#include <CartesianSampler.hh>

Public Member Functions
	CartesianSampler ()

	CartesianSampler (utility::vector1< core::fragment::FragSetOP > fragments_in)

void	init ()

void	apply (core::pose::Pose &pose)

void	set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_fa_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

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

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

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	set_userpos (std::set< core::Size > const &user_pos_in)

void	set_strategy (std::string strategy_in)

void	set_rms_cutoff (core::Real rms_cutoff_in)

void	set_fullatom (bool fullatom_in)

void	set_bbmove (bool bbmove_in)

void	set_restore_csts (bool restore_csts_in)

void	set_frag_sizes (utility::vector1< core::Size > const &frag_sizes_in)

void	set_nminsteps (core::Size nminsteps_in)

void	set_ncycles (core::Size ncycles_in)

void	set_overlap (core::Size overlap_in)

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

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...

Protected Member Functions
bool	apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)

void	compute_fragment_bias (core::pose::Pose &pose)

void	update_fragment_library_pointers ()

void	apply_constraints (core::pose::Pose &pose)

core::Real	get_transform (core::pose::Pose const &pose, core::pose::Pose const &frag, core::Size startpos, core::Vector &preT, core::Vector &postT, numeric::xyzMatrix< core::Real > &R)

void	apply_transform (core::pose::Pose &frag, core::Vector const &preT, core::Vector const &postT, numeric::xyzMatrix< core::Real > const &R)

void	apply_fragcsts (core::pose::Pose &working_frag, core::pose::Pose const &pose, core::Size start)

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...

Private Attributes
core::Size	ncycles_

core::Size	overlap_

core::Size	nminsteps_

core::Real	rms_cutoff_

utility::vector1< core::Size >	frag_sizes_

core::Size	nfrags_

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

utility::vector1 < boost::unordered_map < core::Size, core::fragment::Frame > >	library_

std::string	fragment_bias_strategy_

utility::vector1 < numeric::random::WeightedSampler >	frag_bias_

std::set< core::Size >	user_pos_

core::Real	temp_

std::string	selection_bias_

core::pose::Pose	ref_model_

core::Real	ref_cst_weight_

bool	input_as_ref_

bool	restore_csts_

bool	fullatom_

bool	bbmove_

bool	recover_low_

char	force_ss_

LoopsOP	loops_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

core::scoring::ScoreFunctionOP	mc_scorefxn_

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...

Constructor & Destructor Documentation

protocols::hybridization::CartesianSampler::CartesianSampler ( )

References init().

Referenced by clone(), and fresh_instance().

protocols::hybridization::CartesianSampler::CartesianSampler ( utility::vector1< core::fragment::FragSetOP > fragments_in )

References fragments_, init(), and update_fragment_library_pointers().

Member Function Documentation

void protocols::hybridization::CartesianSampler::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References protocols::hotspot_hashing::accept, protocols::moves::Mover::apply(), apply_constraints(), apply_frame(), core::chemical::CENTROID, compute_fragment_bias(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::hybridization::create_fragment_set_no_ssbias(), core::pose::Pose::data(), end, fa_scorefxn_, core::chemical::FA_STANDARD, force_ss_, frag_bias_, frag_sizes_, fragment_bias_strategy_, fragments_, fullatom_, basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), input_as_ref_, core::pose::Pose::is_fullatom(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), j, length, library_, core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), mc, mc_scorefxn_, minimizer, core::pose::datacache::CacheableDataType::NCS_RESIDUE_MAPPING, ncycles_, nfrags_, nminsteps_, nres, numeric::random::random_range(), recover_low_, ref_model_, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), restore_csts_, protocols::hybridization::RG, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), temp_, core::pose::Pose::total_residue(), protocols::hybridization::TR, update_fragment_library_pointers(), user_pos_, and utility_exit_with_message.

void protocols::hybridization::CartesianSampler::apply_constraints ( core::pose::Pose & pose )

protected

void protocols::hybridization::CartesianSampler::apply_fragcsts	(	core::pose::Pose &	working_frag,
		core::pose::Pose const &	pose,
		core::Size	start
	)

protected

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::conformation::Residue::atom(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), j, overlap_, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

Referenced by apply_frame().

bool protocols::hybridization::CartesianSampler::apply_frame	(	core::pose::Pose &	pose,
		core::fragment::Frame &	frame
	)

protected

References core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_bond(), core::fragment::Frame::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), apply_fragcsts(), apply_transform(), core::scoring::symmetry::asymmetrize_scorefunction(), bbmove_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::Pose::data(), core::scoring::elec_dens_fast, fa_scorefxn_, fullatom_, basic::datacache::BasicDataCache::get_ptr(), get_transform(), basic::datacache::BasicDataCache::has(), core::conformation::idealize_position(), core::pose::symmetry::is_symmetric(), j, core::fragment::Frame::length(), core::optimization::MinimizerOptions::max_iter(), core::pose::datacache::CacheableDataType::NCS_RESIDUE_MAPPING, core::fragment::Frame::nr_frags(), overlap_, core::pack::task::TaskFactory::push_back(), numeric::random::random_range(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), rms, rms_cutoff_, core::optimization::AtomTreeMinimizer::run(), runtime_assert, protocols::simple_moves::PackRotamersMover::score_function(), scorefxn_, selection_bias_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::fragment::Frame::shift_to(), core::fragment::Frame::start(), protocols::loops::start, protocols::simple_moves::PackRotamersMover::task_factory(), protocols::hybridization::TR, and utility_exit_with_message.

Referenced by apply().

void protocols::hybridization::CartesianSampler::apply_transform	(	core::pose::Pose &	frag,
		core::Vector const &	preT,
		core::Vector const &	postT,
		numeric::xyzMatrix< core::Real > const &	R
	)

protected

References j, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by apply_frame().

protocols::moves::MoverOP protocols::hybridization::CartesianSampler::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 CartesianSampler().

void protocols::hybridization::CartesianSampler::compute_fragment_bias ( core::pose::Pose & pose )

protected

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), core::scoring::elec_dens_window, protocols::loops::Loops::empty(), core::pose::Pose::energies(), core::scoring::fa_rep, core::pose::Pose::fold_tree(), frag_bias_, fragment_bias_strategy_, fragments_, core::scoring::electron_density::getDensityMap(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::is_fullatom(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::last_backbone_atom(), loops_, core::scoring::electron_density::ElectronDensity::matchRes(), nres, core::pose::Pose::pdb_info(), core::scoring::rama, rama, core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::scoring::electron_density::ElectronDensity::setScoreWindowContext(), core::scoring::electron_density::ElectronDensity::setWindow(), core::scoring::symmetry::symmetrize_scorefunction(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), protocols::hybridization::TR, user_pos_, core::scoring::vdw, and core::conformation::Atom::xyz().

Referenced by apply().

protocols::moves::MoverOP protocols::hybridization::CartesianSampler::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 CartesianSampler().

std::string protocols::hybridization::CartesianSampler::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::hybridization::CartesianSampler::get_transform	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	frag,
		core::Size	startpos,
		core::Vector &	preT,
		core::Vector &	postT,
		numeric::xyzMatrix< core::Real > &	R
	)

protected

void protocols::hybridization::CartesianSampler::init ( void )

References bbmove_, core::scoring::ScoreFunctionFactory::create_score_function(), force_ss_, fragment_bias_strategy_, fullatom_, input_as_ref_, ncycles_, nfrags_, nminsteps_, overlap_, recover_low_, ref_cst_weight_, restore_csts_, rms_cutoff_, selection_bias_, set_fa_scorefunction(), set_scorefunction(), and temp_.

Referenced by CartesianSampler().

void protocols::hybridization::CartesianSampler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		filters::Filters_map const &	filters,
		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 bbmove_, force_ss_, frag_sizes_, fragment_bias_strategy_, fragments_, fullatom_, basic::datacache::DataMap::get(), core::pose::get_resnum_list(), basic::datacache::DataMap::has(), input_as_ref_, loops_, mc_scorefxn_, ncycles_, nfrags_, nminsteps_, overlap_, core::import_pose::pose_from_pdb(), recover_low_, ref_cst_weight_, ref_model_, rms_cutoff_, runtime_assert, selection_bias_, set_fa_scorefunction(), set_scorefunction(), utility::string_split(), temp_, update_fragment_library_pointers(), and user_pos_.

void protocols::hybridization::CartesianSampler::set_bbmove ( bool bbmove_in )

inline

void protocols::hybridization::CartesianSampler::set_fa_scorefunction ( core::scoring::ScoreFunctionOP scorefxn_in )

inline

Referenced by init(), and parse_my_tag().

void protocols::hybridization::CartesianSampler::set_frag_sizes ( utility::vector1< core::Size > const & frag_sizes_in )

inline

void protocols::hybridization::CartesianSampler::set_fullatom ( bool fullatom_in )

inline

void protocols::hybridization::CartesianSampler::set_ncycles ( core::Size ncycles_in )

inline

void protocols::hybridization::CartesianSampler::set_nminsteps ( core::Size nminsteps_in )

inline

void protocols::hybridization::CartesianSampler::set_overlap ( core::Size overlap_in )

inline

void protocols::hybridization::CartesianSampler::set_restore_csts ( bool restore_csts_in )

inline

void protocols::hybridization::CartesianSampler::set_rms_cutoff ( core::Real rms_cutoff_in )

inline

void protocols::hybridization::CartesianSampler::set_scorefunction ( core::scoring::ScoreFunctionOP scorefxn_in )

inline

Referenced by init(), and parse_my_tag().

void protocols::hybridization::CartesianSampler::set_strategy ( std::string strategy_in )

inline

void protocols::hybridization::CartesianSampler::set_userpos ( std::set< core::Size > const & user_pos_in )

inline

void protocols::hybridization::CartesianSampler::update_fragment_library_pointers ( )

protected

References begin, fragments_, j, and library_.

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

Member Data Documentation

bool protocols::hybridization::CartesianSampler::bbmove_

private

Referenced by apply_frame(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::fa_scorefxn_

private

Referenced by apply(), and apply_frame().

char protocols::hybridization::CartesianSampler::force_ss_

private

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

utility::vector1<numeric::random::WeightedSampler> protocols::hybridization::CartesianSampler::frag_bias_

private

Referenced by apply(), and compute_fragment_bias().

utility::vector1<core::Size> protocols::hybridization::CartesianSampler::frag_sizes_

private

Referenced by apply(), and parse_my_tag().

std::string protocols::hybridization::CartesianSampler::fragment_bias_strategy_

private

Referenced by apply(), apply_constraints(), compute_fragment_bias(), init(), and parse_my_tag().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::CartesianSampler::fragments_

private

Referenced by apply(), CartesianSampler(), compute_fragment_bias(), parse_my_tag(), and update_fragment_library_pointers().

bool protocols::hybridization::CartesianSampler::fullatom_

private

Referenced by apply(), apply_frame(), init(), and parse_my_tag().

bool protocols::hybridization::CartesianSampler::input_as_ref_

private

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

utility::vector1<boost::unordered_map<core::Size, core::fragment::Frame> > protocols::hybridization::CartesianSampler::library_

private

Referenced by apply(), and update_fragment_library_pointers().

LoopsOP protocols::hybridization::CartesianSampler::loops_

private

Referenced by apply_constraints(), compute_fragment_bias(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::mc_scorefxn_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::hybridization::CartesianSampler::ncycles_

private

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

core::Size protocols::hybridization::CartesianSampler::nfrags_

private

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

core::Size protocols::hybridization::CartesianSampler::nminsteps_

private

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

core::Size protocols::hybridization::CartesianSampler::overlap_

private

Referenced by apply_fragcsts(), apply_frame(), get_transform(), init(), and parse_my_tag().

bool protocols::hybridization::CartesianSampler::recover_low_

private

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

core::Real protocols::hybridization::CartesianSampler::ref_cst_weight_

private

Referenced by apply_constraints(), init(), and parse_my_tag().

core::pose::Pose protocols::hybridization::CartesianSampler::ref_model_

private

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

bool protocols::hybridization::CartesianSampler::restore_csts_

private

Referenced by apply(), and init().

core::Real protocols::hybridization::CartesianSampler::rms_cutoff_

private

Referenced by apply_frame(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::scorefxn_

private

Referenced by apply(), and apply_frame().

std::string protocols::hybridization::CartesianSampler::selection_bias_

private

Referenced by apply_frame(), init(), and parse_my_tag().

core::Real protocols::hybridization::CartesianSampler::temp_

private

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

std::set<core::Size> protocols::hybridization::CartesianSampler::user_pos_

private

Referenced by apply(), apply_constraints(), compute_fragment_bias(), and parse_my_tag().

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

symlinks/rosetta/src/protocols/hybridization/CartesianSampler.hh
symlinks/rosetta/src/protocols/hybridization/CartesianSampler.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation