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protocols::features::LoopAnchorFeatures Class Reference

#include <LoopAnchorFeatures.hh>

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

 LoopAnchorFeatures ()
 
 LoopAnchorFeatures (LoopAnchorFeatures const &)
 
virtual ~LoopAnchorFeatures ()
 
std::string type_name () const
 return string with class name More...
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const
 generate the table schemas and write them to the database More...
 
utility::vector1< std::string > features_reporter_dependencies () const
 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::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 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)
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
virtual ~FeaturesReporter ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 &, boost::uuids::uuid, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)
 
virtual void delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)
 

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...
 
utility::vector1< Sizestart_residue (Size resNo)
 
utility::vector1< Sizeend_residue (Size resNo)
 
utility::vector1< Sizeatoms ()
 
core::Size min_loop_length (utility::vector1< bool > const &relevant_residue)
 
core::Size max_loop_length (utility::vector1< bool > const &relevant_residue)
 
core::Size determine_correct_length (utility::vector1< bool > const &relevant_residue, Size default_length)
 
numeric::HomogeneousTransform
< core::Real
compute_anchor_transform (core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_begin, utility::vector1< core::Size > const &residue_end, utility::vector1< core::Size > const &atoms)
 
void compute_transform_and_write_to_db (boost::uuids::uuid struct_id, core::Size begin, core::Size end, core::pose::Pose const &pose, cppdb::statement &stmt)
 
core::Real compute_atom_angles (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues, utility::vector1< core::Size > const &atoms)
 

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, boost::uuids::uuid 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...
 

Constructor & Destructor Documentation

protocols::features::LoopAnchorFeatures::LoopAnchorFeatures ( )
protocols::features::LoopAnchorFeatures::LoopAnchorFeatures ( LoopAnchorFeatures const &  src)
protocols::features::LoopAnchorFeatures::~LoopAnchorFeatures ( )
virtual

Member Function Documentation

vector1< Size > protocols::features::LoopAnchorFeatures::atoms ( )
private
HomogeneousTransform< Real > protocols::features::LoopAnchorFeatures::compute_anchor_transform ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  residue_begin,
utility::vector1< core::Size > const &  residue_end,
utility::vector1< core::Size > const &  atoms 
)
private
Real protocols::features::LoopAnchorFeatures::compute_atom_angles ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  residues,
utility::vector1< core::Size > const &  atoms 
)
private
void protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db ( boost::uuids::uuid  struct_id,
core::Size  begin,
core::Size  end,
core::pose::Pose const &  pose,
cppdb::statement &  stmt 
)
private
Size protocols::features::LoopAnchorFeatures::determine_correct_length ( utility::vector1< bool > const &  relevant_residue,
Size  default_length 
)
private
vector1< Size > protocols::features::LoopAnchorFeatures::end_residue ( Size  resNo)
private
utility::vector1< std::string > protocols::features::LoopAnchorFeatures::features_reporter_dependencies ( ) const
virtual

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.

Size protocols::features::LoopAnchorFeatures::max_loop_length ( utility::vector1< bool > const &  relevant_residue)
private
Size protocols::features::LoopAnchorFeatures::min_loop_length ( utility::vector1< bool > const &  relevant_residue)
private
void protocols::features::LoopAnchorFeatures::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
Size protocols::features::LoopAnchorFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  ,
boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual

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::total_residue().

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)
vector1< Size > protocols::features::LoopAnchorFeatures::start_residue ( Size  resNo)
private
string protocols::features::LoopAnchorFeatures::type_name ( ) const
virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

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

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

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

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

Referenced by write_schema_to_db().

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
virtual

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: