repeat_demo.cc File Reference

Example of how to set up a symmetric repeat protein system where you fold through the polypeptide chain. More...

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/variant_util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/relax/FastRelax.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/optimization.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <ObjexxFCL/format.hh>

Namespaces
	my_options

Functions
void	add_my_options ()
void	setup_repeat_symminfo (Size const repeatlen, Size const nrepeat, Size const base_repeat, conformation::symmetry::SymmetryInfo &symminfo)
void	setup_repeat_pose (Size const repeatlen, Size const nrepeat, Size const base_repeat, Pose &pose)
void	rebuild_test ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.phil.repeat_demo")
IntegerOptionKey	my_options::nrepeat ("my:nrepeat")

Detailed Description

Example of how to set up a symmetric repeat protein system where you fold through the polypeptide chain.

Author

Phil Bradley (pbrad.nosp@m.ley@.nosp@m.fredh.nosp@m.utch.nosp@m..org)

Function Documentation

add_my_options()

void add_my_options

(

)

References utility::options::OptionCollection::add(), my_options::nrepeat, and basic::options::option.

Referenced by main().

main()

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

References add_my_options(), argv, test.T009_Exceptions::e, basic::init(), and rebuild_test().

rebuild_test()

void rebuild_test

(

)

References basic::options::OptionKeys::rna::denovo::minimize::deriv_check, test.T009_Exceptions::e, ObjexxFCL::format::F(), basic::options::OptionKeys::abinitio::fastrelax, lactamize::filename, create_a3b_hbs::i, basic::options::OptionKeys::packing::linmem_ig, vancomycin::min_mover, basic::options::OptionKeys::in::file::movemap, my_options::nrepeat, basic::options::OptionKeys::optimization::old_sym_min, basic::options::option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, average_rmsds::rmsd, runtime_assert, setup_repeat_pose(), basic::options::start_file(), basic::options::OptionKeys::symmetry::symmetry_definition, basic::options::TR, basic::Tracer::Trace, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

setup_repeat_pose()

void setup_repeat_pose	(	Size const	repeatlen,
		Size const	nrepeat,
		Size const	base_repeat,
		Pose &	pose
	)

sets up a repeat pose, starting from a non-symmetric pdb with nres=repeatlen*nrepeat

References create_a3b_hbs::f, my_options::nrepeat, beta_nonlocal::pose, runtime_assert, and setup_repeat_symminfo().

Referenced by rebuild_test().

setup_repeat_symminfo()

void setup_repeat_symminfo	(	Size const	repeatlen,
		Size const	nrepeat,
		Size const	base_repeat,
		conformation::symmetry::SymmetryInfo &	symminfo
	)

fills in a SymmetryInfo object with the necessary info

References create_a3b_hbs::i, create_a3b_hbs::j, my_options::nrepeat, and offset.

Referenced by setup_repeat_pose().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.phil.repeat_demo") ( "apps.pilot.phil.repeat_demo"  )

static