#include <SetSecStructEnergies.hh>

Inheritance diagram for protocols::fldsgn::potentials::SetSecStructEnergies:

Collaboration diagram for protocols::fldsgn::potentials::SetSecStructEnergies:

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::jd2::parser::BluePrint	BluePrint

typedef protocols::jd2::parser::BluePrintOP	BluePrintOP

typedef core::conformation::symmetry::SymmetryInfoOP	SymmetryInfoOP

typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential	NatbiasHelixPairPotential

typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP	NatbiasHelixPairPotentialOP

typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential	NatbiasHelicesSheetPotential

typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP	NatbiasHelicesSheetPotentialOP

typedef utility::tag::TagPtr	TagPtr

typedef protocols::filters::Filters_map	Filters_map

typedef protocols::moves::DataMap	DataMap

typedef protocols::moves::Movers_map	Movers_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
	SetSecStructEnergies ()
	default constructor More...

	SetSecStructEnergies (ScoreFunctionOP const sfx, String const &filename, bool const ss_from_blueprint=true)
	value constructor More...

	SetSecStructEnergies (ScoreFunctionOP const sfx, BluePrintOP const blueprintOP, bool const ss_from_blueprint=true)
	value constructor More...

	SetSecStructEnergies (SetSecStructEnergies const &rval)
	copy constructor More...

virtual	~SetSecStructEnergies ()
	default destructor More...

virtual MoverOP	clone () const
	clone this object More...

virtual MoverOP	fresh_instance () const
	create this type of object More...

void	ss_from_blueprint (bool const flag)
	define secondary structrue by blueprint More...

void	scorefunction (ScoreFunction const &sfx)
	set the centroid level score function More...

void	scorefunction (ScoreFunctionOP sfx)
	set the centroid level score function More...

void	set_blueprint (String const &filename)
	set blueprint file by filename More...

void	set_blueprint (BluePrintOP const blp)
	set blueprint file More...

virtual void	apply (Pose &pose)
	apply defined moves to given Pose More...

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

void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
	parse xml file 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

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 Types
typedef protocols::moves::Mover	Super

Private Member Functions
SetSecStructEnergies &	operator= (SetSecStructEnergies const &rval)
	copy assignment More...

String	symmetric_secstruct (SymmetryInfoOP const syminfo, String const &ss)
	make symmetric secstruct More...

Private Attributes
bool	loaded_

BluePrintOP	blueprint_
	bluerprint file for setting build instruction More...

bool	ss_from_blueprint_

ScoreFunctionOP	sfx_
	the centroid scorefunction to use, default "remodel_cen" More...

Real	hh_weight_
	weight for helix and helix pairing potential More...

Real	hs_weight_
	weight for heilx and strand pairing potential More...

Real	ss_weight_
	weight for strand and strand pairing potential More...

Real	stwist_weight_
	weight for sheet twist potential More...

Real	hs_pair_weight_
	weight for hs_pair More...

Real	ss_pair_weight_
	weight for ss_pair More...

Real	rsigma_weight_
	weight for strand and strand pairing potential More...

NatbiasHelixPairPotentialOP	hpairpot_

NatbiasHelicesSheetPotentialOP	hspot_

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 45 of file SetSecStructEnergies.hh.

Member Typedef Documentation

typedef protocols::jd2::parser::BluePrint protocols::fldsgn::potentials::SetSecStructEnergies::BluePrint

Definition at line 67 of file SetSecStructEnergies.hh.

typedef protocols::jd2::parser::BluePrintOP protocols::fldsgn::potentials::SetSecStructEnergies::BluePrintOP

Definition at line 68 of file SetSecStructEnergies.hh.

typedef protocols::moves::DataMap protocols::fldsgn::potentials::SetSecStructEnergies::DataMap

Definition at line 79 of file SetSecStructEnergies.hh.

typedef protocols::filters::Filters_map protocols::fldsgn::potentials::SetSecStructEnergies::Filters_map

Definition at line 78 of file SetSecStructEnergies.hh.

typedef protocols::moves::MoverOP protocols::fldsgn::potentials::SetSecStructEnergies::MoverOP

Definition at line 66 of file SetSecStructEnergies.hh.

typedef protocols::moves::Movers_map protocols::fldsgn::potentials::SetSecStructEnergies::Movers_map

Definition at line 80 of file SetSecStructEnergies.hh.

typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelicesSheetPotential

Definition at line 74 of file SetSecStructEnergies.hh.

typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelicesSheetPotentialOP

Definition at line 75 of file SetSecStructEnergies.hh.

typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelixPairPotential

Definition at line 72 of file SetSecStructEnergies.hh.

typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelixPairPotentialOP

Definition at line 73 of file SetSecStructEnergies.hh.

typedef core::pose::Pose protocols::fldsgn::potentials::SetSecStructEnergies::Pose

Definition at line 61 of file SetSecStructEnergies.hh.

typedef core::pose::PoseOP protocols::fldsgn::potentials::SetSecStructEnergies::PoseOP

Definition at line 62 of file SetSecStructEnergies.hh.

typedef core::Real protocols::fldsgn::potentials::SetSecStructEnergies::Real

Definition at line 59 of file SetSecStructEnergies.hh.

typedef core::scoring::ScoreFunction protocols::fldsgn::potentials::SetSecStructEnergies::ScoreFunction

Definition at line 63 of file SetSecStructEnergies.hh.

typedef core::scoring::ScoreFunctionOP protocols::fldsgn::potentials::SetSecStructEnergies::ScoreFunctionOP

Definition at line 64 of file SetSecStructEnergies.hh.

typedef core::Size protocols::fldsgn::potentials::SetSecStructEnergies::Size

Definition at line 60 of file SetSecStructEnergies.hh.

typedef std::string protocols::fldsgn::potentials::SetSecStructEnergies::String

Definition at line 57 of file SetSecStructEnergies.hh.

typedef protocols::moves::Mover protocols::fldsgn::potentials::SetSecStructEnergies::Super

private

Definition at line 51 of file SetSecStructEnergies.hh.

typedef core::conformation::symmetry::SymmetryInfoOP protocols::fldsgn::potentials::SetSecStructEnergies::SymmetryInfoOP

Definition at line 70 of file SetSecStructEnergies.hh.

typedef utility::tag::TagPtr protocols::fldsgn::potentials::SetSecStructEnergies::TagPtr

Definition at line 77 of file SetSecStructEnergies.hh.

Constructor & Destructor Documentation

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( )

default constructor

Definition at line 81 of file SetSecStructEnergies.cc.

Referenced by clone(), and fresh_instance().

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies	(	ScoreFunctionOP const	sfx,
		String const &	filename,
		bool const	ss_from_blueprint = `true`
	)

value constructor

Definition at line 100 of file SetSecStructEnergies.cc.

References set_blueprint().

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies	(	ScoreFunctionOP const	sfx,
		BluePrintOP const	blueprintOP,
		bool const	ss_from_blueprint = `true`
	)

value constructor

Definition at line 119 of file SetSecStructEnergies.cc.

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( SetSecStructEnergies const & rval)

copy constructor

Definition at line 137 of file SetSecStructEnergies.cc.

protocols::fldsgn::potentials::SetSecStructEnergies::~SetSecStructEnergies ( )

virtual

default destructor

Definition at line 155 of file SetSecStructEnergies.cc.

Member Function Documentation

void protocols::fldsgn::potentials::SetSecStructEnergies::apply ( Pose & pose)

virtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

Definition at line 217 of file SetSecStructEnergies.cc.

References blueprint_, core::pose::Pose::conformation(), hh_weight_, hpairpot_, core::scoring::hs_pair, hs_pair_weight_, hs_weight_, hspot_, core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), loaded_, core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, core::scoring::natbias_stwist, core::scoring::rsigma, rsigma_weight_, core::scoring::SCORE12_PATCH, sfx_, ss_from_blueprint_, core::scoring::ss_pair, ss_pair_weight_, ss_weight_, core::scoring::STANDARD_WTS, stwist_weight_, symmetric_secstruct(), and protocols::fldsgn::potentials::TR().

SetSecStructEnergies::MoverOP protocols::fldsgn::potentials::SetSecStructEnergies::clone ( ) const

virtual

clone this object

Reimplemented from protocols::moves::Mover.

Definition at line 159 of file SetSecStructEnergies.cc.

References SetSecStructEnergies().

SetSecStructEnergies::MoverOP protocols::fldsgn::potentials::SetSecStructEnergies::fresh_instance ( ) const

virtual

create this type of object

Reimplemented from protocols::moves::Mover.

Definition at line 166 of file SetSecStructEnergies.cc.

References SetSecStructEnergies().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 327 of file SetSecStructEnergies.cc.

References protocols::fldsgn::potentials::SetSecStructEnergiesCreator::mover_name().

SetSecStructEnergies& protocols::fldsgn::potentials::SetSecStructEnergies::operator= ( SetSecStructEnergies const & rval)

private

copy assignment

Remarks: Mover base class prevents this from working properly...

void protocols::fldsgn::potentials::SetSecStructEnergies::parse_my_tag	(	TagPtr const	tag,
		DataMap &	data,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &
	)