protocols::fldsgn::filters::SecondaryStructureFilter Class Reference

#include <SecondaryStructureFilter.hh>

Public Types
typedef protocols::filters::Filter	Super
typedef protocols::filters::Filter	Filter
typedef std::string	String
typedef protocols::filters::FilterOP	FilterOP
typedef core::pose::Pose	Pose
typedef utility::tag::TagCOP	TagCOP
typedef protocols::filters::Filters_map	Filters_map
typedef basic::datacache::DataMap	DataMap
typedef protocols::moves::Movers_map	Movers_map

Public Member Functions
	SecondaryStructureFilter ()
	SecondaryStructureFilter (String const &ss)
	SecondaryStructureFilter (SecondaryStructureFilter const &rval)
virtual	~SecondaryStructureFilter ()
virtual FilterOP	clone () const
virtual FilterOP	fresh_instance () const
void	filtered_ss (String const &s)
void	filtered_abego (String const &s)
virtual std::string	name () const
void	set_blueprint (std::string const blueprint_file)
	sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
	parse xml More...
virtual bool	apply (Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
virtual core::Real	report_sm (Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual core::Size	compute (Pose const &pose) const
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
virtual void	report (std::ostream &, core::pose::Pose const &) const
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)

Private Attributes
String	filtered_ss_
utility::vector1< String >	filtered_abego_
bool	use_abego_

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

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::fldsgn::filters::SecondaryStructureFilter::DataMap

typedef protocols::filters::Filter protocols::fldsgn::filters::SecondaryStructureFilter::Filter

typedef protocols::filters::FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::FilterOP

typedef protocols::filters::Filters_map protocols::fldsgn::filters::SecondaryStructureFilter::Filters_map

typedef protocols::moves::Movers_map protocols::fldsgn::filters::SecondaryStructureFilter::Movers_map

typedef core::pose::Pose protocols::fldsgn::filters::SecondaryStructureFilter::Pose

typedef std::string protocols::fldsgn::filters::SecondaryStructureFilter::String

typedef protocols::filters::Filter protocols::fldsgn::filters::SecondaryStructureFilter::Super

typedef utility::tag::TagCOP protocols::fldsgn::filters::SecondaryStructureFilter::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter

(

)

Referenced by clone(), and fresh_instance().

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter

(

String const &

ss

)

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter

(

SecondaryStructureFilter const &

rval

)

virtual protocols::fldsgn::filters::SecondaryStructureFilter::~SecondaryStructureFilter ( )

inlinevirtual

Member Function Documentation

bool protocols::fldsgn::filters::SecondaryStructureFilter::apply ( Pose const &  pose ) const

virtual

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

Implements protocols::filters::Filter.

References compute(), filtered_abego_, filtered_ss_, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and utility_exit_with_message.

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

inlinevirtual

Implements protocols::filters::Filter.

References SecondaryStructureFilter().

core::Size protocols::fldsgn::filters::SecondaryStructureFilter::compute ( Pose const &  pose ) const

virtual

returns the number of residues in the protein that have matching secondary structure WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match

References abego, core::util::ABEGOManager::check_rama(), filtered_abego_, filtered_ss_, core::util::ABEGOManager::get_abego_string(), core::conformation::Residue::is_protein(), j, core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), sec(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), tr, and use_abego_.

Referenced by apply(), and report_sm().

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego

(

String const &

s

)

References filtered_abego_, and use_abego_.

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss

(

String const &

s

)

References filtered_ss_.

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

inlinevirtual

Implements protocols::filters::Filter.

References SecondaryStructureFilter().

virtual std::string protocols::fldsgn::filters::SecondaryStructureFilter::name ( ) const

inlinevirtual

Reimplemented from protocols::filters::Filter.

void protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  , Filters_map const &  , Movers_map const &  , Pose const &    )

virtual

parse xml

Reimplemented from protocols::filters::Filter.

References abego, blueprint, filtered_abego_, filtered_ss_, core::util::ABEGOManager::get_abego_string(), runtime_assert, set_blueprint(), tr, and use_abego_.

core::Real protocols::fldsgn::filters::SecondaryStructureFilter::report_sm ( Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::fldsgn::filters::SecondaryStructureFilter::set_blueprint

(

std::string const

blueprint_file

)

sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.

References filtered_abego_, filtered_ss_, runtime_assert, s1, s2, ss, and tr.

Referenced by parse_my_tag().

Member Data Documentation

utility::vector1< String > protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego_

private

Referenced by apply(), compute(), filtered_abego(), parse_my_tag(), and set_blueprint().

String protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss_

private

Referenced by apply(), compute(), filtered_ss(), parse_my_tag(), and set_blueprint().

bool protocols::fldsgn::filters::SecondaryStructureFilter::use_abego_

private

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

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

• symlinks/rosetta/src/protocols/fldsgn/filters/SecondaryStructureFilter.hh
• symlinks/rosetta/src/protocols/fldsgn/filters/SecondaryStructureFilter.cc