SandwichFeatures.cc File Reference

Extract and analyze beta-sandwich features. More...

#include <protocols/features/strand_assembly/CheckForSandwichFeatures.hh>
#include <protocols/features/strand_assembly/SandwichFeatures.hh>
#include <protocols/features/strand_assembly/WriteToDBFromSandwichFeatures.hh>
#include <protocols/features/strand_assembly/WriteToFileFromSandwichFeatures.hh>
#include <basic/database/schema_generator/DbDataType.hh>
#include <core/pose/Pose.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <utility/tag/Tag.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/features/feature_schemas.hh>
#include <protocols/features/strand_assembly/SandwichFeaturesCreator.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <basic/Tracer.hh>
#include <basic/database/schema_generator/Schema.hh>
#include <iostream>
#include <basic/database/schema_generator/Column.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::features
	protocols::features::strand_assembly

Functions
static basic::Tracer	protocols::features::strand_assembly::TR ("protocols.features.strand_assembly.SandwichFeatures")

Detailed Description

Extract and analyze beta-sandwich features.

Author

Doo Nam Kim (doona.nosp@m.m.ki.nosp@m.m@gma.nosp@m.il.c.nosp@m.om) @overview @ task 0: Determine whether we deal with given pdb file @ task 1: Identify all beta-strands @ task 2: Identify all beta-sheets with these strands @ task 3: Identify all beta-sandwiches with these sheets @ task 3-1: Merge sheets to each other if possible @ task 3-2: Make beta-sandwiches with sheets that are ideal only @ task 3-2-1: Exclude if this_sheet_is_surrounded_by_more_than_1_other_sheet @ task 3-2-2: Exclude sheets that are too close to each other @ task 3-2-3: Exclude sheets that are too distant to each other @ task 3-2-4: Exclude sheets that do not face each other @ task 3-2-4-1: Exclude sheets that do not face each other by an angle with two terminal residues and one central residue @ task 3-2-4-2: Exclude sheets that do not face each other by an angle with four terminal residues in two edge strands @ task 3-4: Test canonical sandwich test @ task 3-4-1: Canonical sandwiches need to have low number of helix or strand residues in any loop (beta-hairpin-loop or inter-sheet-loop) @ task 3-4-2: Canonical sandwiches need to not have same-direction-strands as connecting two beta-sheets @ task 3-4-3: Canonical sandwiches should not be beta-barrel obviously @ task 4: Write beta-sandwiches that passed canonical tests into database @ task 4-1: Write hairpin_loop and inter-sheet loop @ task 4-2: Write starting_loop and endng_loop @ task 4-3: Write ratio_hydrophobic_philic/net_charge @ task 4-4: Write total size of sandwich @ task 5: Write resfiles automatically