scheme_v0_score.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/sicdock.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <utility/io/ozstream.hh>
#include <sstream>
#include <basic/options/option_macros.hh>
#include <utility/io/izstream.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <utility/file/file_sys_util.hh>
#include <core/scoring/motif/motif_hash_stuff.hh>
#include <core/pose/motif/reference_frames.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/kinematics/MoveMap.hh>

Classes
struct	ScoreBreakdown
struct	DesignOpts

Typedefs
typedef numeric::xyzTransform< Real >	Xform

Functions
void	register_options ()
Real	compute_bb_motif_score (char const &ss1, char const &ss2, char const &aa1, char const &aa2, Xform const &x)
Real	motif_score_pose (core::pose::Pose const &pose, bool interchain_only=true)
void	get_motif_hits_common (core::pose::Pose const &pose, core::scoring::motif::MotifHits &hits)
core::pack::task::PackerTaskOP	make_motif_task (core::pose::Pose &pose)
void	design_pose_motifs_only (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP sf, DesignOpts opts)
ScoreBreakdown	extract_scores (core::pose::Pose const &pose, core::scoring::EnergyMap const &weights)
void	centroid_scores_destroys_pose (core::pose::Pose &pose, ScoreBreakdown &cenvalsc, ScoreBreakdown &cenleusc, ScoreBreakdown &cencheatsc)
void	scheme_score ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("scheme_score")
bool	DUMP = false

Typedef Documentation

Xform

typedef numeric::xyzTransform<Real> Xform

Function Documentation

centroid_scores_destroys_pose()

void centroid_scores_destroys_pose	(	core::pose::Pose &	pose,
		ScoreBreakdown &	cenvalsc,
		ScoreBreakdown &	cenleusc,
		ScoreBreakdown &	cencheatsc
	)

References pyrosetta::create_score_function, DUMP, extract_scores(), create_a3b_hbs::nres, and beta_nonlocal::pose.

compute_bb_motif_score()

Real compute_bb_motif_score	(	char const &	ss1,
		char const &	ss2,
		char const &	aa1,
		char const &	aa2,
		Xform const &	x
	)

References basic::options::OptionKeys::mh::match::aa1, basic::options::OptionKeys::mh::match::aa2, numeric::log(), basic::options::option, basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::match::ss2, and x.

Referenced by motif_score_pose().

design_pose_motifs_only()

void design_pose_motifs_only	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	sf,
		DesignOpts	opts
	)

References test.T009_Exceptions::e, make_motif_task(), DesignOpts::minimize_bb, DesignOpts::minimize_chi, DesignOpts::minimize_rb, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by scheme_score().

extract_scores()

ScoreBreakdown extract_scores	(	core::pose::Pose const &	pose,
		core::scoring::EnergyMap const &	weights
	)

References utility::graph::Node::const_upper_edge_list_end(), utility::graph::Edge::get_node(), create_a3b_hbs::nres, beta_nonlocal::pose, legacy_score_vs_rmsd::scores, basic::options::OptionKeys::frags::scoring::scoring, utility_exit_with_message, and weights().

Referenced by centroid_scores_destroys_pose(), dostuff(), get_sc(), and main().

get_motif_hits_common()

void get_motif_hits_common	(	core::pose::Pose const &	pose,
		core::scoring::motif::MotifHits &	hits
	)

References beta_nonlocal::pose, and cache_trajectory::query.

Referenced by make_motif_task().

main()

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

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

make_motif_task()

core::pack::task::PackerTaskOP make_motif_task

(

core::pose::Pose &

pose

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, CREATE_EXCEPTION, DUMP, test.T009_Exceptions::e, get_motif_hits_common(), beta_nonlocal::pose, basic::options::OptionKeys::packing::resfile, vancomycin::task, basic::options::TR, and utility_exit_with_message.

Referenced by design_pose_motifs_only().

motif_score_pose()

Real motif_score_pose	(	core::pose::Pose const &	pose,
		bool	interchain_only = true
	)

References compute_bb_motif_score(), numeric::xyzVector< T >::distance_squared(), numeric::xyzTransform< T >::inverse(), beta_nonlocal::pose, create_a3b_hbs::score, and numeric::xyzTransform< T >::t.

Referenced by scheme_score().

register_options()

void register_options

(

)

References basic::options::OptionKeys::msd::debug, revert_app::design, NEW_OPT, and execute::overwrite.

Referenced by main().

scheme_score()

void scheme_score

(

)

References utility::io::izstream::close(), utility::io::oc::cout, basic::options::OptionKeys::msd::debug, revert_app::design, design_pose_motifs_only(), DUMP, utility::file::file_exists(), basic::options::OptionKeys::in::file::l, DesignOpts::minimize_chi, motif_score_pose(), basic::options::option, execute::overwrite, closure_error::path, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, runtime_assert, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::sf, subloop_histogram::size, basic::options::OptionKeys::symmetry::symmetry_definition, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

Variable Documentation

DUMP

bool DUMP = false

Referenced by centroid_scores_destroys_pose(), make_motif_task(), and scheme_score().

TR

basic::Tracer TR("scheme_score") ( "scheme_score"  )

static