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protocols::features::LoopAnchorFeatures Class Reference

#include <LoopAnchorFeatures.hh>

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

 LoopAnchorFeatures ()
 
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 &) override
 
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...
 
void set_use_relevant_residues_as_loop_length (bool const use_relevant_residues_as_loop_length)
 
void set_use_single_residue_to_define_anchor_transfrom (bool const use_single_residue_to_define_anchor_transfrom)
 
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_loop_anchors_table_schema (utility::sql_database::sessionOP db_session) const
 generate the loop_anchors table schema More...
 
void write_loop_anchor_transforms_table_schema (utility::sql_database::sessionOP db_session) const
 generate the loop_anchor_transforms table schema More...
 
void write_loop_anchor_transforms_three_res_table_schema (utility::sql_database::sessionOP db_session) const
 generate the loop_anchor_transforms_three_res table schema More...
 
core::Size min_loop_length (utility::vector1< bool > const &relevant_residue) const
 
core::Size max_loop_length (utility::vector1< bool > const &relevant_residue) const
 
core::Size determine_correct_length (utility::vector1< bool > const &relevant_residue, core::Size default_length) const
 
numeric::HomogeneousTransform
< core::Real > const 
frame_for_residue (core::conformation::Residue const &residue) const
 
numeric::HomogeneousTransform
< core::Real > const 
compute_anchor_transform (core::pose::Pose const &pose, core::Size const residue_begin, core::Size const residue_end) const
 
void compute_transform_and_write_to_db (StructureID struct_id, core::Size begin, core::Size end, core::pose::Pose const &pose, cppdb::statement &stmt) const
 

Private Attributes

bool use_relevant_residues_as_loop_length_
 
bool use_single_residue_to_define_anchor_transfrom_
 
core::Size min_loop_length_
 
core::Size max_loop_length_
 

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::LoopAnchorFeatures::LoopAnchorFeatures ( )

Member Function Documentation

std::string protocols::features::LoopAnchorFeatures::class_name ( )
static
HomogeneousTransform< Real > const protocols::features::LoopAnchorFeatures::compute_anchor_transform ( core::pose::Pose const &  pose,
core::Size const  residue_begin,
core::Size const  residue_end 
) const
private
void protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db ( StructureID  struct_id,
core::Size  begin,
core::Size  end,
core::pose::Pose const &  pose,
cppdb::statement &  stmt 
) const
private
Size protocols::features::LoopAnchorFeatures::determine_correct_length ( utility::vector1< bool > const &  relevant_residue,
core::Size  default_length 
) const
private
utility::vector1< std::string > protocols::features::LoopAnchorFeatures::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.

HomogeneousTransform< Real > const protocols::features::LoopAnchorFeatures::frame_for_residue ( core::conformation::Residue const &  residue) const
private
Size protocols::features::LoopAnchorFeatures::max_loop_length ( utility::vector1< bool > const &  relevant_residue) const
private
Size protocols::features::LoopAnchorFeatures::min_loop_length ( utility::vector1< bool > const &  relevant_residue) const
private
void protocols::features::LoopAnchorFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::features::LoopAnchorFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::features::LoopAnchorFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  ,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual

collect all the feature data for the pose

An anchor is a take off and landing for a loop. Every residue in the loop must be relevant in order for the loop to be stored.

Implements protocols::features::FeaturesReporter.

References core::conformation::Conformation::chain_endings(), compute_transform_and_write_to_db(), core::pose::Pose::conformation(), core::sequence::end, max_loop_length(), min_loop_length(), set_use_single_residue_to_define_anchor_transfrom(), and core::pose::Pose::size().

void protocols::features::LoopAnchorFeatures::set_use_relevant_residues_as_loop_length ( bool const  use_relevant_residues_as_loop_length)
void protocols::features::LoopAnchorFeatures::set_use_single_residue_to_define_anchor_transfrom ( bool const  use_single_residue_to_define_anchor_transfrom)
std::string protocols::features::LoopAnchorFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the loop_anchor_transforms table schema

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the loop_anchor_transforms_three_res table schema

void protocols::features::LoopAnchorFeatures::write_loop_anchors_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the loop_anchors table schema

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::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 write_loop_anchor_transforms_table_schema(), and write_loop_anchors_table_schema().

Member Data Documentation

core::Size protocols::features::LoopAnchorFeatures::max_loop_length_
private

Referenced by max_loop_length(), and parse_my_tag().

core::Size protocols::features::LoopAnchorFeatures::min_loop_length_
private

Referenced by min_loop_length(), and parse_my_tag().

bool protocols::features::LoopAnchorFeatures::use_relevant_residues_as_loop_length_
private
bool protocols::features::LoopAnchorFeatures::use_single_residue_to_define_anchor_transfrom_
private

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