buns.cc File Reference

#include <algorithm>
#include <cctype>
#include <limits>
#include <devel/init.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/moves/Mover.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/id/AtomID.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/id/AtomID_Map.hh>
#include <core/conformation/PointGraph.hh>
#include <core/conformation/find_neighbors.hh>
#include <core/scoring/sasa.hh>
#include <devel/buns/BuriedUnsatHbondFilter2.hh>
#include <devel/vardist_solaccess/VarSolDRotamerDots.hh>
#include <core/types.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <core/pose/util.hh>

Classes
class	hbond_strat
class	hbond_energy_strat
class	hbond_geom_strat

Functions
void	read_FileVector (const basic::options::FileVectorOptionKey &fv_key, std::vector< std::string > &str_vec)
Size	bunsats (pose::Pose &pose, const Real AHdist_threshold, const hbond_strat &hb_eval, const bool vsasa, const Real probe_radius, const Real burial_cutoff)
int	separation (const std::vector< std::string > &nat_list, const std::vector< std::string > &rlx_list, const Real AHdist_geom_eval_threshold, const hbond_strat &hb_eval, const bool vsasa, const Real probe, const Real burial_cutoff)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.kevin.buns")
basic::options::FileVectorOptionKey const	nat_list_opkey ("nat_list")
basic::options::FileVectorOptionKey const	rlx_list_opkey ("rlx_list")

Function Documentation

bunsats()

Size bunsats	(	pose::Pose &	pose,
		const Real	AHdist_threshold,
		const hbond_strat &	hb_eval,
		const bool	vsasa,
		const Real	probe_radius,
		const Real	burial_cutoff
	)

References end, hbond_strat::evaluate(), find_neighbors(), h, test.T200_Scoring::hbond_set, benchmark_ns::hbonded, basic::options::OptionKeys::legacy_sewing::neighbor_cutoff, create_a3b_hbs::nres, create_a3b_hbs::pdb_info, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, res, and oop_conformations::scorefxn.

Referenced by separation().

main()

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

References utility::options::OptionCollection::add(), argv, utility::io::oc::cout, test.T009_Exceptions::e, basic::init(), nat_list_opkey, basic::options::option, read_FileVector(), rlx_list_opkey, basic::options::OptionKeys::sc::sep, separation(), and TR.

read_FileVector()

void read_FileVector	(	const basic::options::FileVectorOptionKey &	fv_key,
		std::vector< std::string > &	str_vec
	)

References getline(), line, basic::options::OptionKeys::in::file::list, basic::options::option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

separation()

int separation	(	const std::vector< std::string > &	nat_list,
		const std::vector< std::string > &	rlx_list,
		const Real	AHdist_geom_eval_threshold,
		const hbond_strat &	hb_eval,
		const bool	vsasa,
		const Real	probe,
		const Real	burial_cutoff
	)

References bunsats(), create_a3b_hbs::i, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and subloop_histogram::size.

Referenced by main(), and sasa_separation().

Variable Documentation

nat_list_opkey

basic::options::FileVectorOptionKey const nat_list_opkey("nat_list")

(

"nat_list"

)

Referenced by main().

rlx_list_opkey

basic::options::FileVectorOptionKey const rlx_list_opkey("rlx_list")

(

"rlx_list"

)

Referenced by main().

TR

basic::Tracer TR("apps.pilot.kevin.buns") ( "apps.pilot.kevin.buns"  )

static

Referenced by main().