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core::pack::palette::CustomBaseTypePackerPalette Class Reference

CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time). More...

#include <CustomBaseTypePackerPalette.hh>

Inheritance diagram for core::pack::palette::CustomBaseTypePackerPalette:
Inheritance graph
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Public Member Functions

 CustomBaseTypePackerPalette ()
 Default constructor. More...
 
 ~CustomBaseTypePackerPalette () 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...
 
bool has_type (std::string const &type) const
 Test if this CustomBaseTypePackerPalette has the provided type already. Note that this only tests for explicitly added types. It will not test for default types. More...
 
void add_type (std::string const &type)
 Add a ResidueType (by base type full name – not 3-letter code) to the set of ResidueTypes being used for design. More...
 
void parse_additional_residue_types (std::string const &typelist)
 Given a comma-separated list of additional residue types, separate it out and add the additonal types to the types used for design. More...
 
void initialize_from_file_contents (std::string const &file_contents, std::string const &filename)
 Given a whitespace-separated list of residue base names from a file, parse the file contents and set up this CustomBaseTypePackerPalette. More...
 
std::string const & name () const override
 Get the name of this object ("CustomBaseTypePackerPalette"). More...
 
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. 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 add_xsd_options (utility::tag::AttributeList &attlist)
 Add the options for this PackerPalette to the AttributeList. More...
 
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 CustomBaseTypePackerPalette with the default set of position-specific behaviours. More...
 

Private Attributes

utility::vector1< std::string > additional_residue_types_
 

Detailed Description

CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time).

Member Typedef Documentation

The parent class (PackerPalette).

Constructor & Destructor Documentation

core::pack::palette::CustomBaseTypePackerPalette::CustomBaseTypePackerPalette ( )

Default constructor.

References set_up_behaviours().

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

Destructor.

Member Function Documentation

void core::pack::palette::CustomBaseTypePackerPalette::add_type ( std::string const &  type)

Add a ResidueType (by base type full name – not 3-letter code) to the set of ResidueTypes being used for design.

References additional_residue_types_.

Referenced by initialize_from_file_contents(), and parse_additional_residue_types().

void core::pack::palette::CustomBaseTypePackerPalette::add_xsd_options ( utility::tag::AttributeList &  attlist)
static

Add the options for this PackerPalette to the AttributeList.

Referenced by provide_xml_schema().

PackerPaletteOP core::pack::palette::CustomBaseTypePackerPalette::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::CustomBaseTypePackerPalette::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::add_base_residue_type(), additional_residue_types_, and core::pack::palette::PackerPalette::set_up_default_base_types().

bool core::pack::palette::CustomBaseTypePackerPalette::has_type ( std::string const &  type) const

Test if this CustomBaseTypePackerPalette has the provided type already. Note that this only tests for explicitly added types. It will not test for default types.

References additional_residue_types_.

void core::pack::palette::CustomBaseTypePackerPalette::initialize_from_file_contents ( std::string const &  file_contents,
std::string const &  filename 
)

Given a whitespace-separated list of residue base names from a file, parse the file contents and set up this CustomBaseTypePackerPalette.

Appends to any other base types already set up.

References add_type(), and name().

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

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

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

Referenced by initialize_from_file_contents(), parse_my_tag(), and provide_citation_info().

void core::pack::palette::CustomBaseTypePackerPalette::parse_additional_residue_types ( std::string const &  typelist)

Given a comma-separated list of additional residue types, separate it out and add the additonal types to the types used for design.

calls CustomBaseTypePackerPalette::add_type().

References add_type().

Referenced by parse_my_tag().

void core::pack::palette::CustomBaseTypePackerPalette::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 name(), and parse_additional_residue_types().

void core::pack::palette::CustomBaseTypePackerPalette::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual

Provide the citation.

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

References name().

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

Member Data Documentation

utility::vector1< std::string > core::pack::palette::CustomBaseTypePackerPalette::additional_residue_types_
private

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