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

#include <BackrubMover.hh>

Public Member Functions
	BackrubMover ()

	BackrubMover (BackrubMover const &mover)

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

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

void	init_with_options ()

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	apply (Pose &pose)

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

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...

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 ()
	add segments between mainchain atoms using stored parameters More...

core::Size	add_mainchain_segments_from_options ()
	add segments between mainchain atoms using command line options More...

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

utility::vector1< core::Size > const &	pivot_residues () 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...

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...

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

virtual void	set_preserve_detailed_balance (bool preserve_detailed_balance)
	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...

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

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

void	rotate_segment (Pose &pose, 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, 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...

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

virtual	~ThermodynamicMover ()
	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...

virtual core::Real	last_proposal_density_ratio ()
	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_temperature_delta ()
	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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 protocols::filters::Filters_map	Filters_map

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

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...

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

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

References radians().

Referenced by fresh_instance().

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

References canonical_sampling.

Member Function Documentation

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 protocols::backrub::connected_mainchain_atomids(), and runtime_assert.

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

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 runtime_assert, and protocols::TR.

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

add segments between mainchain atoms using stored parameters

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

add segments between mainchain atoms using command line options

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

Detailed:: 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 runtime_assert, protocols::TR, and protocols::backrub::tree_distance().

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

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

virtual

Detailed:

Implements protocols::moves::Mover.

References core::id::AtomID::atomno(), numeric::conversions::degrees(), core::pose::Pose::fold_tree(), fold_tree, numeric::random::RandomGenerator::random_range(), core::pose::Pose::residue_type(), protocols::RG, core::id::AtomID::rsd(), runtime_assert, and protocols::TR.

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

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

inline

get the branch angle optimizer stored in the mover

References branchopt_.

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

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().

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

virtual

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.

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

virtual

get whether rotation angle is customized

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

virtual

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(), pi, runtime_assert, protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), and protocols::backrub::BackrubSegment::start_atomid2().

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

virtual

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.

References BackrubMover().

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

virtual

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

Implements protocols::moves::Mover.

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().

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

References protocols::backrub::init_backrub_mover_with_options().

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

virtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

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

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

get the last rotation angle

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

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

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

get id the last backrub segment moved

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

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

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

get maximum angular displacement for 4 atom segments

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

get maximum angular displacement for 7 atom segments

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

get maximum angular displacement slope for other atom segments

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

get maximum segment length if no segments manually defined

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

get minimum segment length if no segments manually defined

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

get the rotation angle for the next move

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

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

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

inline

get the number of segments

References segments_.

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

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

optimize branching atoms for all segment pivot atoms

References utility::keys::Key3Vector< class >::key1(), utility::keys::Key3Vector< class >::key2(), utility::keys::Key3Vector< class >::key3(), and protocols::TR.

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

void protocols::backrub::BackrubMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References core::pose::get_resnum_list(), and utility::string_split().

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

get atom names to pivot if no segments manually defined

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

get residues to pivot if no segments manually defined

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

virtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

Real protocols::backrub::BackrubMover::random_angle	(	Pose &	pose,
		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 angle, core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::backrub_rotation_constants(), protocols::backrub::BackrubSegment::end_atomid(), numeric::IntervalSet< class >::length(), length, numeric::nearest_angle_radians(), pi, numeric::IntervalSet< class >::random_point(), protocols::RG, numeric::IntervalSet< class >::set(), protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), protocols::backrub::BackrubSegment::start_atomid2(), threshold, and numeric::random::RandomGenerator::uniform().

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

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

void protocols::backrub::BackrubMover::rotate_segment	(	Pose &	pose,
		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

Detailed:: 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(), pi, core::pose::Pose::set_dof(), protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), and protocols::backrub::BackrubSegment::start_atomid2().

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

inline

get a particular segment

References segment_id(), and segments_.

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

Detailed:: if the segment ID does not exist, 0 is returned

References segments_.

Referenced by has_segment(), and segment().

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

virtual

set whether rotation angle is customized

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

set maximum angular displacement for 4 atom segments

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

set maximum angular displacement for 7 atom segments

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

set maximum angular displacement slope for other atom segments

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().

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().

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

set the rotation angle for the next move

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

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

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().

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().

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

virtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

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

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

virtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

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

update string describing the move type

Detailed:: 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, and type.

Member Data Documentation

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

private

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

private

Referenced by branchopt().

bool protocols::backrub::BackrubMover::custom_angle_

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

bool protocols::backrub::BackrubMover::preserve_detailed_balance_

private

bool protocols::backrub::BackrubMover::require_mm_bend_

private

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

Private Attributes
utility::vector1 < protocols::backrub::BackrubSegment >	segments_

protocols::branch_angle::BranchAngleOptimizer	branchopt_

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

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_

bool	preserve_detailed_balance_

bool	require_mm_bend_

bool	custom_angle_

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation