dxdock.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/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.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/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 <set>
#include <apps/pilot/will/sicfast.ihh>

Classes
struct	Hit

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

Functions
void	register_options ()
void	dump_points_pdb (vector1< Vec > &p, string fn, vector1< int > const &d, vector1< int > const &a)
void	get_avail_don_acc (Pose &pose, std::set< Size > &actdon, std::set< Size > &actacc)
bool	cmp (Hit i, Hit j)
void	dock (Pose &init, std::string const &fn, vector1< Vec > const &ssamp)
int	main (int argc, char *argv[])

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

Typedef Documentation

Matf

typedef numeric::xyzMatrix<Real> Matf

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

cmp()

bool cmp	(	Hit	i,
		Hit	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by dock().

dock()

void dock	(	Pose &	init,
		std::string const &	fn,
		vector1< Vec > const &	ssamp
	)

References begin, cmp(), utility::io::oc::cout, end, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_avail_don_acc(), h, has, create_a3b_hbs::i, basic::init(), test.T008_Serialization::iss, min(), 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(), docking::s, sicfast(), subloop_histogram::size, str(), basic::options::OptionKeys::symmetry::symmetry_definition, predPRE::t, tag, tan, basic::options::TR, trans_pose(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

dump_points_pdb()

void dump_points_pdb	(	vector1< Vec > &	p,
		string	fn,
		vector1< int > const &	d,
		vector1< int > const &	a
	)

References a, ObjexxFCL::format::F(), detail::find(), 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.

get_avail_don_acc()

void get_avail_don_acc	(	Pose &	pose,
		std::set< Size > &	actdon,
		std::set< Size > &	actacc
	)

References basic::options::OptionKeys::in::file::dssp, create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by dock().

main()

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

References argv, utility::io::izstream::close(), dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, basic::init(), NSS, basic::database::open(), basic::options::option, pyrosetta.distributed.io::pose_from_file, register_options(), basic::options::OptionKeys::in::file::s, subloop_histogram::size, str(), basic::options::TR, trans_pose(), x, predPRE::y, and predPRE::z.

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().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("dxdock") ( "dxdock"  )

static