supercharge.cc File Reference

#include <devel/init.hh>
#include <protocols/design_opt/Supercharge.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/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/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/pose_metric_calculators/NeighborsByDistanceCalculator.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/file/FileName.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <sstream>
#include <string>
#include <utility/vector1.hh>
#include <utility/sort_predicates.hh>
#include <cmath>

Namespaces
	local

Typedefs
using	Pose = core::pose::Pose
using	SizeSet = std::set< Size >

Functions
int	main (int argc, char *argv[])
	Adds charged residues to a protein surface. More...

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

Pose

using Pose = core::pose::Pose

SizeSet

using SizeSet = std::set<Size>

Function Documentation

main()

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

Adds charged residues to a protein surface.

References argv, local::AvNAPSA_negative, local::AvNAPSA_positive, local::compare_residue_energies_all, local::compare_residue_energies_mut, local::dont_mutate_correct_charge, local::dont_mutate_glyprocys, local::dont_mutate_hbonded_sidechains, test.T009_Exceptions::e, local::include_arg, local::include_asp, local::include_glu, local::include_lys, basic::init(), 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, TR, and basic::options::OptionKeys::inout::dbms::user.

Variable Documentation

TR

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

static

Referenced by main().