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

#include <SmotifFeatures.hh>

Inheritance diagram for protocols::features::SmotifFeatures:
Inheritance graph
[legend]

Public Member Functions

 SmotifFeatures ()
 
 SmotifFeatures (core::scoring::ScoreFunctionOP scfxn)
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 generate the table schemas and write them to the database More...
 
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...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 
void calculate_angles (utility::vector1< numeric::xyzVector< core::Real > > const &ss1_coords, utility::vector1< numeric::xyzVector< core::Real > > const &ss2_coords, core::Real &distance, core::Real &hoist_angle_degrees, core::Real &packing_angle_degrees, core::Real &meridian_angle_degrees)
 
utility::vector1
< SecondaryStructureSegment
get_ss_segments (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, 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)
 

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::SmotifFeatures::SmotifFeatures ( )
default
protocols::features::SmotifFeatures::SmotifFeatures ( core::scoring::ScoreFunctionOP  scfxn)

Member Function Documentation

void protocols::features::SmotifFeatures::calculate_angles ( utility::vector1< numeric::xyzVector< core::Real > > const &  ss1_coords,
utility::vector1< numeric::xyzVector< core::Real > > const &  ss2_coords,
core::Real distance,
core::Real hoist_angle_degrees,
core::Real packing_angle_degrees,
core::Real meridian_angle_degrees 
)

References core::pose::center_of_mass().

Referenced by report_features().

std::string protocols::features::SmotifFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::SmotifFeatures::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.

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

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

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References core::kinematics::distance().


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