Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::features::ProteinRMSDNoSuperpositionFeatures Class Reference

#include <ProteinRMSDNoSuperpositionFeatures.hh>

Public Member Functions

 ProteinRMSDNoSuperpositionFeatures ()
 
 ProteinRMSDNoSuperpositionFeatures (core::pose::PoseCOP reference_pose)
 
 ProteinRMSDNoSuperpositionFeatures (ProteinRMSDNoSuperpositionFeatures const &)
 
virtual ~ProteinRMSDNoSuperpositionFeatures ()
 
std::string type_name () const
 return string with class name More...
 
utility::vector1< std::stringfeatures_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 write_schema_to_db (utility::sql_database::sessionOP db_session) const
 generate the table schemas and write them to the database More...
 
core::pose::PoseCOP reference_pose () const
 
void reference_pose (core::pose::PoseCOP)
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &pose)
 
void reference_pose_from_options (core::pose::Pose const &pose)
 Sets the native pose to the native pose if set, or the starting pose otherwise. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose More...
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 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 &, 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
 

Private Member Functions

void write_protein_rmsd_table_schema (utility::sql_database::sessionOP db_session) const
 generate the protein_rmsd table schema More...
 

Private Attributes

core::pose::PoseCOP reference_pose_
 

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::ProteinRMSDNoSuperpositionFeatures::ProteinRMSDNoSuperpositionFeatures ( )
inline

If you use this constructor, before applying, make sure the reference pose is specified, either through the set_reference_pose method or parse_my_tag.

protocols::features::ProteinRMSDNoSuperpositionFeatures::ProteinRMSDNoSuperpositionFeatures ( core::pose::PoseCOP  reference_pose)
protocols::features::ProteinRMSDNoSuperpositionFeatures::ProteinRMSDNoSuperpositionFeatures ( ProteinRMSDNoSuperpositionFeatures const &  )
inline
virtual protocols::features::ProteinRMSDNoSuperpositionFeatures::~ProteinRMSDNoSuperpositionFeatures ( )
inlinevirtual

Member Function Documentation

utility::vector1< std::string > protocols::features::ProteinRMSDNoSuperpositionFeatures::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.

void protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
)
virtual
PoseCOP protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose ( ) const
void protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose ( core::pose::PoseCOP  )
void protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose_from_options ( core::pose::Pose const &  pose)

Sets the native pose to the native pose if set, or the starting pose otherwise.

References option, pose_from_pdb(), reference_pose(), protocols::features::tr, type_name(), and user.

Referenced by parse_my_tag().

Size protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual
string protocols::features::ProteinRMSDNoSuperpositionFeatures::type_name ( ) const
virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

Referenced by parse_my_tag(), and reference_pose_from_options().

void protocols::features::ProteinRMSDNoSuperpositionFeatures::write_protein_rmsd_table_schema ( utility::sql_database::sessionOP  db_session) const
private
void protocols::features::ProteinRMSDNoSuperpositionFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_protein_rmsd_table_schema().

Member Data Documentation

core::pose::PoseCOP protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose_
private

Referenced by reference_pose(), and report_features().


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