cxdock.cc File Reference

#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/option_macros.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <numeric/conversions.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/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <utility/excn/Exceptions.hh>
#include <apps/pilot/will/sicfast.ihh>

Classes
class	SphereSampler
struct	Hit

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat

Functions
void	register_options ()
void	dump_points_pdb (vector1< Vec > const &p, string fn)
void	dump_points_pdb_contacts (vector1< Vec > const &p, string fn)
utility::vector1< core::Real >	get_ang_samp ()
void	dock (Pose const &init, std::string const &fn, SphereSampler const &ssamp)
void	testone (vector1< Vec > const &bb0, vector1< Vec > const &cb0, int i, int j, int k)
void	visualize (Pose const &init)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("cxdock")
static core::io::silent::SilentFileData	sfd

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

dock()

void dock	(	Pose const &	init,
		std::string const &	fn,
		SphereSampler const &	ssamp
	)

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, count, dump_points_pdb_contacts(), ObjexxFCL::format::F(), get_ang_samp(), h, SphereSampler::half_begin(), SphereSampler::half_end(), SphereSampler::half_w_nbr(), SphereSampler::half_w_nbr_size(), has, create_a3b_hbs::i, basic::init(), test.T008_Serialization::iss, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, max(), SphereSampler::nbr_begin(), SphereSampler::nbr_end(), basic::options::OptionKeys::out::file::o, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::constants::d::pi, docking::R, rot, rot_pose(), numeric::rotation_matrix_degrees(), sicfast(), SphereSampler::size(), str(), basic::options::OptionKeys::symmetry::symmetry_definition, predPRE::t, tan, basic::options::TR, trans_pose(), and utility_exit_with_message.

Referenced by main().

dump_points_pdb()

void dump_points_pdb	(	vector1< Vec > const &	p,
		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.

Referenced by testone().

dump_points_pdb_contacts()

void dump_points_pdb_contacts	(	vector1< Vec > const &	p,
		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.

Referenced by dock().

get_ang_samp()

utility::vector1<core::Real> get_ang_samp

(

)

References create_a3b_hbs::i, enumerate_junctions::int, basic::options::option, numeric::constants::d::pi, pi, round(), and basic::options::TR.

Referenced by dock().

main()

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

References argv, dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::init(), NSS, basic::options::option, pyrosetta.distributed.io::pose_from_file, register_options(), basic::options::OptionKeys::in::file::s, subloop_histogram::size, basic::options::TR, and trans_pose().

register_options()

void register_options

(

)

References basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::sicdock::contact_dis, NEW_OPT, OPT, and basic::options::OptionKeys::in::file::s.

Referenced by main().

testone()

void testone	(	vector1< Vec > const &	bb0,
		vector1< Vec > const &	cb0,
		int	i,
		int	j,
		int	k
	)

References numeric::xyzVector< T >::cross(), dump_points_pdb(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, N, docking::R, numeric::rotation_matrix_degrees(), sicfast(), test_mm_lj::step, str(), predPRE::t, and basic::options::TR.

visualize()

void visualize

(

Pose const &

init

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, utility::io::oc::cerr, utility::io::oc::cout, numeric::xyzVector< T >::cross(), ObjexxFCL::format::F(), utility::io::ocstream::flush(), basic::options::OptionKeys::docking::ligand::grid::grid, has, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, create_a3b_hbs::k, max(), min(), N, docking::R, numeric::rotation_matrix_degrees(), sicfast(), test_mm_lj::step, predPRE::t, and basic::options::TR.

Referenced by MembraneViewMover::apply(), MPFoldingMover::apply(), mp::visualize::embedding(), main(), mp::visualize::plane_radius(), mp::visualize::spacing(), mp::visualize::thickness(), mp::visualize::visualize(), and mp::visualize::width().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("cxdock") ( "cxdock"  )

static