protocols::simple_filters::SymmetricMotifFilter Class Reference

#include <SymmetricMotifFilter.hh>

Inheritance diagram for protocols::simple_filters::SymmetricMotifFilter:

Collaboration diagram for protocols::simple_filters::SymmetricMotifFilter:

Public Member Functions
	SymmetricMotifFilter ()
	SymmetricMotifFilter (utility::vector1< core::pose::PoseOP > reference_motifs, std::string symm_type_in="D2")
void	set_defaults ()
bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
void	add_motif (core::pose::PoseOP motif)
void	set_symm (std::string symm_type_in)
void	set_thresholds (core::Real angle_thresh_in, core::Real trans_thresh_in, core::Real rmsd_thresh_in, core::Size)
void	set_weights (core::Real angle_thresh_in, core::Real trans_thresh_in, core::Real rmsd_thresh_in)
void	process_motifs ()
protocols::filters::FilterOP	clone () const
protocols::filters::FilterOP	fresh_instance () const
void	report (std::ostream &out, core::pose::Pose const &pose) const
bool	compute (core::pose::Pose const &pose, core::Real &best_score, std::string &motifhit) const
bool	compute_d2 (core::pose::Pose const &pose, core::Real &best_score, std::string &motifhit) const
core::Real	score_d2 (core::Real rms, core::Real angle, core::Real trans, core::Size clash) const
core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual	~SymmetricMotifFilter ()
void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data_map, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &reference_pose)
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::string	symm_type_
utility::vector1 < core::pose::PoseOP >	ref_motifs_
core::Size	nsegs_
core::Real	angle_thresh_
core::Real	trans_thresh_
core::Real	rmsd_thresh_
core::Size	clash_thresh_
core::Real	angle_wt_
core::Real	trans_wt_
core::Real	rmsd_wt_
core::Real	clash_wt_
utility::vector1< int >	forced_pos_
utility::vector1< Quat >	Qs
utility::vector1 < numeric::xyzMatrix < core::Real > >	Rdimers
utility::vector1 < numeric::xyzVector < core::Real > >	delta_coms
utility::vector1 < numeric::xyzVector < core::Real > >	symm_axes
utility::vector1< core::Real >	symm_orders
utility::vector1 < utility::vector1 < numeric::xyzVector < core::Real > > >	cas_chainA
utility::vector1 < utility::vector1 < numeric::xyzVector < core::Real > > >	cas_chainB
utility::vector1 < utility::vector1< core::Size > >	motif_cuts

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

Constructor & Destructor Documentation

protocols::simple_filters::SymmetricMotifFilter::SymmetricMotifFilter

(

)

References set_defaults().

Referenced by clone(), and fresh_instance().

protocols::simple_filters::SymmetricMotifFilter::SymmetricMotifFilter	(	utility::vector1< core::pose::PoseOP >	reference_motifs,
		std::string	symm_type_in = "D2"
	)

References process_motifs(), ref_motifs_, and set_defaults().

protocols::simple_filters::SymmetricMotifFilter::~SymmetricMotifFilter ( )

virtual

Member Function Documentation

void protocols::simple_filters::SymmetricMotifFilter::add_motif

(

core::pose::PoseOP

motif)

References ref_motifs_.

bool protocols::simple_filters::SymmetricMotifFilter::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(), and protocols::simple_filters::TR().

protocols::filters::FilterOP protocols::simple_filters::SymmetricMotifFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References SymmetricMotifFilter().

bool protocols::simple_filters::SymmetricMotifFilter::compute	(	core::pose::Pose const &	pose,
		core::Real &	best_score,
		std::string &	motifhit
	)		const

References compute_d2(), and symm_type_.

Referenced by apply(), and report().

bool protocols::simple_filters::SymmetricMotifFilter::compute_d2	(	core::pose::Pose const &	pose,
		core::Real &	best_score,
		std::string &	motifhit
	)		const

References angle_thresh_, core::conformation::Residue::atom(), cas_chainA, clash_thresh_, core::pose::Pose::conformation(), delta_coms, core::kinematics::distance(), forced_pos_, core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), motif_cuts, core::scoring::packstat::overlap(), Rdimers, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rms, rmsd_thresh_, protocols::simple_filters::RMSwrapper(), score_d2(), symm_axes, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), protocols::simple_filters::TR(), trans_thresh_, and core::conformation::Atom::xyz().

Referenced by compute().

protocols::filters::FilterOP protocols::simple_filters::SymmetricMotifFilter::fresh_instance ( ) const

inlinevirtual

Implements protocols::filters::Filter.

References SymmetricMotifFilter().

void protocols::simple_filters::SymmetricMotifFilter::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::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 angle_thresh_, angle_wt_, clash_thresh_, clash_wt_, forced_pos_, nsegs_, core::import_pose::pose_from_pdb(), process_motifs(), ref_motifs_, rmsd_thresh_, rmsd_wt_, symm_type_, protocols::simple_filters::TR(), trans_thresh_, and trans_wt_.

void protocols::simple_filters::SymmetricMotifFilter::process_motifs

(

)

References cas_chainA, cas_chainB, delta_coms, motif_cuts, nsegs_, core::scoring::omega, Qs, protocols::simple_filters::quat2R(), protocols::simple_filters::R2quat(), Rdimers, ref_motifs_, core::scoring::rms, protocols::simple_filters::RMSwrapper(), core::io::serialization::size(), symm_axes, symm_orders, symm_type_, and protocols::simple_filters::TR().

Referenced by parse_my_tag(), and SymmetricMotifFilter().

void protocols::simple_filters::SymmetricMotifFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::simple_filters::TR().

core::Real protocols::simple_filters::SymmetricMotifFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

core::Real protocols::simple_filters::SymmetricMotifFilter::score_d2 ( core::Real  rms, core::Real  angle, core::Real  trans, core::Size  clash  ) const

inline

References angle_thresh_, angle_wt_, clash_thresh_, clash_wt_, rmsd_thresh_, rmsd_wt_, trans_thresh_, and trans_wt_.

Referenced by compute_d2().

void protocols::simple_filters::SymmetricMotifFilter::set_defaults

(

)

References angle_thresh_, angle_wt_, clash_thresh_, clash_wt_, rmsd_thresh_, rmsd_wt_, trans_thresh_, and trans_wt_.

Referenced by SymmetricMotifFilter().

void protocols::simple_filters::SymmetricMotifFilter::set_symm ( std::string  symm_type_in)

inline

References symm_type_.

void protocols::simple_filters::SymmetricMotifFilter::set_thresholds ( core::Real  angle_thresh_in, core::Real  trans_thresh_in, core::Real  rmsd_thresh_in, core::Size    )

inline

References angle_thresh_, rmsd_thresh_, and trans_thresh_.

void protocols::simple_filters::SymmetricMotifFilter::set_weights ( core::Real  angle_thresh_in, core::Real  trans_thresh_in, core::Real  rmsd_thresh_in  )

inline

References angle_thresh_, rmsd_thresh_, and trans_thresh_.

Member Data Documentation

core::Real protocols::simple_filters::SymmetricMotifFilter::angle_thresh_

private

Referenced by compute_d2(), parse_my_tag(), score_d2(), set_defaults(), set_thresholds(), and set_weights().

core::Real protocols::simple_filters::SymmetricMotifFilter::angle_wt_

private

Referenced by parse_my_tag(), score_d2(), and set_defaults().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > protocols::simple_filters::SymmetricMotifFilter::cas_chainA

private

Referenced by compute_d2(), and process_motifs().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > protocols::simple_filters::SymmetricMotifFilter::cas_chainB

private

Referenced by process_motifs().

core::Size protocols::simple_filters::SymmetricMotifFilter::clash_thresh_

private

Referenced by compute_d2(), parse_my_tag(), score_d2(), and set_defaults().

core::Real protocols::simple_filters::SymmetricMotifFilter::clash_wt_

private

Referenced by parse_my_tag(), score_d2(), and set_defaults().

utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_filters::SymmetricMotifFilter::delta_coms

private

Referenced by compute_d2(), and process_motifs().

utility::vector1< int > protocols::simple_filters::SymmetricMotifFilter::forced_pos_

private

Referenced by compute_d2(), and parse_my_tag().

utility::vector1< utility::vector1< core::Size > > protocols::simple_filters::SymmetricMotifFilter::motif_cuts

private

Referenced by compute_d2(), and process_motifs().

core::Size protocols::simple_filters::SymmetricMotifFilter::nsegs_

private

Referenced by parse_my_tag(), and process_motifs().

utility::vector1< Quat > protocols::simple_filters::SymmetricMotifFilter::Qs

private

Referenced by process_motifs().

utility::vector1< numeric::xyzMatrix< core::Real > > protocols::simple_filters::SymmetricMotifFilter::Rdimers

private

Referenced by compute_d2(), and process_motifs().

utility::vector1<core::pose::PoseOP> protocols::simple_filters::SymmetricMotifFilter::ref_motifs_

private

Referenced by add_motif(), parse_my_tag(), process_motifs(), and SymmetricMotifFilter().

core::Real protocols::simple_filters::SymmetricMotifFilter::rmsd_thresh_

private

Referenced by compute_d2(), parse_my_tag(), score_d2(), set_defaults(), set_thresholds(), and set_weights().

core::Real protocols::simple_filters::SymmetricMotifFilter::rmsd_wt_

private

Referenced by parse_my_tag(), score_d2(), and set_defaults().

utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_filters::SymmetricMotifFilter::symm_axes

private

Referenced by compute_d2(), and process_motifs().

utility::vector1< core::Real > protocols::simple_filters::SymmetricMotifFilter::symm_orders

private

Referenced by process_motifs().

std::string protocols::simple_filters::SymmetricMotifFilter::symm_type_

private

Referenced by compute(), parse_my_tag(), process_motifs(), and set_symm().

core::Real protocols::simple_filters::SymmetricMotifFilter::trans_thresh_

private

Referenced by compute_d2(), parse_my_tag(), score_d2(), set_defaults(), set_thresholds(), and set_weights().

core::Real protocols::simple_filters::SymmetricMotifFilter::trans_wt_

private

Referenced by parse_my_tag(), score_d2(), and set_defaults().

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

• src/protocols/simple_filters/SymmetricMotifFilter.hh
• src/protocols/simple_filters/SymmetricMotifFilter.cc