filters based on an upper bound # of buried unsatisfied polar residues More...

#include <SymUnsatHbondFilter.hh>

Inheritance diagram for protocols::matdes::SymUnsatHbondFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	SymUnsatHbondFilter ()

	SymUnsatHbondFilter (core::Size const upper_cutoff, core::Size const jump, std::string const sym_dofs, bool verb, bool write, std::string const mode, bool compare_to_ref, core::pose::PoseOP const reference_pose)

	SymUnsatHbondFilter (SymUnsatHbondFilter const &rval)

	~SymUnsatHbondFilter () override=default

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

void	upper_threshold (core::Size const upper_cutoff)

void	jump_num (core::Size const jump)

void	sym_dof_names (std::string const sym_dofs)

void	verbose (bool const verb)

void	write2pdb (bool const write)

void	mode (std::string const mode)

void	reference_pose (core::pose::PoseOP const reference_pose)

void	compare_to_ref (bool const compare_to_ref)

core::Size	upper_threshold () const

core::Size	jump_num () const

std::string	sym_dof_names () const

bool	verbose () const

bool	write2pdb () const

std::string	mode () const

core::pose::PoseOP	reference_pose () const

bool	compare_to_ref () const

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...

void	report (std::ostream &out, core::pose::Pose const &pose) const override

core::Real	compute (core::pose::Pose const &pose, bool const &verb, bool const &write) const

void	write_to_pdb (core::pose::Pose const &pose, std::string const mode, std::string const residue_name, core::Size const residue, std::string const atom_name) const

void	write_pymol_string_to_pdb (std::string const pymol_selection) const

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

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 std::string	class_name ()

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

Private Attributes
core::Size	upper_threshold_

core::Size	jump_num_

std::string	sym_dof_names_

bool	verbose_

bool	write2pdb_

std::string	mode_

bool	compare_to_ref_

core::pose::PoseOP	reference_pose_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

filters based on an upper bound # of buried unsatisfied polar residues

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::matdes::SymUnsatHbondFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::matdes::SymUnsatHbondFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::matdes::SymUnsatHbondFilter::Pose

◆ Real

typedef core::Real protocols::matdes::SymUnsatHbondFilter::Real

◆ Super

typedef protocols::filters::Filter protocols::matdes::SymUnsatHbondFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::matdes::SymUnsatHbondFilter::TagCOP

Constructor & Destructor Documentation

◆ SymUnsatHbondFilter() [1/3]

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( )

◆ SymUnsatHbondFilter() [2/3]

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter	(	core::Size const	upper_cutoff,
		core::Size const	jump,
		std::string const	sym_dofs,
		bool	verb,
		bool	write,
		std::string const	mode,
		bool	compare_to_ref,
		core::pose::PoseOP const	reference_pose
	)

◆ SymUnsatHbondFilter() [3/3]

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( SymUnsatHbondFilter const & rval )

default

◆ ~SymUnsatHbondFilter()

protocols::matdes::SymUnsatHbondFilter::~SymUnsatHbondFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::matdes::SymUnsatHbondFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), protocols::matdes::TR(), and upper_threshold().

◆ class_name()

std::string protocols::matdes::SymUnsatHbondFilter::class_name ( )

static

Referenced by protocols::matdes::SymUnsatHbondFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compare_to_ref() [1/2]

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref ( ) const

References compare_to_ref_.

Referenced by compare_to_ref(), and parse_my_tag().

◆ compare_to_ref() [2/2]

void protocols::matdes::SymUnsatHbondFilter::compare_to_ref ( bool const compare_to_ref )

References compare_to_ref(), and compare_to_ref_.

◆ compute()

core::Real protocols::matdes::SymUnsatHbondFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	verb,
		bool const &	write
	)		const

◆ fresh_instance()

protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ jump_num() [1/2]

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num ( ) const

References jump_num_.

Referenced by compute(), and parse_my_tag().

◆ jump_num() [2/2]

void protocols::matdes::SymUnsatHbondFilter::jump_num ( core::Size const jump )

References jump_num_.

◆ mode() [1/2]

std::string protocols::matdes::SymUnsatHbondFilter::mode ( ) const

References mode_.

Referenced by mode(), parse_my_tag(), and write_to_pdb().

◆ mode() [2/2]

void protocols::matdes::SymUnsatHbondFilter::mode ( std::string const mode )

References mode(), and mode_.

◆ name()

std::string protocols::matdes::SymUnsatHbondFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_pymol_string_to_pdb(), and write_to_pdb().

◆ parse_my_tag()

void protocols::matdes::SymUnsatHbondFilter::parse_my_tag	(	TagCOP	,
		basic::datacache::DataMap &
	)

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References compare_to_ref(), jump_num(), mode(), mode_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), reference_pose_, protocols::rosetta_scripts::saved_reference_pose(), sym_dof_names(), protocols::matdes::TR(), upper_threshold(), verbose(), and write2pdb().

◆ provide_xml_schema()

void protocols::matdes::SymUnsatHbondFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::attributes_for_saved_reference_pose(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::matdes::SymUnsatHbondFilterCreator::provide_xml_schema().

◆ reference_pose() [1/2]

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose ( ) const

References reference_pose_.

Referenced by reference_pose().

◆ reference_pose() [2/2]

void protocols::matdes::SymUnsatHbondFilter::reference_pose ( core::pose::PoseOP const reference_pose )

References reference_pose(), and reference_pose_.

◆ report()

void protocols::matdes::SymUnsatHbondFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::membrane::out, verbose(), and write2pdb().

◆ report_sm()

core::Real protocols::matdes::SymUnsatHbondFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ sym_dof_names() [1/2]

std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

◆ sym_dof_names() [2/2]

void protocols::matdes::SymUnsatHbondFilter::sym_dof_names ( std::string const sym_dofs )

References sym_dof_names_.

◆ upper_threshold() [1/2]

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold ( ) const

References upper_threshold_.

Referenced by apply(), and parse_my_tag().

◆ upper_threshold() [2/2]

void protocols::matdes::SymUnsatHbondFilter::upper_threshold ( core::Size const upper_cutoff )

References upper_threshold_.

◆ verbose() [1/2]

bool protocols::matdes::SymUnsatHbondFilter::verbose ( ) const

References verbose_.

Referenced by parse_my_tag(), and report().

◆ verbose() [2/2]

void protocols::matdes::SymUnsatHbondFilter::verbose ( bool const verb )

References verbose_.

◆ write2pdb() [1/2]

bool protocols::matdes::SymUnsatHbondFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag(), and report().

◆ write2pdb() [2/2]

void protocols::matdes::SymUnsatHbondFilter::write2pdb ( bool const write )

References write2pdb_.

◆ write_pymol_string_to_pdb()

void protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb ( std::string const pymol_selection ) const

References protocols::jd2::add_string_to_current_job(), protocols::jd2::current_output_name(), protocols::filters::Filter::get_user_defined_name(), and name().

Referenced by compute().

◆ write_to_pdb()

void protocols::matdes::SymUnsatHbondFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		std::string const	mode,
		std::string const	residue_name,
		core::Size const	residue,
		std::string const	atom_name
	)		const

References protocols::jd2::add_string_to_current_job(), protocols::filters::Filter::get_user_defined_name(), mode(), name(), and core::pose::Pose::pdb_info().

Referenced by compute().

Member Data Documentation

◆ compare_to_ref_

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref_

private

Referenced by compare_to_ref(), and compute().

◆ jump_num_

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num_

private

Referenced by jump_num().

◆ mode_

std::string protocols::matdes::SymUnsatHbondFilter::mode_

private

Referenced by compute(), mode(), and parse_my_tag().

◆ reference_pose_

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose_

private

Referenced by compute(), parse_my_tag(), and reference_pose().

◆ sym_dof_names_

std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names_

private

Referenced by sym_dof_names().

◆ upper_threshold_

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold_

private

Referenced by upper_threshold().

◆ verbose_

bool protocols::matdes::SymUnsatHbondFilter::verbose_

private

Referenced by verbose().

◆ write2pdb_

bool protocols::matdes::SymUnsatHbondFilter::write2pdb_

private

Referenced by write2pdb().

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

src/protocols/matdes/SymUnsatHbondFilter.hh
src/protocols/matdes/SymUnsatHbondFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ SymUnsatHbondFilter() [1/3]

◆ SymUnsatHbondFilter() [2/3]

◆ SymUnsatHbondFilter() [3/3]

◆ ~SymUnsatHbondFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compare_to_ref() [1/2]

◆ compare_to_ref() [2/2]

◆ compute()

◆ fresh_instance()

◆ jump_num() [1/2]

◆ jump_num() [2/2]

◆ mode() [1/2]

◆ mode() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reference_pose() [1/2]

◆ reference_pose() [2/2]

◆ report()

◆ report_sm()

◆ sym_dof_names() [1/2]

◆ sym_dof_names() [2/2]

◆ upper_threshold() [1/2]

◆ upper_threshold() [2/2]

◆ verbose() [1/2]

◆ verbose() [2/2]

◆ write2pdb() [1/2]

◆ write2pdb() [2/2]

◆ write_pymol_string_to_pdb()

◆ write_to_pdb()

Member Data Documentation

◆ compare_to_ref_

◆ jump_num_

◆ mode_

◆ reference_pose_

◆ sym_dof_names_

◆ upper_threshold_

◆ verbose_

◆ write2pdb_