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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:
Inheritance graph
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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
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
void core::pack::task::PIKAA::residue_action ( PackerTask ,
Size  resid 
) const
overridevirtual

Member Data Documentation

utility::vector1< std::string > core::pack::task::PIKAA::basenames_to_keep_
private
bool core::pack::task::PIKAA::initialized_ = false
private

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