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:

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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...

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...

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.".