#include <cmath>
#include <cstdlib>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/types.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/pose/util.hh>
#include <numeric/constants.hh>
#include <utility/string_util.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/Tracer.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/conformation/ResidueFactory.hh>
#include <numeric/conversions.hh>
#include <utility/io/ozstream.hh>

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

	basic::options

	basic::options::OptionKeys

	hbscan

Functions
bool	fast_clash_check (Pose const &pose, vector1< id::AtomID > const check_atids, Real const clash_dist_cut)

Size	max_atom_hbonds (chemical::ResidueType const &restype, Size const &atomno)

void	get_n_hbonds_from_pair (Pose const pose, Size const rec_seqpos, Size const lig_seqpos, int const &lig_min_atom_sep, Real const &hbond_wtd_energy_cutoff, Size &n_sc_hbonds, Size &n_bb_hbonds, Size &n_hbonds, std::string &hbond_pairs_str)

void	print_cst_file (std::string const filename, std::string const &r1, char const &r2, std::string const &r1a1, std::string const &r1a2, std::string const &r1a3, std::string const &r2a1, std::string const &r2a2, std::string const &r2a3, Real const &distab, Real const &anga, Real const &angb, Real const &tora, Real const &torab, Real const &torb)

void	scan_hbond_jumps (pose::Pose pose, scoring::ScoreFunctionOP scorefxn, Size seqpos, Size atomno, conformation::Residue new_rsd, Size new_atomno)

void	byres_analysis (pose::Pose pose)

void	load_coords ()

void *	my_main (void *)

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

Variables
static basic::Tracer	TR ("apps.pilot.chrisk.hbscan")

basic::options::StringOptionKey	hbscan::tag ("hbscan:tag")

basic::options::RealOptionKey	hbscan::repeat ("hbscan:repeat")

basic::options::IntegerOptionKey	hbscan::nloop_hbscan ("hbscan:nloop_hbscan")

basic::options::RealOptionKey	hbscan::hbond_sc_cutoff ("hbscan:hbond_sc_cutoff")

basic::options::RealOptionKey	hbscan::fa_rep_cutoff ("hbscan:fa_rep_cutoff")

basic::options::IntegerOptionKey	hbscan::lig_seqpos ("hbscan:lig_seqpos")

basic::options::StringOptionKey	hbscan::restypes ("hbscan:restypes")

basic::options::IntegerOptionKey	hbscan::lig_min_atom_sep ("hbscan:lig_min_atom_sep")

basic::options::RealOptionKey	hbscan::hbond_wtd_energy_cutoff ("hbscan:hbond_wtd_energy_cutoff")

basic::options::BooleanOptionKey	hbscan::write_cst_file ("hbscan:write_cst_file")

core::scoring::hbonds::HBondDatabaseCOP	hb_database_

Function Documentation

◆ byres_analysis()

void byres_analysis ( pose::Pose pose )

References hb_database_, hbscan::lig_seqpos, create_a3b_hbs::nres, option, predPRE::pdbname, beta_nonlocal::pose, hbscan::restypes, scan_hbond_jumps(), oop_conformations::scorefxn, ObjexxFCL::string_of(), utility::string_split(), hbscan::tag, tag, tag_from_pose(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by load_coords().

◆ fast_clash_check()

bool fast_clash_check	(	Pose const &	pose,
		vector1< id::AtomID > const	check_atids,
		Real const	clash_dist_cut
	)

References numeric::xyzVector< T >::distance_squared(), natoms(), beta_nonlocal::pose, and erraser_analysis::res2.

Referenced by scan_hbond_jumps().

◆ get_n_hbonds_from_pair()

void get_n_hbonds_from_pair	(	Pose const	pose,
		Size const	rec_seqpos,
		Size const	lig_seqpos,
		int const &	lig_min_atom_sep,
		Real const &	hbond_wtd_energy_cutoff,
		Size &	n_sc_hbonds,
		Size &	n_bb_hbonds,
		Size &	n_hbonds,
		std::string &	hbond_pairs_str
	)

References hbscan::hbond_wtd_energy_cutoff, create_a3b_hbs::i, hbscan::lig_min_atom_sep, hbscan::lig_seqpos, max_atom_hbonds(), and beta_nonlocal::pose.

Referenced by scan_hbond_jumps().

◆ load_coords()

void load_coords ( )

References byres_analysis(), create_a3b_hbs::i, gaussian-sampling::input, option, beta_nonlocal::pose, hbscan::repeat, and in::file::residue_type_set().

Referenced by my_main().

◆ main()

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

References argv, test.T009_Exceptions::e, hbscan::fa_rep_cutoff, hbscan::hbond_sc_cutoff, hbscan::hbond_wtd_energy_cutoff, basic::init(), hbscan::lig_min_atom_sep, hbscan::lig_seqpos, my_main(), hbscan::nloop_hbscan, option, hbscan::repeat, hbscan::restypes, hbscan::tag, viewer_main(), and hbscan::write_cst_file.

◆ max_atom_hbonds()

Size max_atom_hbonds	(	chemical::ResidueType const &	restype,
		Size const &	atomno
	)

References enumerate_junctions::default, and build_restypes::restype.

Referenced by get_n_hbonds_from_pair().

◆ my_main()

void* my_main ( void * )

References utility::options::OptionKeys::options::exit, and load_coords().

Referenced by main().

◆ print_cst_file()

void print_cst_file	(	std::string const	filename,
		std::string const &	r1,
		char const &	r2,
		std::string const &	r1a1,
		std::string const &	r1a2,
		std::string const &	r1a3,
		std::string const &	r2a1,
		std::string const &	r2a2,
		std::string const &	r2a3,
		Real const &	distab,
		Real const &	anga,
		Real const &	angb,
		Real const &	tora,
		Real const &	torab,
		Real const &	torb
	)