BuriedUnsatPolarsFinder2.cc File Reference

#include <devel/init.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/MetricValue.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <devel/vardist_solaccess/VarSolDRotamerDots.hh>
#include <devel/vardist_solaccess/LoadVarSolDistSasaCalculatorMover.hh>
#include <numeric/xyzVector.hh>
#include <core/scoring/sasa.hh>
#include <numeric/conversions.hh>

Classes
class	BuriedUnsatPolarsFinder

Typedefs
typedef numeric::xyzVector< core::Real >	Vector
typedef utility::pointer::owning_ptr< BuriedUnsatPolarsFinder >	BuriedUnsatPolarsFinderOP

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

Variables
static basic::Tracer	TR ("apps.pilot.bder.BuriedUnsatPolarsFinder")
basic::options::BooleanOptionKey const	use_varsoldist_sasa_calc ("use_varsoldist_sasa_calc")
basic::options::BooleanOptionKey const	use_regular_sasa_calc ("use_regular_sasa_calc")
basic::options::BooleanOptionKey const	generous_hbond_settings ("generous_hbond_settings")
basic::options::RealOptionKey const	sasa_cutoff ("bunsat_sasa_cutoff")
basic::options::RealOptionKey const	AHD_cutoff ("bunsat_AHD_cutoff")
basic::options::RealOptionKey const	dist_cutoff ("bunsat_dist_cutoff")
basic::options::RealOptionKey const	hydroxyl_dist_cutoff ("bunsat_hydroxyl_dist_cutoff")
basic::options::RealOptionKey const	sulphur_dist_cutoff ("bunsat_sulphur_dist_cutoff")
basic::options::RealOptionKey const	metal_dist_cutoff ("bunsat_metal_dist_cutoff")

Detailed Description

Author

Kevin Houlihan

Bryan Der

Typedef Documentation

BuriedUnsatPolarsFinderOP

typedef utility::pointer::owning_ptr<BuriedUnsatPolarsFinder> BuriedUnsatPolarsFinderOP

Vector

typedef numeric::xyzVector< core::Real > Vector

Function Documentation

main()

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

References utility::options::OptionCollection::add(), AHD_cutoff, argv, utility::options::ScalarOption_T_< K, T >::def(), dist_cutoff, test.T009_Exceptions::e, generous_hbond_settings, hydroxyl_dist_cutoff, basic::init(), metal_dist_cutoff, basic::options::option, sasa_cutoff, sulphur_dist_cutoff, basic::options::TR, use_regular_sasa_calc, and use_varsoldist_sasa_calc.

Variable Documentation

AHD_cutoff

basic::options::RealOptionKey const AHD_cutoff("bunsat_AHD_cutoff")

(

"bunsat_AHD_cutoff"

)

Referenced by BuriedUnsatPolarsFinder::acc_geom_check(), BuriedUnsatPolarsFinder::don_geom_check(), and main().

dist_cutoff

basic::options::RealOptionKey const dist_cutoff("bunsat_dist_cutoff")

(

"bunsat_dist_cutoff"

)

Referenced by BuriedUnsatPolarsFinder::acc_geom_check(), InteractionDistMinimizer::apply(), calculate_burial(), concave_hull(), BuriedUnsatPolarsFinder::don_geom_check(), is_atom_clash(), main(), output_interface_graphviz(), and BuriedUnsatPolarsFinder::single_bunsat_thorough_check().

generous_hbond_settings

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

(

"generous_hbond_settings"

)

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

hydroxyl_dist_cutoff

basic::options::RealOptionKey const hydroxyl_dist_cutoff("bunsat_hydroxyl_dist_cutoff")

(

"bunsat_hydroxyl_dist_cutoff"

)

Referenced by BuriedUnsatPolarsFinder::acc_geom_check(), and main().

metal_dist_cutoff

basic::options::RealOptionKey const metal_dist_cutoff("bunsat_metal_dist_cutoff")

(

"bunsat_metal_dist_cutoff"

)

Referenced by main(), and BuriedUnsatPolarsFinder::metal_check().

sasa_cutoff

basic::options::RealOptionKey const sasa_cutoff("bunsat_sasa_cutoff")

(

"bunsat_sasa_cutoff"

)

Referenced by BuriedUnsatPolarsFinder::apply(), is_buried_ring(), and main().

sulphur_dist_cutoff

basic::options::RealOptionKey const sulphur_dist_cutoff("bunsat_sulphur_dist_cutoff")

(

"bunsat_sulphur_dist_cutoff"

)

Referenced by main(), and BuriedUnsatPolarsFinder::sulphur_bond_check().

TR

basic::Tracer TR("apps.pilot.bder.BuriedUnsatPolarsFinder") ( "apps.pilot.bder.BuriedUnsatPolarsFinder"  )

static

use_regular_sasa_calc

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

(

"use_regular_sasa_calc"

)

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

use_varsoldist_sasa_calc

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

(

"use_varsoldist_sasa_calc"

)

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