core::pack::task::PIKAA Class Reference

PIKAA allows residues specifed in a following string. More...

#include <ResfileReader.hh>

Inheritance diagram for core::pack::task::PIKAA:

Public Member Functions
	PIKAA ()=default
	Default constructor. More...
	PIKAA (PIKAA const &)=default
	Default copy constructor. More...
ResfileCommandOP	clone () const override
void	initialize_from_tokens (utility::vector1< std::string > const &tokens, Size &which_token, Size resid) override
	PIKAA allows residues specifed in a following string. More...
void	add_base_name_to_keep (std::string const &basename)
	Add a base name to the list of base names to keep. More...
void	residue_action (PackerTask &, Size resid) const override
	Modify the packer task with the command that was read in. More...
std::string	get_name () override
Public Member Functions inherited from core::pack::task::ResfileCommand
	~ResfileCommand () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

Static Public Member Functions
static std::string	name ()

Private Attributes
bool	initialized_ = false
utility::vector1< std::string >	basenames_to_keep_

Detailed Description

PIKAA allows residues specifed in a following string.

In actuality, it is PROHIBITING any residue that is NOT in the following string. The string should be formatted as an all-caps string of one-letter codes. Noncanonical amino acids can be included using X[<full base="" name>="">]. For example, to allow tyrosine, threonine, tryptophan, and 2-aminoisobutyric acid, you would use "PIKAA YTWX[AIB]".

Author

Original author unknown.

Noncanonical pruning support added by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Constructor & Destructor Documentation

core::pack::task::PIKAA::PIKAA ( )

default

Default constructor.

core::pack::task::PIKAA::PIKAA ( PIKAA const &  )

default

Default copy constructor.

Member Function Documentation

void core::pack::task::PIKAA::add_base_name_to_keep

(

std::string const &

basename

)

Add a base name to the list of base names to keep.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

ResfileCommandOP core::pack::task::PIKAA::clone ( ) const

inlineoverridevirtual

Implements core::pack::task::ResfileCommand.

std::string core::pack::task::PIKAA::get_name ( )

inlineoverridevirtual

Implements core::pack::task::ResfileCommand.

References name().

void core::pack::task::PIKAA::initialize_from_tokens ( utility::vector1< std::string > const &  tokens, Size &  which_token, Size  resid  )

overridevirtual

PIKAA allows residues specifed in a following string.

In actuality, it is PROHIBITING any residue that is NOT in the following string. The string should be formatted as an all-caps string of one-letter codes. Noncanonical amino acids can be included using X[<full base="" name>="">]. For example, to allow tyrosine, threonine, tryptophan, and 2-aminoisobutyric acid, you would use "PIKAA YTWX[AIB]".

Author

Original author unknown.

Noncanonical pruning support added by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implements core::pack::task::ResfileCommand.

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), protocols::vip::base_name(), core::pack::task::get_token(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, core::chemical::name_from_aa(), core::chemical::num_canonical_aas, core::chemical::oneletter_code_specifies_aa(), and core::pack::task::TR().

static std::string core::pack::task::PIKAA::name ( )

inlinestatic

Referenced by core::pack::task::create_command_map(), and get_name().

void core::pack::task::PIKAA::residue_action ( PackerTask &  , Size  resid  ) const

overridevirtual

Modify the packer task with the command that was read in.

Implements core::pack::task::ResfileCommand.

References core::pack::task::PackerTask::nonconst_residue_task(), and core::pack::task::ResidueLevelTask::restrict_restypes().

Member Data Documentation

utility::vector1< std::string > core::pack::task::PIKAA::basenames_to_keep_

private

bool core::pack::task::PIKAA::initialized_ = false

private

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

• src/core/pack/task/ResfileReader.hh
• src/core/pack/task/ResfileReader.cc