#include <MapHotspot.hh>

Public Member Functions
	MapHotspot ()

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

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

void	GenerateMap (core::pose::Pose const &start_pose, core::pose::Pose &curr_pose, core::Size const jump_number)
	this is the recursive function where the functionality takes place More...

void	MinimizeHotspots (core::pose::Pose &pose)
	minimizes rb and sc dofs for all of the hotspots More...

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...

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	output_pose (core::pose::Pose const &pose) const

RotamerSetOP	create_rotamer_set (core::pose::Pose const &, core::Size const hotspot_resnum, core::Size const explosion) const

virtual	~MapHotspot ()

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 Attributes
bool	clash_check_

std::map< core::Size, core::Size >	explosion_

SizeFilter_map	jump_filters_

std::map< core::Size, std::string >	allowed_aas_per_jump_

std::map< core::Size, core::scoring::ScoreFunctionCOP >	minimization_scorefxns_

std::map< core::Size, protocols::moves::MoverOP >	jump_movers_

std::string	file_name_prefix_

Additional Inherited Members
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...

Member Typedef Documentation

typedef core::pose::Pose protocols::protein_interface_design::movers::MapHotspot::Pose

typedef core::conformation::Residue protocols::protein_interface_design::movers::MapHotspot::Residue

typedef core::pack::rotamer_set::RotamerSetOP protocols::protein_interface_design::movers::MapHotspot::RotamerSetOP

typedef core::scoring::ScoreFunction protocols::protein_interface_design::movers::MapHotspot::ScoreFunction

typedef core::scoring::ScoreFunctionCOP protocols::protein_interface_design::movers::MapHotspot::ScoreFunctionCOP

typedef std::map< core::Size, protocols::filters::FilterCOP > protocols::protein_interface_design::movers::MapHotspot::SizeFilter_map

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::MapHotspot::MapHotspot ( )

Referenced by clone().

protocols::protein_interface_design::movers::MapHotspot::~MapHotspot ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::MapHotspot::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References protocols::moves::FAIL_DO_NOT_RETRY, GenerateMap(), protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::split_by_chain().

protocols::moves::MoverOP protocols::protein_interface_design::movers::MapHotspot::clone ( ) const

inlinevirtual

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 MapHotspot().

core::pack::rotamer_set::RotamerSetOP protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set	(	core::pose::Pose const &	pose,
		core::Size const	hotspot_resnum,
		core::Size const	explosion
	)		const

utility function for creating a rotamer set an managing all of the rotamer options

References EX_THREE_THIRD_STEP_STDDEVS, get_score_function(), core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSet::set_resid(), core::pose::Pose::total_residue(), and protocols::protein_interface_design::movers::TR.

Referenced by GenerateMap().

protocols::moves::MoverOP protocols::protein_interface_design::movers::MapHotspot::fresh_instance ( ) const

inlinevirtual

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.

void protocols::protein_interface_design::movers::MapHotspot::GenerateMap	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	curr_pose,
		core::Size const	jump_number
	)

this is the recursive function where the functionality takes place

A function that recursively goes over all jumps. Within each function, the residue-identities related to that jump are cycled, and for each of those, it iterates over the rotamer set. for each residue type, the best-energy (scorefxn) rotamer, that fulfills all of the user-defined filters is chosen and then we move deeper into the recursion with the next jump. Stopping condition is the final iteration over the final jump at which point a decoy is output, or if no rotamer for the particular residue identity meets all filters (exit with no decoy generation).

References aa_from_oneletter_code(), allowed_aas_per_jump_, core::conformation::Conformation::chain_begin(), protocols::simple_filters::ScoreTypeFilter::compute(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), create_rotamer_set(), explosion_, get_score_function(), jump_filters_, jump_movers_, MinimizeHotspots(), name_from_aa(), core::pose::Pose::num_jump(), output_pose(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), restype, rot(), total_score, and protocols::protein_interface_design::movers::TR.

Referenced by apply().

std::string protocols::protein_interface_design::movers::MapHotspot::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::MapHotspotCreator::mover_name().

void protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots ( core::pose::Pose & pose )

minimizes rb and sc dofs for all of the hotspots

function for minimizing the interface

References empty, core::pose::Pose::fold_tree(), protocols::protein_interface_design::make_hotspot_foldtree(), minimization_scorefxns_, MinimizeInterface(), core::pose::Pose::num_jump(), core::pose::Pose::total_residue(), and protocols::protein_interface_design::movers::TR.

Referenced by GenerateMap().

void protocols::protein_interface_design::movers::MapHotspot::output_pose ( core::pose::Pose const & pose ) const

utility function for dumping out a pose from GenerateMap

References chain, core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), file_name_prefix_, protocols::moves::Mover::name(), core::conformation::Residue::name1(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), and residues.

Referenced by GenerateMap().

void protocols::protein_interface_design::movers::MapHotspot::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 allowed_aas_per_jump_, clash_check_, explosion_, file_name_prefix_, protocols::environment::find_mover(), protocols::rosetta_scripts::get_score_function_name(), basic::datacache::DataMap::has(), jump_filters_, jump_movers_, minimization_scorefxns_, core::pose::Pose::num_jump(), protocols::rosetta_scripts::parse_score_function(), runtime_assert, and protocols::protein_interface_design::movers::TR.

Member Data Documentation

std::map< core::Size, std::string > protocols::protein_interface_design::movers::MapHotspot::allowed_aas_per_jump_

private

Referenced by GenerateMap(), and parse_my_tag().

bool protocols::protein_interface_design::movers::MapHotspot::clash_check_

private

Referenced by parse_my_tag().

std::map< core::Size, core::Size > protocols::protein_interface_design::movers::MapHotspot::explosion_

private

Referenced by GenerateMap(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::MapHotspot::file_name_prefix_

private

Referenced by output_pose(), and parse_my_tag().

SizeFilter_map protocols::protein_interface_design::movers::MapHotspot::jump_filters_

private

Referenced by GenerateMap(), and parse_my_tag().

std::map< core::Size, protocols::moves::MoverOP > protocols::protein_interface_design::movers::MapHotspot::jump_movers_

private

Referenced by GenerateMap(), and parse_my_tag().

std::map< core::Size, core::scoring::ScoreFunctionCOP > protocols::protein_interface_design::movers::MapHotspot::minimization_scorefxns_

private

Referenced by MinimizeHotspots(), and parse_my_tag().

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

src/protocols/protein_interface_design/movers/MapHotspot.hh
src/protocols/protein_interface_design/movers/MapHotspot.cc

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::pose::Pose	Pose

typedef core::conformation::Residue	Residue

typedef core::pack::rotamer_set::RotamerSetOP	RotamerSetOP

typedef std::map< core::Size, protocols::filters::FilterCOP >	SizeFilter_map

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

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation