#include <AtomInResidueAtomInResiduePairFeatures.hh>

Public Member Functions
	AtomInResidueAtomInResiduePairFeatures ()

	AtomInResidueAtomInResiduePairFeatures (AtomInResidueAtomInResiduePairFeatures const &src)

virtual	~AtomInResidueAtomInResiduePairFeatures ()

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...

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...

void	report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
	Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595. 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	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

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_atom_in_residue_pairs_table_schema (utility::sql_database::sessionOP db_session) const
	generate the atom_in_residue_pairs table schema More...

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::AtomInResidueAtomInResiduePairFeatures::AtomInResidueAtomInResiduePairFeatures ( )

protocols::features::AtomInResidueAtomInResiduePairFeatures::AtomInResidueAtomInResiduePairFeatures ( AtomInResidueAtomInResiduePairFeatures const & src )

protocols::features::AtomInResidueAtomInResiduePairFeatures::~AtomInResidueAtomInResiduePairFeatures ( )

virtual

Member Function Documentation

utility::vector1< std::string > protocols::features::AtomInResidueAtomInResiduePairFeatures::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::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.

This is very similar in spirit to the potential described in

Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.

However, they use different distance bins. Here, [0,1), ..., [9,10) are used because they are easy and as they report the the paper, most of the signal comes in the 3.5-6.5 range. To get the molar fraction of atom types–since the types are unique within each residue type, there is exactly one per residue of that type. Therefore this information can be extracted from the Residues table when needed. It may make sense to include it here if it turns to to be too cumbersom to get those quantities.

TODO: Expand for not just canonical residue types

References aa1, aa2, protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::graph::Edge::get_node(), num_canonical_aas, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), runtime_assert, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), core::conformation::Conformation::structure_moved(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by report_features().

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

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References report_atom_pairs().

string protocols::features::AtomInResidueAtomInResiduePairFeatures::type_name ( ) const

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::AtomInResidueAtomInResiduePairFeatures::write_atom_in_residue_pairs_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the atom_in_residue_pairs table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_constraint(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::AtomInResidueAtomInResiduePairFeatures::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_atom_in_residue_pairs_table_schema().

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

symlinks/rosetta/src/protocols/features/AtomInResidueAtomInResiduePairFeatures.hh
symlinks/rosetta/src/protocols/features/AtomInResidueAtomInResiduePairFeatures.cc

Public Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation