SandwichFeatures.cc File Reference

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

#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <boost/uuid/uuid.hpp>
#include <protocols/features/strand_assembly/SandwichFeatures.hh>
#include <basic/database/sql_utils.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <numeric/xyz.functions.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <core/id/NamedAtomID.hh>
#include <math.h>
#include <cppdb/frontend.h>
#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/strand_assembly.OptionKeys.gen.hh>
#include <basic/database/schema_generator/PrimaryKey.hh>
#include <basic/database/schema_generator/ForeignKey.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/Schema.hh>
#include <basic/database/schema_generator/Constraint.hh>
#include <algorithm>
#include <fstream>
#include <iostream>
#include <cmath>
#include <numeric>
#include <stdlib.h>
#include <vector>
#include <utility/excn/Exceptions.hh>
#include <utility/exit.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <basic/datacache/DataMap.hh>

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

Functions
template<typename T , size_t N>
const T *	mybegin (const T(&a)[N])
template<typename T , size_t N>
const T *	myend (const T(&a)[N])

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

Detailed Description

Extract and analyze beta-sandwich features.

Author

Doo Nam Kim (based on Tim Jacobs' helix_assembly) @ 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 3-3: Write AA distribution @ 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

Function Documentation

template<typename T , size_t N>

const T* mybegin

(

const T(&)

a[N]

)

template<typename T , size_t N>

const T* myend

(

const T(&)

a[N]

)

References protocols::forge::build::SegmentInsertConnectionScheme::N.

Variable Documentation

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

static