avrg_silent.cc File Reference

#include <basic/options/option.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <core/scoring/rms_util.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>
#include <ObjexxFCL/format.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>

Functions
utility::vector1< Real >	calculate_variations (utility::vector1< utility::vector1< Real > > const deviation)
void	smoothen_values (utility::vector1< Real > &CAvars, core::Size const winsize=9)
void	add_deviations (pose::Pose ref_pose, utility::vector1< Vector > &crds, utility::vector1< id::AtomID > const &atomid, utility::vector1< utility::vector1< Real > > &deviation)
utility::vector1< Vector >	get_avrgcrd (utility::vector1< utility::vector1< Vector > > const &crds, Size const n, utility::vector1< bool > const &exclid)
void	report (utility::vector1< Real > const &CAvars)
utility::vector1< Vector >	get_aligned_crd (pose::Pose pose_ref, pose::Pose pose, core::Real &rmsd, core::Real &Sd, utility::vector1< id::AtomID > const &atomid)
utility::vector1< id::AtomID >	get_atomindex (pose::Pose const &pose_ref)
pose::Pose	get_avrgpose (utility::vector1< Vector > const &avrgcrd, pose::Pose const &pose_ref, utility::vector1< Real > const &CAvar, utility::vector1< id::AtomID > const &atomid, utility::vector1< Size > &constres, Real const varcut)
bool	myComparison (const std::pair< Real, Size > &a, const std::pair< Real, Size > &b)
Size	get_close_and_lowE (utility::vector1< Real > const &scores, utility::vector1< bool > const &excluded)
void	relax_with_restraints_on_constres (pose::Pose &pose_avrg, utility::vector1< Size > const &constres, scoring::ScoreFunctionCOP sfxn)
bool	reavrg (utility::vector1< Vector > &avrgcrd, utility::vector1< utility::vector1< Vector > > const &crds, Real const dcut, bool const use_Sd, utility::vector1< Size > &exclid)
utility::vector1< Size >	get_exclid (utility::vector1< Real > const &dists, Real &dcut, bool dcut_dynamic)
void	calc_rmsf_and_avrg ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("app.public.comparative_modeling.avrg_silent")

Function Documentation

add_deviations()

void add_deviations	(	pose::Pose	ref_pose,
		utility::vector1< Vector > &	crds,
		utility::vector1< id::AtomID > const &	atomid,
		utility::vector1< utility::vector1< Real > > &	deviation
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, numeric::xyzVector< T >::distance(), and create_a3b_hbs::i.

Referenced by calc_rmsf_and_avrg().

calc_rmsf_and_avrg()

void calc_rmsf_and_avrg

(

)

References add_deviations(), begin, calculate_variations(), pyrosetta::create_score_function, get_aligned_crd(), get_atomindex(), get_avrgcrd(), get_avrgpose(), get_close_and_lowE(), get_exclid(), create_a3b_hbs::i, subloop_histogram::iterator, natoms(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, out::prefix(), reavrg(), relax_with_restraints_on_constres(), report(), average_rmsds::rmsd, legacy_score_vs_rmsd::scores, sfd, test.T120_core::sfxn, in::file::silent(), cm::similarity_cut(), smoothen_values(), extract_by_sidechain_sasa_score::tags, in::file::template_pdb(), TR, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by main().

calculate_variations()

utility::vector1< Real > calculate_variations

(

utility::vector1< utility::vector1< Real > > const

deviation

)

References create_a3b_hbs::i, and average_rmsds::rmsd.

Referenced by calc_rmsf_and_avrg().

get_aligned_crd()

utility::vector1< Vector > get_aligned_crd	(	pose::Pose	pose_ref,
		pose::Pose	pose,
		core::Real &	rmsd,
		core::Real &	Sd,
		utility::vector1< id::AtomID > const &	atomid
	)

References numeric::xyzVector< T >::distance_squared(), create_a3b_hbs::i, beta_nonlocal::pose, and average_rmsds::rmsd.

Referenced by calc_rmsf_and_avrg().

get_atomindex()

utility::vector1< id::AtomID > get_atomindex

(

pose::Pose const &

pose_ref

)

Referenced by calc_rmsf_and_avrg().

get_avrgcrd()

utility::vector1< Vector > get_avrgcrd	(	utility::vector1< utility::vector1< Vector > > const &	crds,
		Size const	n,
		utility::vector1< bool > const &	exclid
	)

References create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by calc_rmsf_and_avrg(), and reavrg().

get_avrgpose()

pose::Pose get_avrgpose	(	utility::vector1< Vector > const &	avrgcrd,
		pose::Pose const &	pose_ref,
		utility::vector1< Real > const &	CAvar,
		utility::vector1< id::AtomID > const &	atomid,
		utility::vector1< Size > &	constres,
		Real const	varcut
	)

References create_a3b_hbs::i, and TR.

Referenced by calc_rmsf_and_avrg().

get_close_and_lowE()

Size get_close_and_lowE	(	utility::vector1< Real > const &	scores,
		utility::vector1< bool > const &	excluded
	)

References create_a3b_hbs::i, myComparison(), legacy_score_vs_rmsd::scores, and TR.

Referenced by calc_rmsf_and_avrg().

get_exclid()

utility::vector1< Size > get_exclid	(	utility::vector1< Real > const &	dists,
		Real &	dcut,
		bool	dcut_dynamic
	)

References utility::io::oc::cout, create_a3b_hbs::i, option, in::file::template_pdb(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by calc_rmsf_and_avrg().

main()

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

References argv, calc_rmsf_and_avrg(), test.T009_Exceptions::e, and basic::init().

myComparison()

bool myComparison	(	const std::pair< Real, Size > &	a,
		const std::pair< Real, Size > &	b
	)

References a, and compute_difference::b.

Referenced by get_close_and_lowE().

reavrg()

bool reavrg	(	utility::vector1< Vector > &	avrgcrd,
		utility::vector1< utility::vector1< Vector > > const &	crds,
		Real const	dcut,
		bool const	use_Sd,
		utility::vector1< Size > &	exclid
	)

References get_avrgcrd(), create_a3b_hbs::i, average_rmsds::rmsd, and TR.

Referenced by calc_rmsf_and_avrg().

relax_with_restraints_on_constres()

void relax_with_restraints_on_constres	(	pose::Pose &	pose_avrg,
		utility::vector1< Size > const &	constres,
		scoring::ScoreFunctionCOP	sfxn
	)

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, basic::options::OptionKeys::abinitio::relax, test.T120_core::sfxn, and basic::options::OptionKeys::in::file::xyz.

Referenced by calc_rmsf_and_avrg().

report()

void report

(

utility::vector1< Real > const &

CAvars

)

References ObjexxFCL::format::F(), test.T110_numeric::I, and TR.

Referenced by calc_rmsf_and_avrg().

smoothen_values()

void smoothen_values	(	utility::vector1< Real > &	CAvars,
		core::Size const	winsize = 9
	)

References w.

Referenced by calc_rmsf_and_avrg().

Variable Documentation

TR

basic::Tracer TR("app.public.comparative_modeling.avrg_silent") ( "app.public.comparative_modeling.avrg_silent"  )

static

Referenced by calc_rmsf_and_avrg(), get_avrgpose(), get_close_and_lowE(), reavrg(), and report().