byres_data.cc File Reference

#include <math.h>
#include <stdlib.h>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/PoseInputStream.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/scoring/types.hh>
#include <core/scoring/ScoringManager.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/hbonds.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/etable/count_pair/CountPairAll.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/sasa.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/tools/make_map.hh>
#include <utility/string_util.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/rtmin.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMinMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <protocols/pose_metric_calculators/MetricValueGetter.hh>
#include <basic/MetricValue.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/pose_metric_calculators/SemiExplicitWaterUnsatisfiedPolarsCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/rot_anl.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.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
	byres_data

Functions
bool	fast_clash_check (Pose const &pose, vector1< id::AtomID > const check_atids, Real const clash_dist_cut)
void	set_pose_occ_and_bfac (Pose &pose, Pose const native_pose, vector1< Size > const native_seqpos_map)
Pose	remove_pose_water (pose::Pose pose)
Real	normalize_residue_sasa (pose::Pose pose, Size const seqpos, Real const res_sasa)
Real	get_atom_lk_energy_by_residue_no_count_pair (scoring::ScoreFunctionOP scorefxn, conformation::Residue const &rsd1, Size const atom1, conformation::Residue const &rsd2)
Real	get_atom_lk_energy (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, Size const iatom)
Real	get_atom_lk_burial (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, Size const iatom)
Real	get_res_avg_lk_burial (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, bool incl_bb, bool incl_sc)
void	get_n_hbonds (Pose const pose, Size const seqpos, Size &n_sc_hbonds, Size &n_bb_hbonds, Size &n_sc_wat_hbonds, Size &n_bb_wat_hbonds, Size &n_hbonds, Size &n_unsat)
Real	get_res_water_energy (pose::Pose pose, ScoreFunction scorefxn, Size seqpos)
Real	get_sc_bfactor (Pose const native_pose, Size const seqpos)
Real	get_ca_distance (Pose pose, Pose ref_pose, Size const seqpos, Size const ref_seqpos)
Real	get_sc_automorphic_rmsd (Pose pose, Pose ref_pose, Size const seqpos, Size const ref_seqpos, bool const super)
void	split_fa_dun (Pose const pose, Size const seqpos, Real &fa_dun_rot, Real &fa_dun_dev, pack::dunbrack::RotVector &rotvec)
std::string	get_aa_torsion_string (Pose const pose, Size const seqpos)
void	get_res_data_ss (io::silent::SilentStructOP &ss, Pose pose, Pose const native_pose, Size const native_seqpos, Size const seqpos, ScoreFunctionOP scorefxn, ScoreFunctionOP scorefxn_edens, bool const do_sc_rmsd)
void	byres_analysis (pose::Pose pose)
void	load_coords ()
void	register_calcs ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("chrisk.byres_data")
static basic::Tracer	TR_unsat ("chrisk.unsat_calc")
basic::options::StringOptionKey	byres_data::tag ("byres_data:tag")
basic::options::BooleanOptionKey	byres_data::solvate ("byres_data:solvate")
basic::options::BooleanOptionKey	byres_data::calcs_only ("byres_data:calcs_only")
basic::options::BooleanOptionKey	byres_data::solv_unsat_calc ("byres_data:solv_unsat_calc")
basic::options::RealOptionKey	byres_data::repeat ("byres_data:repeat")
basic::options::IntegerOptionKey	byres_data::nloop_solvadd ("byres_data:nloop_solvadd")
basic::options::IntegerOptionKey	byres_data::nloop_solvdock ("byres_data:nloop_solvdock")
basic::options::IntegerOptionKey	byres_data::nloop_hbscan ("byres_data:nloop_hbscan")
basic::options::BooleanOptionKey	byres_data::align_native_seq ("byres_data:align_native_seq")

Function Documentation

byres_analysis()

void byres_analysis

(

pose::Pose

pose

)

References byres_data::align_native_seq, byres_data::calcs_only, get_atom_lk_burial(), get_res_data_ss(), edensity::mapfile(), in::file::native(), docking::native_pose, create_a3b_hbs::nres, option, demo.D050_Packer_task::packer_task(), predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, packing::resfile(), oop_conformations::scorefxn, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, basic::options::OptionKeys::relax::sequence, set_pose_occ_and_bfac(), byres_data::solv_unsat_calc, challenge::ss, ObjexxFCL::string_of(), utility::string_split(), byres_data::tag, tag, tag_from_pose(), TR, basic::options::OptionKeys::inout::dbms::user, basic::MetricValue< T >::value(), and value.

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.

get_aa_torsion_string()

std::string get_aa_torsion_string	(	Pose const	pose,
		Size const	seqpos
	)

References beta_nonlocal::pose, and ObjexxFCL::string_of().

get_atom_lk_burial()

Real get_atom_lk_burial	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		Size const	iatom
	)

References get_atom_lk_energy(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by byres_analysis(), and get_res_avg_lk_burial().

get_atom_lk_energy()

Real get_atom_lk_energy	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		Size const	iatom
	)

References utility::graph::Node::const_edge_list_end(), get_atom_lk_energy_by_residue_no_count_pair(), utility::graph::Edge::get_node(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_atom_lk_burial().

get_atom_lk_energy_by_residue_no_count_pair()

Real get_atom_lk_energy_by_residue_no_count_pair	(	scoring::ScoreFunctionOP	scorefxn,
		conformation::Residue const &	rsd1,
		Size const	atom1,
		conformation::Residue const &	rsd2
	)

References numeric::xyzVector< T >::distance_squared(), test.T009_Exceptions::e, ObjexxFCL::FArray3D< T >::index(), test.G201_Module_Structure::l1, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and oop_conformations::scorefxn.

Referenced by get_atom_lk_energy().

get_ca_distance()

Real get_ca_distance	(	Pose	pose,
		Pose	ref_pose,
		Size const	seqpos,
		Size const	ref_seqpos
	)

References beta_nonlocal::pose.

Referenced by get_res_data_ss().

get_n_hbonds()

void get_n_hbonds	(	Pose const	pose,
		Size const	seqpos,
		Size &	n_sc_hbonds,
		Size &	n_bb_hbonds,
		Size &	n_sc_wat_hbonds,
		Size &	n_bb_wat_hbonds,
		Size &	n_hbonds,
		Size &	n_unsat
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

get_res_avg_lk_burial()

Real get_res_avg_lk_burial	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		bool	incl_bb,
		bool	incl_sc
	)

References get_atom_lk_burial(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_res_data_ss().

get_res_data_ss()

void get_res_data_ss	(	io::silent::SilentStructOP &	ss,
		Pose	pose,
		Pose const	native_pose,
		Size const	native_seqpos,
		Size const	seqpos,
		ScoreFunctionOP	scorefxn,
		ScoreFunctionOP	scorefxn_edens,
		bool const	do_sc_rmsd
	)

References ObjexxFCL::abs(), get_ca_distance(), get_res_avg_lk_burial(), get_res_water_energy(), get_sc_automorphic_rmsd(), get_sc_bfactor(), create_a3b_hbs::i, create_a3b_hbs::ii, edensity::mapfile(), docking::native_pose, option, beta_nonlocal::pose, ObjexxFCL::pow(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, split_fa_dun(), challenge::ss, utility::string_split(), basic::options::OptionKeys::inout::dbms::user, value, and weights().

Referenced by byres_analysis().

get_res_water_energy()

Real get_res_water_energy	(	pose::Pose	pose,
		ScoreFunction	scorefxn,
		Size	seqpos
	)

References utility::graph::Node::const_edge_list_end(), test.T200_Scoring::emap, utility::graph::Edge::get_node(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_res_data_ss().

get_sc_automorphic_rmsd()

Real get_sc_automorphic_rmsd	(	Pose	pose,
		Pose	ref_pose,
		Size const	seqpos,
		Size const	ref_seqpos,
		bool const	super
	)

References beta_nonlocal::pose.

Referenced by get_res_data_ss().

get_sc_bfactor()

Real get_sc_bfactor	(	Pose const	native_pose,
		Size const	seqpos
	)

References count, create_a3b_hbs::ii, and docking::native_pose.

Referenced by get_res_data_ss().

load_coords()

void load_coords

(

)

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

Referenced by my_main().

main()

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

References byres_data::align_native_seq, argv, byres_data::calcs_only, test.T009_Exceptions::e, basic::init(), my_main(), byres_data::nloop_hbscan, byres_data::nloop_solvadd, byres_data::nloop_solvdock, option, byres_data::repeat, byres_data::solv_unsat_calc, byres_data::solvate, byres_data::tag, and viewer_main().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

normalize_residue_sasa()

Real normalize_residue_sasa	(	pose::Pose	pose,
		Size const	seqpos,
		Real const	res_sasa
	)

References enumerate_junctions::default, and beta_nonlocal::pose.

register_calcs()

void register_calcs

(

)

References option, oop_conformations::scorefxn, and byres_data::solv_unsat_calc.

Referenced by my_main().

remove_pose_water()

Pose remove_pose_water

(

pose::Pose

pose

)

References create_a3b_hbs::nres, and beta_nonlocal::pose.

set_pose_occ_and_bfac()

void set_pose_occ_and_bfac	(	Pose &	pose,
		Pose const	native_pose,
		vector1< Size > const	native_seqpos_map
	)

References create_a3b_hbs::ii, docking::native_pose, and beta_nonlocal::pose.

Referenced by byres_analysis().

split_fa_dun()

void split_fa_dun	(	Pose const	pose,
		Size const	seqpos,
		Real &	fa_dun_rot,
		Real &	fa_dun_dev,
		pack::dunbrack::RotVector &	rotvec
	)

References ObjexxFCL::abs(), corrections::score::dun10(), option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::path::scratch, and basic::options::OptionKeys::inout::dbms::user.

Referenced by get_res_data_ss().

Variable Documentation

TR

basic::Tracer TR("chrisk.byres_data") ( "chrisk.byres_data"  )

static

Referenced by byres_analysis().

TR_unsat

basic::Tracer TR_unsat("chrisk.unsat_calc") ( "chrisk.unsat_calc"  )

static