ca_to_allatom.cc File Reference

An app which constructs an all atom model from a CA-only input trace. The inputs are the starting CA trace, a list of residue ranges corresponding to secondary structure elements (as best as can be inferred from the initial trace) and a set of backbone torsion fragments. More...

#include <protocols/jd2/JobDistributor.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/RBSegmentRelax.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/id/AtomID.hh>
#include <protocols/rbsegment_relax/RBSegmentRelax.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/simple_filters/RmsdEvaluator.hh>
#include <protocols/evaluation/EvaluatorFactory.hh>
#include <protocols/viewer/viewers.hh>
#include <utility/vector1.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <string>
#include <core/fragment/FragSet.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/rbsegment_relax/RBSegment.hh>
#include <numeric/xyzVector.io.hh>
#include <core/kinematics/FoldTree.hh>
#include <utility/excn/Exceptions.hh>

Classes
class	CaToAllAtom

Typedefs
using	CaToAllAtomOP = utility::pointer::shared_ptr< CaToAllAtom >

Functions
numeric::xyzVector< core::Real >	recenter_with_missing (core::pose::Pose &pose)
void *	ca_to_allatom_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TZ ("pilot_apps::ca_to_allatom")

Detailed Description

An app which constructs an all atom model from a CA-only input trace. The inputs are the starting CA trace, a list of residue ranges corresponding to secondary structure elements (as best as can be inferred from the initial trace) and a set of backbone torsion fragments.

Author

Frank DiMaio

Typedef Documentation

CaToAllAtomOP

using CaToAllAtomOP = utility::pointer::shared_ptr<CaToAllAtom>

Function Documentation

ca_to_allatom_main()

void* ca_to_allatom_main

(

void *

)

References basic::options::OptionKeys::constraints::constraints, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

main()

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

References argv, ca_to_allatom_main(), test.T009_Exceptions::e, basic::init(), NEW_OPT, and viewer_main().

recenter_with_missing()

numeric::xyzVector< core::Real > recenter_with_missing

(

core::pose::Pose &

pose

)

References count, numeric::xyzVector< T >::length(), beta_nonlocal::pose, and TZ.

Variable Documentation

TZ

basic::Tracer TZ("pilot_apps::ca_to_allatom") ( "pilot_apps::ca_to_allatom"  )

static

Referenced by recenter_with_missing(), and test_chi_xform().