cycgly_target.cc File Reference

#include <basic/basic.hh>
#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 <core/import_pose/import_pose.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/optimizeH.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.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/backrub/BackrubMover.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/minimization_packing/PackRotamersMover.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>
#include <time.h>

Classes
class	AbsFunc
class	CycBBMover
class	MoveThenFixH
class	MoveThenFixHMin

Typedefs
typedef unsigned long	BINTYPE

Functions
Real	mod360 (Real x)
void	bb_sample (Pose &pose, ScoreFunctionOP sf, Size niter)
void	BBG8T3A_sample (Pose &pose, ScoreFunctionOP sf, Size niter, Real temp=2.0)
void	minimize (Pose &pose, ScoreFunctionOP sf)
Pose	cyclic_perm (Pose const &orig, Size start, bool mirror=false)
Real	cyclic_all_atom_rmsd (Pose const &pose, Pose const &other)
Real	cyclic_ca_rmsd (Pose const &pose, Pose const &other)
void	cyclic_superimpose (Pose &move, Pose const &ref)
std::string	printbits (BINTYPE nn)
std::string	bin2string (BINTYPE bin, Size nres)
BINTYPE	makemask (Size n)
BINTYPE	mirror_bin (BINTYPE bin, Size nres)
BINTYPE	cyclic_unique_bin (BINTYPE bin, Size nres)
BINTYPE	pose2bin (core::pose::Pose const &pose)
Size	compute_num_bins (Size nres)
void	fixH (core::pose::Pose &pose)
void	cyclize_pose (core::pose::Pose &pose)
void	target_constraints (core::pose::Pose &pose, core::pose::Pose const &refpose, utility::vector1< utility::vector1< Size > > poseres, utility::vector1< utility::vector1< Size > > refres)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("cycgly_target")
BINTYPE const	BINBITS = 2
BINTYPE const	BINSIZE = 4

Typedef Documentation

BINTYPE

typedef unsigned long BINTYPE

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.

BBG8T3A_sample()

void BBG8T3A_sample	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	niter,
		Real	temp = 2.0
	)

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

bin2string()

std::string bin2string	(	BINTYPE	bin,
		Size	nres
	)

References create_a3b_hbs::bin, BINBITS, BINSIZE, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), create_a3b_hbs::nres, and docking::s.

compute_num_bins()

Size compute_num_bins

(

Size

nres

)

References create_a3b_hbs::bin, BINSIZE, cyclic_unique_bin(), create_a3b_hbs::nres, ObjexxFCL::pow(), and basic::options::TR.

cyclic_all_atom_rmsd()

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

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

cyclic_ca_rmsd()

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

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

cyclic_perm()

Pose cyclic_perm	(	Pose const &	orig,
		Size	start,
		bool	mirror = false
	)

References create_a3b_hbs::i, create_a3b_hbs::j, natoms(), beta_nonlocal::pose, basic::options::OptionKeys::cutoutdomain::start, and basic::options::OptionKeys::in::file::xyz.

Referenced by cyclic_all_atom_rmsd(), cyclic_ca_rmsd(), and cyclic_superimpose().

cyclic_superimpose()

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

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

Referenced by main().

cyclic_unique_bin()

BINTYPE cyclic_unique_bin	(	BINTYPE	bin,
		Size	nres
	)

References create_a3b_hbs::bin, BINBITS, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, makemask(), mirror_bin(), and create_a3b_hbs::nres.

Referenced by compute_num_bins(), and pose2bin().

cyclize_pose()

void cyclize_pose

(

core::pose::Pose &

pose

)

References docking::a1, docking::a2, docking::b1, docking::b2, basic::options::OptionKeys::constraints::constraints, fixH(), create_a3b_hbs::i, N, and beta_nonlocal::pose.

Referenced by main().

fixH()

void fixH

(

core::pose::Pose &

pose

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, h, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by MoveThenFixH::apply(), MoveThenFixHMin::apply(), and cyclize_pose().

main()

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

References docking::a1, docking::a2, argv, docking::b1, docking::b2, create_a3b_hbs::bin, basic::options::OptionKeys::constraints::constraints, pyrosetta::create_score_function, cyclic_superimpose(), cyclize_pose(), test.T009_Exceptions::e, ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, ObjexxFCL::format::I(), basic::init(), ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, N, create_a3b_hbs::nres, out::nstruct(), basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::option, erraser_single_res_analysis::out, beta_nonlocal::pose, pose2bin(), pyrosetta.io::poses_from_files(), basic::options::OptionKeys::remodel::rama, register_options(), in::file::s(), beta_sc_scan::seq, basic::options::OptionKeys::out::sf, sfd, out::file::silent(), subloop_histogram::size, ObjexxFCL::string_of(), tag, target_constraints(), erraser_analysis::temp, local::temperature, basic::options::OptionKeys::recces::temps, basic::options::TR, gaussian-sampling::trial, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

makemask()

BINTYPE makemask

(

Size

n

)

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

Referenced by cyclic_unique_bin().

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.

mirror_bin()

BINTYPE mirror_bin	(	BINTYPE	bin,
		Size	nres
	)

References create_a3b_hbs::bin, BINBITS, BINSIZE, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::nres, and numeric::constants::f::two.

Referenced by cyclic_unique_bin().

mod360()

Real mod360

(

Real

x

)

References x.

pose2bin()

BINTYPE pose2bin

(

core::pose::Pose const &

pose

)

References create_a3b_hbs::bin, BINBITS, BINSIZE, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, cyclic_unique_bin(), numeric::dihedral_degrees(), create_a3b_hbs::i, enumerate_junctions::int, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, oop_conformations::phi, beta_nonlocal::pose, oop_conformations::psi, basic::unsigned_periodic_range(), and basic::options::OptionKeys::in::file::xyz.

Referenced by main().

printbits()

std::string printbits

(

BINTYPE

nn

)

References create_a3b_hbs::i, basic::options::OptionKeys::cm::nn, and docking::s.

target_constraints()

void target_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	refpose,
		utility::vector1< utility::vector1< Size > >	poseres,
		utility::vector1< utility::vector1< Size > >	refres
	)

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::pose, runtime_assert, subloop_histogram::size, and basic::options::TR.

Referenced by main().

Variable Documentation

BINBITS

BINTYPE const BINBITS = 2

Referenced by bin2string(), cyclic_unique_bin(), mirror_bin(), and pose2bin().

BINSIZE

BINTYPE const BINSIZE = 4

Referenced by bin2string(), compute_num_bins(), mirror_bin(), and pose2bin().

TR

basic::Tracer TR("cycgly_target") ( "cycgly_target"  )

static