PackerPalette.hh File Reference

PackerPalette: a class for storing the set of ResidueTypes and VariantTypes that the packer uses by default, in the absence of any TaskOperations that limit the set actually used. More...

#include <core/pack/palette/PackerPalette.fwd.hh>
#include <core/chemical/ResidueProperty.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.fwd.hh>
#include <basic/datacache/DataMap.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/VirtualBase.hh>
#include <utility/thread/mutable_cache.hh>
#include <basic/citation_manager/CitationCollectionBase.fwd.hh>
#include <map>
#include <list>
#include <utility/vector1.hh>

Classes
class	core::pack::palette::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	core::pack::palette::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...

Namespaces
	core
	A class for reading in the atom type properties.
	core::pack
	core::pack::palette

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

Detailed Description

PackerPalette: a class for storing the set of ResidueTypes and VariantTypes that the packer uses by default, in the absence of any TaskOperations that limit the set actually used.

The PackerPalette says, "Here are the types that you're allowed to use, and which are on in the absence of TaskOperations." TaskOperations then prune this, turning OFF types that have been enabled. This allows users to turn on noncanonicals for design, and then use TaskOperations with the same commutativity rules (turning OFF types only) that are used for canonicals, making mixed design with canonicals and noncanonicals much easier.\nThis was implemented as part of the 2016 Chemical XRW (eXtreme Rosetta Workshop).

Author

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu).