#include <RelativePoseFilter.hh>

Inheritance diagram for protocols::simple_filters::RelativePoseFilter:

Collaboration diagram for protocols::simple_filters::RelativePoseFilter:

Public Member Functions
	RelativePoseFilter ()
	default ctor More...

virtual bool	apply (core::pose::Pose const &pose) const
	Constructor with a single target residue. More...

virtual void	report (std::ostream &out, core::pose::Pose const &pose) const

virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

virtual protocols::filters::FilterOP	clone () const

virtual protocols::filters::FilterOP	fresh_instance () const

core::Real	compute (core::pose::Pose const &pose) const

virtual	~RelativePoseFilter ()

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

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

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 Types
typedef protocols::filters::Filter	parent

Private Attributes
protocols::filters::FilterOP	filter_

protocols::moves::MoverOP	relax_mover_

std::map< core::Size, core::Size >	alignment_

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_

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

Detailed Description

Definition at line 34 of file RelativePoseFilter.hh.

Member Typedef Documentation

typedef protocols::filters::Filter protocols::simple_filters::RelativePoseFilter::parent

private

Definition at line 37 of file RelativePoseFilter.hh.

Constructor & Destructor Documentation

protocols::simple_filters::RelativePoseFilter::RelativePoseFilter ( )

default ctor

Definition at line 55 of file RelativePoseFilter.cc.

References alignment_.

Referenced by clone(), protocols::simple_filters::RelativePoseFilterCreator::create_filter(), and fresh_instance().

protocols::simple_filters::RelativePoseFilter::~RelativePoseFilter ( )

virtual

Definition at line 350 of file RelativePoseFilter.cc.

Member Function Documentation

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

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

Definition at line 125 of file RelativePoseFilter.cc.

References filter(), and thread_seq().

bool protocols::simple_filters::RelativePoseFilter::baseline ( ) const

Definition at line 384 of file RelativePoseFilter.cc.

References baseline_.

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

void protocols::simple_filters::RelativePoseFilter::baseline ( bool const b)

Definition at line 389 of file RelativePoseFilter.cc.

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

core::Real protocols::simple_filters::RelativePoseFilter::baseline_val ( ) const

Definition at line 394 of file RelativePoseFilter.cc.

References baseline(), and baseline_val_.

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

void protocols::simple_filters::RelativePoseFilter::baseline_val ( core::Real const b)

Definition at line 400 of file RelativePoseFilter.cc.

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

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

virtual

Implements protocols::filters::Filter.

Definition at line 353 of file RelativePoseFilter.cc.

References RelativePoseFilter().

core::Real protocols::simple_filters::RelativePoseFilter::compute ( core::pose::Pose const & pose) const

Definition at line 220 of file RelativePoseFilter.cc.

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

Referenced by report_sm().

bool protocols::simple_filters::RelativePoseFilter::copy_stretch ( ) const

inline

Definition at line 77 of file RelativePoseFilter.hh.

References copy_stretch_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::copy_stretch ( bool const b)

inline

Definition at line 78 of file RelativePoseFilter.hh.

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

std::string protocols::simple_filters::RelativePoseFilter::dump_pose_fname ( ) const

Definition at line 95 of file RelativePoseFilter.cc.

References dump_pose_fname_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::RelativePoseFilter::dump_pose_fname ( std::string const s)

Definition at line 100 of file RelativePoseFilter.cc.

References dump_pose_fname_.

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

Definition at line 115 of file RelativePoseFilter.cc.

References filter(), and filter_.

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

Definition at line 120 of file RelativePoseFilter.cc.

References filter_.

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

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

Definition at line 421 of file RelativePoseFilter.cc.

References filter_name_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::RelativePoseFilter::filter_name ( std::string const s)

Definition at line 416 of file RelativePoseFilter.cc.

References filter_name_.

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

virtual

Implements protocols::filters::Filter.

Definition at line 346 of file RelativePoseFilter.cc.

References RelativePoseFilter().

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

Definition at line 85 of file RelativePoseFilter.cc.

References packing_shell_.

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

Definition at line 90 of file RelativePoseFilter.cc.

References packing_shell_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	p
	)

virtual

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.

Definition at line 260 of file RelativePoseFilter.cc.

References alignment_, baseline(), baseline_val(), 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::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), core::pose::Pose::pdb_info(), pdb_name(), pose(), pose_, core::import_pose::pose_from_pdb(), relax_mover(), report_sm(), rtmin(), scorefxn(), symmdata_, symmetry_definition_, thread(), core::pose::Pose::total_residue(), and unbound().