tcdock.cc File Reference

#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/scores/MotifHashRigidScore.hh>
#include <protocols/sic_dock/util.hh>
#include <protocols/sic_dock/types.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/mh.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/conformation/symmetry/SymmetricConformation.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/io/izstream.hh>
#include <utility/string_util.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.hh>
#include <core/scoring/methods/RG_Energy_Fast.hh>
#include <numeric/xyzTransform.hh>
#include <basic/database/open.hh>
#include <protocols/sic_dock/xyzStripeHashPose.hh>

Classes
class	Arch
class	ArchT32
class	ArchT33
class	ArchO32
class	ArchO42
class	ArchO43
class	ArchI32
class	ArchI52
class	ArchI53
class	ArchP6_32
class	ArchP6m_32d
class	ArchP4_42
class	ArchP4m_42d
class	ArchP4g_42d
struct	LMAX
struct	TCDock

Typedefs
typedef utility::pointer::shared_ptr< Arch >	ArchOP
typedef utility::pointer::shared_ptr< Arch const >	ArchCOP

Functions
void	initsyms ()
void	register_options ()
void	prune_cb_pairs (vector1< Vec > &cba, vector1< Vec > &cbb, vector1< Real > &wa_in, vector1< Real > &wb_in, Real CTD2)
int	compareLMAX (const LMAX a, const LMAX b)
Real	sphere_coverage (vector1< Vec > points, vector1< Xform > const &xforms)
int	main (int argc, char *argv[])

Variables
static numeric::Xforms	SYMOCT
static numeric::Xforms	SYMTET
static numeric::Xforms	SYMICS
static basic::Tracer	TR ("symdock_enum")

Typedef Documentation

ArchCOP

typedef utility::pointer::shared_ptr<Arch const> ArchCOP

ArchOP

typedef utility::pointer::shared_ptr<Arch > ArchOP

Function Documentation

compareLMAX()

int compareLMAX	(	const LMAX	a,
		const LMAX	b
	)

References a, and compute_difference::b.

Referenced by TCDock::run().

initsyms()

void initsyms

(

)

References numeric::xyzMatrix< Real >::rows(), SYMICS, SYMOCT, and SYMTET.

Referenced by main().

main()

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

References argv, utility::io::oc::cerr, utility::io::oc::cout, utility::file::create_directory_recursive(), test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), initsyms(), create_a3b_hbs::j, basic::options::OptionKeys::mh::harvest::max_res, out::file::o(), basic::options::option, option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, pyrosetta.distributed.io::pose_from_file, register_options(), TCDock::run(), TR, utility_exit_with_message, and basic::Tracer::Warning.

prune_cb_pairs()

void prune_cb_pairs	(	vector1< Vec > &	cba,
		vector1< Vec > &	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::ddg::dump_pdbs, basic::options::OptionKeys::mh::harvest::max_res, NEW_OPT, OPT, reverse(), and in::file::s().

Referenced by main().

sphere_coverage()

Real sphere_coverage	(	vector1< Vec >	points,
		vector1< Xform > const &	xforms
	)

References utility::io::izstream::close(), gpu_set_args::done, create_a3b_hbs::i, basic::database::open(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, docking::s, x, predPRE::y, and predPRE::z.

Referenced by TCDock::dump_top_hits().

Variable Documentation

SYMICS

numeric::Xforms SYMICS

static

Referenced by TCDock::dump_top_hits(), and initsyms().

SYMOCT

numeric::Xforms SYMOCT

static

Referenced by TCDock::dump_top_hits(), and initsyms().

SYMTET

numeric::Xforms SYMTET

static

Referenced by TCDock::dump_top_hits(), and initsyms().

TR

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

static

Referenced by TCDock::dump_top_hits(), TCDock::gather_hits(), TCDock::init(), and main().