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core::pack::palette Namespace Reference

Classes

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  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  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< CustomBaseTypePackerPaletteCustomBaseTypePackerPaletteOP
 
typedef utility::pointer::shared_ptr< CustomBaseTypePackerPalette const > CustomBaseTypePackerPaletteCOP
 
typedef utility::pointer::shared_ptr< DefaultPackerPaletteDefaultPackerPaletteOP
 
typedef utility::pointer::shared_ptr< DefaultPackerPalette const > DefaultPackerPaletteCOP
 
typedef utility::pointer::shared_ptr< NCAADefaultPackerPaletteNCAADefaultPackerPaletteOP
 
typedef utility::pointer::shared_ptr< NCAADefaultPackerPalette const > NCAADefaultPackerPaletteCOP
 
typedef utility::pointer::shared_ptr< NoDesignPackerPaletteNoDesignPackerPaletteOP
 
typedef utility::pointer::shared_ptr< NoDesignPackerPalette const > NoDesignPackerPaletteCOP
 
typedef utility::pointer::shared_ptr< PackerPalettePackerPaletteOP
 
typedef utility::pointer::shared_ptr< PackerPalette const > PackerPaletteCOP
 
typedef utility::pointer::shared_ptr< PackerPaletteCreatorPackerPaletteCreatorOP
 
typedef utility::pointer::shared_ptr< PackerPaletteCreator const > PackerPaletteCreatorCOP
 
typedef utility::pointer::shared_ptr< PackerPaletteFactoryPackerPaletteFactoryOP
 
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

◆ CustomBaseTypePackerPaletteCOP

◆ CustomBaseTypePackerPaletteOP

◆ DefaultPackerPaletteCOP

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

◆ DefaultPackerPaletteOP

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

◆ NCAADefaultPackerPaletteCOP

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

◆ NCAADefaultPackerPaletteOP

◆ NoDesignPackerPaletteCOP

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

◆ NoDesignPackerPaletteOP

◆ PackerPaletteCOP

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

◆ PackerPaletteCreatorCOP

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

◆ PackerPaletteCreatorOP

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

◆ PackerPaletteFactoryCOP

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

◆ PackerPaletteFactoryOP

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

◆ PackerPaletteOP

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

Enumeration Type Documentation

◆ 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

◆ complex_type_name_for_packer_palette()

std::string core::pack::palette::complex_type_name_for_packer_palette ( std::string const &  packer_palette_name)

◆ TR() [1/6]

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

◆ TR() [2/6]

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

◆ TR() [3/6]

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

◆ TR() [4/6]

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

◆ TR() [5/6]

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

◆ TR() [6/6]

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

◆ xsd_type_definition_w_attributes()

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 
)

◆ xsd_type_definition_w_attributes_and_repeatable_subelements()

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().