cycgly_canonical.cc File Reference

#include <basic/options/after_opts.hh>
#include <basic/options/keys/backrub.OptionKeys.gen.hh>
#include <basic/options/keys/bbg.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/cyclic.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/mc.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/DOF_ID.hh>
#include <devel/init.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/MPIFileBufJobDistributor.hh>
#include <protocols/jd2/NoOutputJobOutputter.hh>
#include <protocols/simple_moves/BBGaussianMover.hh>
#include <protocols/canonical_sampling/CanonicalSamplingMover.fwd.hh>
#include <protocols/canonical_sampling/CanonicalSamplingMover.hh>
#include <protocols/moves/mc_convergence_checks/MPIBPool_ConvergenceCheck.hh>
#include <protocols/moves/mc_convergence_checks/MPIHPool_ConvergenceCheck.hh>
#include <protocols/moves/mc_convergence_checks/MPIPool_ConvergenceCheck.hh>
#include <protocols/moves/mc_convergence_checks/Pool_ConvergenceCheck.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMCMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/toolbox/SwitchResidueTypeSet.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>

Classes
class	AbsFunc
class	CycBBMover

Functions
Real	mod360 (Real x)
void	bb_sample (Pose &pose, ScoreFunctionOP sf, Size niter)
void	minimize (Pose &pose, ScoreFunctionOP sf)
Pose	cyclic_perm (Pose const &orig, Size start)
Real	cyclic_all_atom_rms (Pose const &pose, Pose const &other)
void	cyclic_superimpose (Pose &move, Pose const &ref)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("cycgly_canonical")

Function Documentation

bb_sample()

void bb_sample	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	niter
	)

References basic::options::OptionKeys::MonteCarlo::MonteCarlo, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by main().

cyclic_all_atom_rms()

Real cyclic_all_atom_rms	(	Pose const &	pose,
		Pose const &	other
	)

References cyclic_perm(), create_a3b_hbs::i, beta_nonlocal::pose, and create_a3b_hbs::r.

cyclic_perm()

Pose cyclic_perm	(	Pose const &	orig,
		Size	start
	)

References create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by cyclic_all_atom_rms(), and cyclic_superimpose().

cyclic_superimpose()

void cyclic_superimpose	(	Pose &	move,
		Pose const &	ref
	)

References cyclic_perm(), create_a3b_hbs::i, basic::options::OptionKeys::stepwise::move, and create_a3b_hbs::r.

main()

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

References docking::a1, docking::a2, argv, docking::b1, docking::b2, bb_sample(), basic::options::OptionKeys::constraints::constraints, pyrosetta::create_score_function, test.T009_Exceptions::e, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves_ntrials, create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::canonical_sampling::probabilities::localbb, minimize(), basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_bcast, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_sync_pools, NEW_OPT, basic::options::OptionKeys::canonical_sampling::probabilities::no_jd2_output, create_a3b_hbs::nres, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::remodel::rama, register_options(), basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent, basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_withinrot, beta_sc_scan::seq, basic::options::OptionKeys::out::sf, sfd, test.T120_core::sfxn, vancomycin::task, basic::options::TR, numeric::random::uniform(), and basic::options::OptionKeys::canonical_sampling::probabilities::use_hierarchical_clustering.

minimize()

void minimize	(	Pose &	pose,
		ScoreFunctionOP	sf
	)

References test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by main().

mod360()

Real mod360

(

Real

x

)

References x.

Variable Documentation

TR

basic::Tracer TR("cycgly_canonical") ( "cycgly_canonical"  )

static