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:

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

Public Types
typedef TaskOperation	parent
Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr
typedef pose::Pose	Pose

Public Member Functions
	DisallowIfNonnative ()
	DisallowIfNonnative (utility::vector1< bool > disallowed_aas)
	DisallowIfNonnative (utility::vector1< bool > disallowed_aas, utility::vector1< core::Size > res_selection)
virtual	~DisallowIfNonnative ()
virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...
virtual void	apply (pose::Pose const &, PackerTask &) const
	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 &cannonical_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)
virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...
virtual void	parse_def (utility::lua::LuaObject const &def)
Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

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.

Definition at line 123 of file TaskOperations.hh.

Member Typedef Documentation

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

Definition at line 126 of file TaskOperations.hh.

Constructor & Destructor Documentation

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

(

)

Definition at line 213 of file TaskOperations.cc.

Referenced by clone().

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

(

utility::vector1< bool >

disallowed_aas)

Definition at line 218 of file TaskOperations.cc.

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

Definition at line 223 of file TaskOperations.cc.

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

virtual

Definition at line 229 of file TaskOperations.cc.

Member Function Documentation

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

virtual

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.

Definition at line 257 of file TaskOperations.cc.

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().

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

(

)

Definition at line 241 of file TaskOperations.cc.

References allowed_aas_, disallowed_aas_, and residue_selection_.

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

virtual

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

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

Definition at line 236 of file TaskOperations.cc.

References DisallowIfNonnative().

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

(

utility::vector1< bool > const &

cannonical_disallowed)

Definition at line 272 of file TaskOperations.cc.

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

Referenced by parse_def(), and parse_tag().

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

(

std::string const &

aa_string)

Definition at line 277 of file TaskOperations.cc.

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

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

private

Definition at line 249 of file TaskOperations.cc.

References disallowed_aas_.

Referenced by disallow_aas().

void core::pack::task::operation::DisallowIfNonnative::parse_def ( utility::lua::LuaObject const &  def)

virtual

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

Definition at line 309 of file TaskOperations.cc.

References disallow_aas(), and restrict_to_residue().

void core::pack::task::operation::DisallowIfNonnative::parse_tag ( TagPtr  tag)

virtual

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

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

Definition at line 304 of file TaskOperations.cc.

References disallow_aas(), and restrict_to_residue().

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

(

core::Size const &

resid)

Definition at line 295 of file TaskOperations.cc.

References residue_selection_.

Referenced by parse_def(), and parse_tag().

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

(

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

residues)

Definition at line 299 of file TaskOperations.cc.

References residue_selection_.

Member Data Documentation

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

private

Definition at line 155 of file TaskOperations.hh.

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

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

private

Definition at line 154 of file TaskOperations.hh.

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

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

private

Definition at line 153 of file TaskOperations.hh.

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