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/chemical/ResidueTypeSet.fwd.hh>
#include <core/scoring/ScoreFunction.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/Pose.fwd.hh>
#include <core/pose/util.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/keys/out.OptionKeys.gen.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/io/silent/SilentStructFactory.hh>
#include <core/id/AtomID.hh>
#include <core/io/silent/silent.fwd.hh>
#include <protocols/rbsegment_relax/RBSegmentRelax.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loops.hh>
#include <utility/options/OptionCollection.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 <numeric/random/random.hh>
#include <platform/types.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/fragment/FragSet.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/evaluation/util.hh>
#include <protocols/moves/MoverStatistics.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
typedef utility::pointer::shared_ptr < CaToAllAtom >	CaToAllAtomOP

Functions
static THREAD_LOCAL basic::Tracer	TZ ("pilot_apps::ca_to_allatom")
numeric::xyzVector< core::Real >	recenter_with_missing (core::pose::Pose &pose)
void *	ca_to_allatom_main (void *)
int	main (int argc, char *argv[])

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

typedef utility::pointer::shared_ptr< CaToAllAtom > CaToAllAtomOP

Function Documentation

void* ca_to_allatom_main

(

void *

)

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

Referenced by main().

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

References ca_to_allatom_main(), utility::io::oc::cout, devel::init(), utility::excn::EXCN_Base::msg(), and NEW_OPT.

numeric::xyzVector< core::Real > recenter_with_missing

(

core::pose::Pose &

pose

)

References clean_pdb_keep_ligand::count, numeric::xyzVector< typename >::length(), and TZ().

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

static

Referenced by recenter_with_missing().