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protocols::features::WaterFeatures Class Reference

#include <WaterFeatures.hh>

Inheritance diagram for protocols::features::WaterFeatures:
Inheritance graph
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Public Member Functions

 WaterFeatures ()
 
 WaterFeatures (core::Real acc_dist_cutoff, core::Real don_dist_cutoff)
 
core::Real acc_dist_cutoff () const
 
core::Real don_dist_cutoff () const
 
void acc_dist_cutoff (core::Real d)
 
void don_dist_cutoff (core::Real d)
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 return string with class name More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 
utility::vector1< std::string > features_reporter_dependencies () const override
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &, StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Static Public Member Functions

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

Private Member Functions

void write_water_hbond_geom_table_schema (utility::sql_database::sessionOP db_session) const
 generate the salt_bridges table schema More...
 

Private Attributes

core::Real acc_dist_cutoff_
 
core::Real don_dist_cutoff_
 
core::Real ahd_cutoff_
 
utility::vector1< std::pair
< std::string, std::string > > 
names_for_water_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::features::WaterFeatures::WaterFeatures ( )
protocols::features::WaterFeatures::WaterFeatures ( core::Real  acc_dist_cutoff,
core::Real  don_dist_cutoff 
)

Member Function Documentation

core::Real protocols::features::WaterFeatures::acc_dist_cutoff ( ) const
inline

References acc_dist_cutoff_.

void protocols::features::WaterFeatures::acc_dist_cutoff ( core::Real  d)
inline

References acc_dist_cutoff_.

std::string protocols::features::WaterFeatures::class_name ( )
static
core::Real protocols::features::WaterFeatures::don_dist_cutoff ( ) const
inline

References don_dist_cutoff_.

void protocols::features::WaterFeatures::don_dist_cutoff ( core::Real  d)
inline

References don_dist_cutoff_.

utility::vector1< std::string > protocols::features::WaterFeatures::features_reporter_dependencies ( ) const
overridevirtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::WaterFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::features::WaterFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::features::WaterFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  ,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
std::string protocols::features::WaterFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::WaterFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
overridevirtual

return string with class name

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_water_hbond_geom_table_schema().

void protocols::features::WaterFeatures::write_water_hbond_geom_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the salt_bridges table schema

Referenced by write_schema_to_db().

Member Data Documentation

core::Real protocols::features::WaterFeatures::acc_dist_cutoff_
private
core::Real protocols::features::WaterFeatures::ahd_cutoff_
private

Referenced by parse_my_tag().

core::Real protocols::features::WaterFeatures::don_dist_cutoff_
private
utility::vector1< std::pair<std::string, std::string> > protocols::features::WaterFeatures::names_for_water_
private

Referenced by parse_my_tag(), and report_features().


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