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protocols::simple_filters::DdgFilter Class Reference

#include <DdgFilter.hh>

Inheritance diagram for protocols::simple_filters::DdgFilter:
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Collaboration diagram for protocols::simple_filters::DdgFilter:
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Public Member Functions

 DdgFilter ()
 
 DdgFilter (core::Real const ddg_threshold, core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1, core::Size const repeats=1, bool const symmetry=false)
 
bool apply (core::pose::Pose const &pose) const
 Returns true if the given pose passes the filter, false otherwise. More...
 
filters::FilterOP clone () const
 
filters::FilterOP fresh_instance () const
 
void repack (bool const repack)
 
bool repack () const
 
void repeats (core::Size const repeats)
 
void repack_bound (bool rpb)
 
bool repack_bound () const
 
void relax_bound (bool rlb)
 
bool relax_bound () const
 
core::Size repeats () const
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
core::pack::task::TaskFactoryOP task_factory () const
 
void use_custom_task (bool uct)
 
bool use_custom_task () const
 
void report (std::ostream &out, core::pose::Pose const &pose) const
 
core::Real report_sm (core::pose::Pose const &pose) const
 used to report filter internals through a score or silent file More...
 
core::Real compute (core::pose::Pose const &pose) const
 
virtual ~DdgFilter ()
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 
void relax_mover (protocols::moves::MoverOP m)
 
protocols::moves::MoverOP relax_mover () 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)
 
virtual std::string name () const
 

Static Public Attributes

static const core::Real DEFAULT_TRANSLATION_DISTANCE = 100.0
 

Private Member Functions

void initPB ()
 

Private Attributes

core::Real ddg_threshold_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size rb_jump_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool use_custom_task_
 
bool repack_bound_
 
bool relax_bound_
 
utility::vector1< core::Sizechain_ids_
 
core::Size repeats_
 
bool symmetry_
 
bool repack_
 
protocols::moves::MoverOP relax_mover_
 
bool pb_enabled_
 is PB enabled? More...
 
core::Real translate_by_
 translation distance in A More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::simple_filters::DdgFilter::DdgFilter ( )
protocols::simple_filters::DdgFilter::DdgFilter ( core::Real const  ddg_threshold,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  rb_jump = 1,
core::Size const  repeats = 1,
bool const  symmetry = false 
)
protocols::simple_filters::DdgFilter::~DdgFilter ( )
virtual

Member Function Documentation

bool protocols::simple_filters::DdgFilter::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(), ddg_threshold_, and protocols::simple_filters::TR().

filters::FilterOP protocols::simple_filters::DdgFilter::clone ( ) const
virtual

Implements protocols::filters::Filter.

References DdgFilter().

Referenced by parse_def().

core::Real protocols::simple_filters::DdgFilter::compute ( core::pose::Pose const &  pose) const
filters::FilterOP protocols::simple_filters::DdgFilter::fresh_instance ( ) const
virtual

Implements protocols::filters::Filter.

References DdgFilter().

void protocols::simple_filters::DdgFilter::initPB ( )
private
void protocols::simple_filters::DdgFilter::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks 
)
virtual
void protocols::simple_filters::DdgFilter::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
filters::Filters_map const &  ,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &   
)
virtual
void protocols::simple_filters::DdgFilter::relax_bound ( bool  rlb)
inline

References relax_bound_.

bool protocols::simple_filters::DdgFilter::relax_bound ( ) const
inline

References relax_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::relax_mover ( protocols::moves::MoverOP  m)

References relax_mover_.

protocols::moves::MoverOP protocols::simple_filters::DdgFilter::relax_mover ( ) const

References relax_mover_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repack ( bool const  repack)
bool protocols::simple_filters::DdgFilter::repack ( ) const

References repack_.

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

void protocols::simple_filters::DdgFilter::repack_bound ( bool  rpb)
inline

References repack_bound_.

bool protocols::simple_filters::DdgFilter::repack_bound ( ) const
inline

References repack_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repeats ( core::Size const  repeats)

References repeats(), and repeats_.

core::Size protocols::simple_filters::DdgFilter::repeats ( ) const

References repeats_.

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

void protocols::simple_filters::DdgFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
virtual

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::simple_filters::DdgFilter::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::simple_filters::DdgFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)
inline

References task_factory(), and task_factory_.

Referenced by task_factory().

core::pack::task::TaskFactoryOP protocols::simple_filters::DdgFilter::task_factory ( ) const
inline

References task_factory_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::use_custom_task ( bool  uct)
inline

References use_custom_task_.

bool protocols::simple_filters::DdgFilter::use_custom_task ( ) const
inline

References use_custom_task_.

Referenced by compute().

Member Data Documentation

utility::vector1<core::Size> protocols::simple_filters::DdgFilter::chain_ids_
private

Referenced by compute(), and parse_def().

core::Real protocols::simple_filters::DdgFilter::ddg_threshold_
private

Referenced by apply(), and parse_def().

const core::Real protocols::simple_filters::DdgFilter::DEFAULT_TRANSLATION_DISTANCE = 100.0
static

Distance in A to separate the molecules away from bound-state. NOTES by Sachko Honda: This value used to be hard coded to 1000 for unbound poses, whereas the default 100 was used for bounded. The choice of value 1000 was arbitrary by the original author. The value is now reduced to 100 in order to help the PDE solver (APBS) from blowing up, by default, but can be a user-defined value via RosettaScript option or command-line option.

Referenced by parse_def().

bool protocols::simple_filters::DdgFilter::pb_enabled_
private

is PB enabled?

Referenced by DdgFilter().

core::Size protocols::simple_filters::DdgFilter::rb_jump_
private

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::relax_bound_
private

Referenced by parse_def(), and relax_bound().

protocols::moves::MoverOP protocols::simple_filters::DdgFilter::relax_mover_
private

Referenced by relax_mover().

bool protocols::simple_filters::DdgFilter::repack_
private

Referenced by repack().

bool protocols::simple_filters::DdgFilter::repack_bound_
private

Referenced by parse_def(), and repack_bound().

core::Size protocols::simple_filters::DdgFilter::repeats_
private

Referenced by compute(), and repeats().

core::scoring::ScoreFunctionOP protocols::simple_filters::DdgFilter::scorefxn_
private

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

bool protocols::simple_filters::DdgFilter::symmetry_
private

Referenced by compute(), and parse_def().

core::pack::task::TaskFactoryOP protocols::simple_filters::DdgFilter::task_factory_
private

Referenced by task_factory().

core::Real protocols::simple_filters::DdgFilter::translate_by_
private

translation distance in A

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::use_custom_task_
private

Referenced by use_custom_task().


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