denovo_density.cc File Reference

#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/init_id_map.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/DensitySymmInfo.hh>
#include <protocols/electron_density/DockFragmentsIntoDensityMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/scoring/electron_density/ElectronDensity.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/xyzVector.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/random/random.hh>
#include <utility/string_util.hh>
#include <tuple>
#include <basic/Tracer.hh>
#include <string>
#include <algorithm>
#include <utility/file/FileName.hh>
#include <fstream>
#include <core/chemical/AtomTypeSet.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

main()

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

main

References argv, test.T009_Exceptions::e, basic::init(), in::missing_density_to_jump(), SmotifHasher::mode, 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(), extract_by_sidechain_sasa_score::scorefile, TR, and basic::options::OptionKeys::sc::verbose.

operator<()

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

References x, and predPRE::y.

ReadCAsFromPDB()

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

References cal_vdw_radius_pool::buf, getline(), and clean_pdb_keep_ligand::pdbfile.

Referenced by DockFragmentsMover::run().

Variable Documentation

TR

basic::Tracer TR("denovo_density") ( "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().