helix_assembly.cc File Reference

#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <devel/init.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzTransform.hh>
#include <numeric/xyz.io.hh>
#include <numeric/xyzVector.hh>
#include <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/util.hh>
#include <protocols/sic_dock/read_biounit.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/fixedsizearray1.hh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	HelixHit

Macros
#define	HELIX_ROT   99.3646
#define	HELIX_TRANS   1.55642

Typedefs
typedef numeric::xyzVector< core::Real >	Vec
typedef numeric::xyzMatrix< core::Real >	Mat
typedef numeric::xyzTransform< core::Real >	Xform

Functions
int	num_threads ()
int	thread_num ()
static std::string const	chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcba")
void	register_options ()
void	get_pose_chains (Pose const &pose, int nres, vector1< int > &chainlower, vector1< int > &chainupper, bool const)
Real	alignhelix (Pose &helix, Pose const &pose, int ir, int jr, int &cen)
Real	alignhelix (Pose &helix, Pose const &pose, int ir, int jr)
Vec	proj (Vec u, Vec v)
string	fname2pdbcode (string const &fname)
ostream &	operator<< (ostream &out, HelixHit const &h)
int	main (int argc, char *argv[])

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

Macro Definition Documentation

HELIX_ROT

#define HELIX_ROT   99.3646

HELIX_TRANS

#define HELIX_TRANS   1.55642

Typedef Documentation

Mat

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

Vec

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

Xform

typedef numeric::xyzTransform<core::Real> Xform

Function Documentation

alignhelix() [1/2]

Real alignhelix	(	Pose &	helix,
		Pose const &	pose,
		int	ir,
		int	jr
	)

References alignhelix(), and beta_nonlocal::pose.

alignhelix() [2/2]

Real alignhelix	(	Pose &	helix,
		Pose const &	pose,
		int	ir,
		int	jr,
		int &	cen
	)

References enumerate_junctions::int, create_a3b_hbs::k, natoms(), beta_nonlocal::pose, loops_kic::rms, and superimpose_pose().

Referenced by alignhelix(), and main().

chr_chains()

static std::string const chr_chains ( )

static

Referenced by main().

fname2pdbcode()

string fname2pdbcode

(

string const &

fname

)

References utility::file_basename(), PREcst::fname, kic_runner::pdb, erraser_analysis::pdb1, and utility_exit_with_message.

Referenced by main().

get_pose_chains()

void get_pose_chains	(	Pose const &	pose,
		int	nres,
		vector1< int > &	chainlower,
		vector1< int > &	chainupper,
		bool const
	)

References create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::TR, and utility_exit_with_message.

Referenced by main().

main()

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

References a, ObjexxFCL::abs(), alignhelix(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, argv, compute_difference::b, begin, utility::io::oc::cerr, predPRE::chain, chr_chains(), utility::io::oc::cout, basic::options::OptionKeys::msd::debug, PyMOL-Rosetta-relay-client::DEBUG, numeric::conversions::degrees(), numeric::xyzVector< T >::dot(), basic::options::OptionKeys::in::file::dssp, ObjexxFCL::format::F(), utility::file_basename(), fname2pdbcode(), get_pose_chains(), HELIX_ROT, HELIX_TRANS, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, basic::init(), enumerate_junctions::int, beta_nonlocal::jj, test_terpenes::lower, max(), basic::options::OptionKeys::mh::harvest::max_res, min(), numeric::xyzVector< T >::normalized(), basic::options::option, adapt_rotamers::ori, kic_runner::pdb, clean_pdb_keep_ligand::pdbcode, pdbs, beta_nonlocal::pose, proj(), projperp(), docking::R, numeric::xyzTransform< T >::R, numeric::conversions::radians(), register_options(), loops_kic::rms, numeric::xyzTransform< core::Real >::rot_deg(), numeric::rotation_axis(), basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, ObjexxFCL::string_of(), test_terpenes::upper, x, numeric::xyzVector< T >::x(), predPRE::y, numeric::xyzVector< T >::y(), predPRE::z, and numeric::xyzVector< T >::z().

num_threads()

int num_threads

(

)

operator<<()

ostream& operator<<	(	ostream &	out,
		HelixHit const &	h
	)

References h, test.T110_numeric::I, and erraser_single_res_analysis::out.

proj()

Vec proj	(	Vec	u,
		Vec	v
	)

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

Referenced by main().

register_options()

void register_options

(

)

References basic::options::OptionKeys::msd::debug, basic::options::OptionKeys::mh::harvest::max_res, and NEW_OPT.

Referenced by main().

thread_num()

int thread_num

(

)

Variable Documentation

TR

basic::Tracer TR("helix_assembly") ( "helix_assembly"  )

static