Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_filters::DdgFilter Class Reference

#include <DdgFilter.hh>

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 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
 
core::Size repeats () const
 
void repeats (core::Size const repeats)
 
void repack (bool const repack)
 
bool repack () const
 
void repack_bound (bool rpb)
 
bool repack_bound () const
 
void relax_bound (bool rlb)
 
bool relax_bound () const
 
void translate_by (core::Real const translate_by)
 
core::Real translate_by () 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::TagCOP tag, basic::datacache::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
 
void filter (protocols::filters::FilterOP m)
 
protocols::filters::FilterOP filter () const
 
void extreme_value_removal (bool const b)
 
bool extreme_value_removal () 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
 

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 repack_
 
protocols::moves::MoverOP relax_mover_
 
protocols::filters::FilterOP filter_
 
bool pb_enabled_
 is PB enabled? More...
 
core::Real translate_by_
 translation distance in A More...
 
bool extreme_value_removal_
 

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 
)
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

References protocols::rigid::RigidBodyTransMover::apply(), protocols::simple_moves::ddG::calculate(), chain_ids_, ddg, extreme_value_removal(), filter(), protocols::simple_moves::ddG::filter(), filter_, core::pose::get_jump_id_from_chain_id(), rb_jump_, relax_bound(), protocols::simple_moves::ddG::relax_bound(), relax_mover(), protocols::simple_moves::ddG::relax_mover(), repack(), repack_bound(), protocols::simple_moves::ddG::repack_bound(), repeats(), repeats_, protocols::simple_moves::ddG::report_ddG(), runtime_assert, scorefxn_, protocols::stepwise::modeler::split_pose(), protocols::rigid::RigidBodyTransMover::step_size(), protocols::simple_moves::ddG::sum_ddG(), task_factory(), protocols::simple_moves::ddG::task_factory(), core::scoring::total_score, protocols::simple_filters::TR, protocols::rigid::RigidBodyTransMover::trans_axis(), protocols::stepwise::sampler::rigid_body::translate(), translate_by(), protocols::simple_moves::ddG::translate_by(), translate_by_, use_custom_task(), protocols::simple_moves::ddG::use_custom_task(), and utility_exit_with_message.

Referenced by apply(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::simple_filters::AlaScan::report(), report(), report_sm(), and protocols::simple_filters::AlaScan::report_symmetry().

void protocols::simple_filters::DdgFilter::extreme_value_removal ( bool const  b)
inline
bool protocols::simple_filters::DdgFilter::extreme_value_removal ( ) const
inline

References extreme_value_removal_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::filter ( protocols::filters::FilterOP  m)

References filter_.

protocols::filters::FilterOP protocols::simple_filters::DdgFilter::filter ( ) const

References filter_.

Referenced by compute().

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::TagCOP  tag,
basic::datacache::DataMap data,
filters::Filters_map const &  filters,
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().

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

References repeats_.

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

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

References repeats(), 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::translate_by ( core::Real const  translate_by)

References translate_by(), and translate_by_.

core::Real protocols::simple_filters::DdgFilter::translate_by ( ) const

References translate_by_.

Referenced by compute(), and translate_by().

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().

bool protocols::simple_filters::DdgFilter::extreme_value_removal_
private

Referenced by extreme_value_removal().

protocols::filters::FilterOP protocols::simple_filters::DdgFilter::filter_
private

Referenced by compute(), and filter().

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().

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(), parse_def(), and translate_by().

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: