supercharge Class Reference

Adds charged residues to a protein surface. More...

Inheritance diagram for supercharge:

Public Member Functions
	supercharge ()
virtual	~supercharge ()
virtual void	apply (Pose &pose)
virtual void	AvNAPSA_values (Pose const &pose)
virtual void	set_resfile_AvNAPSA (Pose const &pose)
virtual void	design_supercharge_AvNAPSA (Pose const &starting_pose, Pose &pose)
virtual void	prepack_input_structure (Pose &pose)
void	set_surface (Pose const &pose)
void	set_resfile (Pose const &pose)
utility::vector1< Real >	set_reference_energies ()
void	design_supercharge (Pose const &starting_pose, Pose &pose)
void	print_netcharge_and_mutations (Pose const &starting_pose, Pose const &pose)
int	get_net_charge (Pose const &pose)
void	energy_comparison (Pose &native, Pose &pose)
virtual std::string	get_name () const

Private Attributes
SizeSet	surface_res_
std::string	outputname_
std::string	out_path_
utility::vector1< Real >	AvNAPSA_values_
Size	largest_mutated_AvNAPSA_
Pose	native_
core::scoring::ScoreFunctionOP	scorefxn_

Detailed Description

Adds charged residues to a protein surface.

Constructor & Destructor Documentation

supercharge::supercharge ( )

inline

virtual supercharge::~supercharge ( )

inlinevirtual

Member Function Documentation

virtual void supercharge::apply ( Pose &  pose )

inlinevirtual

References local::AvNAPSA_negative, local::AvNAPSA_positive, basic::options::OptionKeys::run::chain, local::compare_residue_energies_all, local::compare_residue_energies_mut, pyrosetta::get_score_function, local::include_arg, local::include_asp, local::include_glu, local::include_lys, basic::options::OptionKeys::in::file::native, basic::options::option, option, options, basic::options::OptionKeys::in::path::path, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, test.Workshop7test::starting_pose, local::target_net_charge, local::target_net_charge_active, TR(), and basic::options::OptionKeys::packing::use_input_sc.

Referenced by src.protocols.jd2.RosettaScriptWrapper::apply_to_failure().

virtual void supercharge::AvNAPSA_values ( Pose const &  pose )

inlinevirtual

References local::AvNAPSA_negative, local::AvNAPSA_positive, test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, basic::options::option, and TR().

void supercharge::design_supercharge ( Pose const &  starting_pose, Pose &  pose  )

inline

References ObjexxFCL::abs(), demo.D060_Folding::counter, basic::options::OptionKeys::optE::fixed, pyrosetta::get_score_function, local::include_arg, local::include_asp, local::include_glu, local::include_lys, local::nstruct, option, options, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::in::file::s, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, local::target_net_charge, local::target_net_charge_active, app.delta_score_per_mutation::task, TR(), basic::options::OptionKeys::inout::dbms::user, and value.

virtual void supercharge::design_supercharge_AvNAPSA ( Pose const &  starting_pose, Pose &  pose  )

inlinevirtual

References local::AvNAPSA_positive, pyrosetta::get_score_function, option, options, basic::options::OptionKeys::packing::resfile, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, app.delta_score_per_mutation::task, TR(), and basic::options::OptionKeys::inout::dbms::user.

void supercharge::energy_comparison ( Pose &  native, Pose &  pose  )

inline

References local::compare_residue_energies_all, local::compare_residue_energies_mut, basic::options::OptionKeys::optE::fixed, test.T200_Scoring::ii, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::option, options, basic::options::OptionKeys::corrections::score::p_aa_pp, basic::options::OptionKeys::remodel::rama, app.delta_score_per_mutation::task, and TR().

virtual std::string supercharge::get_name ( ) const

inlinevirtual

int supercharge::get_net_charge ( Pose const &  pose )

inline

virtual void supercharge::prepack_input_structure ( Pose &  pose )

inlinevirtual

References pyrosetta::get_score_function, basic::options::option, options, local::pre_packminpack, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, app.delta_score_per_mutation::task, and TR().

void supercharge::print_netcharge_and_mutations ( Pose const &  starting_pose, Pose const &  pose  )

inline

References TR().

utility::vector1< Real > supercharge::set_reference_energies ( )

inline

References option, options, local::refweight_arg, local::refweight_asp, local::refweight_glu, and local::refweight_lys.

void supercharge::set_resfile ( Pose const &  pose )

inline

References local::dont_mutate_correct_charge, local::dont_mutate_glyprocys, local::dont_mutate_hbonded_sidechains, basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::mp::scoring::hbond, test.T200_Scoring::hbond_set, local::include_arg, local::include_asp, local::include_glu, local::include_lys, basic::options::OptionKeys::frags::j, utility::io::ozstream::open(), option, options, TR(), and value.

virtual void supercharge::set_resfile_AvNAPSA ( Pose const &  pose )

inlinevirtual

References local::AvNAPSA_negative, local::AvNAPSA_positive, basic::options::OptionKeys::frags::j, utility::io::ozstream::open(), basic::options::option, local::surface_atom_cutoff, local::target_net_charge, local::target_net_charge_active, and TR().

void supercharge::set_surface ( Pose const &  pose )

inline

References test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, basic::options::option, app.delta_score_per_mutation::res, local::surface_atom_cutoff, local::surface_residue_cutoff, TR(), basic::options::OptionKeys::inout::dbms::user, basic::MetricValue< T >::value(), value, and basic::Warning().

Member Data Documentation

utility::vector1< Real > supercharge::AvNAPSA_values_

private

Size supercharge::largest_mutated_AvNAPSA_

private

Pose supercharge::native_

private

std::string supercharge::out_path_

private

std::string supercharge::outputname_

private

core::scoring::ScoreFunctionOP supercharge::scorefxn_

private

SizeSet supercharge::surface_res_

private

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The documentation for this class was generated from the following file:

• src/apps/public/design/supercharge.cc