#include <MapHotspot.hh>

Inheritance diagram for protocols::protein_interface_design::movers::MapHotspot:

Collaboration diagram for protocols::protein_interface_design::movers::MapHotspot:

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::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

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::TagPtr const tag, protocols::moves::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
	clone has to be overridden only if clone invocation is expected. More...

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	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

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

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. 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

Definition at line 33 of file MapHotspot.hh.

Member Typedef Documentation

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

Definition at line 38 of file MapHotspot.hh.

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

Definition at line 39 of file MapHotspot.hh.

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

Definition at line 40 of file MapHotspot.hh.

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

Definition at line 37 of file MapHotspot.hh.

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

Definition at line 36 of file MapHotspot.hh.

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

Definition at line 41 of file MapHotspot.hh.

Constructor & Destructor Documentation

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

Definition at line 88 of file MapHotspot.cc.

Referenced by clone().

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

virtual

Definition at line 90 of file MapHotspot.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 264 of file MapHotspot.cc.

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

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 57 of file MapHotspot.hh.

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

Definition at line 170 of file MapHotspot.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, and core::pose::Pose::total_residue().

Referenced by GenerateMap().

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

inlinevirtual

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 58 of file MapHotspot.hh.

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 (score12) 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).

Definition at line 202 of file MapHotspot.cc.

References core::chemical::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(), core::scoring::ScoreFunctionFactory::create_score_function(), explosion_, jump_filters_, jump_movers_, MinimizeHotspots(), core::chemical::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(), rot(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, and core::scoring::total_score.

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.

Definition at line 273 of file MapHotspot.cc.

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

Definition at line 94 of file MapHotspot.cc.

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

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

Definition at line 123 of file MapHotspot.cc.

References 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(), and core::pose::Pose::residue().

Referenced by GenerateMap().

void protocols::protein_interface_design::movers::MapHotspot::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 278 of file MapHotspot.cc.

References allowed_aas_per_jump_, clash_check_, explosion_, file_name_prefix_, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), jump_filters_, jump_movers_, minimization_scorefxns_, and core::pose::Pose::num_jump().