Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_ddg::DdgFilter Class Reference

#include <DdgFilter.hh>

Inheritance diagram for protocols::simple_ddg::DdgFilter:
Inheritance graph
[legend]

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 override
 Returns true if the given pose passes the filter, false otherwise. More...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
core::Size repeats () const
 
void repeats (core::Size const repeats)
 
void repack (bool const repack)
 
bool repack () const
 
void repack_bound (bool const rpb)
 
bool repack_bound () const
 
void repack_unbound (bool const rpu)
 
bool repack_unbound () const
 
void relax_bound (bool const rlb)
 
bool relax_bound () const
 
void relax_unbound (bool const rlu)
 
bool relax_unbound () 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 override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
core::Real compute (core::pose::Pose const &pose) const
 
 ~DdgFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
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
 
void dump_pdbs (bool const dp)
 
bool dump_pdbs () const
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
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 bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

void initPB ()
 

Private Attributes

core::Real ddg_threshold_
 
core::Real ddg_threshold_min_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size rb_jump_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool use_custom_task_
 
bool repack_bound_
 
bool repack_unbound_
 
bool relax_bound_
 
bool relax_unbound_
 
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_
 
bool dump_pdbs_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_ddg::DdgFilter::DdgFilter ( )
protocols::simple_ddg::DdgFilter::DdgFilter ( core::Real const  ddg_threshold,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  rb_jump = 1,
core::Size const  repeats = 1 
)
protocols::simple_ddg::DdgFilter::~DdgFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_ddg::DdgFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), ddg_threshold_, ddg_threshold_min_, and protocols::simple_ddg::TR().

std::string protocols::simple_ddg::DdgFilter::class_name ( )
static
filters::FilterOP protocols::simple_ddg::DdgFilter::clone ( ) const
overridevirtual
core::Real protocols::simple_ddg::DdgFilter::compute ( core::pose::Pose const &  pose) const

References protocols::simple_ddg::ddG::calculate(), chain_ids_, dump_pdbs(), protocols::simple_ddg::ddG::dump_pdbs(), extreme_value_removal(), filter(), protocols::simple_ddg::ddG::filter(), filter_, core::pose::get_jump_id_from_chain_id(), rb_jump_, relax_bound(), protocols::simple_ddg::ddG::relax_bound(), relax_mover(), protocols::simple_ddg::ddG::relax_mover(), relax_unbound(), protocols::simple_ddg::ddG::relax_unbound(), repack(), repack_bound(), protocols::simple_ddg::ddG::repack_bound(), repeats(), repeats_, protocols::simple_ddg::ddG::report_ddG(), scorefxn_, protocols::stepwise::modeler::split_pose(), protocols::simple_ddg::ddG::sum_ddG(), task_factory(), protocols::simple_ddg::ddG::task_factory(), protocols::simple_ddg::TR(), protocols::toolbox::rigid_body::translate(), translate_by(), protocols::simple_ddg::ddG::translate_by(), translate_by_, use_custom_task(), protocols::simple_ddg::ddG::use_custom_task(), and protocols::hybridization::val.

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

void protocols::simple_ddg::DdgFilter::dump_pdbs ( bool const  dp)
inline

References dump_pdbs_.

bool protocols::simple_ddg::DdgFilter::dump_pdbs ( ) const
inline

References dump_pdbs_.

Referenced by compute(), and parse_my_tag().

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

References extreme_value_removal_.

Referenced by compute(), and parse_my_tag().

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

References filter_.

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

References filter_.

Referenced by compute(), and parse_my_tag().

filters::FilterOP protocols::simple_ddg::DdgFilter::fresh_instance ( ) const
overridevirtual
void protocols::simple_ddg::DdgFilter::initPB ( )
private
std::string protocols::simple_ddg::DdgFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_ddg::DdgFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::simple_ddg::DdgFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_ddg::DdgFilter::relax_bound ( bool const  rlb)
inline

References relax_bound_.

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

References relax_bound_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::relax_mover ( protocols::moves::MoverOP  m)
protocols::moves::MoverOP protocols::simple_ddg::DdgFilter::relax_mover ( ) const

References relax_mover_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::relax_unbound ( bool const  rlu)
inline

References relax_unbound_.

bool protocols::simple_ddg::DdgFilter::relax_unbound ( ) const
inline

References relax_unbound_.

Referenced by compute(), and parse_my_tag().

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

References repack_.

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

void protocols::simple_ddg::DdgFilter::repack_bound ( bool const  rpb)
inline

References repack_bound_.

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

References repack_bound_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::repack_unbound ( bool const  rpu)
inline

References repack_unbound_.

bool protocols::simple_ddg::DdgFilter::repack_unbound ( ) const
inline

References repack_unbound_.

Referenced by parse_my_tag().

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

References repeats_.

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

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

References repeats(), and repeats_.

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

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::simple_ddg::DdgFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_ddg::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_ddg::DdgFilter::task_factory ( ) const
inline

References task_factory_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::translate_by ( core::Real const  translate_by)

References translate_by(), and translate_by_.

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

References translate_by_.

Referenced by compute(), and translate_by().

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

References use_custom_task_.

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

References use_custom_task_.

Referenced by compute(), and parse_my_tag().

Member Data Documentation

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

Referenced by compute(), and parse_my_tag().

core::Real protocols::simple_ddg::DdgFilter::ddg_threshold_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::simple_ddg::DdgFilter::ddg_threshold_min_
private

Referenced by apply(), and parse_my_tag().

bool protocols::simple_ddg::DdgFilter::dump_pdbs_
private

Referenced by dump_pdbs().

bool protocols::simple_ddg::DdgFilter::extreme_value_removal_
private

Referenced by extreme_value_removal().

protocols::filters::FilterOP protocols::simple_ddg::DdgFilter::filter_
private

Referenced by compute(), and filter().

bool protocols::simple_ddg::DdgFilter::pb_enabled_
private

is PB enabled?

Referenced by DdgFilter(), and parse_my_tag().

core::Size protocols::simple_ddg::DdgFilter::rb_jump_
private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_ddg::DdgFilter::relax_bound_
private

Referenced by relax_bound().

protocols::moves::MoverOP protocols::simple_ddg::DdgFilter::relax_mover_
private

Referenced by relax_mover().

bool protocols::simple_ddg::DdgFilter::relax_unbound_
private

Referenced by relax_unbound().

bool protocols::simple_ddg::DdgFilter::repack_
private

Referenced by repack().

bool protocols::simple_ddg::DdgFilter::repack_bound_
private

Referenced by repack_bound().

bool protocols::simple_ddg::DdgFilter::repack_unbound_
private

Referenced by repack_unbound().

core::Size protocols::simple_ddg::DdgFilter::repeats_
private

Referenced by compute(), and repeats().

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

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

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

Referenced by task_factory().

core::Real protocols::simple_ddg::DdgFilter::translate_by_
private

translation distance in A

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

bool protocols::simple_ddg::DdgFilter::use_custom_task_
private

Referenced by use_custom_task().


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