supercharge.cc File Reference

#include <devel/init.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/toolbox/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/toolbox/task_operations/RestrictToInterface.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/MetricValue.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/file/FileName.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <sstream>
#include <string>
#include <fstream>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/sort_predicates.hh>
#include <math.h>

Classes
class	supercharge
	Adds charged residues to a protein surface. More...

Namespaces
	local

Typedefs
typedef core::pose::Pose	Pose
typedef std::set< Size >	SizeSet
typedef utility::pointer::shared_ptr < supercharge >	superchargeOP

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.design.supercharge")
int	main (int argc, char *argv[])

Variables
basic::options::BooleanOptionKey const	local::AvNAPSA_positive ("AvNAPSA_positive")
basic::options::BooleanOptionKey const	local::AvNAPSA_negative ("AvNAPSA_negative")
basic::options::BooleanOptionKey const	local::target_net_charge_active ("target_net_charge_active")
basic::options::IntegerOptionKey const	local::target_net_charge ("target_net_charge")
basic::options::IntegerOptionKey const	local::surface_atom_cutoff ("surface_atom_cutoff")
basic::options::IntegerOptionKey const	local::surface_residue_cutoff ("surface_residue_cutoff")
basic::options::BooleanOptionKey const	local::include_arg ("include_arg")
basic::options::BooleanOptionKey const	local::include_lys ("include_lys")
basic::options::BooleanOptionKey const	local::include_asp ("include_asp")
basic::options::BooleanOptionKey const	local::include_glu ("include_glu")
basic::options::RealOptionKey const	local::refweight_arg ("refweight_arg")
basic::options::RealOptionKey const	local::refweight_lys ("refweight_lys")
basic::options::RealOptionKey const	local::refweight_asp ("refweight_asp")
basic::options::RealOptionKey const	local::refweight_glu ("refweight_glu")
basic::options::BooleanOptionKey const	local::dont_mutate_glyprocys ("dont_mutate_glyprocys")
basic::options::BooleanOptionKey const	local::dont_mutate_correct_charge ("dont_mutate_correct_charge")
basic::options::BooleanOptionKey const	local::dont_mutate_hbonded_sidechains ("dont_mutate_hbonded_sidechains")
basic::options::BooleanOptionKey const	local::pre_packminpack ("pre_packminpack")
basic::options::IntegerOptionKey const	local::nstruct ("nstruct")
basic::options::BooleanOptionKey const	local::compare_residue_energies_all ("compare_residue_energies_all")
basic::options::BooleanOptionKey const	local::compare_residue_energies_mut ("compare_residue_energies_mut")

Typedef Documentation

typedef core::pose::Pose Pose

typedef std::set< Size > SizeSet

typedef utility::pointer::shared_ptr< supercharge > superchargeOP

Function Documentation

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

References local::AvNAPSA_negative, local::AvNAPSA_positive, local::compare_residue_energies_all, local::compare_residue_energies_mut, utility::io::oc::cout, local::dont_mutate_correct_charge, local::dont_mutate_glyprocys, local::dont_mutate_hbonded_sidechains, local::include_arg, local::include_asp, local::include_glu, local::include_lys, devel::init(), utility::excn::EXCN_Base::msg(), local::nstruct, basic::options::option, option, local::pre_packminpack, local::refweight_arg, local::refweight_asp, local::refweight_glu, local::refweight_lys, local::surface_atom_cutoff, local::surface_residue_cutoff, local::target_net_charge, local::target_net_charge_active, and TR().

static THREAD_LOCAL basic::Tracer TR ( "apps.public.design.supercharge"  )

static

Referenced by supercharge::apply(), supercharge::AvNAPSA_values(), supercharge::design_supercharge(), supercharge::design_supercharge_AvNAPSA(), supercharge::energy_comparison(), main(), supercharge::prepack_input_structure(), supercharge::print_netcharge_and_mutations(), supercharge::set_resfile(), supercharge::set_resfile_AvNAPSA(), and supercharge::set_surface().