exposed_strand_finder.cc File Reference

finds exposed strands with option to check rmsd to another strand More...

#include <devel/init.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/excn/EXCN_Base.hh>
#include <utility/vector1.functions.hh>
#include <utility/vector1.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/methods/EnergyMethod.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID_Map.hh>
#include <numeric/xyzVector.hh>
#include <basic/MetricValue.hh>
#include <basic/Tracer.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/StructureRestrictor.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <sstream>
#include <iostream>
#include <string>
#include <math.h>
#include <utility>
#include <core/pose/util.tmpl.hh>
#include <utility/vector0.hh>

Classes
class	ExposedStrandMover

Enumerations
enum	Index {   chain_index = 1, start_index = 2, end_index = 3, max_neighbors = 16,   trans = 1, rot = 2 }

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.beta_strand_homodimer_design.exposed_strand_finder")
static THREAD_LOCAL basic::Tracer	TRout ("ExposedStrand")
int	main (int argc, char *argv[])

Variables
basic::options::BooleanOptionKey const	check_rmsd ("check_rmsd")
basic::options::StringVectorOptionKey const	strand_span ("strand_span")
basic::options::IntegerOptionKey const	beta_length ("beta_length")
basic::options::IntegerOptionKey const	sat_allow ("sat_allow")
basic::options::RealOptionKey const	max_E_allow ("max_E_allow")
basic::options::RealOptionKey const	max_RMSD ("max_RMSD")
basic::options::StringOptionKey const	struct_file ("struct_file")

Detailed Description

finds exposed strands with option to check rmsd to another strand

Enumeration Type Documentation

enum Index

Enumerator
chain_index
start_index
end_index
max_neighbors
trans
rot

Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

References beta_length, check_rmsd, utility::io::oc::cout, devel::init(), max_E_allow, max_RMSD, utility::excn::EXCN_Base::msg(), option, sat_allow, strand_span, and struct_file.

static THREAD_LOCAL basic::Tracer TR ( "apps.public.beta_strand_homodimer_design.exposed_strand_finder"  )

static

Referenced by ExposedStrandMover::apply(), ExposedStrandMover::bb_score(), ExposedStrandMover::is_exposed(), and ExposedStrandMover::parse_strand_ids().

static THREAD_LOCAL basic::Tracer TRout ( "ExposedStrand"  )

static

Referenced by ExposedStrandMover::print_sheets(), and ExposedStrandMover::print_sheets_extras().

Variable Documentation

basic::options::IntegerOptionKey const beta_length("beta_length")

Referenced by ExposedStrandMover::ExposedStrandMover(), and main().

basic::options::BooleanOptionKey const check_rmsd("check_rmsd")

Referenced by ExposedStrandMover::ExposedStrandMover(), and main().

basic::options::RealOptionKey const max_E_allow("max_E_allow")

Referenced by ExposedStrandMover::apply(), and main().

basic::options::RealOptionKey const max_RMSD("max_RMSD")

Referenced by ExposedStrandMover::apply(), and main().

basic::options::IntegerOptionKey const sat_allow("sat_allow")

Referenced by ExposedStrandMover::ExposedStrandMover(), and main().

basic::options::StringVectorOptionKey const strand_span("strand_span")

Referenced by ExposedStrandMover::apply(), and main().

basic::options::StringOptionKey const struct_file("struct_file")

Referenced by ExposedStrandMover::apply(), and main().