_

bool	preserve_detailed_balance_

bool	require_mm_bend_

bool	custom_angle_

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

class for applying backrub moves to arbitrary protein segments

Constructor & Destructor Documentation

◆ BackrubMover() [1/2]

protocols::backrub::BackrubMover::BackrubMover ( )

References init_with_options().

◆ BackrubMover() [2/2]

protocols::backrub::BackrubMover::BackrubMover ( BackrubMover const & mover )

default

Member Function Documentation

◆ add_mainchain_segments() [1/3]

core::Size protocols::backrub::BackrubMover::add_mainchain_segments ( Pose const & pose )

add segments between mainchain atoms for the given pose, using stored parameters

◆ add_mainchain_segments() [2/3]

core::Size protocols::backrub::BackrubMover::add_mainchain_segments	(	utility::vector1< core::id::AtomID >	atomids,
		core::Size	min_atoms,
		core::Size	max_atoms
	)

add segments between a list of mainchain atomids

References core::chemical::aa_pro, protocols::denovo_design::components::add_segment(), and protocols::backrub::connected_mainchain_atomids().

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move().

◆ add_mainchain_segments() [3/3]

core::Size protocols::backrub::BackrubMover::add_mainchain_segments	(	utility::vector1< core::Size >	resnums,
		utility::vector1< std::string >	atomnames,
		core::Size	min_atoms,
		core::Size	max_atoms
	)

add segments between mainchain atoms in contiguous stretches of residues

References protocols::TR().

◆ add_mainchain_segments_from_options()

core::Size protocols::backrub::BackrubMover::add_mainchain_segments_from_options ( Pose const & pose )

add segments between mainchain atoms for the given pose, using command line options

◆ add_segment()

Size protocols::backrub::BackrubMover::add_segment	(	core::id::AtomID	start_atomid,
		core::id::AtomID	end_atomid,
		core::Real	max_angle_disp = `0`
	)

add a segment to the mover

The start atom MUST have all three stub atoms defined. However, the end atom may be at the very end of the chain. There must be at least one atom between start and end atoms.

If the segment is for whatever reason invalid, 0 is returned. Otherwise, the segment is added to the end of the segments vector and the ID to the new segment is returned. If the segment already exists, then nothing is changed and the existing segment ID is returned.

There has been absolutely no testing of how the code handles jumps! Use this with jumps at your own risk!

References core::kinematics::tree::Atom::parent(), protocols::TR(), and protocols::backrub::tree_distance().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::backrub().

◆ apply()

void protocols::backrub::BackrubMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::chemical::ResidueType::atom_name(), core::id::AtomID::atomno(), core::pose::Pose::fold_tree(), core::pose::Pose::residue_type(), core::scoring::rg, core::id::AtomID::rsd(), and protocols::TR().

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), and protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move().

◆ branchopt()

protocols::branch_angle::BranchAngleOptimizer& protocols::backrub::BackrubMover::branchopt ( )

inline

get the branch angle optimizer stored in the mover

References branchopt_.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), and protocols::dna::DesignProteinBackboneAroundDNA::backrub().

◆ clear_segments()

void protocols::backrub::BackrubMover::clear_segments ( )

inline

remove all segements

References segments_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), and protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move().

◆ clone()

protocols::moves::MoverOP protocols::backrub::BackrubMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ complex_type_generator_for_backrub_mover()

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::backrub::BackrubMover::complex_type_generator_for_backrub_mover ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), core::select::movemap::attributes_for_parse_movemap_factory_default_attr_name(), protocols::moves::complex_type_name_for_mover(), and core::id::to_string().

◆ custom_angle()

bool protocols::backrub::BackrubMover::custom_angle ( ) const

virtual

get whether rotation angle is customized

◆ dof_id_ranges()

utility::vector1< core::id::DOF_ID_Range > protocols::backrub::BackrubMover::dof_id_ranges ( core::pose::Pose & pose )

overridevirtual

get the DOF_IDs perturbed by the mover during moves, along with their ranges

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::BackrubSegment::end_atomid(), core::kinematics::tree::Atom::get_self_ptr(), core::chemical::rings::PHI, protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), protocols::backrub::BackrubSegment::start_atomid2(), and core::chemical::rings::THETA.

◆ fresh_instance()

protocols::moves::MoverOP protocols::backrub::BackrubMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::backrub::BackrubMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ has_segment()

bool protocols::backrub::BackrubMover::has_segment	(	core::id::AtomID	start_atomid,
		core::id::AtomID	end_atomid
	)

inline

determine whether a given segment exists

References segment_id().

◆ init_with_options()

void protocols::backrub::BackrubMover::init_with_options ( )

References protocols::backrub::init_backrub_mover_with_options().

Referenced by BackrubMover().

◆ initialize_simulation()

void protocols::backrub::BackrubMover::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)

overridevirtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References core::pose::Pose::fold_tree(), core::scoring::mm_bend, protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), and protocols::TR().

◆ last_angle()

core::Real protocols::backrub::BackrubMover::last_angle ( ) const

get the last rotation angle

◆ last_end_atom_name()

std::string protocols::backrub::BackrubMover::last_end_atom_name ( ) const

get the name of the atom at the end of the last segment

◆ last_segment_id()

core::Size protocols::backrub::BackrubMover::last_segment_id ( ) const

get id the last backrub segment moved

◆ last_start_atom_name()

std::string protocols::backrub::BackrubMover::last_start_atom_name ( ) const

get the name of the atom at the start of the last segment

◆ max_angle_disp_4()

core::Real protocols::backrub::BackrubMover::max_angle_disp_4 ( ) const

get maximum angular displacement for 4 atom segments

◆ max_angle_disp_7()

core::Real protocols::backrub::BackrubMover::max_angle_disp_7 ( ) const

get maximum angular displacement for 7 atom segments

◆ max_angle_disp_slope()

core::Real protocols::backrub::BackrubMover::max_angle_disp_slope ( ) const

get maximum angular displacement slope for other atom segments

◆ max_atoms()

core::Size protocols::backrub::BackrubMover::max_atoms ( ) const

get maximum segment length if no segments manually defined

◆ min_atoms()

core::Size protocols::backrub::BackrubMover::min_atoms ( ) const

get minimum segment length if no segments manually defined

◆ mover_name()

std::string protocols::backrub::BackrubMover::mover_name ( )

static

Referenced by protocols::backrub::BackrubMoverCreator::keyname().

◆ next_angle()

core::Real protocols::backrub::BackrubMover::next_angle ( ) const

get the rotation angle for the next move

◆ next_segment_id()

core::Size protocols::backrub::BackrubMover::next_segment_id ( ) const

set the id for the next move (i.e. nonrandom)

◆ num_segments()

core::Size protocols::backrub::BackrubMover::num_segments ( )

inline

get the number of segments

References segments_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply().

◆ optimize_branch_angles()

void protocols::backrub::BackrubMover::optimize_branch_angles ( Pose & pose )

optimize branching atoms for all segment pivot atoms

References protocols::TR().

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply().

◆ parse_movemap_factory()

void protocols::backrub::BackrubMover::parse_movemap_factory	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

References core::select::movemap::parse_movemap_factory(), and protocols::TR().

◆ parse_my_tag()

void protocols::backrub::BackrubMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::pose::get_resnum_selector(), core::select::movemap::parse_movemap_factory(), and protocols::TR().

◆ pivot_atoms()

utility::vector1< std::string > const & protocols::backrub::BackrubMover::pivot_atoms ( ) const

get atom names to pivot if no segments manually defined

◆ pivot_residues()

utility::vector1< core::Size > protocols::backrub::BackrubMover::pivot_residues ( Pose const & pose ) const

get residues to pivot if no segments manually defined

References core::select::get_residues_from_subset().

◆ preserve_detailed_balance()

bool protocols::backrub::BackrubMover::preserve_detailed_balance ( ) const

overridevirtual

get whether detailed balance is preserved (i.e. no branch angle optimization during moves)

Implements protocols::canonical_sampling::ThermodynamicMover.

◆ provide_xml_schema()

void protocols::backrub::BackrubMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Referenced by protocols::backrub::BackrubMoverCreator::provide_xml_schema().

◆ random_angle()

Real protocols::backrub::BackrubMover::random_angle	(	Pose &	pose,
		core::Size	segment_id,
		utility::vector0< core::Real > &	start_constants,
		utility::vector0< core::Real > &	end_constants
	)

get a random angle for a segment subject to bond angle and rotation constraints

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::backrub_rotation_constants(), protocols::backrub::BackrubSegment::end_atomid(), core::kinematics::tree::Atom::get_self_ptr(), core::scoring::rg, protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), and protocols::backrub::BackrubSegment::start_atomid2().

◆ require_mm_bend()

bool protocols::backrub::BackrubMover::require_mm_bend ( ) const

get whether to exit during initialize_simulation if the mm_bend term isn't turned on

◆ rotate_segment()

void protocols::backrub::BackrubMover::rotate_segment	(	Pose &	pose,
		core::Size	segment_id,
		core::Real	angle,
		utility::vector0< core::Real > &	start_constants,
		utility::vector0< core::Real > &	end_constants
	)

do a manual rotation about the given segment

The code currently does not do any optimization of branching atom bond angles.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::backrub_rotation_angles(), protocols::backrub::backrub_rotation_constants(), core::pose::Pose::dof(), protocols::backrub::BackrubSegment::end_atomid(), core::kinematics::tree::Atom::get_self_ptr(), core::chemical::rings::PHI, core::pose::Pose::set_dof(), protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), protocols::backrub::BackrubSegment::start_atomid2(), and core::chemical::rings::THETA.

◆ segment()

BackrubSegment const& protocols::backrub::BackrubMover::segment ( core::Size segment_id )

inline

get a particular segment

References segment_id(), and segments_.

◆ segment_id()

core::Size protocols::backrub::BackrubMover::segment_id	(	core::id::AtomID	start_atomid,
		core::id::AtomID	end_atomid
	)

inline

get the segment ID for a given starting and ending atom

if the segment ID does not exist, 0 is returned

References segments_.

Referenced by has_segment(), and segment().

◆ set_custom_angle()

void protocols::backrub::BackrubMover::set_custom_angle ( bool custom_angle )

virtual

set whether rotation angle is customized

◆ set_max_angle_disp_4()

void protocols::backrub::BackrubMover::set_max_angle_disp_4 ( core::Real max_angle_disp_4 )

set maximum angular displacement for 4 atom segments

◆ set_max_angle_disp_7()

void protocols::backrub::BackrubMover::set_max_angle_disp_7 ( core::Real max_angle_disp_7 )

set maximum angular displacement for 7 atom segments

◆ set_max_angle_disp_slope()

void protocols::backrub::BackrubMover::set_max_angle_disp_slope ( core::Real max_angle_disp_slope )

set maximum angular displacement slope for other atom segments

◆ set_max_atoms()

void protocols::backrub::BackrubMover::set_max_atoms ( core::Size max_atoms )

set maximum segment length if no segments manually defined

Referenced by protocols::backrub::init_backrub_mover_with_options().

◆ set_min_atoms()

void protocols::backrub::BackrubMover::set_min_atoms ( core::Size min_atoms )

set minimum segment length if no segments manually defined

Referenced by protocols::backrub::init_backrub_mover_with_options().

◆ set_movemap()

void protocols::backrub::BackrubMover::set_movemap ( core::kinematics::MoveMapCOP movemap )

Sets Pivot Residues from the Movemap. Each contiguous set of residues with BB enabled will be used as a segment.

References protocols::backrub::get_pivot_residues_from_movemap().

Referenced by protocols::backrub::init_backrub_mover_with_options().

◆ set_movemap_factory()

void protocols::backrub::BackrubMover::set_movemap_factory ( core::select::movemap::MoveMapFactoryCOP mmf )

virtual

Sets up movemap from the movemap factory inputs.

◆ set_next_angle()

void protocols::backrub::BackrubMover::set_next_angle ( core::Real next_angle )

set the rotation angle for the next move

◆ set_next_segment_id()

void protocols::backrub::BackrubMover::set_next_segment_id ( core::Size next_segment_id )

set the id for the next move (i.e. nonrandom)

◆ set_pivot_atoms()

void protocols::backrub::BackrubMover::set_pivot_atoms ( utility::vector1< std::string > const & pivot_atoms )

set atom names to pivot if no segments manually defined

Referenced by protocols::backrub::init_backrub_mover_with_options().

◆ set_pivot_residue_selector()

void protocols::backrub::BackrubMover::set_pivot_residue_selector ( core::select::residue_selector::ResidueSelectorCOP pivot_residues )

◆ set_pivot_residues()

void protocols::backrub::BackrubMover::set_pivot_residues ( utility::vector1< core::Size > const & pivot_residues )

set residues to pivot if no segments manually defined

Referenced by protocols::backrub::init_backrub_mover_with_options().

◆ set_preserve_detailed_balance()

void protocols::backrub::BackrubMover::set_preserve_detailed_balance ( bool preserve_detailed_balance )

overridevirtual

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

Implements protocols::canonical_sampling::ThermodynamicMover.

◆ set_require_mm_bend()

void protocols::backrub::BackrubMover::set_require_mm_bend ( bool require_mm_bend )

set whether to exit during initialize_simulation if the mm_bend term isn't turned on

◆ torsion_id_ranges()

utility::vector1< core::id::TorsionID_Range > protocols::backrub::BackrubMover::torsion_id_ranges ( core::pose::Pose & pose )

overridevirtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.

◆ update_type()

void protocols::backrub::BackrubMover::update_type ( )

update string describing the move type

All move types are prefixed with "br". Sections are divided by underscores. The next two sections indicates the names of the atoms at the start and end of the backrub segment. The last section gives the size of the segment.

References protocols::motifs::mt().

Member Data Documentation

◆ bond_angle_map_

std::map<protocols::backrub::BackrubSegment::BondAngleKey, core::Size> protocols::backrub::BackrubMover::bond_angle_map_

private

◆ branchopt_

protocols::branch_angle::BranchAngleOptimizer protocols::backrub::BackrubMover::branchopt_

private

Referenced by branchopt().

◆ custom_angle_

bool protocols::backrub::BackrubMover::custom_angle_

private

◆ last_angle_

core::Real protocols::backrub::BackrubMover::last_angle_

private

◆ last_end_atom_name_

std::string protocols::backrub::BackrubMover::last_end_atom_name_

private

◆ last_segment_id_

core::Size protocols::backrub::BackrubMover::last_segment_id_

private

◆ last_start_atom_name_

std::string protocols::backrub::BackrubMover::last_start_atom_name_

private

◆ max_angle_disp_4_

core::Real protocols::backrub::BackrubMover::max_angle_disp_4_

private

◆ max_angle_disp_7_

core::Real protocols::backrub::BackrubMover::max_angle_disp_7_

private

◆ max_angle_disp_slope_

core::Real protocols::backrub::BackrubMover::max_angle_disp_slope_

private

◆ max_atoms_

core::Size protocols::backrub::BackrubMover::max_atoms_

private

◆ min_atoms_

core::Size protocols::backrub::BackrubMover::min_atoms_

private

◆ movemap_

core::kinematics::MoveMapOP protocols::backrub::BackrubMover::movemap_

private

◆ movemap_factory_

core::select::movemap::MoveMapFactoryCOP protocols::backrub::BackrubMover::movemap_factory_

private

◆ next_angle_

core::Real protocols::backrub::BackrubMover::next_angle_

private

◆ next_segment_id_

core::Size protocols::backrub::BackrubMover::next_segment_id_

private

◆ pivot_atoms_

utility::vector1<std::string> protocols::backrub::BackrubMover::pivot_atoms_

private

◆ pivot_residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::backrub::BackrubMover::pivot_residue_selector_

private

The pivot residues are a combination of the pivot_residue_selector_ and the explicitly set pivot_residues_

◆ pivot_residues_

utility::vector1<core::Size> protocols::backrub::BackrubMover::pivot_residues_

private

◆ preserve_detailed_balance_

bool protocols::backrub::BackrubMover::preserve_detailed_balance_

private

◆ require_mm_bend_

bool protocols::backrub::BackrubMover::require_mm_bend_

private

◆ segments_

utility::vector1<protocols::backrub::BackrubSegment> protocols::backrub::BackrubMover::segments_

private

Referenced by clear_segments(), num_segments(), segment(), and segment_id().

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

src/protocols/backrub/BackrubMover.hh
src/protocols/backrub/BackrubMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BackrubMover() [1/2]

◆ BackrubMover() [2/2]

Member Function Documentation

◆ add_mainchain_segments() [1/3]

◆ add_mainchain_segments() [2/3]

◆ add_mainchain_segments() [3/3]

◆ add_mainchain_segments_from_options()

◆ add_segment()

◆ apply()

◆ branchopt()

◆ clear_segments()

◆ clone()

◆ complex_type_generator_for_backrub_mover()

◆ custom_angle()

◆ dof_id_ranges()

◆ fresh_instance()

◆ get_name()

◆ has_segment()

◆ init_with_options()

◆ initialize_simulation()

◆ last_angle()

◆ last_end_atom_name()

◆ last_segment_id()

◆ last_start_atom_name()

◆ max_angle_disp_4()

◆ max_angle_disp_7()

◆ max_angle_disp_slope()

◆ max_atoms()

◆ min_atoms()

◆ mover_name()

◆ next_angle()

◆ next_segment_id()

◆ num_segments()

◆ optimize_branch_angles()

◆ parse_movemap_factory()

◆ parse_my_tag()

◆ pivot_atoms()

◆ pivot_residues()

◆ preserve_detailed_balance()

◆ provide_xml_schema()

◆ random_angle()

◆ require_mm_bend()

◆ rotate_segment()

◆ segment()

◆ segment_id()

◆ set_custom_angle()

◆ set_max_angle_disp_4()

◆ set_max_angle_disp_7()

◆ set_max_angle_disp_slope()

◆ set_max_atoms()

◆ set_min_atoms()

◆ set_movemap()

◆ set_movemap_factory()

◆ set_next_angle()

◆ set_next_segment_id()

◆ set_pivot_atoms()

◆ set_pivot_residue_selector()

◆ set_pivot_residues()

◆ set_preserve_detailed_balance()

◆ set_require_mm_bend()

◆ torsion_id_ranges()

◆ update_type()

Member Data Documentation

◆ bond_angle_map_

◆ branchopt_

◆ custom_angle_

◆ last_angle_

◆ last_end_atom_name_

◆ last_segment_id_

◆ last_start_atom_name_

◆ max_angle_disp_4_

◆ max_angle_disp_7_

◆ max_angle_disp_slope_

◆ max_atoms_