Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Types | Private Member Functions | List of all members
core::pack::palette::NCAADefaultPackerPalette Class Reference

The NCAADefaultPackerPalette class gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list. Specifically, the NCAADefaultPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and nothing else.". More...

#include <NCAADefaultPackerPalette.hh>

Inheritance diagram for core::pack::palette::NCAADefaultPackerPalette:
Inheritance graph
[legend]

Public Member Functions

 NCAADefaultPackerPalette ()
 NCAADefault constructor. More...
 
 ~NCAADefaultPackerPalette () override
 Destructor. More...
 
PackerPaletteOP clone () const override
 Clone operator: make a copy and return an owning pointer to the copy. More...
 
void parse_my_tag (utility::tag::TagCOP const &tag, basic::datacache::DataMap const &datamap) override
 Function to parse XML tags, implemented by derived classes. More...
 
std::string const & name () const override
 Get the name of this object ("NCAADefaultPackerPalette"). More...
 
bool packer_palette_is_unpublished () const override
 Returns true (this packer palette is unpublished). More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Returns Andy Watkins as the author. More...
 
- Public Member Functions inherited from core::pack::palette::PackerPalette
 PackerPalette ()
 Default constructor. More...
 
 ~PackerPalette () override
 Destructor. More...
 
PackerPaletteCOP get_self_ptr () const
 Self pointers (const). More...
 
PackerPaletteOP get_self_ptr ()
 Self pointers (non-const). More...
 
void initialize_residue_level_task (core::conformation::Residue const &existing_residue, core::chemical::ResidueTypeSetCOP restypeset, std::list< chemical::ResidueTypeCOP > &residue_type_list) const
 The initialize_residue_level_task ("apply") function – called during rotamer setup for the packer to get the list of all ResidueTypes that are allowed. More...
 
void set_up_default_special_behaviours ()
 Set the special behaviours to their default values. More...
 
virtual bool packer_palette_provides_citation_info () const
 Does this packer palette provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 

Static Public Member Functions

static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Provide information about the XML options available for this PackerPalette. More...
 

Protected Member Functions

BaseTypeList get_base_residue_types (core::chemical::ResidueTypeSetCOP const &restypeset) const override
 Generate a list of possible base residue types. More...
 
- Protected Member Functions inherited from core::pack::palette::PackerPalette
BaseTypeList const & get_base_residue_types_cached (core::chemical::ResidueTypeSetCOP const &restypeset) const
 Get a list of possible base residue types Will preferentially grab them from a cached list for the given ResidueTypeSet If we don't have a cached version, generate one (and cache it) using get_base_residue_types() More...
 
void set_up_default_base_types (core::chemical::ResidueTypeSet const &restypeset, BaseTypeList &base_types) const
 Set up the default base types for a particular ResidueTypeSet. More...
 
void set_up_expanded_base_types (core::chemical::ResidueTypeSet const &restypeset, BaseTypeList &base_types) const
 Set up the default base types for a particular ResidueTypeSet. More...
 
void add_base_residue_type (std::string const &name, core::chemical::ResidueTypeSet const &restypeset, BaseTypeList &base_types) const
 Add a base residue type name to the list of base residue type names. More...
 
void add_base_residue_types_by_properties (utility::vector1< core::chemical::ResidueProperty > const &properties, core::chemical::ResidueTypeSet const &restypeset, BaseTypeList &base_types) const
 Add a group of base ResidueTypes and names to the PackerPalette from a particular ResidueTypeSet by properties. More...
 
void set_only_design_protein_peptoid_dna_saccharide (bool const setting)
 Set whether design is only limited to protein/peptoid/dna/saccharide positions, or can happen everywhere. More...
 
void set_force_existing_base_type (bool const setting)
 Set whether we're forcing the existing base type. More...
 
void set_only_design_polymer_residues (bool const setting)
 Set whether design is only limited to polymer positions, or can happen everywhere. More...
 
utility::vector1< std::string > get_base_names_by_properties (core::chemical::ResidueTypeSet const &restypeset, utility::vector1< core::chemical::ResidueProperty > const &properties) const
 Return a list of base ResidueType names to be added to the PackerPalette from a particular ResidueTypeSet by properties. More...
 

Private Types

typedef PackerPalette parent
 The parent class (PackerPalette). More...
 

Private Member Functions

void set_up_behaviours ()
 Set up the NCAADefaultPackerPalette with the default set of position-specific behaviours. More...
 

Detailed Description

The NCAADefaultPackerPalette class gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list. Specifically, the NCAADefaultPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and nothing else.".

Member Typedef Documentation

The parent class (PackerPalette).

Constructor & Destructor Documentation

core::pack::palette::NCAADefaultPackerPalette::NCAADefaultPackerPalette ( )

NCAADefault constructor.

References set_up_behaviours().

core::pack::palette::NCAADefaultPackerPalette::~NCAADefaultPackerPalette ( )
override

Destructor.

Member Function Documentation

PackerPaletteOP core::pack::palette::NCAADefaultPackerPalette::clone ( ) const
overridevirtual

Clone operator: make a copy and return an owning pointer to the copy.

Clone operator.

Derived classes MUST implement this.

Implements core::pack::palette::PackerPalette.

BaseTypeList core::pack::palette::NCAADefaultPackerPalette::get_base_residue_types ( core::chemical::ResidueTypeSetCOP const &  restypeset) const
overrideprotectedvirtual

Generate a list of possible base residue types.

Parameters
[in]restypesetThe ResidueTypeSet to use as a reference for related types.
Returns
A list of basename:base residue type pairs

Implements core::pack::palette::PackerPalette.

References core::pack::palette::PackerPalette::set_up_expanded_base_types().

std::string const & core::pack::palette::NCAADefaultPackerPalette::name ( ) const
overridevirtual

Get the name of this object ("NCAADefaultPackerPalette").

Implements core::pack::palette::PackerPalette.

Referenced by provide_authorship_info_for_unpublished().

bool core::pack::palette::NCAADefaultPackerPalette::packer_palette_is_unpublished ( ) const
overridevirtual

Returns true (this packer palette is unpublished).

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

Reimplemented from core::pack::palette::PackerPalette.

void core::pack::palette::NCAADefaultPackerPalette::parse_my_tag ( utility::tag::TagCOP const &  tag,
basic::datacache::DataMap const &  datamap 
)
overridevirtual

Function to parse XML tags, implemented by derived classes.

Failure to implement this results in a warning message, but does not prevent compilation or program execution.

Reimplemented from core::pack::palette::PackerPalette.

References core::pack::palette::TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::pack::palette::NCAADefaultPackerPalette::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Returns Andy Watkins as the author.

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

Reimplemented from core::pack::palette::PackerPalette.

References name().

void core::pack::palette::NCAADefaultPackerPalette::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::pack::palette::NCAADefaultPackerPalette::set_up_behaviours ( )
private

Set up the NCAADefaultPackerPalette with the default set of position-specific behaviours.

References core::pack::palette::PackerPalette::set_up_default_special_behaviours(), and core::pack::palette::TR().

Referenced by NCAADefaultPackerPalette().


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