core::pack::palette Namespace Reference

Classes
class	BaseTypeList
	A small utility class which allows you to do a map-like addition of name/ResidueType pairs, but keeps things in the added order. More...
class	CustomBaseTypePackerPalette
	CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time). More...
class	CustomBaseTypePackerPaletteCreator
	The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class. More...
class	DefaultPackerPalette
	The DefaultPackerPalette 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 DefaultPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and nothing else.". More...
class	DefaultPackerPaletteCreator
	The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class. More...
class	NCAADefaultPackerPalette
	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...
class	NCAADefaultPackerPaletteCreator
	The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class. More...
class	NoDesignPackerPalette
	The NoDesignPackerPalette 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 NoDesignPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and nothing else.". More...
class	NoDesignPackerPaletteCreator
	The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class. More...
class	PackerPalette
	The PackerPalette 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. More...
class	PackerPaletteCreator
	The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class. More...
class	PackerPaletteFactory
class	PackerPaletteRegistrator
	This templated class will register an instance of an PackerPalettteCreator (class T) with the PackerPaletteFactory. It will ensure that no PackerPaletteCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

Typedefs
typedef utility::pointer::shared_ptr < CustomBaseTypePackerPalette >	CustomBaseTypePackerPaletteOP
typedef utility::pointer::shared_ptr < CustomBaseTypePackerPalette const >	CustomBaseTypePackerPaletteCOP
typedef utility::pointer::shared_ptr < DefaultPackerPalette >	DefaultPackerPaletteOP
typedef utility::pointer::shared_ptr < DefaultPackerPalette const >	DefaultPackerPaletteCOP
typedef utility::pointer::shared_ptr < NCAADefaultPackerPalette >	NCAADefaultPackerPaletteOP
typedef utility::pointer::shared_ptr < NCAADefaultPackerPalette const >	NCAADefaultPackerPaletteCOP
typedef utility::pointer::shared_ptr < NoDesignPackerPalette >	NoDesignPackerPaletteOP
typedef utility::pointer::shared_ptr < NoDesignPackerPalette const >	NoDesignPackerPaletteCOP
typedef utility::pointer::shared_ptr < PackerPalette >	PackerPaletteOP
typedef utility::pointer::shared_ptr < PackerPalette const >	PackerPaletteCOP
typedef utility::pointer::shared_ptr < PackerPaletteCreator >	PackerPaletteCreatorOP
typedef utility::pointer::shared_ptr < PackerPaletteCreator const >	PackerPaletteCreatorCOP
typedef utility::pointer::shared_ptr < PackerPaletteFactory >	PackerPaletteFactoryOP
typedef utility::pointer::shared_ptr < PackerPaletteFactory const >	PackerPaletteFactoryCOP

Enumerations
enum	SpecialPackerPaletteBehaviour {   KEEP_EXISTING_BASE_TYPE = 1, FORCE_EXISTING_BASE_TYPE, ONLY_DESIGN_POLYMER_RESIDUES, ONLY_DESIGN_PROTEIN_PEPTIOID_DNA_AND_SACCHARIDES,   ONLY_ALPHA_AA_AT_ALPHA_POSITIONS, ONLY_BETA_AA_AT_BETA_POSITIONS, ONLY_GAMMA_AA_AT_GAMMA_POSITIONS, ONLY_DNA_AT_DNA_POSITIONS,   ONLY_OLIGOUREA_AT_OLIGOUREA_POSITIONS, ONLY_ARAMID_AT_ARAMID_POSITIONS, ONLY_SACCHARIDES_AT_SACCHARIDE_POSITIONS, ONLY_LIGAND_AT_LIGAND_POSITIONS,   ONLY_MATCHING_LIGAND_NAMES, ALL_DNA_TYPES_ON, ONLY_RNA_AT_RNA_POSITIONS, EXCLUDE_ADDUCT_VARIANT_AT_DNA_POSITIONS,   STRIP_VIRTUAL_SIDE_CHAIN, pH_MODE_EXCEPTIONS, HYDROXYPROLINE_EXCEPTIONS, KEEP_EXISTING_TERMINAL_VARIANT_TYPES_AT_POSITIONS,   KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_FOR_EXISTING_BASE_TYPE, KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_AND_DISALLLOW_INCOMPATIBLE_BASE_TYPES, KEEP_EXISTING_DISULFIDES, NO_METAPATCHES,   ALLOW_ALTERNATE_BACKBONE_MATCHING, INVALID_BEHAVIOUR, END_OF_BEHAVIOUR_LIST = INVALID_BEHAVIOUR }

Functions
static basic::Tracer	TR ("core.pack.palette.CustomBaseTypePackerPalette")
static basic::Tracer	TR ("core.pack.palette.DefaultPackerPalette")
static basic::Tracer	TR ("core.pack.palette.NCAADefaultPackerPalette")
static basic::Tracer	TR ("core.pack.palette.NoDesignPackerPalette")
static basic::Tracer	TR ("core.pack.palette.PackerPalette")
static basic::Tracer	TR ("core.pack.palette.PackerPaletteFactory")
std::string	complex_type_name_for_packer_palette (std::string const &packer_palette_name)
	Construct a type name for a PackerPalette. More...
void	xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &packer_palette_type, std::string const &description, utility::tag::AttributeList const &attributes)
	Add a type definition for a PackerPalette. More...
void	xsd_type_definition_w_attributes_and_repeatable_subelements (utility::tag::XMLSchemaDefinition &xsd, std::string const &packer_palette_type, std::string const &description, utility::tag::AttributeList const &attributes, utility::tag::XMLSchemaSimpleSubelementList const &subelements)
	Add a type definition for a PackerPalette, with sub-elements. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< CustomBaseTypePackerPalette const > core::pack::palette::CustomBaseTypePackerPaletteCOP

typedef utility::pointer::shared_ptr< CustomBaseTypePackerPalette > core::pack::palette::CustomBaseTypePackerPaletteOP

typedef utility::pointer::shared_ptr< DefaultPackerPalette const > core::pack::palette::DefaultPackerPaletteCOP

typedef utility::pointer::shared_ptr< DefaultPackerPalette > core::pack::palette::DefaultPackerPaletteOP

typedef utility::pointer::shared_ptr< NCAADefaultPackerPalette const > core::pack::palette::NCAADefaultPackerPaletteCOP

typedef utility::pointer::shared_ptr< NCAADefaultPackerPalette > core::pack::palette::NCAADefaultPackerPaletteOP

typedef utility::pointer::shared_ptr< NoDesignPackerPalette const > core::pack::palette::NoDesignPackerPaletteCOP

typedef utility::pointer::shared_ptr< NoDesignPackerPalette > core::pack::palette::NoDesignPackerPaletteOP

typedef utility::pointer::shared_ptr< PackerPalette const > core::pack::palette::PackerPaletteCOP

typedef utility::pointer::shared_ptr< PackerPaletteCreator const > core::pack::palette::PackerPaletteCreatorCOP

typedef utility::pointer::shared_ptr< PackerPaletteCreator > core::pack::palette::PackerPaletteCreatorOP

typedef utility::pointer::shared_ptr< PackerPaletteFactory const > core::pack::palette::PackerPaletteFactoryCOP

typedef utility::pointer::shared_ptr< PackerPaletteFactory > core::pack::palette::PackerPaletteFactoryOP

typedef utility::pointer::shared_ptr< PackerPalette > core::pack::palette::PackerPaletteOP

Enumeration Type Documentation

enum core::pack::palette::SpecialPackerPaletteBehaviour

Enumerator
KEEP_EXISTING_BASE_TYPE
FORCE_EXISTING_BASE_TYPE
ONLY_DESIGN_POLYMER_RESIDUES
ONLY_DESIGN_PROTEIN_PEPTIOID_DNA_AND_SACCHARIDES
ONLY_ALPHA_AA_AT_ALPHA_POSITIONS
ONLY_BETA_AA_AT_BETA_POSITIONS
ONLY_GAMMA_AA_AT_GAMMA_POSITIONS
ONLY_DNA_AT_DNA_POSITIONS
ONLY_OLIGOUREA_AT_OLIGOUREA_POSITIONS
ONLY_ARAMID_AT_ARAMID_POSITIONS
ONLY_SACCHARIDES_AT_SACCHARIDE_POSITIONS
ONLY_LIGAND_AT_LIGAND_POSITIONS
ONLY_MATCHING_LIGAND_NAMES
ALL_DNA_TYPES_ON
ONLY_RNA_AT_RNA_POSITIONS
EXCLUDE_ADDUCT_VARIANT_AT_DNA_POSITIONS
STRIP_VIRTUAL_SIDE_CHAIN
pH_MODE_EXCEPTIONS
HYDROXYPROLINE_EXCEPTIONS
KEEP_EXISTING_TERMINAL_VARIANT_TYPES_AT_POSITIONS
KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_FOR_EXISTING_BASE_TYPE
KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_AND_DISALLLOW_INCOMPATIBLE_BASE_TYPES
KEEP_EXISTING_DISULFIDES
NO_METAPATCHES
ALLOW_ALTERNATE_BACKBONE_MATCHING
INVALID_BEHAVIOUR
END_OF_BEHAVIOUR_LIST

Function Documentation

std::string core::pack::palette::complex_type_name_for_packer_palette

(

std::string const &

packer_palette_name

)

Construct a type name for a PackerPalette.

Referenced by core::pack::palette::PackerPaletteFactory::define_packer_palette_xml_schema(), xsd_type_definition_w_attributes(), and xsd_type_definition_w_attributes_and_repeatable_subelements().

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.CustomBaseTypePackerPalette"  )

static

Referenced by core::pack::palette::PackerPalette::add_base_residue_type(), core::pack::palette::PackerPalette::add_residue_types_to_list(), core::pack::palette::PackerPalette::initialize_residue_level_task(), core::pack::palette::PackerPaletteFactory::newPackerPalette(), core::pack::palette::PackerPaletteFactory::newPackerPalettes(), core::pack::palette::NCAADefaultPackerPalette::parse_my_tag(), core::pack::palette::DefaultPackerPalette::parse_my_tag(), core::pack::palette::NoDesignPackerPalette::parse_my_tag(), core::pack::palette::PackerPalette::parse_my_tag(), core::pack::palette::NoDesignPackerPalette::set_up_behaviours(), core::pack::palette::NCAADefaultPackerPalette::set_up_behaviours(), and core::pack::palette::DefaultPackerPalette::set_up_behaviours().

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.NCAADefaultPackerPalette"  )

static

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.NoDesignPackerPalette"  )

static

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.DefaultPackerPalette"  )

static

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.PackerPaletteFactory"  )

static

static basic::Tracer core::pack::palette::TR ( "core.pack.palette.PackerPalette"  )

static

void core::pack::palette::xsd_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	packer_palette_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Add a type definition for a PackerPalette.

References complex_type_name_for_packer_palette().

Referenced by core::pack::palette::CustomBaseTypePackerPalette::provide_xml_schema(), core::pack::palette::NCAADefaultPackerPalette::provide_xml_schema(), core::pack::palette::DefaultPackerPalette::provide_xml_schema(), core::pack::palette::NoDesignPackerPalette::provide_xml_schema(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::provide_xml_schema(), protocols::antibody::residue_selector::AntibodyRegionSelector::provide_xml_schema(), and protocols::antibody::residue_selector::CDRResidueSelector::provide_xml_schema().

void core::pack::palette::xsd_type_definition_w_attributes_and_repeatable_subelements	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	packer_palette_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes,
		utility::tag::XMLSchemaSimpleSubelementList const &	subelements
	)

Add a type definition for a PackerPalette, with sub-elements.

References complex_type_name_for_packer_palette().