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protocols::simple_filters::InterfaceHbondsFilter Class Reference

#include <InterfaceHbondsFilter.hh>

Inheritance diagram for protocols::simple_filters::InterfaceHbondsFilter:
Inheritance graph
[legend]

Public Member Functions

 InterfaceHbondsFilter ()
 
 InterfaceHbondsFilter (core::Size hbonds_num_threshold_in, core::Real hbonds_energy_cutoff_in=0.0, core::Size jump_in=1, core::scoring::ScoreFunctionOP scorefxn_in=nullptr, bool salt_bridge_mode_in=false, bool include_His_chain_terminus_in=false, core::Real salt_bridge_distance_cutoff_in=4.0)
 
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
 
InterfaceHbondsFilteroperator= (InterfaceHbondsFilter const &ot)
 
 InterfaceHbondsFilter (InterfaceHbondsFilter const &init)
 
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::Size compute (core::pose::Pose const &pose) const
 
 ~InterfaceHbondsFilter () 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...
 
std::string name () const override
 
void set_jump (core::Size const jump_in)
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_hbonds_num_threshold (core::Size hbonds_num_threshold_in)
 
void set_hbonds_energy_cutoff (core::Real hbonds_energy_cutoff_in)
 
void set_salt_bridge_mode (bool salt_bridge_mode_in)
 
void set_include_His_chain_terminus (bool include_His_chain_terminus_in)
 
void set_salt_bridge_distance_cutoff (bool salt_bridge_distance_cutoff_in)
 
- 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 Types

enum  CHARGE { POSITIVE, NEGATIVE }
 
typedef std::pair< std::string,
CHARGE
Charged_Group
 

Private Member Functions

core::Size compute_hbonds (core::pose::Pose const &pose) const
 
core::Size compute_salt_bridges (core::pose::Pose const &pose) const
 
void initialize_charged_residue_map ()
 

Private Attributes

core::Size hbonds_num_threshold_
 
core::Real hbonds_energy_cutoff_
 
core::Size jump_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool salt_bridge_mode_
 
bool include_His_chain_terminus_
 
core::Real salt_bridge_distance_cutoff_
 
std::unordered_map
< std::string, std::vector
< Charged_Group > > 
charged_res_
 

Additional Inherited Members

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

Member Typedef Documentation

Member Enumeration Documentation

Enumerator
POSITIVE 
NEGATIVE 

Constructor & Destructor Documentation

protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter ( )
protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter ( core::Size  hbonds_num_threshold_in,
core::Real  hbonds_energy_cutoff_in = 0.0,
core::Size  jump_in = 1,
core::scoring::ScoreFunctionOP  scorefxn_in = nullptr,
bool  salt_bridge_mode_in = false,
bool  include_His_chain_terminus_in = false,
core::Real  salt_bridge_distance_cutoff_in = 4.0 
)
protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter ( InterfaceHbondsFilter const &  init)
inline

References core::init::init().

protocols::simple_filters::InterfaceHbondsFilter::~InterfaceHbondsFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::InterfaceHbondsFilter::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(), and hbonds_num_threshold_.

std::string protocols::simple_filters::InterfaceHbondsFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::InterfaceHbondsFilter::clone ( ) const
inlineoverridevirtual
core::Size protocols::simple_filters::InterfaceHbondsFilter::compute ( core::pose::Pose const &  pose) const
core::Size protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds ( core::pose::Pose const &  pose) const
private
core::Size protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges ( core::pose::Pose const &  pose) const
private
filters::FilterOP protocols::simple_filters::InterfaceHbondsFilter::fresh_instance ( ) const
inlineoverridevirtual
void protocols::simple_filters::InterfaceHbondsFilter::initialize_charged_residue_map ( )
private
std::string protocols::simple_filters::InterfaceHbondsFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

InterfaceHbondsFilter& protocols::simple_filters::InterfaceHbondsFilter::operator= ( InterfaceHbondsFilter const &  ot)
inline
void protocols::simple_filters::InterfaceHbondsFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References hbonds_energy_cutoff_, hbonds_num_threshold_, include_His_chain_terminus_, initialize_charged_residue_map(), jump_, core::scoring::parse_score_function(), salt_bridge_distance_cutoff_, salt_bridge_mode_, and set_scorefxn().

void protocols::simple_filters::InterfaceHbondsFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::InterfaceHbondsFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and jump_.

core::Real protocols::simple_filters::InterfaceHbondsFilter::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_filters::InterfaceHbondsFilter::set_hbonds_energy_cutoff ( core::Real  hbonds_energy_cutoff_in)
inline

References hbonds_energy_cutoff_.

void protocols::simple_filters::InterfaceHbondsFilter::set_hbonds_num_threshold ( core::Size  hbonds_num_threshold_in)
inline

References hbonds_num_threshold_.

void protocols::simple_filters::InterfaceHbondsFilter::set_include_His_chain_terminus ( bool  include_His_chain_terminus_in)
inline
void protocols::simple_filters::InterfaceHbondsFilter::set_jump ( core::Size const  jump_in)
inline

References jump_.

void protocols::simple_filters::InterfaceHbondsFilter::set_salt_bridge_distance_cutoff ( bool  salt_bridge_distance_cutoff_in)
inline
void protocols::simple_filters::InterfaceHbondsFilter::set_salt_bridge_mode ( bool  salt_bridge_mode_in)
inline
void protocols::simple_filters::InterfaceHbondsFilter::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

References scorefxn_.

Referenced by parse_my_tag().

Member Data Documentation

std::unordered_map<std::string, std::vector<Charged_Group > > protocols::simple_filters::InterfaceHbondsFilter::charged_res_
private
core::Real protocols::simple_filters::InterfaceHbondsFilter::hbonds_energy_cutoff_
private
core::Size protocols::simple_filters::InterfaceHbondsFilter::hbonds_num_threshold_
private
bool protocols::simple_filters::InterfaceHbondsFilter::include_His_chain_terminus_
private
core::Size protocols::simple_filters::InterfaceHbondsFilter::jump_
private
core::Real protocols::simple_filters::InterfaceHbondsFilter::salt_bridge_distance_cutoff_
private
bool protocols::simple_filters::InterfaceHbondsFilter::salt_bridge_mode_
private
core::scoring::ScoreFunctionOP protocols::simple_filters::InterfaceHbondsFilter::scorefxn_
private

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