symdock_enum_3_1.cc File Reference

#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/sicdock.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/sasa.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <devel/init.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <core/scoring/methods/RG_Energy_Fast.hh>
#include <numeric/xyzTransform.hh>

Classes
struct	LMAX
struct	TCDock

Typedefs
typedef numeric::xyzVector< core::Real >	Vec
typedef numeric::xyzMatrix< core::Real >	Mat
typedef numeric::xyzVector< Real >	Vecf
typedef numeric::xyzMatrix< Real >	Matf

Functions
void	register_options ()
numeric::xyzTransform< core::Real > const	toXform (core::kinematics::Stub const &stub)
template<typename T >
T	sqr (T x)
Real	sigmoid (Real const &sqdist, Real const &start, Real const &stop)
void	dump_points_pdb (utility::vector1< Vecf > const &p, std::string fn)
void	dump_points_pdb (utility::vector1< Vecf > const &p, Vec t, std::string fn)
void	xform_pose (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres=1, Size eres=0)
void	xform_pose_rev (core::pose::Pose &pose, core::kinematics::Stub const &s)
void	trans_pose (Pose &pose, Vecf const &trans, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Mat const &rot, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Mat const &rot, Vecf const &cen, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Vecf const &axis, Real const &ang, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Vecf const &axis, Real const &ang, Vecf const &cen, Size start=1, Size end=0)
void	alignaxis (Pose &pose, Vecf newaxis, Vecf oldaxis, Vecf cen=Vecf(0, 0, 0))
Vec	projperp (Vec const &u, Vec const &v)
void	prune_cb_pairs (vector1< Vecf > &cba, vector1< Vecf > &cbb, vector1< Real > &wa_in, vector1< Real > &wb_in, Real CTD2)
int	neighbor_count (Pose const &pose, int ires, Real distance_threshold=10.0)
Real	brute_mindis (vector1< Vecf > const &pa, vector1< Vecf > const &pb, Vecf const ofst)
int	compareLMAX (const LMAX a, const LMAX b)
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef numeric::xyzMatrix<core::Real> Mat

Matf

typedef numeric::xyzMatrix<Real> Matf

Vec

typedef numeric::xyzVector<core::Real> Vec

Vecf

typedef numeric::xyzVector<Real> Vecf

Function Documentation

alignaxis()

void alignaxis	(	Pose &	pose,
		Vecf	newaxis,
		Vecf	oldaxis,
		Vecf	cen = Vecf(0,0,0)
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::xyzVector< T >::cross(), numeric::xyzVector< T >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< T >::normalize(), numeric::xyzVector< T >::normalized(), numeric::constants::f::pi, beta_nonlocal::pose, and rot_pose().

brute_mindis()

Real brute_mindis	(	vector1< Vecf > const &	pa,
		vector1< Vecf > const &	pb,
		Vecf const	ofst
	)

References create_a3b_hbs::i, create_a3b_hbs::j, and min().

compareLMAX()

int compareLMAX	(	const LMAX	a,
		const LMAX	b
	)

References a, and compute_difference::b.

Referenced by TCDock::run().

dump_points_pdb() [1/2]

void dump_points_pdb	(	utility::vector1< Vecf > const &	p,
		std::string	fn
	)

References ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, basic::options::OptionKeys::out::file::o, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, x, predPRE::y, and predPRE::z.

dump_points_pdb() [2/2]

void dump_points_pdb	(	utility::vector1< Vecf > const &	p,
		Vec	t,
		std::string	fn
	)

References ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, basic::options::OptionKeys::out::file::o, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, predPRE::t, x, predPRE::y, and predPRE::z.

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, TCDock::justone(), basic::options::OptionKeys::mh::harvest::max_res, basic::options::option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, pyrosetta.distributed.io::pose_from_file(), register_options(), TCDock::run(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

neighbor_count()

int neighbor_count	(	Pose const &	pose,
		int	ires,
		Real	distance_threshold = 10.0
	)

References build_jacobian::distance, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by TCDock::TCDock().

projperp()

Vec projperp ( Vec const &  u, Vec const &  v  )

inline

References numeric::projection_matrix(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by TCDock::dump_pdb(), and TCDock::min_termini_proj().

prune_cb_pairs()

void prune_cb_pairs	(	vector1< Vecf > &	cba,
		vector1< Vecf > &	cbb,
		vector1< Real > &	wa_in,
		vector1< Real > &	wb_in,
		Real	CTD2
	)

References a, compute_difference::b, and wa.

Referenced by TCDock::precompute_intra().

register_options()

void register_options

(

)

References basic::options::OptionKeys::msd::debug, execute::dry_run, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::mh::harvest::max_res, NEW_OPT, OPT, reverse(), and basic::options::OptionKeys::in::file::s.

Referenced by main().

rot_pose() [1/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Size	start = 1,
		Size	end = 0
	)

References end, natoms(), beta_nonlocal::pose, rot, and basic::options::OptionKeys::cutoutdomain::start.

rot_pose() [2/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Vecf const &	cen,
		Size	start = 1,
		Size	end = 0
	)

References end, beta_nonlocal::pose, rot, rot_pose(), basic::options::OptionKeys::cutoutdomain::start, and trans_pose().

rot_pose() [3/4]

void rot_pose	(	Pose &	pose,
		Vecf const &	axis,
		Real const &	ang,
		Size	start = 1,
		Size	end = 0
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, end, beta_nonlocal::pose, rot_pose(), numeric::rotation_matrix_degrees(), and basic::options::OptionKeys::cutoutdomain::start.

rot_pose() [4/4]

void rot_pose	(	Pose &	pose,
		Vecf const &	axis,
		Real const &	ang,
		Vecf const &	cen,
		Size	start = 1,
		Size	end = 0
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, end, beta_nonlocal::pose, rot_pose(), numeric::rotation_matrix_degrees(), and basic::options::OptionKeys::cutoutdomain::start.

sigmoid()

Real sigmoid ( Real const &  sqdist, Real const &  start, Real const &  stop  )

inline

References dist(), and basic::options::OptionKeys::cutoutdomain::start.

Referenced by TCDock::precompute_intra().

sqr()

template<typename T >

T sqr ( T  x )

inline

References x.

Referenced by TCDock::precompute_intra().

toXform()

numeric::xyzTransform<core::Real> const toXform ( core::kinematics::Stub const &  stub )

inline

References stub().

Referenced by TCDock::__dock_base__(), TCDock::dump_pdb(), and TCDock::run().

trans_pose()

void trans_pose	(	Pose &	pose,
		Vecf const &	trans,
		Size	start = 1,
		Size	end = 0
	)

References end, natoms(), beta_nonlocal::pose, basic::options::OptionKeys::cutoutdomain::start, and trans.

xform_pose()

void xform_pose	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s,
		Size	sres = 1,
		Size	eres = 0
	)

References natoms(), beta_nonlocal::pose, and docking::s.

Referenced by TCDock::dump_pdb().

xform_pose_rev()

void xform_pose_rev	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s
	)

References natoms(), beta_nonlocal::pose, and docking::s.

Variable Documentation

TR

basic::Tracer TR("symdock_enum") ( "symdock_enum"  )

static