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protocols::calc_taskop_filters::RelativePoseFilter Class Reference

#include <RelativePoseFilter.hh>

Inheritance diagram for protocols::calc_taskop_filters::RelativePoseFilter:
Inheritance graph
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Public Member Functions

 RelativePoseFilter ()
 default ctor More...
 
bool apply (core::pose::Pose const &pose) const override
 Constructor with a single target residue. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
core::Real compute (core::pose::Pose const &pose) const
 
 ~RelativePoseFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 
void filter (protocols::filters::FilterOP filter)
 
protocols::filters::FilterOP filter () const
 
protocols::moves::MoverOP relax_mover () const
 
void relax_mover (protocols::moves::MoverOP const mover)
 
core::pose::PoseOP pose () const
 
void pose (core::pose::PoseOP p)
 
void pdb_name (std::string const &pdb_name)
 
std::string dump_pose_fname () const
 
void dump_pose_fname (std::string const &s)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void scorefxn (core::scoring::ScoreFunctionOP const s)
 
void packing_shell (core::Real const s)
 
core::Real packing_shell () const
 
core::pose::PoseOP thread_seq (core::pose::Pose const &p) const
 
bool thread () const
 
void thread (bool const t)
 
bool baseline () const
 
void baseline (bool const b)
 
core::Real baseline_val () const
 
void baseline_val (core::Real const )
 
bool unbound () const
 
void unbound (bool const b)
 
bool copy_stretch () const
 
void copy_stretch (bool const b)
 
void symmetry_definition (std::string const &s)
 
std::string symmetry_definition () const
 
std::string filter_name () const
 
void filter_name (std::string const &s)
 
void rtmin (bool const b)
 
bool rtmin () const
 
utility::vector1< std::string > copy_comments () const
 
void copy_comments (utility::vector1< std::string > const &s)
 
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 bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void attributes (utility::tag::AttributeList &attlist)
 

Protected Member Functions

std::map< core::Size, core::Sizeget_alignment (core::pose::Pose const &p) const
 

Private Types

typedef protocols::filters::Filter parent
 

Private Attributes

protocols::filters::FilterOP filter_
 
protocols::moves::MoverOP relax_mover_
 
std::string alignment_str_
 
std::string dump_pose_fname_
 
core::pose::PoseOP pose_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real packing_shell_
 
bool thread_
 
bool baseline_
 
core::Real baseline_val_
 
bool unbound_
 
bool copy_stretch_
 
std::string symmetry_definition_
 
core::conformation::symmetry::SymmDataOP symmdata_
 
std::string filter_name_
 
bool rtmin_
 
utility::vector1< std::string > copy_comments_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::calc_taskop_filters::RelativePoseFilter::RelativePoseFilter ( )

default ctor

References copy_comments_.

protocols::calc_taskop_filters::RelativePoseFilter::~RelativePoseFilter ( )
overridedefault

Member Function Documentation

bool protocols::calc_taskop_filters::RelativePoseFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References filter(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::attributes ( utility::tag::AttributeList &  attlist)
static
bool protocols::calc_taskop_filters::RelativePoseFilter::baseline ( ) const

References baseline_.

Referenced by baseline_val(), compute(), parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::baseline ( bool const  b)
core::Real protocols::calc_taskop_filters::RelativePoseFilter::baseline_val ( ) const

References baseline(), and baseline_val_.

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

void protocols::calc_taskop_filters::RelativePoseFilter::baseline_val ( core::Real const  b)
std::string protocols::calc_taskop_filters::RelativePoseFilter::class_name ( )
static
protocols::filters::FilterOP protocols::calc_taskop_filters::RelativePoseFilter::clone ( ) const
overridevirtual
core::Real protocols::calc_taskop_filters::RelativePoseFilter::compute ( core::pose::Pose const &  pose) const
utility::vector1< std::string > protocols::calc_taskop_filters::RelativePoseFilter::copy_comments ( ) const
inline

References copy_comments_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::copy_comments ( utility::vector1< std::string > const &  s)
inline

References copy_comments_.

bool protocols::calc_taskop_filters::RelativePoseFilter::copy_stretch ( ) const
inline

References copy_stretch_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::copy_stretch ( bool const  b)
inline
std::string protocols::calc_taskop_filters::RelativePoseFilter::dump_pose_fname ( ) const

References dump_pose_fname_.

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::RelativePoseFilter::dump_pose_fname ( std::string const &  s)

References dump_pose_fname_.

void protocols::calc_taskop_filters::RelativePoseFilter::filter ( protocols::filters::FilterOP  filter)

References filter(), and filter_.

protocols::filters::FilterOP protocols::calc_taskop_filters::RelativePoseFilter::filter ( ) const

References filter_.

Referenced by apply(), compute(), filter(), and parse_my_tag().

std::string protocols::calc_taskop_filters::RelativePoseFilter::filter_name ( ) const

References filter_name_.

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::RelativePoseFilter::filter_name ( std::string const &  s)

References filter_name_.

protocols::filters::FilterOP protocols::calc_taskop_filters::RelativePoseFilter::fresh_instance ( ) const
overridevirtual
std::map< core::Size, core::Size > protocols::calc_taskop_filters::RelativePoseFilter::get_alignment ( core::pose::Pose const &  p) const
protected
std::string protocols::calc_taskop_filters::RelativePoseFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::calc_taskop_filters::RelativePoseFilter::packing_shell ( core::Real const  s)

References packing_shell_.

core::Real protocols::calc_taskop_filters::RelativePoseFilter::packing_shell ( ) const

References packing_shell_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

alignment is expecting X1:Y1,X2:Y2,X3:Y3... where X is the protein on disk (target) and Y is the active structure (starting structure). When no alignment is given it is implied that the poses are trivially aligned 1..nres Feb2012 added option to align entire chains: A:B,D:C. Notice that no testing is made to ensure correct lengths etc., simply aligns from the start to end of the chains sequentially.

Reimplemented from protocols::filters::Filter.

References alignment_str_, baseline(), baseline_val(), copy_comments(), copy_stretch(), dump_pose_fname(), core::pose::symmetry::extract_asymmetric_unit(), filter(), filter_name(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_pose(), packing_shell(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::import_pose::PDB_file, pdb_name(), pose(), pose_, core::import_pose::pose_from_file(), relax_mover(), report_sm(), rtmin(), scorefxn(), symmdata_, symmetry_definition_, thread(), protocols::calc_taskop_filters::TR(), and unbound().

void protocols::calc_taskop_filters::RelativePoseFilter::pdb_name ( std::string const &  pdb_name)
core::pose::PoseOP protocols::calc_taskop_filters::RelativePoseFilter::pose ( ) const

References pose_.

Referenced by get_alignment(), parse_my_tag(), pdb_name(), pose(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::pose ( core::pose::PoseOP  p)

References pose(), and pose_.

void protocols::calc_taskop_filters::RelativePoseFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
protocols::moves::MoverOP protocols::calc_taskop_filters::RelativePoseFilter::relax_mover ( ) const

References relax_mover_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::relax_mover ( protocols::moves::MoverOP const  mover)

References relax_mover_.

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

Reimplemented from protocols::filters::Filter.

core::Real protocols::calc_taskop_filters::RelativePoseFilter::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().

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::RelativePoseFilter::rtmin ( bool const  b)
bool protocols::calc_taskop_filters::RelativePoseFilter::rtmin ( ) const

References rtmin_.

Referenced by parse_my_tag(), and thread_seq().

core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RelativePoseFilter::scorefxn ( ) const

References scorefxn_.

Referenced by compute(), parse_my_tag(), scorefxn(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::scorefxn ( core::scoring::ScoreFunctionOP const  s)

References scorefxn(), and scorefxn_.

void protocols::calc_taskop_filters::RelativePoseFilter::symmetry_definition ( std::string const &  s)

References symmetry_definition_.

std::string protocols::calc_taskop_filters::RelativePoseFilter::symmetry_definition ( ) const

References symmetry_definition_.

bool protocols::calc_taskop_filters::RelativePoseFilter::thread ( ) const

References thread_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::thread ( bool const  t)
core::pose::PoseOP protocols::calc_taskop_filters::RelativePoseFilter::thread_seq ( core::pose::Pose const &  p) const
bool protocols::calc_taskop_filters::RelativePoseFilter::unbound ( ) const
inline

References unbound_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::calc_taskop_filters::RelativePoseFilter::unbound ( bool const  b)
inline

Member Data Documentation

std::string protocols::calc_taskop_filters::RelativePoseFilter::alignment_str_
private

Referenced by get_alignment(), and parse_my_tag().

bool protocols::calc_taskop_filters::RelativePoseFilter::baseline_
private

Referenced by baseline().

core::Real protocols::calc_taskop_filters::RelativePoseFilter::baseline_val_
private

Referenced by baseline_val().

utility::vector1< std::string > protocols::calc_taskop_filters::RelativePoseFilter::copy_comments_
private
bool protocols::calc_taskop_filters::RelativePoseFilter::copy_stretch_
private

Referenced by copy_stretch().

std::string protocols::calc_taskop_filters::RelativePoseFilter::dump_pose_fname_
private

Referenced by dump_pose_fname().

protocols::filters::FilterOP protocols::calc_taskop_filters::RelativePoseFilter::filter_
private

Referenced by filter().

std::string protocols::calc_taskop_filters::RelativePoseFilter::filter_name_
private

Referenced by filter_name().

core::Real protocols::calc_taskop_filters::RelativePoseFilter::packing_shell_
private

Referenced by packing_shell().

core::pose::PoseOP protocols::calc_taskop_filters::RelativePoseFilter::pose_
private

Referenced by parse_my_tag(), and pose().

protocols::moves::MoverOP protocols::calc_taskop_filters::RelativePoseFilter::relax_mover_
private

Referenced by relax_mover().

bool protocols::calc_taskop_filters::RelativePoseFilter::rtmin_
private

Referenced by rtmin().

core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RelativePoseFilter::scorefxn_
private

Referenced by scorefxn().

core::conformation::symmetry::SymmDataOP protocols::calc_taskop_filters::RelativePoseFilter::symmdata_
private

Referenced by parse_my_tag().

std::string protocols::calc_taskop_filters::RelativePoseFilter::symmetry_definition_
private
bool protocols::calc_taskop_filters::RelativePoseFilter::thread_
private

Referenced by thread().

bool protocols::calc_taskop_filters::RelativePoseFilter::unbound_
private

Referenced by unbound().


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