CycDsulf.cc File Reference

#include <numeric/constants.hh>
#include <core/pose/Pose.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <utility/graph/Graph.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/optimization/MinimizerMap.hh>
#include <core/scoring/Energies.fwd.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <basic/Tracer.hh>
#include <devel/init.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/util.hh>
#include <protocols/relax/loop/LoopRelaxMover.fwd.hh>
#include <protocols/relax/loop/LoopRelaxMover.hh>
#include <core/kinematics/FoldTree.hh>
#include <numeric/random/random.hh>
#include <protocols/loops/Loops.hh>
#include <core/chemical/VariantType.hh>
#include <core/pose/disulfide_util.hh>
#include <protocols/loops/LoopRelaxMover.fwd.hh>
#include <core/scoring/rms_util.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loop.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <core/types.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/Edge.fwd.hh>
#include <core/conformation/Conformation.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/basic.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/disulfides/FullatomDisulfidePotential.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <core/io/raw_data/ScoreFileData.hh>
#include <ObjexxFCL/format.hh>
#include <sstream>
#include <fstream>
#include <iostream>
#include <algorithm>
#include <string>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>

Namespaces
	ss_loop_builder

Macros
#define	INF   99999999
#define	CYSPOS   2

Functions
std::string	int2string (int n)
void	modelSSLoop (Size startCys, Size endCys, pose::Pose &workpose, core::scoring::ScoreFunctionOP scorefxn)
void	printEnergies (pose::Pose &workpose)
void	rotateUntilCys (pose::Pose &workpose, Size untilCys)
void	updateSSAtoms (pose::Pose &workpose, Size upNum, utility::vector1_int &vec, Size pepsize)
core::scoring::constraints::ConstraintSetOP	createConstraintSet (pose::Pose &workpose, utility::vector1< std::pair< Size, Size > > &dss)
void	printScoreTermsPose (pose::Pose &workpose, std::string filename)
core::scoring::constraints::ConstraintSetOP	createMinimizationConstraint (pose::Pose &workpose)
void	deleteEdge (core::scoring::EnergyGraph &g)
core::scoring::constraints::ConstraintSetOP	createDihedralConstraint (pose::Pose &workpose)
void	performMinimization (pose::Pose &workpose, core::scoring::ScoreFunctionOP scorefxn)
void	packRotamers (pose::Pose &workpose, core::scoring::ScoreFunctionOP scorefxn)
void	writeScores (pose::Pose &workpose, pose::Pose &nativePose, const std::string filename, Real score)
int	main (int argc, char **argv)

Variables
basic::options::IntegerOptionKey	ss_loop_builder::start_cys ("ss_loop_builder:start")
basic::options::IntegerOptionKey	ss_loop_builder::end_cys ("ss_loop_builder:end")
basic::options::IntegerOptionKey	ss_loop_builder::ncycles ("ss_loop_builder:ncycles")

Macro Definition Documentation

CYSPOS

#define CYSPOS   2

INF

#define INF   99999999

Function Documentation

createConstraintSet()

core::scoring::constraints::ConstraintSetOP createConstraintSet	(	pose::Pose &	workpose,
		utility::vector1< std::pair< Size, Size > > &	dss
	)

References create_a3b_hbs::i.

createDihedralConstraint()

core::scoring::constraints::ConstraintSetOP createDihedralConstraint

(

pose::Pose &

workpose

)

Referenced by main().

createMinimizationConstraint()

core::scoring::constraints::ConstraintSetOP createMinimizationConstraint

(

pose::Pose &

workpose

)

References dist().

deleteEdge()

void deleteEdge

(

core::scoring::EnergyGraph &

g

)

References g().

int2string()

std::string int2string

(

int

n

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and str().

Referenced by main().

main()

int main	(	int	argc,
		char **	argv
	)

References argv, createDihedralConstraint(), test.T009_Exceptions::e, create_a3b_hbs::first, out::file::fullatom(), create_a3b_hbs::i, basic::init(), int2string(), modelSSLoop(), local::nstruct, out::nstruct(), option, packRotamers(), performMinimization(), pyrosetta.distributed.io::pose_from_file, rotateUntilCys(), docking::s, oop_conformations::scorefxn, basic::options::start_file(), TR, updateSSAtoms(), and writeScores().

modelSSLoop()

void modelSSLoop	(	Size	startCys,
		Size	endCys,
		pose::Pose &	workpose,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References utility::io::oc::cout, create_a3b_hbs::i, internal_coordinates::loop, and oop_conformations::scorefxn.

Referenced by main().

packRotamers()

void packRotamers	(	pose::Pose &	workpose,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References utility::io::oc::cout, oop_conformations::scorefxn, and vancomycin::task.

Referenced by main().

performMinimization()

void performMinimization	(	pose::Pose &	workpose,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References utility::io::oc::cout, and oop_conformations::scorefxn.

Referenced by main().

printEnergies()

void printEnergies

(

pose::Pose &

workpose

)

References utility::io::oc::cout, and create_a3b_hbs::i.

printScoreTermsPose()

void printScoreTermsPose	(	pose::Pose &	workpose,
		std::string	filename
	)

References utility::io::oc::cout, lactamize::filename, and sfd.

rotateUntilCys()

void rotateUntilCys	(	pose::Pose &	workpose,
		Size	untilCys
	)

References demo.D060_Folding::counter, utility::io::oc::cout, create_a3b_hbs::j, and pna::resi.

Referenced by main().

updateSSAtoms()

void updateSSAtoms	(	pose::Pose &	workpose,
		Size	upNum,
		utility::vector1_int &	vec,
		Size	pepsize
	)

References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and vec().

Referenced by main().

writeScores()

void writeScores	(	pose::Pose &	workpose,
		pose::Pose &	nativePose,
		const std::string	filename,
		Real	score
	)

References job_manager::app, lactamize::filename, and average_rmsds::rmsd.

Referenced by main().