Rosetta 3.4
Public Member Functions
protocols::protein_interface_design::filters::BoltzmannFilter Class Reference

#include <BoltzmannFilter.hh>

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List of all members.

Public Member Functions

 BoltzmannFilter ()
 default ctor
virtual bool apply (core::pose::Pose const &pose) const
 Constructor with a single target residue.
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
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::Realanchors () 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
core::Real fitness_threshold () const
void fitness_threshold (core::Real const f)

Constructor & Destructor Documentation

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

default ctor

Referenced by clone(), and fresh_instance().

protocols::protein_interface_design::filters::BoltzmannFilter::~BoltzmannFilter ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::filters::BoltzmannFilter::add_negative_filter ( protocols::filters::FilterOP  f)

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::add_positive_filter ( protocols::filters::FilterOP  f)

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::anchors ( utility::vector1< core::Real > const  anchors)

References anchors().

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

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.

References compute(), and fitness_threshold().

protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::clone ( ) const [virtual]
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

References get_negative_filters(), get_positive_filters(), report_sm(), and temperature().

Referenced by apply(), and report_sm().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold ( ) const

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold ( core::Real const  f)
protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::fresh_instance ( ) const [virtual]
utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_negative_filters ( ) const

Referenced by compute(), and parse_my_tag().

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_positive_filters ( ) const

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
) [virtual]
void protocols::protein_interface_design::filters::BoltzmannFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const [virtual]

Reimplemented from protocols::filters::Filter.

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.

References compute().

Referenced by compute().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature ( ) const

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::temperature ( core::Real const  temp)

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