#include <PreProlineFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::PreProlineFilter:

Public Member Functions
	PreProlineFilter ()
	Initialize PreProlineFilter. More...

virtual	~PreProlineFilter ()
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Parses the PreProlineFilter tags. More...

virtual std::string	get_name () const
	Return the name of this mover. More...

virtual protocols::filters::FilterOP	clone () const
	return a fresh instance of this class in an owning pointer More...

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

virtual core::Real	report_sm (core::pose::Pose const &pose) const
	Apply the PreProlineFilter. Overloaded apply function from filter base class. More...

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

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

virtual bool	apply (core::pose::Pose const &pose) const
	Does the PreProline Filtering. More...

void	set_use_statistical_potential (bool const use_stat)

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector)

void	setup_spline ()

core::Real	compute_simple (core::pose::Pose const &pose, utility::vector1< bool > const &selection) const

core::Real	compute_spline (core::pose::Pose const &pose, utility::vector1< bool > const &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 core::Real	score (core::pose::Pose &pose)

virtual std::string	name () const

Private Attributes
core::Real	threshold_
	If total calculated filter score is <= theshold_, the filter passes, otherwise it fails. More...

bool	use_statistical_potential_
	If set, spline based on statistical potential will be used, otherwise only preproline residues not in beta conformation will be counted (default = True) More...

core::select::residue_selector::ResidueSelectorCOP	selector_

numeric::interpolation::spline::BicubicSpline	spline_

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

Detailed Description

Definition at line 37 of file PreProlineFilter.hh.

Constructor & Destructor Documentation

protocols::denovo_design::filters::PreProlineFilter::PreProlineFilter ( )

Initialize PreProlineFilter.

PreProlineFilter main code:

Definition at line 69 of file PreProlineFilter.cc.

References setup_spline().

Referenced by clone(), and fresh_instance().

protocols::denovo_design::filters::PreProlineFilter::~PreProlineFilter ( )

virtual

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Definition at line 81 of file PreProlineFilter.cc.

Member Function Documentation

bool protocols::denovo_design::filters::PreProlineFilter::apply ( core::pose::Pose const & pose ) const

virtual

Does the PreProline Filtering.

Implements protocols::filters::Filter.

Definition at line 222 of file PreProlineFilter.cc.

References compute(), and threshold_.

protocols::filters::FilterOP protocols::denovo_design::filters::PreProlineFilter::clone ( ) const

virtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Implements protocols::filters::Filter.

Definition at line 87 of file PreProlineFilter.cc.

References PreProlineFilter().

core::Real protocols::denovo_design::filters::PreProlineFilter::compute ( core::pose::Pose const & pose ) const

virtual

Definition at line 140 of file PreProlineFilter.cc.

References compute_simple(), compute_spline(), selector_, core::pose::Pose::total_residue(), and use_statistical_potential_.

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

core::Real protocols::denovo_design::filters::PreProlineFilter::compute_simple	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	selection
	)		const

Definition at line 185 of file PreProlineFilter.cc.

References core::pose::motif::a(), protocols::denovo_design::abego_str(), core::sequence::get_abego(), core::pose::is_upper_terminus(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and protocols::TR().

Referenced by compute().

core::Real protocols::denovo_design::filters::PreProlineFilter::compute_spline	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	selection
	)		const

Definition at line 156 of file PreProlineFilter.cc.

References core::pose::is_upper_terminus(), core::conformation::Residue::name1(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), spline_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by compute().

protocols::filters::FilterOP protocols::denovo_design::filters::PreProlineFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

Definition at line 93 of file PreProlineFilter.cc.

References PreProlineFilter().

std::string protocols::denovo_design::filters::PreProlineFilter::get_name ( ) const

virtual

Return the name of this mover.

Definition at line 116 of file PreProlineFilter.cc.

void protocols::denovo_design::filters::PreProlineFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Parses the PreProlineFilter tags.

Reimplemented from protocols::filters::Filter.

Definition at line 99 of file PreProlineFilter.cc.

References protocols::rosetta_scripts::parse_residue_selector(), selector_, threshold_, and use_statistical_potential_.

void protocols::denovo_design::filters::PreProlineFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 128 of file PreProlineFilter.cc.

References compute().

core::Real protocols::denovo_design::filters::PreProlineFilter::report_sm ( core::pose::Pose const & pose ) const

virtual

Apply the PreProlineFilter. Overloaded apply function from filter base class.

Reimplemented from protocols::filters::Filter.

Definition at line 134 of file PreProlineFilter.cc.

References compute().

void protocols::denovo_design::filters::PreProlineFilter::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Definition at line 122 of file PreProlineFilter.cc.

References selector_.

void protocols::denovo_design::filters::PreProlineFilter::set_use_statistical_potential ( bool const use_stat )

Definition at line 308 of file PreProlineFilter.cc.

References use_statistical_potential_.

void protocols::denovo_design::filters::PreProlineFilter::setup_spline ( )

Definition at line 259 of file PreProlineFilter.cc.

References protocols::denovo_design::filters::parse_matrix(), spline_, protocols::loops::start, and protocols::TR().

Referenced by PreProlineFilter().

Member Data Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::filters::PreProlineFilter::selector_

private

Definition at line 88 of file PreProlineFilter.hh.

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

numeric::interpolation::spline::BicubicSpline protocols::denovo_design::filters::PreProlineFilter::spline_

private

Definition at line 89 of file PreProlineFilter.hh.

Referenced by compute_spline(), and setup_spline().

core::Real protocols::denovo_design::filters::PreProlineFilter::threshold_

private

If total calculated filter score is <= theshold_, the filter passes, otherwise it fails.

Definition at line 82 of file PreProlineFilter.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::denovo_design::filters::PreProlineFilter::use_statistical_potential_

private

If set, spline based on statistical potential will be used, otherwise only preproline residues not in beta conformation will be counted (default = True)

Definition at line 85 of file PreProlineFilter.hh.

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

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

src/protocols/denovo_design/filters/PreProlineFilter.hh
src/protocols/denovo_design/filters/PreProlineFilter.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

PreProlineFilter main code:

Member Function Documentation

Member Data Documentation