nisod.cc File Reference

#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/FragSet.hh>
#include <devel/init.hh>
#include <basic/database/open.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <basic/Tracer.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/abinitio/FragmentMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>

Classes
struct	CCParam

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef utility::vector1< Vec >	Vecs
typedef numeric::xyzMatrix< Real >	Mat

Functions
Vec	helix_axis (core::pose::Pose const &pose)
Vec	center_of_mass (core::pose::Pose const &pose, Size nres=0)
void	trans_pose (core::pose::Pose &pose, Vec const &trans)
void	rot_pose (core::pose::Pose &pose, Mat const &rot)
void	rot_pose (core::pose::Pose &pose, Mat const &rot, Vec const &cen)
void	rot_pose (core::pose::Pose &pose, Vec const &axis, Real const &ang)
void	rot_pose (core::pose::Pose &pose, Vec const &axis, Real const &ang, Vec const &cen)
core::pose::Pose	make_helix (std::string seq)
core::conformation::symmetry::SymmData	make_symm_data (core::pose::Pose const &pose, core::Real rot, core::Real trans, core::Size n)
core::pose::Pose	make_coiled_coil (CCParam &p)
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

center_of_mass()

Vec center_of_mass ( core::pose::Pose const &  pose, Size  nres = 0  )

inline

References count, natoms(), create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by make_helix().

helix_axis()

Vec helix_axis

(

core::pose::Pose const &

pose

)

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

Referenced by make_helix().

main()

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

References argv, basic::options::OptionKeys::cp::cp, test.T009_Exceptions::e, basic::init(), make_coiled_coil(), beta_nonlocal::pose, and numeric::random::uniform().

make_coiled_coil()

core::pose::Pose make_coiled_coil

(

CCParam &

p

)

References create_a3b_hbs::i, make_helix(), make_symm_data(), natoms(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, rot_pose(), beta_sc_scan::seq, basic::options::OptionKeys::symmetry::symmetry, trans_pose(), and predPRE::z.

Referenced by main().

make_helix()

core::pose::Pose make_helix

(

std::string

seq

)

References center_of_mass(), utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, helix_axis(), create_a3b_hbs::i, beta_sc_scan::name3, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, rot, rot_pose(), numeric::rotation_matrix_radians(), beta_sc_scan::seq, trans_pose(), and predPRE::z.

Referenced by make_coiled_coil().

make_symm_data()

core::conformation::symmetry::SymmData make_symm_data	(	core::pose::Pose const &	pose,
		core::Real	rot,
		core::Real	trans,
		core::Size	n
	)

References basic::options::OptionKeys::AnchoredDesign::anchor, create_a3b_hbs::i, test.T008_Serialization::iss, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, rot, docking::s, ObjexxFCL::string_of(), and trans.

Referenced by make_coiled_coil().

rot_pose() [1/4]

void rot_pose ( core::pose::Pose &  pose, Mat const &  rot  )

inline

References natoms(), beta_nonlocal::pose, and rot.

Referenced by make_coiled_coil(), make_helix(), and rot_pose().

rot_pose() [2/4]

void rot_pose ( core::pose::Pose &  pose, Mat const &  rot, Vec const &  cen  )

inline

References beta_nonlocal::pose, rot, rot_pose(), and trans_pose().

rot_pose() [3/4]

void rot_pose ( core::pose::Pose &  pose, Vec const &  axis, Real const &  ang  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

rot_pose() [4/4]

void rot_pose ( core::pose::Pose &  pose, Vec const &  axis, Real const &  ang, Vec const &  cen  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

trans_pose()

void trans_pose ( core::pose::Pose &  pose, Vec const &  trans  )

inline

References natoms(), beta_nonlocal::pose, and trans.

Referenced by make_coiled_coil(), make_helix(), and rot_pose().

Variable Documentation

TR

basic::Tracer TR("dubois") ( "dubois"  )

static

Referenced by CCParam::show().