protocols::comparative_modeling::LoopRelaxMover Class Reference

#include <LoopRelaxMover.hh>

Public Member Functions
	LoopRelaxMover ()
	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::Loops const &loops)
	Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::LoopsFileData const &loops_from_file)
	Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::GuardedLoopsFromFileOP guarded_loops)
	GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
	LoopRelaxMover (LoopRelaxMover const &src)
	Copy-ctor; Shallow copy of all data. More...
LoopRelaxMover const &	operator= (LoopRelaxMover const &rhs)
	assignment operator; Shallow copy of all data. More...
virtual	~LoopRelaxMover ()
virtual void	apply (core::pose::Pose &pose)
	Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	scorefxns (core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn)
void	fa_scorefxn (core::scoring::ScoreFunctionOP fa_scorefxn)
void	cen_scorefxn (core::scoring::ScoreFunctionOP cen_scorefxn)
void	cmd_line_csts (bool setting)
void	copy_sidechains (bool setting)
void	rebuild_filter (core::Real setting)
void	n_rebuild_tries (core::Size setting)
void	remodel (std::string val)
void	intermedrelax (std::string val)
void	refine (std::string val)
void	relax (std::string val)
void	resolve_loopfile_indices (core::pose::Pose const &pose)
	Must be called before the Loops data can be read from. More...
void	loops (protocols::loops::LoopsOP const val)
	set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor More...
void	loops_file_data (loops::LoopsFileData const &loopfiledata)
	Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called. More...
void	frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
bool	cmd_line_csts () const
bool	copy_sidechains () const
core::Size	n_rebuild_tries () const
core::Real	rebuild_filter () const
protocols::loops::LoopsOP	get_loops ()
	Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...
protocols::loops::LoopsCOP	get_loops () const
	Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...
std::string	remodel () const
std::string	relax () const
std::string	intermedrelax () const
std::string	refine () const
utility::vector1 < core::fragment::FragSetOP >	frag_libs () const
protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
void	compute_rmsd (bool const c)
bool	compute_rmsd () const
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...
virtual core::Real	last_proposal_density_ratio ()
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...

Private Member Functions
void	set_defaults_ ()

Private Attributes
bool	cmd_line_csts_
bool	copy_sidechains_
core::Size	n_rebuild_tries_
core::Real	rebuild_filter_
std::string	remodel_
std::string	intermedrelax_
std::string	refine_
std::string	relax_
loops::GuardedLoopsFromFileOP	guarded_loops_
core::scoring::ScoreFunctionOP	cen_scorefxn_
core::scoring::ScoreFunctionOP	fa_scorefxn_
utility::vector1 < core::fragment::FragSetOP >	frag_libs_
bool	compute_rmsd_

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...

Constructor & Destructor Documentation

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover

(

)

References loops, and set_defaults_().

Referenced by clone(), protocols::comparative_modeling::LoopRelaxMoverCreator::create_mover(), and fresh_instance().

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::Loops const &	loops
	)

Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::LoopsFileData const &	loops_from_file
	)

Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

References loops.

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::GuardedLoopsFromFileOP	guarded_loops
	)

GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover

(

LoopRelaxMover const &

src

)

Copy-ctor; Shallow copy of all data.

Copy-ctor; shallow copy of all data object.

protocols::comparative_modeling::LoopRelaxMover::~LoopRelaxMover ( )

virtual

Member Function Documentation

void protocols::comparative_modeling::LoopRelaxMover::apply ( core::pose::Pose &  pose )

virtual

Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::evaluation::EvaluatorFactory::add_all_evaluators(), protocols::viewer::add_conformation_viewer(), core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), protocols::loops::add_cutpoint_variants(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::loops::loop_mover::LoopMover::add_fragments(), core::scoring::angle_constraint, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), protocols::relax::MiniRelax::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::LoopRebuild::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::big_bin_constraint, core::id::BOGUS_ATOM_ID, core::scoring::CA_rmsd(), cen_scorefxn_, core::pose::Pose::center(), core::chemical::CENTROID, core::scoring::chainbreak, protocols::checkpoint::CheckPointer::checkpoint(), cmd_line_csts(), compute_rmsd(), core::pose::Pose::conformation(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, coordinate_constraint, copy_sidechains(), debug, protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::chemical::DISULFIDE, core::io::raw_data::DisulfideFile::disulfides(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), fa_scorefxn_, core::chemical::FA_STANDARD, protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), in::fix_disulf, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), frag_libs(), out::file::fullatom, protocols::relax::generate_relax_from_cmd(), protocols::loops::loop_mover::LoopMover::get_checkpoints(), protocols::moves::Mover::get_current_tag(), protocols::loops::LoopMoverFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), get_loops(), guarded_loops_, core::chemical::ResidueType::has(), core::conformation::Residue::has_variant_type(), core::pose::initialize_atomid_map(), intermedrelax(), core::pose::Pose::is_fullatom(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_polymer(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), length, core::scoring::linear_chainbreak, protocols::loops::loop_rmsd(), loops(), core::pose::symmetry::make_residue_mask_symmetric(), core::pose::symmetry::make_symmetric_movemap(), edensity::mapfile, max_cycles, cm::min_loop_size, protocols::moves::MS_SUCCESS, n_rebuild_tries(), core::chemical::ResidueTypeSet::name_map(), in::file::native, core::scoring::native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), core::conformation::Residue::natoms(), basic::options::option, option, options, core::scoring::overlap_chainbreak, protocols::comparative_modeling::pick_loops_chainbreak(), core::import_pose::pose_from_pdb(), protocol, core::pack::task::TaskFactory::push_back(), basic::options::OptionKeys::loops::random_grow_loops_by, rebuild_filter(), protocols::checkpoint::CheckPointer::recover_checkpoint(), refine(), relax(), remodel(), protocols::loops::remove_cutpoint_variants(), remove_extended_loops, repack_period, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::optimization::AtomTreeMinimizer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), runtime_assert, protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_(), core::kinematics::MoveMap::set_bb(), protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_(), core::kinematics::MoveMap::set_chi(), protocols::moves::Mover::set_current_tag(), protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_(), protocols::moves::Mover::set_last_move_status(), protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::IndependentLoopMover::set_random_order_(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), core::pose::set_ss_from_phipsi(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScore(), setPoseExtraScore(), size(), core::scoring::superimpose_pose(), core::util::switch_to_residue_type_set(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR, numeric::random::uniform(), user, utility_exit_with_message, and core::conformation::Atom::xyz().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().

void protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn

(

core::scoring::ScoreFunctionOP

cen_scorefxn

)

References cen_scorefxn_.

Referenced by parse_my_tag(), and scorefxns().

protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::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.

References LoopRelaxMover().

void protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( bool  setting )

inline

References cmd_line_csts_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

bool protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( ) const

inline

References cmd_line_csts_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( bool const  c )

inline

References compute_rmsd_.

Referenced by protocols::loop_build::LoopBuildMover::apply().

bool protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( ) const

inline

References compute_rmsd_.

Referenced by apply(), parse_my_tag(), and set_defaults_().

void protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( bool  setting )

inline

References copy_sidechains_.

bool protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( ) const

inline

References copy_sidechains_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn

(

core::scoring::ScoreFunctionOP

fa_scorefxn

)

References fa_scorefxn_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), parse_my_tag(), and scorefxns().

void protocols::comparative_modeling::LoopRelaxMover::frag_libs

(

utility::vector1< core::fragment::FragSetOP >

new_libs

)

References frag_libs_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::loop_build::LoopBuild_main().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs

(

)

const

References frag_libs_.

Referenced by apply().

protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::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 LoopRelaxMover().

protocols::loops::LoopsOP protocols::comparative_modeling::LoopRelaxMover::get_loops

(

)

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

Referenced by apply().

protocols::loops::LoopsCOP protocols::comparative_modeling::LoopRelaxMover::get_loops

(

)

const

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

std::string protocols::comparative_modeling::LoopRelaxMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( std::string  val )

inline

References intermedrelax_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().

std::string protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( ) const

inline

References intermedrelax_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::loops

(

protocols::loops::LoopsOP const

val

)

set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor

By setting the loops object directly, the requirement is relaxed that a Pose be first given to the LoopRelax object (through a call to apply() or resolve_loopfile_indices) before the get_loops() function may be called.

References guarded_loops_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::loops_file_data

(

loops::LoopsFileData const &

loopfiledata

)

Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called.

Set the loop file data. This will require that.

References guarded_loops_.

Referenced by protocols::loop_build::LoopBuildMover::setup_loop_definition().

void protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( core::Size  setting )

inline

References n_rebuild_tries_.

core::Size protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( ) const

inline

References n_rebuild_tries_.

Referenced by apply(), and parse_my_tag().

LoopRelaxMover const & protocols::comparative_modeling::LoopRelaxMover::operator=

(

LoopRelaxMover const &

rhs

)

assignment operator; Shallow copy of all data.

References cen_scorefxn_, cmd_line_csts_, compute_rmsd_, copy_sidechains_, fa_scorefxn_, frag_libs_, guarded_loops_, intermedrelax_, n_rebuild_tries_, rebuild_filter_, refine_, relax_, and remodel_.

void protocols::comparative_modeling::LoopRelaxMover::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 cen_scorefxn(), cen_scorefxn_, cmd_line_csts(), compute_rmsd(), copy_sidechains(), fa_scorefxn(), frag_libs_, intermedrelax(), protocols::loops::loops_definers::load_loop_definitions(), loops(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries(), protocols::rosetta_scripts::parse_score_function(), protocols::loops::read_loop_fragments(), rebuild_filter(), refine(), relax(), and remodel().

void protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( core::Real  setting )

inline

References rebuild_filter_.

core::Real protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( ) const

inline

References rebuild_filter_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::refine ( std::string  val )

inline

References refine_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().

std::string protocols::comparative_modeling::LoopRelaxMover::refine ( ) const

inline

References refine_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::relax ( std::string  val )

inline

References relax_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().

std::string protocols::comparative_modeling::LoopRelaxMover::relax ( ) const

inline

References relax_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::remodel ( std::string  val )

inline

References remodel_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::medal::MedalMover::do_loop_closure().

std::string protocols::comparative_modeling::LoopRelaxMover::remodel ( ) const

inline

References remodel_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::resolve_loopfile_indices

(

core::pose::Pose const &

pose

)

Must be called before the Loops data can be read from.

References guarded_loops_.

void protocols::comparative_modeling::LoopRelaxMover::scorefxns	(	core::scoring::ScoreFunctionOP	cen_scorefxn,
		core::scoring::ScoreFunctionOP	fa_scorefxn
	)

References cen_scorefxn(), and fa_scorefxn().

Referenced by protocols::loop_build::LoopBuildMover::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().

void protocols::comparative_modeling::LoopRelaxMover::set_defaults_ ( )

private

References cen_scorefxn_, cmd_line_csts_, compute_rmsd(), copy_sidechains_, fa_scorefxn_, protocols::loops::get_cen_scorefxn(), protocols::loops::get_fa_scorefxn(), intermedrelax_, protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries_, option, rebuild_filter_, refine_, protocols::antibody::design::relax, relax_, and remodel_.

Referenced by LoopRelaxMover().

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn_

private

Referenced by apply(), cen_scorefxn(), operator=(), parse_my_tag(), and set_defaults_().

bool protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts_

private

Referenced by cmd_line_csts(), operator=(), and set_defaults_().

bool protocols::comparative_modeling::LoopRelaxMover::compute_rmsd_

private

Referenced by compute_rmsd(), and operator=().

bool protocols::comparative_modeling::LoopRelaxMover::copy_sidechains_

private

Referenced by copy_sidechains(), operator=(), and set_defaults_().

core::scoring::ScoreFunctionOP protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn_

private

Referenced by apply(), fa_scorefxn(), operator=(), and set_defaults_().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs_

private

Referenced by frag_libs(), operator=(), and parse_my_tag().

loops::GuardedLoopsFromFileOP protocols::comparative_modeling::LoopRelaxMover::guarded_loops_

private

Referenced by apply(), get_loops(), loops(), loops_file_data(), operator=(), and resolve_loopfile_indices().

std::string protocols::comparative_modeling::LoopRelaxMover::intermedrelax_

private

Referenced by intermedrelax(), operator=(), and set_defaults_().

core::Size protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries_

private

Referenced by n_rebuild_tries(), operator=(), and set_defaults_().

core::Real protocols::comparative_modeling::LoopRelaxMover::rebuild_filter_

private

Referenced by operator=(), rebuild_filter(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::refine_

private

Referenced by operator=(), refine(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::relax_

private

Referenced by operator=(), relax(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::remodel_

private

Referenced by operator=(), remodel(), and set_defaults_().

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

• src/protocols/comparative_modeling/LoopRelaxMover.hh
• src/protocols/comparative_modeling/LoopRelaxMover.cc