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

#include <BackrubMover.hh>

Inheritance diagram for protocols::backrub::BackrubMover:

Collaboration diagram for protocols::backrub::BackrubMover:

Public Member Functions
	BackrubMover ()

	BackrubMover (BackrubMover const &mover)

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	init_with_options ()

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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 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	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...

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 ()

virtual	~ThermodynamicMover ()

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 ()
	callback for proposal density ratio of 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 More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers 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

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
	this function informs 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
	this function informs 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

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

Definition at line 55 of file BackrubMover.hh.

Constructor & Destructor Documentation

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

Definition at line 96 of file BackrubMover.cc.

Referenced by fresh_instance().

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

Definition at line 108 of file BackrubMover.cc.

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

Definition at line 526 of file BackrubMover.cc.

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

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

Definition at line 583 of file BackrubMover.cc.

References protocols::TR().

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

add segments between mainchain atoms using stored parameters

Definition at line 641 of file BackrubMover.cc.

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

add segments between mainchain atoms using command line options

Definition at line 654 of file BackrubMover.cc.

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!

Definition at line 337 of file BackrubMover.cc.

References 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.

Definition at line 235 of file BackrubMover.cc.

References core::id::AtomID::atomno(), core::pose::Pose::fold_tree(), core::pose::Pose::residue_type(), protocols::RG(), core::id::AtomID::rsd(), 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

Definition at line 311 of file BackrubMover.hh.

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

Definition at line 133 of file BackrubMover.hh.

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

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 132 of file BackrubMover.cc.

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.

Definition at line 813 of file BackrubMover.cc.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::BackrubSegment::end_atomid(), core::id::PHI, protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), protocols::backrub::BackrubSegment::start_atomid2(), and core::id::THETA.

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

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Definition at line 133 of file BackrubMover.cc.

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.

Definition at line 294 of file BackrubMover.cc.

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

inline

determine whether a given segment exists

Definition at line 114 of file BackrubMover.hh.

References segment_id().

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

Definition at line 155 of file BackrubMover.cc.

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

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Definition at line 195 of file BackrubMover.cc.

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

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

get the last rotation angle

Definition at line 1164 of file BackrubMover.cc.

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

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

Definition at line 1158 of file BackrubMover.cc.

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

get id the last backrub segment moved

Definition at line 1146 of file BackrubMover.cc.

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

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

Definition at line 1152 of file BackrubMover.cc.

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

get maximum angular displacement for 4 atom segments

Definition at line 735 of file BackrubMover.cc.

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

get maximum angular displacement for 7 atom segments

Definition at line 749 of file BackrubMover.cc.

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

get maximum angular displacement slope for other atom segments

Definition at line 763 of file BackrubMover.cc.

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

get maximum segment length if no segments manually defined

Definition at line 721 of file BackrubMover.cc.

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

get minimum segment length if no segments manually defined

Definition at line 707 of file BackrubMover.cc.

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

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

Definition at line 1132 of file BackrubMover.cc.

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

inline

get the number of segments

Definition at line 140 of file BackrubMover.hh.

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

Definition at line 662 of file BackrubMover.cc.

References protocols::TR().

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

void protocols::backrub::BackrubMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::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.

Definition at line 161 of file BackrubMover.cc.

References core::pose::get_resnum_list().

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

get atom names to pivot if no segments manually defined

Definition at line 693 of file BackrubMover.cc.

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

get residues to pivot if no segments manually defined

Definition at line 679 of file BackrubMover.cc.

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.

Definition at line 777 of file BackrubMover.cc.

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

Definition at line 897 of file BackrubMover.cc.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), protocols::backrub::backrub_rotation_constants(), protocols::backrub::BackrubSegment::end_atomid(), protocols::RG(), protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), and protocols::backrub::BackrubSegment::start_atomid2().

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

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

Definition at line 791 of file BackrubMover.cc.

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.

Definition at line 1009 of file BackrubMover.cc.

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::id::PHI, core::pose::Pose::set_dof(), protocols::backrub::BackrubSegment::start_atomid(), protocols::backrub::BackrubSegment::start_atomid1(), protocols::backrub::BackrubSegment::start_atomid2(), and core::id::THETA.

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

inline

get a particular segment

Definition at line 124 of file BackrubMover.hh.

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

Definition at line 100 of file BackrubMover.hh.

References segments_.

Referenced by has_segment(), and segment().

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

set maximum angular displacement for 4 atom segments

Definition at line 741 of file BackrubMover.cc.

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

set maximum angular displacement for 7 atom segments

Definition at line 755 of file BackrubMover.cc.

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

set maximum angular displacement slope for other atom segments

Definition at line 769 of file BackrubMover.cc.

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

set maximum segment length if no segments manually defined

Definition at line 727 of file BackrubMover.cc.

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

Definition at line 713 of file BackrubMover.cc.

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

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

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

Definition at line 1138 of file BackrubMover.cc.

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

set atom names to pivot if no segments manually defined

Definition at line 699 of file BackrubMover.cc.

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

Definition at line 685 of file BackrubMover.cc.

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.

Definition at line 783 of file BackrubMover.cc.

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

Definition at line 797 of file BackrubMover.cc.

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.

Definition at line 805 of file BackrubMover.cc.

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.

Definition at line 1174 of file BackrubMover.cc.

References protocols::motifs::mt().

Member Data Documentation

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

private

Definition at line 350 of file BackrubMover.hh.

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

private

Definition at line 349 of file BackrubMover.hh.

Referenced by branchopt().

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

private

Definition at line 362 of file BackrubMover.hh.

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

private

Definition at line 361 of file BackrubMover.hh.

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

private

Definition at line 359 of file BackrubMover.hh.

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

private

Definition at line 360 of file BackrubMover.hh.

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

private

Definition at line 355 of file BackrubMover.hh.

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

private

Definition at line 356 of file BackrubMover.hh.

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

private

Definition at line 357 of file BackrubMover.hh.

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

private

Definition at line 354 of file BackrubMover.hh.

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

private

Definition at line 353 of file BackrubMover.hh.

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

private

Definition at line 358 of file BackrubMover.hh.

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

private

Definition at line 352 of file BackrubMover.hh.

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

private

Definition at line 351 of file BackrubMover.hh.

bool protocols::backrub::BackrubMover::preserve_detailed_balance_

private

Definition at line 363 of file BackrubMover.hh.

bool protocols::backrub::BackrubMover::require_mm_bend_

private

Definition at line 364 of file BackrubMover.hh.

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

private

Definition at line 348 of file BackrubMover.hh.

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	last_angle_

bool	preserve_detailed_balance_

bool	require_mm_bend_

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation