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.

Definition at line 143 of file supercharge.cc.

Constructor & Destructor Documentation

supercharge::supercharge ( )

inline

Definition at line 145 of file supercharge.cc.

virtual supercharge::~supercharge ( )

inlinevirtual

Definition at line 146 of file supercharge.cc.

Member Function Documentation

virtual void supercharge::apply ( Pose & pose )

inlinevirtual

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

inlinevirtual

Definition at line 236 of file supercharge.cc.

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

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

inline

Definition at line 768 of file supercharge.cc.

References ObjexxFCL::abs(), demo.D060_Folding::counter, local::include_arg, local::include_asp, local::include_glu, local::include_lys, local::nstruct, option, options, app.pyrosetta_toolkit.modules.SQLPDB::s, PyMOL_demo::scorefxn, local::target_net_charge, local::target_net_charge_active, app.delta_score_per_mutation::task, TR(), utility::options::OptionKeys::options::user, and value.

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

inlinevirtual

Definition at line 406 of file supercharge.cc.

References local::AvNAPSA_positive, option, options, PyMOL_demo::scorefxn, app.delta_score_per_mutation::task, TR(), and utility::options::OptionKeys::options::user.

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

inline

Definition at line 1041 of file supercharge.cc.

References local::compare_residue_energies_all, local::compare_residue_energies_mut, test.T200_Scoring::ii, basic::options::option, options, app.delta_score_per_mutation::task, and TR().

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

inlinevirtual

Definition at line 1324 of file supercharge.cc.

int supercharge::get_net_charge ( Pose const & pose )

inline

Definition at line 1026 of file supercharge.cc.

virtual void supercharge::prepack_input_structure ( Pose & pose )

inlinevirtual

Definition at line 473 of file supercharge.cc.

References basic::options::option, options, local::pre_packminpack, PyMOL_demo::scorefxn, app.delta_score_per_mutation::task, and TR().

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

inline

Definition at line 987 of file supercharge.cc.

References TR().

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

inline

Definition at line 739 of file supercharge.cc.

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

void supercharge::set_resfile ( Pose const & pose )

inline

Definition at line 634 of file supercharge.cc.

References local::dont_mutate_correct_charge, local::dont_mutate_glyprocys, local::dont_mutate_hbonded_sidechains, end, test.T200_Scoring::hbond_set, local::include_arg, local::include_asp, local::include_glu, local::include_lys, utility::io::ozstream::open(), option, options, TR(), and value.

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

inlinevirtual

Definition at line 305 of file supercharge.cc.

References local::AvNAPSA_negative, local::AvNAPSA_positive, 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

Definition at line 536 of file supercharge.cc.

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

Member Data Documentation

utility::vector1< Real > supercharge::AvNAPSA_values_

private

Definition at line 1331 of file supercharge.cc.

Size supercharge::largest_mutated_AvNAPSA_

private

Definition at line 1332 of file supercharge.cc.

Pose supercharge::native_

private

Definition at line 1333 of file supercharge.cc.

std::string supercharge::out_path_

private

Definition at line 1330 of file supercharge.cc.

std::string supercharge::outputname_

private

Definition at line 1329 of file supercharge.cc.

core::scoring::ScoreFunctionOP supercharge::scorefxn_

private

Definition at line 1335 of file supercharge.cc.

SizeSet supercharge::surface_res_

private

Definition at line 1328 of file supercharge.cc.

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

src/apps/public/design/supercharge.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation