density_grid.cc File Reference

#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <devel/init.hh>
#include <basic/database/open.hh>
#include <basic/prof.hh>
#include <core/sequence/util.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/id/NamedAtomID.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <numeric/kdtree/util.hh>
#include <numeric/kdtree/KDTree.hh>
#include <numeric/kdtree/KDPoint.hh>
#include <numeric/kdtree/KDPointList.hh>
#include <numeric/kdtree/WrappedReal.hh>
#include <apps/pilot/james/james_util.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/james.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>

Typedefs
typedef WrappedPrimitive< std::pair< char, char > >	SS_Prediction
typedef utility::pointer::owning_ptr< SS_Prediction >	SS_PredictionOP

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

Variables
static basic::Tracer	tr ("density_grid")

Detailed Description

Author

James Thompson

Typedef Documentation

SS_Prediction

typedef WrappedPrimitive< std::pair< char, char > > SS_Prediction

SS_PredictionOP

typedef utility::pointer::owning_ptr< SS_Prediction > SS_PredictionOP

Function Documentation

main()

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

References ObjexxFCL::abs(), in::file::alignment(), cm::aln_format(), argv, calc_blosum_scores(), calc_dgaps(), calculate_burial(), utility::io::oc::cout, james::debug(), basic::Tracer::Debug, DistanceMatrix::distance(), test.T009_Exceptions::e, end, errors, numeric::kdtree::get_percentile_bounds(), get_pose_by_id(), get_ss(), getline(), create_a3b_hbs::ii, basic::init(), gaussian-sampling::input, beta_nonlocal::jj, basic::KDTREE_CONSTRUCT, basic::KDTREE_SEARCH, oop_conformations::length, line, max(), basic::options::OptionKeys::james::min_seqsep, numeric::kdtree::nearest_neighbors(), basic::options::OptionKeys::frags::contacts::neighbors, basic::options::OptionKeys::cm::nn, cm::nn(), option, basic::prof_show(), PROF_START, PROF_STOP, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, in::file::s(), legacy_score_vs_rmsd::scores, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::frags::ss_pred, tr, numeric::kdtree::transform_percentile(), numeric::kdtree::transform_percentile_single_pt(), numeric::kdtree::WrappedPrimitive< T >::val(), and test.T040_Types::values.

Variable Documentation

tr

basic::Tracer tr("density_grid") ( "density_grid"  )

static

Referenced by main().