make_motif_tables.cc File Reference

#include <core/scoring/motif/motif_hash_stuff.hh>
#include <core/scoring/motif/util.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/keys/mh.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/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/motif/reference_frames.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.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/etable/Etable.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.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/xyz.io.hh>
#include <numeric/xyzVector.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/util.hh>
#include <protocols/sic_dock/read_biounit.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/constraint_movers/AddConstraintsToCurrentConformationMover.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/fixedsizearray1.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <numeric/HomogeneousTransform.hh>
#include <boost/foreach.hpp>

Typedefs
typedef numeric::xyzVector < core::Real >	Vec
typedef numeric::xyzMatrix < core::Real >	Mat
typedef numeric::xyzTransform < core::Real >	Xform
typedef utility::vector1 < core::id::AtomID >	AIDs

Functions
Size	sicdock_max_threads ()
Size	sicdock_num_threads ()
Size	sicdock_thread_num ()
void	print_motifs (std::ostream &out)
void	merge_motifs ()
template<class T >
T	sqr (T const &x)
void	harvest_scores ()
void	print_scores ()
bool	harvest_motifs_one (ResPairMotifs &motifs, string const &tag0, Pose const &pose, core::scoring::dssp::Dssp &dssp, Size const &ir, core::scoring::EnergyEdge const &edge, vector1< Real > const &, vector1< Real > const &bfactors, vector1< Real > const &, vector1< Real > const &nbrs, int &nbad, int &, int &nbadocc, int &, int &)
void	harvest_motifs ()
int	main (int argc, char *argv[])

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

Typedef Documentation

typedef utility::vector1<core::id::AtomID> AIDs

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

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

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

Function Documentation

void harvest_motifs ( )

inline

References utility::graph::Node::const_upper_edge_list_end(), basic::options::OptionKeys::in::file::dssp, basic::Tracer::Error, utility::file::file_exists(), basic::options::OptionKeys::mh::filter::filter_harvest, pyrosetta.tests.distributed.test_dask::format, utility::graph::Edge::get_node(), basic::options::OptionKeys::mh::harvest_motifs, harvest_motifs_one(), test.T110_Numeric::I, basic::options::OptionKeys::mh::harvest::max_res, basic::options::OptionKeys::mh::motif_out_file, basic::options::OptionKeys::mh::path::motifs, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::mh::filter::occupancy, basic::options::option, erraser_single_res_analysis::out, erraser_single_res_analysis::outfile, demo.D010_Pose_structure::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, tag, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

bool harvest_motifs_one ( ResPairMotifs &  motifs, string const &  tag0, Pose const &  pose, core::scoring::dssp::Dssp &  dssp, Size const &  ir, core::scoring::EnergyEdge const &  edge, vector1< Real > const &  , vector1< Real > const &  bfactors, vector1< Real > const &  , vector1< Real > const &  nbrs, int &  nbad, int &  , int &  nbadocc, int &  , int &    )

inline

References utility::io::oc::cout, utility::file::create_directory_recursive(), basic::options::OptionKeys::mh::harvest::dump, basic::options::OptionKeys::mh::filter::hb_bb_sc, basic::options::OptionKeys::mh::filter::hb_sc, basic::options::OptionKeys::out::file::o, basic::options::option, demo.D010_Pose_structure::pose, loops_kic::rms, ObjexxFCL::string_of(), tag, and utility_exit_with_message.

Referenced by harvest_motifs().

void harvest_scores ( )

inline

References basic::options::OptionKeys::mh::harvest::agg_with_max, utility::io::oc::cout, utility::file::create_directory_recursive(), basic::options::OptionKeys::mh::harvest::dump, basic::options::OptionKeys::cutoutdomain::end, ObjexxFCL::format::F(), basic::options::OptionKeys::mh::harvest_scores, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, test.T200_Scoring::ii, basic::options::key(), test.T110_Numeric::m, max(), min(), basic::options::OptionKeys::mh::harvest::min_bin_val, basic::options::OptionKeys::mh::motif_out_file, basic::options::OptionKeys::mh::filter::motif_type, basic::options::OptionKeys::mh::path::motifs, basic::options::OptionKeys::mh::harvest::multiplier, basic::options::option, basic::options::OptionKeys::score::fiber_diffraction::p, PATH, basic::options::OptionKeys::canonical_sampling::probabilities::sc, sicdock_max_threads(), sicdock_thread_num(), basic::options::OptionKeys::mh::harvest::smoothing_factor, sqr(), basic::options::TR, DRRAFTER::type, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, test.T850_SubClassing::v, basic::options::OptionKeys::mh::harvest::weight_by_energy, and revert_app::wt.

Referenced by main().

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

References utility::io::oc::cerr, utility::io::oc::cout, basic::options::OptionKeys::mh::dump_input_pdb, test.T009_Exceptions::e, basic::Tracer::Error, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::mh::harvest_motifs, harvest_motifs(), basic::options::OptionKeys::mh::harvest_scores, harvest_scores(), devel::init(), basic::options::OptionKeys::mh::harvest::max_res, basic::options::OptionKeys::mh::merge_motifs, merge_motifs(), utility::excn::Exception::msg(), basic::options::OptionKeys::mh::filter::occupancy, basic::options::option, demo.D010_Pose_structure::pose, basic::options::OptionKeys::mh::print_motifs, print_motifs(), basic::options::OptionKeys::mh::print_scores, print_scores(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

void merge_motifs ( )

inline

References test.T110_Numeric::m, basic::options::OptionKeys::mh::merge_motifs, basic::options::OptionKeys::mh::motif_out_file, basic::options::OptionKeys::mh::path::motifs, basic::options::option, basic::options::OptionKeys::score::fiber_diffraction::p, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

void print_motifs ( std::ostream &  out )

inline

References basic::options::OptionKeys::mh::path::motifs, basic::options::option, and basic::options::OptionKeys::mh::print_motifs.

Referenced by main().

void print_scores ( )

inline

References utility::io::oc::cout, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, basic::options::option, basic::options::OptionKeys::mh::print_scores, ObjexxFCL::read_binary(), and basic::options::TR.

Referenced by main().

Size sicdock_max_threads ( )

inline

Referenced by harvest_scores().

Size sicdock_num_threads ( )

inline

Size sicdock_thread_num ( )

inline

Referenced by harvest_scores().

template<class T >

T sqr

(

T const &

x

)

References numeric::crick_equations::x().

Referenced by numeric::expression_parser::DivideExpression::differentiate(), harvest_scores(), and numeric::linear_algebra::qzval().

Variable Documentation

basic::Tracer TR("motif_hash_util")

static