core::pack::task::operation::DesignRestrictions Class Reference

Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely. More...

#include <DesignRestrictions.hh>

Inheritance diagram for core::pack::task::operation::DesignRestrictions:

Public Member Functions
	DesignRestrictions ()
	DesignRestrictions (DesignRestrictions const &src)
	~DesignRestrictions () override
core::pack::task::operation::TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...
void	add_selector_rlto_pair (select::residue_selector::ResidueSelectorCOP selector, ResLvlTaskOperationCOP rlto)
void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Configure from a RosettaScripts XML tag. More...
void	apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
Public Member Functions inherited from core::pack::task::operation::TaskOperation
	~TaskOperation () override
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	keyname ()
	Return the name used to construct this TaskOperation from an XML file. More...
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Describe the format of XML file used to initialize this TaskOperation. More...

Private Types
typedef std::pair < select::residue_selector::ResidueSelectorCOP, std::list < ResLvlTaskOperationCOP > >	action_pair

Private Attributes
std::list< action_pair >	actions_

Additional Inherited Members
Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap
typedef pose::Pose	Pose

Detailed Description

Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely.

Basically, we want to be able to encode layer design as follows: <RESIDUE_SELECTORS> 
 <Layer name="surface" select_core="false" select_boundary="false" select_surface="true" use_sidechain_neighbors="true"> <Layer name="boundary" select_core="false" select_boundary="true" select_surface="false" use_sidechain_neighbors="true"> <Layer name="core" select_core="true" select_boundary="false" select_surface="false" use_sidechain_neighbors="true"> <SecondaryStructure name="helix" overlap="0" minh="3" include_terminal_loops="false" use_dssp="true" ss="H"> <SecondaryStructure name="sheet" overlap="0" mine="3" include_terminal_loops="false" use_dssp="true" ss="E"> <SecondaryStructure name="loop" overlap="0" minh="3" mine="3" include_terminal_loops="true" use_dssp="true" ss="L"> </RESIDUE_SELECTORS> <TASKOPERATIONS> 
 <DesignRestrictions name="layer_design"> <Action selector_logic="surface AND ( helix OR sheet) " aas="DEHKNQRST"> <Action selector_logic="surface AND loop" aas="DEGHKNPQRST"> <Action selector_logic="boundary AND helix" aas="ADEIKLMNQRSTVWY"> <Action selector_logic="boundary AND sheet" aas="DEFIKLNQRSTVWY"> <Action selector_logic="boundary AND loop" aas="ADEFGIKLMNPQRSTVWY"> <Action selector_logic="core AND helix" aas="AFILMVWY"> <Action selector_logic="core AND sheet" aas="FILVWY"> <Action selector_logic="core AND loop" aas="AFILMPVWY"> </DesignRestrictions> 
 </TASKOPERATIONS> So that it then becomes easy to adapt it to change the logic; e.g. if residues 19, 21, and 23 should keep their native amino acid, and still be allowed to pack, then it will look like this

<RESIDUE_SELECTORS> ... the surface, boundary, core, helix, sheet and loop selectors listed above ... <ResidueIndexSelector name="special_res" resnums="19,21,23"> <RESIDUE_LEVEL_TASK_OPERATIONS> <RestrictToRepackingRLT name="rtr"> <RESIDUE_LEVEL_TASK_OPERATIONS> <TASKOPERATIONS> 
 <DesignRestrictions name="custom_layer_design"> <Action residue_selector="special_res" residue_level_operations="rtr"> <Action selector_logic="!special_res AND surface AND ( helix OR sheet) " aas="DEHKNQRST"> <Action selector_logic="!special_res AND surface AND loop" aas="DEGHKNPQRST"> <Action selector_logic="!special_res AND boundary AND helix" aas="ADEIKLMNQRSTVWY"> <Action selector_logic="!special_res AND boundary AND sheet" aas="DEFIKLNQRSTVWY"> <Action selector_logic="!special_res AND boundary AND loop" aas="ADEFGIKLMNPQRSTVWY"> <Action selector_logic="!special_res AND core AND helix" aas="AFILMVWY"> <Action selector_logic="!special_res AND core AND sheet" aas="FILVWY"> <Action selector_logic="!special_res AND core AND loop" aas="AFILMPVWY"> </DesignRestrictions> 
 </TASKOPERATIONS> Where the second "Action" above is saying "apply this to residues besides the special residues that are on surface loops"

Member Typedef Documentation

typedef std::pair< select::residue_selector::ResidueSelectorCOP, std::list< ResLvlTaskOperationCOP > > core::pack::task::operation::DesignRestrictions::action_pair

private

Constructor & Destructor Documentation

core::pack::task::operation::DesignRestrictions::DesignRestrictions

(

)

core::pack::task::operation::DesignRestrictions::DesignRestrictions

(

DesignRestrictions const &

src

)

core::pack::task::operation::DesignRestrictions::~DesignRestrictions ( )

override

Member Function Documentation

void core::pack::task::operation::DesignRestrictions::add_selector_rlto_pair	(	select::residue_selector::ResidueSelectorCOP	selector,
		ResLvlTaskOperationCOP	rlto
	)

References actions_.

void core::pack::task::operation::DesignRestrictions::apply ( core::pose::Pose const &  , core::pack::task::PackerTask &    ) const

overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

References actions_, and core::pack::task::PackerTask::nonconst_residue_task().

TaskOperationOP core::pack::task::operation::DesignRestrictions::clone ( ) const

overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

std::string core::pack::task::operation::DesignRestrictions::keyname ( )

static

Return the name used to construct this TaskOperation from an XML file.

Referenced by core::pack::task::operation::DesignRestrictionsCreator::keyname(), and provide_xml_schema().

void core::pack::task::operation::DesignRestrictions::parse_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  dm  )

overridevirtual

Configure from a RosettaScripts XML tag.

Reimplemented from core::pack::task::operation::TaskOperation.

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), actions_, core::chemical::is_canonical_L_aa_or_gly(), core::chemical::oneletter_code_specifies_aa(), core::pack::task::operation::parse_residue_level_task_operations(), core::select::residue_selector::parse_residue_selector(), and core::select::residue_selector::parse_residue_selector_logic_string().

void core::pack::task::operation::DesignRestrictions::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

Describe the format of XML file used to initialize this TaskOperation.

References core::pack::task::operation::attributes_for_parse_residue_level_operations(), core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), core::select::residue_selector::attributes_for_parse_residue_selector_logic_string(), core::pack::task::operation::complex_type_name_for_task_op(), and keyname().

Referenced by core::pack::task::operation::DesignRestrictionsCreator::provide_xml_schema().

Member Data Documentation

std::list< action_pair > core::pack::task::operation::DesignRestrictions::actions_

private

Referenced by add_selector_rlto_pair(), apply(), and parse_tag().

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

• src/core/pack/task/operation/DesignRestrictions.hh
• src/core/pack/task/operation/DesignRestrictions.cc