#include <StructFragmentMover.hh>

Inheritance diagram for protocols::struct_fragment::StructFragmentMover:

[legend]

Public Member Functions
	StructFragmentMover ()
	Empty Constructor. More...

	~StructFragmentMover () override
	Destructor. More...

void	apply (core::pose::Pose &pose) override
	Apply Mover. More...

protocols::moves::MoverOP	clone () const override
	Create clone of this mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Create a fresh instance of this mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse RosettaScripts options for this mover. More...

std::string	get_name () const override
	Get mover name. More...

core::Size	get_n_candidates () const
	Get the number of fragment candidates per position. More...

core::Size	get_n_frags () const
	Get the number of fragments per position. More...

core::Real	get_loop_angle_conf () const
	Get the confidence for phi and psi angles. More...

core::Size	get_small_frag_size () const
	Get the size of small fragments. More...

core::Size	get_large_frag_size () const
	Get the size of large fragments. More...

std::string	get_small_frag_file () const
	Get the path to the small fragment file. More...

std::string	get_large_frage_file () const
	Get the parth to the large fragment file. More...

std::string	get_prefix () const
	Get the prefix for the fragment file output. More...

bool	get_output_frag_files () const
	Check if fragment files should be outputted. More...

bool	get_steal_small_frags () const
	Check if small fragments are being stolen. More...

bool	get_steal_large_frags () const
	Check if large fragments are being stolen. More...

std::string	get_frag_weight_file () const
	Get the path to the fragment weight file. More...

std::string	get_sequence_profile () const
	Get the path to a sequence profile. More...

std::string	get_vall_file () const
	Get the path to the vall file. More...

void	set_n_candidates (core::Size n_candidates)
	Set the number of fragment candidates per position. More...

void	set_n_frags (core::Size n_frags)
	Set the number of fragments per position. More...

void	set_loop_angle_conf (core::Real loop_angle_conf)
	Set the confidence for phi and psi angles. More...

void	set_small_frag_size (core::Size small_frag_size)
	Set the size of small fragments. More...

void	set_large_frag_size (core::Size large_frag_size)
	Set the size of large fragments. More...

void	set_small_frag_file (std::string small_frag_file)
	Set the path to the small fragment file. More...

void	set_large_frag_file (std::string large_frag_file)
	Set the parth to the large fragment file. More...

void	set_prefix (std::string prefix)
	Set the prefix for the fragment file output. More...

void	set_output_frag_files (bool output_frag_files)
	Set whether fragment files should be outputted. More...

void	set_steal_small_frags (bool steal_small_frags)
	Set whether small fragments are being stolen. More...

void	set_steal_large_frags (bool steal_large_frags)
	Set whether large fragments are being stolen. More...

void	set_frag_weight_file (std::string frag_weight_file)
	Set the path to the fragment weight file. More...

void	set_sequence_profile (std::string sequence_profile)
	Set the path to a sequence profile. More...

void	set_vall_file (std::string vall_file)
	Set the path to the vall file. More...

void	set_secstruct (std::string const &ss)
	sets the secondary structure to be used for constraint generation More...

void	set_use_dssp (bool const use_dssp)
	If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used. 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	mover_name ()
	Return mover name. More...

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
std::string	get_secstruct (core::pose::Pose const &pose) const
	returns secondary structure to be used in this constraint generator 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...

Private Member Functions
core::Size	evaluate_job ()
	evaluates which process to run More...

utility::vector1< core::fragment::FragSetOP >	get_fragments (core::pose::Pose const &pose)
	Collect fragments for the specified input structure. More...

protocols::frag_picker::FragmentPickerOP	make_fragment_picker (core::pose::Pose pose, std::string vall_file_name)
	Create fragment picker for the specified input structure. More...

core::fragment::FragSetOP	steal_fragments_by_size (core::pose::Pose const &pose, core::fragment::FragSetOP fset, core::Size size)

utility::vector1< core::fragment::FragSetOP >	steal_fragments (core::pose::Pose const &pose, utility::vector1< core::fragment::FragSetOP > fsets)

void	collector_to_picker (protocols::frag_picker::FragmentPickerOP pickIt, core::Size size, core::Size seqlength)

core::fragment::FragSetOP	get_fragset (protocols::frag_picker::FragmentPickerOP pickIt, core::Size position, core::Size size)

core::fragment::FragSetOP	shift_fragset (core::fragment::FragSetOP fset, core::id::SequenceMapping const &seqmap)

core::fragment::FragSetOP	read_frag_file (std::string frag_file)
	Read existing fragment file. More...

utility::vector1< core::fragment::FragSetOP >	read_frag_files (std::string small_frag_file, std::string large_frag_file)
	Read small and large fragment file and combine the fragments. More...

Static Private Member Functions
static core::Real	default_value_for_loop_angle_conf ()
	Default value for the confidence of phi and psi angles. More...

static core::Size	default_value_for_small_frag_size ()
	Default value for the small fragment size. More...

static core::Size	default_value_for_large_frag_size ()
	Default value for the large fragment size. More...

static bool	default_value_for_output_frag_files ()
	Default value for outputting fragment files. More...

static bool	default_value_for_steal_small_frags ()
	Default value for stealing small fragments. More...

static bool	default_value_for_steal_large_frags ()
	Default value for stealing large fragments. More...

static std::string	default_value_for_empty_file ()
	Default value for empty file. More...

static core::Size	default_value_for_n_candidates ()
	Default value for fragment candidates per position. More...

static core::Size	default_value_for_n_frags ()
	Default value for the number of fragments per position. More...

static std::string	default_value_for_prefix ()
	Default prefix for fragment output files. More...

static std::string	default_value_for_secstruct ()
	Default value for empty file. More...

Private Attributes
protocols::frag_picker::FragmentPickerOP	structPicker_

core::Real	loop_angle_conf_

core::Size	small_frag_size_

core::Size	large_frag_size_

std::string	small_frag_file_

std::string	large_frag_file_

bool	output_frag_files_

bool	steal_small_frags_

bool	steal_large_frags_

bool	changed_frags_

std::string	frag_weight_file_

std::string	sequence_profile_

std::string	vall_file_

core::fragment::FragSetOP	smallF_

core::fragment::FragSetOP	largeF_

bool	use_dssp_

std::string	secstruct_

Additional Inherited Members
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

Constructor & Destructor Documentation

◆ StructFragmentMover()

protocols::struct_fragment::StructFragmentMover::StructFragmentMover ( )

Empty Constructor.

References default_value_for_n_candidates(), default_value_for_n_frags(), default_value_for_prefix(), and structPicker_.

◆ ~StructFragmentMover()

protocols::struct_fragment::StructFragmentMover::~StructFragmentMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::struct_fragment::StructFragmentMover::apply ( core::pose::Pose & pose )

overridevirtual

Apply Mover.

Implements protocols::moves::Mover.

References changed_frags_, core::pose::Pose::empty(), evaluate_job(), get_fragments(), large_frag_file_, large_frag_size_, largeF_, output_frag_files_, read_frag_files(), small_frag_file_, small_frag_size_, smallF_, steal_fragments(), structPicker_, core::id::to_string(), protocols::struct_fragment::TR(), and core::fragment::FragmentIO::write_data().

◆ clone()

protocols::moves::MoverOP protocols::struct_fragment::StructFragmentMover::clone ( ) const

inlineoverridevirtual

Create clone of this mover.

Reimplemented from protocols::moves::Mover.

◆ collector_to_picker()

void protocols::struct_fragment::StructFragmentMover::collector_to_picker	(	protocols::frag_picker::FragmentPickerOP	pickIt,
		core::Size	size,
		core::Size	seqlength
	)

private

Referenced by get_fragments().

◆ default_value_for_empty_file()

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_empty_file ( )

inlinestaticprivate

Default value for empty file.

Referenced by parse_my_tag().

◆ default_value_for_large_frag_size()

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_large_frag_size ( )

inlinestaticprivate

Default value for the large fragment size.

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_value_for_loop_angle_conf()

static core::Real protocols::struct_fragment::StructFragmentMover::default_value_for_loop_angle_conf ( )

inlinestaticprivate

Default value for the confidence of phi and psi angles.

◆ default_value_for_n_candidates()

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_n_candidates ( )

inlinestaticprivate

Default value for fragment candidates per position.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

◆ default_value_for_n_frags()

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_n_frags ( )

inlinestaticprivate

Default value for the number of fragments per position.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

◆ default_value_for_output_frag_files()

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_output_frag_files ( )

inlinestaticprivate

Default value for outputting fragment files.

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_value_for_prefix()

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_prefix ( )

inlinestaticprivate

Default prefix for fragment output files.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

◆ default_value_for_secstruct()

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_secstruct ( )

inlinestaticprivate

Default value for empty file.

Referenced by provide_xml_schema().

◆ default_value_for_small_frag_size()

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_small_frag_size ( )

inlinestaticprivate

Default value for the small fragment size.

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_value_for_steal_large_frags()

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_steal_large_frags ( )

inlinestaticprivate

Default value for stealing large fragments.

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_value_for_steal_small_frags()

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_steal_small_frags ( )

inlinestaticprivate

Default value for stealing small fragments.

Referenced by parse_my_tag(), and provide_xml_schema().

◆ evaluate_job()

core::Size protocols::struct_fragment::StructFragmentMover::evaluate_job ( )

private

evaluates which process to run

References large_frag_file_, small_frag_file_, steal_large_frags_, steal_small_frags_, and vall_file_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::struct_fragment::StructFragmentMover::fresh_instance ( ) const

inlineoverridevirtual

Create a fresh instance of this mover.

Reimplemented from protocols::moves::Mover.

◆ get_frag_weight_file()

std::string protocols::struct_fragment::StructFragmentMover::get_frag_weight_file ( ) const

inline

Get the path to the fragment weight file.

References frag_weight_file_.

◆ get_fragments()

utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::get_fragments ( core::pose::Pose const & pose )

private

Collect fragments for the specified input structure.

References changed_frags_, collector_to_picker(), get_fragset(), large_frag_size_, make_fragment_picker(), core::pose::Pose::pdb_info(), small_frag_size_, steal_large_frags_, steal_small_frags_, core::pose::Pose::total_residue(), protocols::struct_fragment::TR(), and vall_file_.

Referenced by apply().

◆ get_fragset()

cf::FragSetOP protocols::struct_fragment::StructFragmentMover::get_fragset	(	protocols::frag_picker::FragmentPickerOP	pickIt,
		core::Size	position,
		core::Size	size
	)

private

References protocols::cluster::calibur::aa, core::scoring::omega, core::conformation::membrane::out, and protocols::struct_fragment::TR().

Referenced by get_fragments().

◆ get_large_frag_size()

core::Size protocols::struct_fragment::StructFragmentMover::get_large_frag_size ( ) const

inline

Get the size of large fragments.

References large_frag_size_.

◆ get_large_frage_file()

std::string protocols::struct_fragment::StructFragmentMover::get_large_frage_file ( ) const

inline

Get the parth to the large fragment file.

References large_frag_file_.

◆ get_loop_angle_conf()

core::Real protocols::struct_fragment::StructFragmentMover::get_loop_angle_conf ( ) const

inline

Get the confidence for phi and psi angles.

References loop_angle_conf_.

◆ get_n_candidates()

core::Size protocols::struct_fragment::StructFragmentMover::get_n_candidates ( ) const

inline

Get the number of fragment candidates per position.

References structPicker_.

◆ get_n_frags()

core::Size protocols::struct_fragment::StructFragmentMover::get_n_frags ( ) const

inline

Get the number of fragments per position.

References structPicker_.

◆ get_name()

std::string protocols::struct_fragment::StructFragmentMover::get_name ( ) const

inlineoverridevirtual

Get mover name.

Implements protocols::moves::Mover.

References mover_name().

◆ get_output_frag_files()

bool protocols::struct_fragment::StructFragmentMover::get_output_frag_files ( ) const

inline

Check if fragment files should be outputted.

References output_frag_files_.

◆ get_prefix()

std::string protocols::struct_fragment::StructFragmentMover::get_prefix ( ) const

inline

Get the prefix for the fragment file output.

References structPicker_.

◆ get_secstruct()

std::string protocols::struct_fragment::StructFragmentMover::get_secstruct ( core::pose::Pose const & pose ) const

protected

returns secondary structure to be used in this constraint generator

Parameters

[in] pose Input pose

Returns

Secondary stucture of the pose according to the following rules:

secstruct_ if it is non-empty
DSSP secondary structure of the input pose if use_dssp_ is true
Pose secondary structure if use_dssp_ is false

References protocols::simple_filters::dssp(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Referenced by make_fragment_picker().

◆ get_sequence_profile()

std::string protocols::struct_fragment::StructFragmentMover::get_sequence_profile ( ) const

inline

Get the path to a sequence profile.

References sequence_profile_.

◆ get_small_frag_file()

std::string protocols::struct_fragment::StructFragmentMover::get_small_frag_file ( ) const

inline

Get the path to the small fragment file.

References small_frag_file_.

◆ get_small_frag_size()

core::Size protocols::struct_fragment::StructFragmentMover::get_small_frag_size ( ) const

inline

Get the size of small fragments.

References small_frag_size_.

◆ get_steal_large_frags()

bool protocols::struct_fragment::StructFragmentMover::get_steal_large_frags ( ) const

inline

Check if large fragments are being stolen.

References steal_large_frags_.

◆ get_steal_small_frags()

bool protocols::struct_fragment::StructFragmentMover::get_steal_small_frags ( ) const

inline

Check if small fragments are being stolen.

References steal_small_frags_.

◆ get_vall_file()

std::string protocols::struct_fragment::StructFragmentMover::get_vall_file ( ) const

inline

Get the path to the vall file.

References vall_file_.

◆ make_fragment_picker()

pfp::FragmentPickerOP protocols::struct_fragment::StructFragmentMover::make_fragment_picker	(	core::pose::Pose	pose,
		std::string	vall_file_name
	)

private

Create fragment picker for the specified input structure.

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), frag_weight_file_, get_secstruct(), core::conformation::Residue::is_protein(), loop_angle_conf_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::sequence(), sequence_profile_, structPicker_, core::pose::Pose::total_residue(), and protocols::struct_fragment::TR().

Referenced by get_fragments().

◆ mover_name()

static std::string protocols::struct_fragment::StructFragmentMover::mover_name ( )

inlinestatic

Return mover name.

Referenced by get_name(), protocols::struct_fragment::StructFragmentMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::struct_fragment::StructFragmentMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

◆ provide_xml_schema()

void protocols::struct_fragment::StructFragmentMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References default_value_for_large_frag_size(), default_value_for_n_candidates(), default_value_for_n_frags(), default_value_for_output_frag_files(), default_value_for_prefix(), default_value_for_secstruct(), default_value_for_small_frag_size(), default_value_for_steal_large_frags(), default_value_for_steal_small_frags(), mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::struct_fragment::StructFragmentMoverCreator::provide_xml_schema().

◆ read_frag_file()

cf::FragSetOP protocols::struct_fragment::StructFragmentMover::read_frag_file ( std::string frag_file )

private

Read existing fragment file.

References core::fragment::FragmentIO::read_data(), and protocols::struct_fragment::TR().

Referenced by read_frag_files().

◆ read_frag_files()

utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::read_frag_files	(	std::string	small_frag_file,
		std::string	large_frag_file
	)

private

Read small and large fragment file and combine the fragments.

References read_frag_file().

Referenced by apply().

◆ set_frag_weight_file()

void protocols::struct_fragment::StructFragmentMover::set_frag_weight_file ( std::string frag_weight_file )

inline

Set the path to the fragment weight file.

References frag_weight_file_.

◆ set_large_frag_file()

void protocols::struct_fragment::StructFragmentMover::set_large_frag_file ( std::string large_frag_file )

inline

Set the parth to the large fragment file.

References large_frag_file_.

◆ set_large_frag_size()

void protocols::struct_fragment::StructFragmentMover::set_large_frag_size ( core::Size large_frag_size )

inline

Set the size of large fragments.

References large_frag_size_.

◆ set_loop_angle_conf()

void protocols::struct_fragment::StructFragmentMover::set_loop_angle_conf ( core::Real loop_angle_conf )

inline

Set the confidence for phi and psi angles.

References loop_angle_conf_.

◆ set_n_candidates()

void protocols::struct_fragment::StructFragmentMover::set_n_candidates ( core::Size n_candidates )

inline

Set the number of fragment candidates per position.

References structPicker_.

◆ set_n_frags()

void protocols::struct_fragment::StructFragmentMover::set_n_frags ( core::Size n_frags )

inline

Set the number of fragments per position.

References structPicker_.

◆ set_output_frag_files()

void protocols::struct_fragment::StructFragmentMover::set_output_frag_files ( bool output_frag_files )

inline

Set whether fragment files should be outputted.

References output_frag_files_.

◆ set_prefix()

void protocols::struct_fragment::StructFragmentMover::set_prefix ( std::string prefix )

inline

Set the prefix for the fragment file output.

References structPicker_.

◆ set_secstruct()

void protocols::struct_fragment::StructFragmentMover::set_secstruct ( std::string const & ss )

sets the secondary structure to be used for constraint generation

returns secondary structure to be used in this constraint generator

Parameters

[in] pose Input pose

Returns: Pose secondary structure

References secstruct_.

Referenced by parse_my_tag().

◆ set_sequence_profile()

void protocols::struct_fragment::StructFragmentMover::set_sequence_profile ( std::string sequence_profile )

inline

Set the path to a sequence profile.

References sequence_profile_.

◆ set_small_frag_file()

void protocols::struct_fragment::StructFragmentMover::set_small_frag_file ( std::string small_frag_file )

inline

Set the path to the small fragment file.

References small_frag_file_.

◆ set_small_frag_size()

void protocols::struct_fragment::StructFragmentMover::set_small_frag_size ( core::Size small_frag_size )

inline

Set the size of small fragments.

References small_frag_size_.

◆ set_steal_large_frags()

void protocols::struct_fragment::StructFragmentMover::set_steal_large_frags ( bool steal_large_frags )

inline

Set whether large fragments are being stolen.

References steal_large_frags_.

◆ set_steal_small_frags()

void protocols::struct_fragment::StructFragmentMover::set_steal_small_frags ( bool steal_small_frags )

inline

Set whether small fragments are being stolen.

References steal_small_frags_.

◆ set_use_dssp()

void protocols::struct_fragment::StructFragmentMover::set_use_dssp ( bool const use_dssp )

If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used.

Parameters

[in] use_dssp Desired value

References use_dssp_.

Referenced by parse_my_tag().

◆ set_vall_file()

void protocols::struct_fragment::StructFragmentMover::set_vall_file ( std::string vall_file )

inline

Set the path to the vall file.

References vall_file_.

◆ shift_fragset()

core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::shift_fragset	(	core::fragment::FragSetOP	fset,
		core::id::SequenceMapping const &	seqmap
	)

private

◆ steal_fragments()

utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::steal_fragments	(	core::pose::Pose const &	pose,
		utility::vector1< core::fragment::FragSetOP >	fsets
	)

private

References protocols::idealize::IdealizeMover::apply(), changed_frags_, protocols::idealize::IdealizeMover::fast(), large_frag_size_, core::pose::Pose::pdb_info(), small_frag_size_, steal_fragments_by_size(), steal_large_frags_, and steal_small_frags_.

Referenced by apply().

◆ steal_fragments_by_size()

cf::FragSetOP protocols::struct_fragment::StructFragmentMover::steal_fragments_by_size	(	core::pose::Pose const &	pose,
		core::fragment::FragSetOP	fset,
		core::Size	size
	)

private

References core::pose::Pose::total_residue(), and protocols::struct_fragment::TR().

Referenced by steal_fragments().

Member Data Documentation

◆ changed_frags_

bool protocols::struct_fragment::StructFragmentMover::changed_frags_

private

Referenced by apply(), get_fragments(), and steal_fragments().

◆ frag_weight_file_

std::string protocols::struct_fragment::StructFragmentMover::frag_weight_file_

private

Referenced by get_frag_weight_file(), make_fragment_picker(), parse_my_tag(), and set_frag_weight_file().

◆ large_frag_file_

std::string protocols::struct_fragment::StructFragmentMover::large_frag_file_

private

Referenced by apply(), evaluate_job(), get_large_frage_file(), parse_my_tag(), and set_large_frag_file().

◆ large_frag_size_

core::Size protocols::struct_fragment::StructFragmentMover::large_frag_size_

private

Referenced by apply(), get_fragments(), get_large_frag_size(), parse_my_tag(), set_large_frag_size(), and steal_fragments().

◆ largeF_

core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::largeF_

private

Referenced by apply(), and parse_my_tag().

◆ loop_angle_conf_

core::Real protocols::struct_fragment::StructFragmentMover::loop_angle_conf_

private

Referenced by get_loop_angle_conf(), make_fragment_picker(), and set_loop_angle_conf().

◆ output_frag_files_

bool protocols::struct_fragment::StructFragmentMover::output_frag_files_

private

Referenced by apply(), get_output_frag_files(), parse_my_tag(), and set_output_frag_files().

◆ secstruct_

std::string protocols::struct_fragment::StructFragmentMover::secstruct_

private

Referenced by get_secstruct(), parse_my_tag(), and set_secstruct().

◆ sequence_profile_

std::string protocols::struct_fragment::StructFragmentMover::sequence_profile_

private

Referenced by get_sequence_profile(), make_fragment_picker(), parse_my_tag(), and set_sequence_profile().

◆ small_frag_file_

std::string protocols::struct_fragment::StructFragmentMover::small_frag_file_

private

Referenced by apply(), evaluate_job(), get_small_frag_file(), parse_my_tag(), and set_small_frag_file().

◆ small_frag_size_

core::Size protocols::struct_fragment::StructFragmentMover::small_frag_size_

private

Referenced by apply(), get_fragments(), get_small_frag_size(), parse_my_tag(), set_small_frag_size(), and steal_fragments().

◆ smallF_

core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::smallF_

private

Referenced by apply(), and parse_my_tag().

◆ steal_large_frags_

bool protocols::struct_fragment::StructFragmentMover::steal_large_frags_

private

Referenced by evaluate_job(), get_fragments(), get_steal_large_frags(), parse_my_tag(), set_steal_large_frags(), and steal_fragments().

◆ steal_small_frags_

bool protocols::struct_fragment::StructFragmentMover::steal_small_frags_

private

Referenced by evaluate_job(), get_fragments(), get_steal_small_frags(), parse_my_tag(), set_steal_small_frags(), and steal_fragments().

◆ structPicker_

protocols::frag_picker::FragmentPickerOP protocols::struct_fragment::StructFragmentMover::structPicker_

private

Referenced by apply(), get_n_candidates(), get_n_frags(), get_prefix(), make_fragment_picker(), parse_my_tag(), set_n_candidates(), set_n_frags(), set_prefix(), and StructFragmentMover().

◆ use_dssp_

bool protocols::struct_fragment::StructFragmentMover::use_dssp_

private

Referenced by get_secstruct(), parse_my_tag(), and set_use_dssp().

◆ vall_file_

std::string protocols::struct_fragment::StructFragmentMover::vall_file_

private

Referenced by evaluate_job(), get_fragments(), get_vall_file(), parse_my_tag(), and set_vall_file().

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

src/protocols/struct_fragment/StructFragmentMover.hh
src/protocols/struct_fragment/StructFragmentMover.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StructFragmentMover()

◆ ~StructFragmentMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ collector_to_picker()

◆ default_value_for_empty_file()

◆ default_value_for_large_frag_size()

◆ default_value_for_loop_angle_conf()

◆ default_value_for_n_candidates()

◆ default_value_for_n_frags()

◆ default_value_for_output_frag_files()

◆ default_value_for_prefix()

◆ default_value_for_secstruct()

◆ default_value_for_small_frag_size()

◆ default_value_for_steal_large_frags()

◆ default_value_for_steal_small_frags()

◆ evaluate_job()

◆ fresh_instance()

◆ get_frag_weight_file()

◆ get_fragments()

◆ get_fragset()

◆ get_large_frag_size()

◆ get_large_frage_file()

◆ get_loop_angle_conf()

◆ get_n_candidates()

◆ get_n_frags()

◆ get_name()

◆ get_output_frag_files()

◆ get_prefix()

◆ get_secstruct()

◆ get_sequence_profile()

◆ get_small_frag_file()

◆ get_small_frag_size()

◆ get_steal_large_frags()

◆ get_steal_small_frags()

◆ get_vall_file()

◆ make_fragment_picker()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ read_frag_file()

◆ read_frag_files()

◆ set_frag_weight_file()

◆ set_large_frag_file()

◆ set_large_frag_size()

◆ set_loop_angle_conf()

◆ set_n_candidates()

◆ set_n_frags()

◆ set_output_frag_files()

◆ set_prefix()

◆ set_secstruct()

◆ set_sequence_profile()

◆ set_small_frag_file()

◆ set_small_frag_size()

◆ set_steal_large_frags()

◆ set_steal_small_frags()

◆ set_use_dssp()

◆ set_vall_file()

◆ shift_fragset()

◆ steal_fragments()

◆ steal_fragments_by_size()

Member Data Documentation

◆ changed_frags_

◆ frag_weight_file_

◆ large_frag_file_

◆ large_frag_size_

◆ largeF_

◆ loop_angle_conf_

◆ output_frag_files_

◆ secstruct_

◆ sequence_profile_