core::pack::task::operation::DisallowIfNonnative Class Reference

DisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below. More...

#include <TaskOperations.hh>

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

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

Public Member Functions
	DisallowIfNonnative ()
	DisallowIfNonnative (utility::vector1< bool > const &disallowed_aas)
	DisallowIfNonnative (utility::vector1< bool > const &disallowed_aas, utility::vector1< core::Size > const &res_selection)
	~DisallowIfNonnative () override
TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...
void	apply (pose::Pose const &, PackerTask &) 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...
void	clear ()
void	disallow_aas (utility::vector1< bool > const &canonical_disallowed)
void	disallow_aas (std::string const &aa_string)
void	restrict_to_residue (core::Size const &resid)
void	restrict_to_residue (utility::vector1< core::Size > const &residues)
void	parse_tag (TagCOP, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. 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 ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
utility::vector1< bool >	invert_vector (utility::vector1< bool > disallowed_aas)

Private Attributes
utility::vector1< core::Size >	residue_selection_
utility::vector1< bool >	disallowed_aas_
utility::vector1< bool >	allowed_aas_

Detailed Description

DisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below.

Member Typedef Documentation

parent

typedef TaskOperation core::pack::task::operation::DisallowIfNonnative::parent

Constructor & Destructor Documentation

DisallowIfNonnative() [1/3]

core::pack::task::operation::DisallowIfNonnative::DisallowIfNonnative

(

)

DisallowIfNonnative() [2/3]

core::pack::task::operation::DisallowIfNonnative::DisallowIfNonnative

(

utility::vector1< bool > const &

disallowed_aas

)

DisallowIfNonnative() [3/3]

core::pack::task::operation::DisallowIfNonnative::DisallowIfNonnative	(	utility::vector1< bool > const &	disallowed_aas,
		utility::vector1< core::Size > const &	res_selection
	)

~DisallowIfNonnative()

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

overridedefault

Member Function Documentation

apply()

void core::pack::task::operation::DisallowIfNonnative::apply ( pose::Pose const &  , 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 allowed_aas_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, residue_selection_, core::pack::task::ResidueLevelTask::restrict_nonnative_canonical_aas(), and core::pack::task::PackerTask::total_residue().

clear()

void core::pack::task::operation::DisallowIfNonnative::clear

(

)

References allowed_aas_, disallowed_aas_, and residue_selection_.

clone()

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

overridevirtual

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

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

disallow_aas() [1/2]

void core::pack::task::operation::DisallowIfNonnative::disallow_aas

(

std::string const &

aa_string

)

References core::chemical::aa_from_oneletter_code(), allowed_aas_, disallowed_aas_, invert_vector(), core::chemical::num_canonical_aas, and core::chemical::oneletter_code_specifies_aa().

disallow_aas() [2/2]

void core::pack::task::operation::DisallowIfNonnative::disallow_aas

(

utility::vector1< bool > const &

canonical_disallowed

)

References allowed_aas_, disallowed_aas_, invert_vector(), and core::chemical::num_canonical_aas.

Referenced by parse_tag().

invert_vector()

utility::vector1< bool > core::pack::task::operation::DisallowIfNonnative::invert_vector ( utility::vector1< bool >  disallowed_aas )

private

References disallowed_aas_.

Referenced by disallow_aas().

keyname()

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

static

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

parse_tag()

void core::pack::task::operation::DisallowIfNonnative::parse_tag ( TagCOP  tag, DataMap &    )

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

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

References disallow_aas(), and restrict_to_residue().

provide_xml_schema()

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

static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

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

restrict_to_residue() [1/2]

void core::pack::task::operation::DisallowIfNonnative::restrict_to_residue

(

core::Size const &

resid

)

References residue_selection_.

Referenced by parse_tag().

restrict_to_residue() [2/2]

void core::pack::task::operation::DisallowIfNonnative::restrict_to_residue

(

utility::vector1< core::Size > const &

residues

)

References residue_selection_.

Member Data Documentation

allowed_aas_

utility::vector1< bool > core::pack::task::operation::DisallowIfNonnative::allowed_aas_

private

Referenced by apply(), clear(), and disallow_aas().

disallowed_aas_

utility::vector1< bool > core::pack::task::operation::DisallowIfNonnative::disallowed_aas_

private

Referenced by clear(), disallow_aas(), and invert_vector().

residue_selection_

utility::vector1< core::Size > core::pack::task::operation::DisallowIfNonnative::residue_selection_

private

Referenced by apply(), clear(), and restrict_to_residue().

---

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

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