rescore_i213.cc File Reference

#include <basic/database/open.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/options/keys/holes.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/packing/HolesParams.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <fstream>
#include <iostream>
#include <math.h>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/docking/util.hh>
#include <protocols/jobdist/not_universal_main.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <string>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <protocols/protein_interface_design/movers/ddG.hh>
#include <protocols/pose_metric_calculators/RotamerBoltzCalculator.hh>
#include <protocols/calc_taskop_filters/RotamerBoltzmannWeight.hh>
#include <core/pack/task/ResfileReader.hh>

Typedefs
typedef vector1< Size >	Sizes

Functions
void	new_sc (core::pose::Pose &pose, Real &int_area, Real &sc)
utility::vector1< Real >	sidechain_sasa (Pose const &pose, Real probe_radius)
Real	average_degree (Pose const &pose, vector1< Size > mutalyze_pos, Real distance_threshold=10.0)
vector1< Size >	get_des_pos (core::pose::Pose &pose_for_design)
void	rescore (core::pose::Pose &pose, string tag)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("rescore_i213")
core::io::silent::SilentFileData	sfd

Typedef Documentation

Sizes

typedef vector1<Size> Sizes

Function Documentation

average_degree()

Real average_degree	(	Pose const &	pose,
		vector1< Size >	mutalyze_pos,
		Real	distance_threshold = 10.0
	)

References count_neighbors(), build_jacobian::distance, create_a3b_hbs::i, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by rescore().

get_des_pos()

vector1<Size> get_des_pos

(

core::pose::Pose &

pose_for_design

)

References basic::options::OptionKeys::matdes::design::contact_dist, pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, and basic::options::OptionKeys::out::sf.

Referenced by rescore().

main()

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

References argv, test.T009_Exceptions::e, PREcst::fname, basic::init(), basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, pyrosetta.distributed.io::pose_from_file(), rescore(), basic::options::OptionKeys::in::file::s, and subloop_histogram::size.

new_sc()

void new_sc	(	core::pose::Pose &	pose,
		Real &	int_area,
		Real &	sc
	)

References create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::OptionKeys::canonical_sampling::probabilities::sc.

Referenced by rescore().

rescore()

void rescore	(	core::pose::Pose &	pose,
		string	tag
	)

References average_degree(), get_des_pos(), create_a3b_hbs::i, new_sc(), basic::options::OptionKeys::out::file::o, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::canonical_sampling::probabilities::sc, sfd, basic::options::OptionKeys::out::file::silent, and tag.

Referenced by main(), and my_main().

sidechain_sasa()

utility::vector1<Real> sidechain_sasa	(	Pose const &	pose,
		Real	probe_radius
	)

References basic::options::OptionKeys::edensity::atom_mask, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and bur_nodon_tyr::probe_radius.

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

Referenced by rescore().

TR

basic::Tracer TR("rescore_i213") ( "rescore_i213"  )

static