denovo_density.cc File Reference

#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/conformation/ResidueFactory.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/electron_density/DensitySymmInfo.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/electron_density/DockIntoDensityMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/idealize/IdealizeMover.fwd.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/OptH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/random/random.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <boost/tuple/tuple.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <basic/Tracer.hh>
#include <iostream>
#include <string>
#include <list>
#include <algorithm>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>

Classes
struct	CAtrace
struct	FragID
class	DockFragmentsMover
class	ScoreFragmentSetMover
class	FragmentAssemblyMover
class	ConsensusFragmentMover
class	SolutionRescoreMover

Functions
void	ReadCAsFromPDB (std::string pdbfile, utility::vector1< numeric::xyzVector< core::Real > > &cas)
bool	operator< (const FragID &x, const FragID &y)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("denovo_density")

Function Documentation

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

main

References utility::io::oc::cout, test.T009_Exceptions::e, devel::init(), in::missing_density_to_jump(), basic::options::OptionKeys::dna::specificity::mode, utility::excn::Exception::msg(), NEW_OPT, out::nooutput(), basic::options::OptionKeys::loodo::num_frags, option, make_symmdef_file_denovo::pos, DockFragmentsMover::run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), basic::options::OptionKeys::out::file::scorefile, TR, and basic::options::OptionKeys::sc::verbose.

bool operator<	(	const FragID &	x,
		const FragID &	y
	)

References FragID::pos_, and FragID::tag_.

void ReadCAsFromPDB	(	std::string	pdbfile,
		utility::vector1< numeric::xyzVector< core::Real > > &	cas
	)

References ObjexxFCL::getline().

Referenced by DockFragmentsMover::run().

Variable Documentation

basic::Tracer TR("denovo_density")

static

Referenced by DockFragmentsMover::cluster_frags(), main(), DockFragmentsMover::process_fragfile(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), and FragmentAssemblyMover::score().