protocols::matdes::SymUnsatHbondFilter Class Reference

filters based on an upper bound # of buried unsatisfied polar residues More...

#include <SymUnsatHbondFilter.hh>

Public Types
typedef protocols::filters::Filter	Super
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP
typedef core::Real	Real
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
	SymUnsatHbondFilter ()
	SymUnsatHbondFilter (core::Size const upper_cutoff, core::Size const jump, std::string const sym_dofs, bool verb, bool write, std::string const mode, bool compare_to_ref, core::pose::PoseOP const reference_pose)
	SymUnsatHbondFilter (SymUnsatHbondFilter const &rval)
virtual	~SymUnsatHbondFilter ()
virtual protocols::filters::FilterOP	clone () const
virtual protocols::filters::FilterOP	fresh_instance () const
virtual std::string	name () const
void	upper_threshold (core::Size const upper_cutoff)
void	jump_num (core::Size const jump)
void	sym_dof_names (std::string const sym_dofs)
void	verbose (bool const verb)
void	write2pdb (bool const write)
void	mode (std::string const mode)
void	reference_pose (core::pose::PoseOP const reference_pose)
void	compare_to_ref (bool const compare_to_ref)
core::Size	upper_threshold () const
core::Size	jump_num () const
std::string	sym_dof_names () const
bool	verbose () const
bool	write2pdb () const
std::string	mode () const
core::pose::PoseOP	reference_pose () const
bool	compare_to_ref () const
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, Movers_map const &, Pose const &)
void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual void	report (std::ostream &out, core::pose::Pose const &pose) const
core::Real	compute (core::pose::Pose const &pose, bool const &verb, bool const &write) const
void	write_to_pdb (core::pose::Pose const &pose, std::string const mode, std::string const residue_name, core::Size const residue, std::string const atom_name) const
void	write_pymol_string_to_pdb (std::string const pymol_selection) 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)

Private Attributes
core::Size	upper_threshold_
core::Size	jump_num_
std::string	sym_dof_names_
bool	verbose_
bool	write2pdb_
std::string	mode_
bool	compare_to_ref_
core::pose::PoseOP	reference_pose_

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

Detailed Description

filters based on an upper bound # of buried unsatisfied polar residues

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::matdes::SymUnsatHbondFilter::DataMap

typedef protocols::filters::Filter protocols::matdes::SymUnsatHbondFilter::Filter

typedef protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::FilterOP

typedef protocols::filters::Filters_map protocols::matdes::SymUnsatHbondFilter::Filters_map

typedef protocols::moves::Movers_map protocols::matdes::SymUnsatHbondFilter::Movers_map

typedef core::pose::Pose protocols::matdes::SymUnsatHbondFilter::Pose

typedef core::Real protocols::matdes::SymUnsatHbondFilter::Real

typedef protocols::filters::Filter protocols::matdes::SymUnsatHbondFilter::Super

typedef utility::tag::TagCOP protocols::matdes::SymUnsatHbondFilter::TagCOP

Constructor & Destructor Documentation

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter

(

)

Referenced by clone(), and fresh_instance().

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter	(	core::Size const	upper_cutoff,
		core::Size const	jump,
		std::string const	sym_dofs,
		bool	verb,
		bool	write,
		std::string const	mode,
		bool	compare_to_ref,
		core::pose::PoseOP const	reference_pose
	)

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter

(

SymUnsatHbondFilter const &

rval

)

virtual protocols::matdes::SymUnsatHbondFilter::~SymUnsatHbondFilter ( )

inlinevirtual

Member Function Documentation

bool protocols::matdes::SymUnsatHbondFilter::apply ( core::pose::Pose const &  pose ) const

virtual

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

Implements protocols::filters::Filter.

References compute(), protocols::matdes::TR, and upper_threshold().

protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References SymUnsatHbondFilter().

void protocols::matdes::SymUnsatHbondFilter::compare_to_ref

(

bool const

compare_to_ref

)

References compare_to_ref(), and compare_to_ref_.

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref

(

)

const

References compare_to_ref_.

Referenced by compare_to_ref(), and parse_my_tag().

core::Real protocols::matdes::SymUnsatHbondFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	verb,
		bool const &	write
	)		const

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), compare_to_ref_, core::pose::Pose::conformation(), protocols::jd2::JobDistributor::current_output_name(), protocols::jd2::JobDistributor::get_instance(), core::pose::symmetry::get_sym_aware_jump_num(), core::conformation::symmetry::is_symmetric(), jump_num(), mode_, core::pose::Pose::n_residue(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), basic::options::option, core::pose::Pose::pdb_info(), reference_pose_, basic::options::OptionKeys::out::file::renumber_pdb, core::pose::Pose::residue(), utility::string_split(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names(), core::pose::symmetry::symmetry_info(), protocols::matdes::TR, utility_exit_with_message, basic::MetricValue< T >::value(), write_pymol_string_to_pdb(), and write_to_pdb().

Referenced by apply(), report(), and report_sm().

protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References SymUnsatHbondFilter().

void protocols::matdes::SymUnsatHbondFilter::jump_num

(

core::Size const

jump

)

References jump_num_.

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num

(

)

const

References jump_num_.

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

void protocols::matdes::SymUnsatHbondFilter::mode

(

std::string const

mode

)

References mode(), and mode_.

std::string protocols::matdes::SymUnsatHbondFilter::mode

(

)

const

References mode_.

Referenced by mode(), and parse_my_tag().

virtual std::string protocols::matdes::SymUnsatHbondFilter::name ( ) const

inlinevirtual

Reimplemented from protocols::filters::Filter.

Referenced by write_pymol_string_to_pdb(), and write_to_pdb().

void protocols::matdes::SymUnsatHbondFilter::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented from protocols::filters::Filter.

References jump_num(), protocols::matdes::TR, upper_threshold(), verbose(), and write2pdb().

void protocols::matdes::SymUnsatHbondFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  , Movers_map const &  , Pose const &    )

virtual

Reimplemented from protocols::filters::Filter.

References compare_to_ref(), jump_num(), mode(), mode_, basic::options::OptionKeys::in::file::native, basic::options::option, core::import_pose::pose_from_pdb(), reference_pose_, protocols::rosetta_scripts::saved_reference_pose(), sym_dof_names(), protocols::matdes::TR, upper_threshold(), user, utility_exit_with_message, verbose(), and write2pdb().

void protocols::matdes::SymUnsatHbondFilter::reference_pose

(

core::pose::PoseOP const

reference_pose

)

References reference_pose(), and reference_pose_.

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose

(

)

const

References reference_pose_.

Referenced by reference_pose().

void protocols::matdes::SymUnsatHbondFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), verbose(), and write2pdb().

core::Real protocols::matdes::SymUnsatHbondFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::matdes::SymUnsatHbondFilter::sym_dof_names

(

std::string const

sym_dofs

)

References sym_dof_names_.

std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names

(

)

const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

void protocols::matdes::SymUnsatHbondFilter::upper_threshold

(

core::Size const

upper_cutoff

)

References upper_threshold_.

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold

(

)

const

References upper_threshold_.

Referenced by apply(), parse_def(), and parse_my_tag().

void protocols::matdes::SymUnsatHbondFilter::verbose

(

bool const

verb

)

References verbose_.

bool protocols::matdes::SymUnsatHbondFilter::verbose

(

)

const

References verbose_.

Referenced by parse_def(), parse_my_tag(), and report().

void protocols::matdes::SymUnsatHbondFilter::write2pdb

(

bool const

write

)

References write2pdb_.

bool protocols::matdes::SymUnsatHbondFilter::write2pdb

(

)

const

References write2pdb_.

Referenced by parse_def(), parse_my_tag(), and report().

void protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb

(

std::string const

pymol_selection

)

const

References protocols::jd2::Job::add_string(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::current_output_name(), protocols::jd2::JobDistributor::get_instance(), protocols::filters::Filter::get_user_defined_name(), and name().

Referenced by compute().

void protocols::matdes::SymUnsatHbondFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		std::string const	mode,
		std::string const	residue_name,
		core::Size const	residue,
		std::string const	atom_name
	)		const

References protocols::jd2::Job::add_string(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::filters::Filter::get_user_defined_name(), name(), basic::options::option, core::pose::Pose::pdb_info(), and basic::options::OptionKeys::out::file::renumber_pdb.

Referenced by compute().

Member Data Documentation

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref_

private

Referenced by compare_to_ref(), and compute().

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num_

private

Referenced by jump_num().

std::string protocols::matdes::SymUnsatHbondFilter::mode_

private

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

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose_

private

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

std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names_

private

Referenced by sym_dof_names().

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold_

private

Referenced by upper_threshold().

bool protocols::matdes::SymUnsatHbondFilter::verbose_

private

Referenced by verbose().

bool protocols::matdes::SymUnsatHbondFilter::write2pdb_

private

Referenced by write2pdb().

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

• src/protocols/matdes/SymUnsatHbondFilter.hh
• src/protocols/matdes/SymUnsatHbondFilter.cc