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protocols::simple_filters::SymmetricMotifFilter Class Reference

#include <SymmetricMotifFilter.hh>

Inheritance diagram for protocols::simple_filters::SymmetricMotifFilter:
Inheritance graph
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Public Member Functions

 SymmetricMotifFilter ()
 
 SymmetricMotifFilter (utility::vector1< core::pose::PoseOP > const &reference_motifs, std::string const &symm_type_in="D2")
 
void set_defaults ()
 
bool apply (core::pose::Pose const &pose) const override
 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 override
 
protocols::filters::FilterOP fresh_instance () const override
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
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 override
 used to report filter internals through a score or silent file More...
 
 ~SymmetricMotifFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter 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

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().

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

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

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

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
overridevirtual

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

Implements protocols::filters::Filter.

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

std::string protocols::simple_filters::SymmetricMotifFilter::class_name ( )
static

Referenced by protocols::simple_filters::SymmetricMotifFilterCreator::keyname(), name(), and provide_xml_schema().

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

Implements protocols::filters::Filter.

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::ResidueTypeBase::is_protein(), core::pose::symmetry::is_symmetric(), protocols::mean_field::max(), 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(), core::pose::Pose::size(), symm_axes, protocols::simple_filters::TR(), trans_thresh_, and core::conformation::Atom::xyz().

Referenced by compute().

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

Implements protocols::filters::Filter.

std::string protocols::simple_filters::SymmetricMotifFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::SymmetricMotifFilter::parse_my_tag ( utility::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 angle_thresh_, angle_wt_, clash_thresh_, clash_wt_, forced_pos_, nsegs_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), 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(), symm_axes, symm_orders, symm_type_, and protocols::simple_filters::TR().

Referenced by parse_my_tag(), and SymmetricMotifFilter().

void protocols::simple_filters::SymmetricMotifFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

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

Referenced by protocols::simple_filters::SymmetricMotifFilterCreator::provide_xml_schema().

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

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
overridevirtual

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().

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