template_features.cc File Reference

#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/vector1.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/sequence/util.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <protocols/comparative_modeling/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/conformation/Residue.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/option.hh>
#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 <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <utility/excn/Exceptions.hh>

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.comparative_modeling.thread_local")
utility::vector1< int >	calculate_burial (core::pose::Pose &mypose, core::Real const dist_cutoff)
int	main (int argc, char *argv[])

Function Documentation

utility::vector1< int > calculate_burial	(	core::pose::Pose &	mypose,
		core::Real const	dist_cutoff
	)

References basic::options::OptionKeys::in::file::burial, coordlib::dist(), distance(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::cmiles::jumping::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by main().

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

References ObjexxFCL::format::A(), basic::options::OptionKeys::in::file::alignment, basic::options::OptionKeys::cm::aln_format, basic::options::OptionKeys::in::file::burial, calculate_burial(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::bunsat_calc2::dist_cutoff, basic::options::OptionKeys::james::dist_thresholds, distance(), basic::options::OptionKeys::cutoutdomain::end, basic::Tracer::Error, ObjexxFCL::format::F(), BuildPackagedBindings::format, ObjexxFCL::format::I(), test.T200_Scoring::ii, devel::init(), max(), utility::excn::EXCN_Base::msg(), basic::options::option, options, basic::options::OptionKeys::cp::output, app.surface_docking.surface_docking::pose, poses_from_cmd_line(), basic::options::OptionKeys::cmiles::jumping::resi, basic::options::OptionKeys::cmiles::jumping::resj, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::template_pdb, basic::options::TR(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::mp::visualize::width.

static THREAD_LOCAL basic::Tracer TR ( "apps.public.comparative_modeling.thread_local"  )

static