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:

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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

typedef PackerPalette core::pack::palette::CustomBaseTypePackerPalette::parent

private

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] restypeset The 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

Provide information about the XML options available for this PackerPalette.

References add_xsd_options(), and core::pack::palette::xsd_type_definition_w_attributes().

Referenced by core::pack::palette::CustomBaseTypePackerPaletteCreator::provide_xml_schema().

void core::pack::palette::CustomBaseTypePackerPalette::set_up_behaviours ( )

private

Set up the CustomBaseTypePackerPalette with the default set of position-specific behaviours.

References core::pack::palette::PackerPalette::set_only_design_polymer_residues(), core::pack::palette::PackerPalette::set_only_design_protein_peptoid_dna_saccharide(), and core::pack::palette::PackerPalette::set_up_default_special_behaviours().

Referenced by CustomBaseTypePackerPalette().

Member Data Documentation

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

private

Referenced by add_type(), get_base_residue_types(), and has_type().

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

src/core/pack/palette/CustomBaseTypePackerPalette.hh
src/core/pack/palette/CustomBaseTypePackerPalette.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation