protocols::calc_taskop_filters::RelativePoseFilter Class Reference

#include <RelativePoseFilter.hh>

Inheritance diagram for protocols::calc_taskop_filters::RelativePoseFilter:

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 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)
static void	attributes (utility::tag::AttributeList &attlist)

Protected Member Functions
std::map< core::Size, core::Size >	get_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

typedef protocols::filters::Filter protocols::calc_taskop_filters::RelativePoseFilter::parent

private

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

References core::scoring::attributes_for_parse_score_function().

Referenced by protocols::calc_taskop_filters::MultipleSigmoids::provide_xml_schema(), and provide_xml_schema().

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

)

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

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

)

References protocols::match::upstream::b, baseline(), and baseline_val_.

std::string protocols::calc_taskop_filters::RelativePoseFilter::class_name ( )

static

Referenced by protocols::calc_taskop_filters::RelativePoseFilterCreator::keyname(), name(), and provide_xml_schema().

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

overridevirtual

Implements protocols::filters::Filter.

core::Real protocols::calc_taskop_filters::RelativePoseFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::simple_moves::DumpPdb::apply(), baseline(), baseline_val(), dump_pose_fname(), filter(), filter_name(), report_sm(), scorefxn(), protocols::simple_moves::DumpPdb::set_scorefxn(), thread_seq(), and protocols::calc_taskop_filters::TR().

Referenced by report_sm().

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

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

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

Implements protocols::filters::Filter.

std::map< core::Size, core::Size > protocols::calc_taskop_filters::RelativePoseFilter::get_alignment ( core::pose::Pose const &  p ) const

protected

References core::scoring::alignment, alignment_str_, core::pose::parse_resnum(), core::pose::Pose::pdb_info(), pose(), and core::pose::Pose::size().

Referenced by thread_seq().

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

)

References core::import_pose::PDB_file, pose(), and core::import_pose::pose_from_file().

Referenced by parse_my_tag().

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

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

Referenced by protocols::calc_taskop_filters::RelativePoseFilterCreator::provide_xml_schema().

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

)

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

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

)

References protocols::hybridization::t, and thread_.

core::pose::PoseOP protocols::calc_taskop_filters::RelativePoseFilter::thread_seq

(

core::pose::Pose const &

p

)

const

References protocols::cluster::calibur::aa, core::pose::add_comment(), core::scoring::alignment, protocols::rigid::RigidBodyTransMover::apply(), baseline(), baseline_val(), core::pose::Pose::conformation(), copy_comments(), copy_stretch(), get_alignment(), core::pose::get_comment(), core::conformation::Residue::name1(), core::chemical::num_canonical_aas, packing_shell(), pose(), relax_mover(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), rtmin(), scorefxn(), protocols::rigid::RigidBodyTransMover::step_size(), thread(), protocols::calc_taskop_filters::TR(), unbound(), and protocols::hybridization::val.

Referenced by apply(), and compute().

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

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

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

Referenced by copy_comments(), and RelativePoseFilter().

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

Referenced by parse_my_tag(), and symmetry_definition().

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:

• src/protocols/calc_taskop_filters/RelativePoseFilter.hh
• src/protocols/calc_taskop_filters/RelativePoseFilter.cc