#include <SetSecStructEnergies.hh>

Inheritance 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 core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::parser::BluePrint	BluePrint

typedef protocols::parser::BluePrintOP	BluePrintOP

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

typedef core::conformation::symmetry::SymmetryInfoCOP	SymmetryInfoCOP

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::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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 () override
	default destructor More...

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

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

ScoreFunctionOP	scorefunction_ptr () const
	access ptr to the modified score function More...

void	set_scorefunction_ptr (ScoreFunctionOP sfx)
	set the centroid level score function to be modified More...

void	set_secstruct (String const &secstruct)
	sets the secondary structure to be used for computation More...

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

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml file More...

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 ()

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 const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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 Types
typedef protocols::moves::Mover	Super

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

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

std::string	get_secstruct (Pose const &pose) const
	chooses and return the secondary structure to be used in computation More...

std::string	get_helix_pairings (Pose const &pose) const

void	init_from_blueprint (BluePrint const &bp, bool const ss_from_blueprint)
	initializes pairings and secondary structure from blueprint file More...

Private Attributes
std::string	secstruct_
	Secondary structure to be used. More...

bool	use_dssp_
	If true, and secstruct is not set, DSSP will be used to determine secondary structure. More...

std::string	hh_pair_
	HHPAIR definition to be used. More...

std::string	ss_pair_
	strand pairing definition to be used More...

std::string	hss_triplet_
	helix-strand-strand triplet definition to be used More...

ScoreFunctionCOP	sfx_orig_
	Original copy of the centroid scorefunction to use. More...

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...

bool	add_symmetry_
	if this option is set, a copy of the input pose will have symmetry added to it, and this symmetry will be used to modify the secondary structure. The input pose will be unchanged. I can't think of any reason why anyone would want this to be true if the input pose is already symmetric. More...

NatbiasHelixPairPotentialOP	hpairpot_

NatbiasHelicesSheetPotentialOP	hspot_

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 protocols::parser::BluePrint protocols::fldsgn::potentials::SetSecStructEnergies::BluePrint

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

typedef basic::datacache::DataMap protocols::fldsgn::potentials::SetSecStructEnergies::DataMap

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

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

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

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

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

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

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

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

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

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

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

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

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

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

private

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

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

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

Constructor & Destructor Documentation

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

default constructor

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

value constructor

References init_from_blueprint().

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

value constructor

References init_from_blueprint().

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

overridedefault

default destructor

Member Function Documentation

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

overridevirtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

References get_secstruct(), hh_pair_, hh_weight_, hpairpot_, core::scoring::hs_pair, hs_pair_weight_, hs_weight_, hspot_, hss_triplet_, core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, core::scoring::natbias_stwist, core::scoring::rsigma, rsigma_weight_, sfx_, sfx_orig_, core::scoring::ss_pair, ss_pair_, ss_pair_weight_, ss_weight_, stwist_weight_, and protocols::fldsgn::potentials::TR().

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

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

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

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_helix_pairings ( Pose const & pose ) const

private

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct ( Pose const & pose ) const

private

chooses and return the secondary structure to be used in computation

Parameters

[in] pose Input pose

If secstruct_ is set, returns that. If use_dssp_ is set, returns DSSP secstruct string Otherwise, returns pose secondary structure

References add_symmetry_, core::pose::Pose::conformation(), protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), core::pose::Pose::secstruct(), secstruct_, symmetric_secstruct(), and use_dssp_.

Referenced by apply().

void protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint	(	BluePrint const &	bp,
		bool const	ss_from_blueprint
	)

private

initializes pairings and secondary structure from blueprint file

Parameters

[in]	bp	BluePrint object
[in]	ss_from_blueprint	If true, secstruct_ will be set from the blueprint. If false, secstruct_ will be unchanged, and only the pairings will be set.

References protocols::parser::BluePrint::helix_pairings(), hh_pair_, hss_triplet_, protocols::parser::BluePrint::hss_triplets(), protocols::parser::BluePrint::secstruct(), secstruct_, ss_pair_, and protocols::parser::BluePrint::strand_pairings().

Referenced by parse_my_tag(), and SetSecStructEnergies().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::mover_name ( )

static

Referenced by get_name(), protocols::fldsgn::potentials::SetSecStructEnergiesCreator::keyname(), and provide_xml_schema().

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	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml file

parse xml

Reimplemented from protocols::moves::Mover.

References add_symmetry_, hh_pair_, hh_weight_, hpairpot_, hs_pair_weight_, hs_weight_, hspot_, hss_triplet_, init_from_blueprint(), rsigma_weight_, secstruct_, set_scorefunction_ptr(), ss_pair_, ss_pair_weight_, ss_weight_, stwist_weight_, protocols::fldsgn::potentials::TR(), and use_dssp_.

void protocols::fldsgn::potentials::SetSecStructEnergies::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::fldsgn::potentials::SetSecStructEnergiesCreator::provide_xml_schema().

SetSecStructEnergies::ScoreFunctionOP protocols::fldsgn::potentials::SetSecStructEnergies::scorefunction_ptr ( ) const

access ptr to the modified score function

References sfx_.

void protocols::fldsgn::potentials::SetSecStructEnergies::set_scorefunction_ptr ( ScoreFunctionOP sfx )

set the centroid level score function to be modified

set the centroid level score function

this also clones the object of ptr isn't null and stores the clone in sfx_orig_

References sfx_, and sfx_orig_.

Referenced by parse_my_tag().

void protocols::fldsgn::potentials::SetSecStructEnergies::set_secstruct ( String const & secstruct )

sets the secondary structure to be used for computation

Parameters

[in] secstruct Secondary structure to be forced on the pose

If this is non-empty, it will be used as the pose secondary structure to determine secondary structure elements in the pose

References secstruct_.

SetSecStructEnergies::String protocols::fldsgn::potentials::SetSecStructEnergies::symmetric_secstruct	(	SymmetryInfoCOP const	syminfo,
		String const &	ss
	)		const

private

make symmetric secstruct

Referenced by get_secstruct().

Member Data Documentation

bool protocols::fldsgn::potentials::SetSecStructEnergies::add_symmetry_

private

if this option is set, a copy of the input pose will have symmetry added to it, and this symmetry will be used to modify the secondary structure. The input pose will be unchanged. I can't think of any reason why anyone would want this to be true if the input pose is already symmetric.

TL: this is added as a hack to work around behavior by SetupForSymmetryMover. SetupForSymmetry sets this command line flag to a bogus value in its parse_my_tag() function. Therefore, the presence of the option at runtime does not indicate the user's intentions. As a workaround, the option is queried set at parse time and this variable is used after than. WARNING: You should declare your SetupForSymmetry movers AFTER this one, or you will probably get crashes. Default is the value of option[ symmetry::symmetry_definition ].active() at parse-time

Referenced by get_secstruct(), and parse_my_tag().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::hh_pair_

private

HHPAIR definition to be used.

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

Real protocols::fldsgn::potentials::SetSecStructEnergies::hh_weight_

private

weight for helix and helix pairing potential

Referenced by apply(), and parse_my_tag().

NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::hpairpot_

private

Referenced by apply(), and parse_my_tag().