#include <TryRotamers.hh>

Inheritance diagram for protocols::protein_interface_design::movers::TryRotamers:

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

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 Member Functions
	TryRotamers ()

	TryRotamers (core::Size resnum, core::scoring::ScoreFunction const &scorefxn, protocols::filters::Filter const &final_filter, core::Size explosion=0, core::Size jump_num=1, bool clash_check=false, bool solo_res=false, bool include_current=true)

	TryRotamers (core::Size resnum, core::scoring::ScoreFunction const &scorefxn, core::Size explosion=0, core::Size jump_num=1, bool clash_check=false, bool solo_res=false, bool include_current=true)

core::pack::rotamer_set::RotamerSetOP	rotamer_set ()
	EVIL. More...

void	get_rotamer_set (core::pack::rotamer_set::RotamerSetOP const &rs)
	EVIL. More...

void	set_resnum (core::Size const r)

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
	EVIL. More...

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

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

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 &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

core::pack::rotamer_set::Rotamers::const_iterator	begin () const

core::pack::rotamer_set::Rotamers::const_iterator	end () const

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

virtual	~TryRotamers ()

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

	~Mover () override

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string 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...

virtual 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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Attributes
core::scoring::ScoreFunctionCOP	scorefxn_

core::pack::rotamer_set::Rotamers::const_iterator	rotamer_it_

core::pack::rotamer_set::RotamerSetOP	rotset_

core::Size	resnum_

core::Size	jump_num_

bool	clash_check_

bool	solo_res_

bool	include_current_

bool	automatic_connection_

core::Size	explosion_

protocols::filters::FilterOP	final_filter_

utility::vector1< core::Size >	shove_residues_

Additional Inherited Members
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::TryRotamers::Pose

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

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

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

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

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::TryRotamers::TryRotamers ( )

Referenced by clone().

protocols::protein_interface_design::movers::TryRotamers::TryRotamers	(	core::Size	resnum,
		core::scoring::ScoreFunction const &	scorefxn,
		protocols::filters::Filter const &	final_filter,
		core::Size	explosion = `0`,
		core::Size	jump_num = `1`,
		bool	clash_check = `false`,
		bool	solo_res = `false`,
		bool	include_current = `true`
	)

protocols::protein_interface_design::movers::TryRotamers::TryRotamers	(	core::Size	resnum,
		core::scoring::ScoreFunction const &	scorefxn,
		core::Size	explosion = `0`,
		core::Size	jump_num = `1`,
		bool	solo_res = `false`,
		bool	clash_check = `false`,
		bool	include_current = `true`
	)

Parameters

jump_num The jump number of the interface. 0 for no interface

Note: Pass everything through the final filter (True Filter); Pass everything through the final filter (True Filter)

protocols::protein_interface_design::movers::TryRotamers::~TryRotamers ( )

virtual

Member Function Documentation

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

overridevirtual

core::pack::rotamer_set::Rotamers::const_iterator protocols::protein_interface_design::movers::TryRotamers::begin ( ) const

inline

References rotset_.

Referenced by get_rotamer_set().

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

inlineoverridevirtual

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 TryRotamers().

core::pack::rotamer_set::Rotamers::const_iterator protocols::protein_interface_design::movers::TryRotamers::end ( ) const

inline

References rotset_.

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

inlineoverridevirtual

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.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::protein_interface_design::movers::TryRotamers::get_rotamer_set ( core::pack::rotamer_set::RotamerSetOP const & rs )

inline

EVIL.

References begin(), rotamer_it_, and rotset_.

std::string protocols::protein_interface_design::movers::TryRotamers::mover_name ( )

static

Referenced by get_name(), protocols::protein_interface_design::movers::TryRotamersCreator::keyname(), and provide_xml_schema().

void protocols::protein_interface_design::movers::TryRotamers::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
	)

overridevirtual

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 automatic_connection_, clash_check_, explosion_, final_filter_, core::pose::get_resnum(), protocols::rosetta_scripts::get_score_function_name(), include_current_, jump_num_, core::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), resnum_, scorefxn_, shove_residues_, solo_res_, and protocols::protein_interface_design::movers::TR().

void protocols::protein_interface_design::movers::TryRotamers::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pose::attributes_for_get_resnum(), protocols::rosetta_scripts::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::movers::TryRotamersCreator::provide_xml_schema().

core::pack::rotamer_set::RotamerSetOP protocols::protein_interface_design::movers::TryRotamers::rotamer_set ( )

inline

EVIL.

References rotset_.

void protocols::protein_interface_design::movers::TryRotamers::set_resnum ( core::Size const r )

inline

References resnum_.

void protocols::protein_interface_design::movers::TryRotamers::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

inline

EVIL.

References scorefxn_.

void protocols::protein_interface_design::movers::TryRotamers::setup_rotamer_set ( core::pose::Pose & pose )

References clash_check_, core::pack::task::TaskFactory::create_packer_task(), core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, explosion_, include_current_, core::pose::Pose::residue(), resnum_, rotamer_it_, rotset_, scorefxn_, core::pose::Pose::size(), and protocols::protein_interface_design::movers::TR().

Referenced by apply().

Member Data Documentation

bool protocols::protein_interface_design::movers::TryRotamers::automatic_connection_

private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::TryRotamers::clash_check_

private

Referenced by parse_my_tag(), and setup_rotamer_set().

core::Size protocols::protein_interface_design::movers::TryRotamers::explosion_

private

Referenced by parse_my_tag(), and setup_rotamer_set().

protocols::filters::FilterOP protocols::protein_interface_design::movers::TryRotamers::final_filter_

private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::TryRotamers::include_current_

private

Referenced by parse_my_tag(), and setup_rotamer_set().

core::Size protocols::protein_interface_design::movers::TryRotamers::jump_num_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::TryRotamers::resnum_

private

Referenced by apply(), parse_my_tag(), set_resnum(), and setup_rotamer_set().

core::pack::rotamer_set::Rotamers::const_iterator protocols::protein_interface_design::movers::TryRotamers::rotamer_it_

private

Referenced by apply(), get_rotamer_set(), and setup_rotamer_set().

core::pack::rotamer_set::RotamerSetOP protocols::protein_interface_design::movers::TryRotamers::rotset_

private

Referenced by apply(), begin(), end(), get_rotamer_set(), rotamer_set(), and setup_rotamer_set().

core::scoring::ScoreFunctionCOP protocols::protein_interface_design::movers::TryRotamers::scorefxn_

private

Referenced by parse_my_tag(), set_scorefxn(), and setup_rotamer_set().

utility::vector1< core::Size > protocols::protein_interface_design::movers::TryRotamers::shove_residues_

private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::TryRotamers::solo_res_

private

Referenced by apply(), and parse_my_tag().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation