protocols::protein_interface_design::filters::RmsdFilter Class Reference

#include <RmsdFilter.hh>

Public Member Functions
	RmsdFilter ()
	RmsdFilter (std::list< core::Size > const selection, bool const superimpose, core::Real const threshold, core::pose::PoseOP reference_pose)
bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
protocols::filters::FilterOP	clone () const
protocols::filters::FilterOP	fresh_instance () const
void	report (std::ostream &out, core::pose::Pose const &pose) const
void	reference_pose (core::pose::PoseOP ref)
void	selection (std::list< core::Size > const &sele)
void	superimpose (bool s)
bool	superimpose () const
core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose) const
virtual	~RmsdFilter ()
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &reference_pose)
void	superimpose_on_all (bool const b)
bool	superimpose_on_all () const
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

Private Attributes
std::list< core::Size >	selection_
bool	superimpose_
bool	symmetry_
core::Real	threshold_
core::pose::PoseOP	reference_pose_
bool	selection_from_segment_cache_
bool	superimpose_on_all_
bool	specify_both_spans_
bool	CA_only_
core::Size	begin_native_
core::Size	end_native_
core::Size	begin_pose_
core::Size	end_pose_

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

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::RmsdFilter::RmsdFilter

(

)

References filters, and selection_.

Referenced by clone(), protocols::protein_interface_design::filters::RmsdFilterCreator::create_filter(), and fresh_instance().

protocols::protein_interface_design::filters::RmsdFilter::RmsdFilter	(	std::list< core::Size > const	selection,
		bool const	superimpose,
		core::Real const	threshold,
		core::pose::PoseOP	reference_pose
	)

References filters.

protocols::protein_interface_design::filters::RmsdFilter::~RmsdFilter ( )

virtual

Member Function Documentation

bool protocols::protein_interface_design::filters::RmsdFilter::apply ( core::pose::Pose const &  pose ) const

virtual

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

Implements protocols::filters::Filter.

References compute(), rmsd, threshold_, and protocols::protein_interface_design::filters::TR.

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References RmsdFilter().

core::Real protocols::protein_interface_design::filters::RmsdFilter::compute

(

core::pose::Pose const &

pose

)

const

References begin_native_, begin_pose_, CA_only_, calpha_superimpose_pose(), end_native_, core::scoring::is_protein_CA(), numeric::xyzVector< class >::length_squared(), native, reference_pose_, numeric::model_quality::rms_wrapper(), rmsd, core::scoring::rmsd_no_super_subset(), rmsd_with_super_subset(), runtime_assert_msg, selection_, selection_from_segment_cache_, core::pose::datacache::SpecialSegmentsObserver::set_farray_from_sso(), specify_both_spans_, superimpose_, superimpose_on_all(), sym_rmsd_with_super_subset(), symmetry_, and core::pose::Pose::total_residue().

Referenced by apply(), report(), and report_sm().

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdFilter::fresh_instance ( ) const

inlinevirtual

Implements protocols::filters::Filter.

References RmsdFilter().

void protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data_map, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &  reference_pose  )

virtual

Reimplemented from protocols::filters::Filter.

References begin, begin_native_, begin_pose_, CA_only_, chain, core::conformation::Residue::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), end, end_native_, end_pose_, core::pose::get_resnum(), basic::options::OptionKeys::in::file::native, basic::options::option, core::pose::Pose::pdb_info(), core::import_pose::pose_from_pdb(), reference_pose_, core::pose::Pose::residue(), runtime_assert, protocols::rosetta_scripts::saved_reference_pose(), selection_, specify_both_spans_, superimpose_on_all(), symmetry_, core::pose::Pose::total_residue(), protocols::protein_interface_design::filters::TR, and user.

void protocols::protein_interface_design::filters::RmsdFilter::reference_pose ( core::pose::PoseOP  ref )

inline

References reference_pose_.

Referenced by protocols::enzdes::RemoveLigandFilter::report_sm().

void protocols::protein_interface_design::filters::RmsdFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), and rmsd.

core::Real protocols::protein_interface_design::filters::RmsdFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), and rmsd.

Referenced by protocols::enzdes::RemoveLigandFilter::report_sm().

void protocols::protein_interface_design::filters::RmsdFilter::selection ( std::list< core::Size > const &  sele )

inline

References selection_.

Referenced by protocols::enzdes::RemoveLigandFilter::report_sm().

void protocols::protein_interface_design::filters::RmsdFilter::superimpose ( bool  s )

inline

References superimpose_.

Referenced by protocols::enzdes::RemoveLigandFilter::report_sm().

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose ( ) const

inline

References superimpose_.

void protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all ( bool const  b )

inline

References protocols::match::upstream::b, and superimpose_on_all_.

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all ( ) const

inline

References superimpose_on_all_.

Referenced by compute(), and parse_my_tag().

Member Data Documentation

core::Size protocols::protein_interface_design::filters::RmsdFilter::begin_native_

private

Referenced by compute(), and parse_my_tag().

core::Size protocols::protein_interface_design::filters::RmsdFilter::begin_pose_

private

Referenced by compute(), and parse_my_tag().

bool protocols::protein_interface_design::filters::RmsdFilter::CA_only_

private

Referenced by compute(), and parse_my_tag().

core::Size protocols::protein_interface_design::filters::RmsdFilter::end_native_

private

Referenced by compute(), and parse_my_tag().

core::Size protocols::protein_interface_design::filters::RmsdFilter::end_pose_

private

Referenced by parse_my_tag().

core::pose::PoseOP protocols::protein_interface_design::filters::RmsdFilter::reference_pose_

private

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

std::list< core::Size > protocols::protein_interface_design::filters::RmsdFilter::selection_

private

Referenced by compute(), parse_my_tag(), RmsdFilter(), and selection().

bool protocols::protein_interface_design::filters::RmsdFilter::selection_from_segment_cache_

private

Referenced by compute().

bool protocols::protein_interface_design::filters::RmsdFilter::specify_both_spans_

private

Referenced by compute(), and parse_my_tag().

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_

private

Referenced by compute(), and superimpose().

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all_

private

Referenced by superimpose_on_all().

bool protocols::protein_interface_design::filters::RmsdFilter::symmetry_

private

Referenced by compute(), and parse_my_tag().

core::Real protocols::protein_interface_design::filters::RmsdFilter::threshold_

private

Referenced by apply().

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

• symlinks/rosetta/src/protocols/protein_interface_design/filters/RmsdFilter.hh
• symlinks/rosetta/src/protocols/protein_interface_design/filters/RmsdFilter.cc