protocols::protein_interface_design::filters::BoltzmannFilter Class Reference

#include <BoltzmannFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::BoltzmannFilter:

Collaboration diagram for protocols::protein_interface_design::filters::BoltzmannFilter:

Public Member Functions
	BoltzmannFilter ()
	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	~BoltzmannFilter ()
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	add_positive_filter (protocols::filters::FilterOP f)
void	add_negative_filter (protocols::filters::FilterOP f)
void	anchors (utility::vector1< core::Real > const anchors)
utility::vector1< core::Real >	anchors () const
utility::vector1 < protocols::filters::FilterOP >	get_positive_filters () const
utility::vector1 < protocols::filters::FilterOP >	get_negative_filters () const
void	temperature (core::Real const temp)
core::Real	temperature () const
void	triage_threshold (core::Real const t)
core::Real	triage_threshold () const
core::Real	fitness_threshold () const
void	fitness_threshold (core::Real const f)
bool	norm_neg () const
void	norm_neg (bool const n)
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
utility::vector1 < protocols::filters::FilterOP >	positive_filters_
utility::vector1 < protocols::filters::FilterOP >	negative_filters_
utility::vector1< core::Real >	anchors_
core::Real	temperature_
core::Real	fitness_threshold_
core::Real	triage_threshold_
bool	norm_neg_

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

Detailed Description

Definition at line 33 of file BoltzmannFilter.hh.

Member Typedef Documentation

typedef protocols::filters::Filter protocols::protein_interface_design::filters::BoltzmannFilter::parent

private

Definition at line 36 of file BoltzmannFilter.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::BoltzmannFilter::BoltzmannFilter

(

)

default ctor

Definition at line 38 of file BoltzmannFilter.cc.

References anchors_, negative_filters_, and positive_filters_.

Referenced by clone(), and fresh_instance().

protocols::protein_interface_design::filters::BoltzmannFilter::~BoltzmannFilter ( )

virtual

Definition at line 226 of file BoltzmannFilter.cc.

Member Function Documentation

void protocols::protein_interface_design::filters::BoltzmannFilter::add_negative_filter

(

protocols::filters::FilterOP

f)

Definition at line 107 of file BoltzmannFilter.cc.

References negative_filters_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::add_positive_filter

(

protocols::filters::FilterOP

f)

Definition at line 102 of file BoltzmannFilter.cc.

References positive_filters_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::anchors

(

utility::vector1< core::Real > const

anchors)

Definition at line 112 of file BoltzmannFilter.cc.

References anchors(), and anchors_.

utility::vector1< core::Real > protocols::protein_interface_design::filters::BoltzmannFilter::anchors

(

)

const

Definition at line 117 of file BoltzmannFilter.cc.

References anchors_.

Referenced by anchors(), and parse_my_tag().

bool protocols::protein_interface_design::filters::BoltzmannFilter::apply ( core::pose::Pose const &  pose) const

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

Definition at line 122 of file BoltzmannFilter.cc.

References compute(), and fitness_threshold().

protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

Definition at line 229 of file BoltzmannFilter.cc.

References BoltzmannFilter().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::compute

(

core::pose::Pose const &

pose)

const

NOTICE that this returns -Fitness [-1:0] for use in optimization F = Sum_{+}( -E/T ) / [ Sum_{-}( -E/T ) + Sum_{+} ( -E/T ) + Sum_{+}(( E - anchor )/T) ] This is the standard fitness function, except for anchor. Anchor can be (but doesn't have to be) defined for each positive state and sets a threshold above which energy increases in the positive state substantially reduce fitness, irrespective of what happened to all negative states. Can be used to ensure that the stability of a target state is not compromised during design. Set this to a very large number (99999) to eliminate the effects of the anchor, or specify no anchors at all

Definition at line 136 of file BoltzmannFilter.cc.

References anchors_, get_negative_filters(), get_positive_filters(), norm_neg(), report_sm(), core::io::serialization::size(), temperature(), and triage_threshold().

Referenced by apply(), and report_sm().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold

(

)

const

Definition at line 51 of file BoltzmannFilter.cc.

References fitness_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold

(

core::Real const

f)

Definition at line 56 of file BoltzmannFilter.cc.

References fitness_threshold_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

Definition at line 222 of file BoltzmannFilter.cc.

References BoltzmannFilter().

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_negative_filters

(

)

const

Definition at line 97 of file BoltzmannFilter.cc.

References negative_filters_.

Referenced by compute(), and parse_my_tag().

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_positive_filters

(

)

const

Definition at line 92 of file BoltzmannFilter.cc.

References positive_filters_.

Referenced by compute(), and parse_my_tag().

bool protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg

(

)

const

Definition at line 86 of file BoltzmannFilter.cc.

References norm_neg_.

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg

(

bool const

n)

Definition at line 81 of file BoltzmannFilter.cc.

References norm_neg_.

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

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 188 of file BoltzmannFilter.cc.

References add_negative_filter(), add_positive_filter(), anchors(), anchors_, fitness_threshold(), get_negative_filters(), get_positive_filters(), norm_neg(), protocols::rosetta_scripts::parse_filter(), core::io::serialization::size(), temperature(), and triage_threshold().

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

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 183 of file BoltzmannFilter.cc.

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 177 of file BoltzmannFilter.cc.

References compute().

Referenced by compute().

void protocols::protein_interface_design::filters::BoltzmannFilter::temperature

(

core::Real const

temp)

Definition at line 66 of file BoltzmannFilter.cc.

References core::scoring::hbonds::t(), and temperature_.

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature

(

)

const

Definition at line 61 of file BoltzmannFilter.cc.

References temperature_.

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold

(

core::Real const

t)

Definition at line 76 of file BoltzmannFilter.cc.

References core::scoring::hbonds::t(), and triage_threshold_.

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold

(

)

const

Definition at line 71 of file BoltzmannFilter.cc.

References triage_threshold_.

Referenced by compute(), and parse_my_tag().

Member Data Documentation

utility::vector1< core::Real > protocols::protein_interface_design::filters::BoltzmannFilter::anchors_

private

Definition at line 70 of file BoltzmannFilter.hh.

Referenced by anchors(), BoltzmannFilter(), compute(), and parse_my_tag().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold_

private

Definition at line 73 of file BoltzmannFilter.hh.

Referenced by fitness_threshold().

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::negative_filters_

private

Definition at line 69 of file BoltzmannFilter.hh.

Referenced by add_negative_filter(), BoltzmannFilter(), and get_negative_filters().

bool protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg_

private

Definition at line 75 of file BoltzmannFilter.hh.

Referenced by norm_neg().

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::positive_filters_

private

Definition at line 68 of file BoltzmannFilter.hh.

Referenced by add_positive_filter(), BoltzmannFilter(), and get_positive_filters().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature_

private

Definition at line 72 of file BoltzmannFilter.hh.

Referenced by temperature().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold_

private

Definition at line 74 of file BoltzmannFilter.hh.

Referenced by triage_threshold().

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

• src/protocols/protein_interface_design/filters/BoltzmannFilter.hh
• src/protocols/protein_interface_design/filters/BoltzmannFilter.cc