designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

#include <NucleotideMutation.hh>

Inheritance diagram for protocols::evolution::NucleotideMutation:

[legend]

Public Types
typedef core::pose::Pose	Pose

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	NucleotideMutation ()

void	add_nt_seq_to_pose (core::pose::Pose &pose)

void	find_neighbors (utility::vector1< bool > const &is_mutated, core::pose::Pose const &pose, utility::vector1< bool > &is_flexible, core::Real const heavyatom_distance_threshold)

void	compute_folding_energies (core::scoring::ScoreFunctionOP fa_scorefxn, core::pose::Pose &pose, utility::vector1< bool > const &is_flexible, utility::vector1< bool > const &is_mutpos, core::Size bbnbrs, bool flexbb)

void	apply (Pose &pose) override
	Main Method. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

	~NucleotideMutation () override

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::scoring::ScoreFunctionOP	scorefxn () const

void	scorefxn (core::scoring::ScoreFunctionOP sfxn)

std::string	init_sequence () const

void	init_sequence (std::string const &s)

bool	continue_if_silent () const

void	continue_if_silent (bool const c)

bool	flexbb () const

void	flexbb (bool const f)

core::Size	bbnbrs () const

void	bbnbrs (core::Size const n)

bool	cache_task () const

void	cache_task (bool cache)

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

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	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::scoring::ScoreFunctionOP	scorefxn_

std::string	init_sequence_

bool	continue_if_silent_

bool	flexbb_

core::Size	bbnbrs_

core::pose::PoseOP	reference_pose_

bool	cache_task_

core::pack::task::PackerTaskCOP	task_

Additional Inherited Members
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

Member Typedef Documentation

◆ Pose

typedef core::pose::Pose protocols::evolution::NucleotideMutation::Pose

Constructor & Destructor Documentation

◆ NucleotideMutation()

protocols::evolution::NucleotideMutation::NucleotideMutation ( )

◆ ~NucleotideMutation()

protocols::evolution::NucleotideMutation::~NucleotideMutation ( )

overridedefault

Member Function Documentation

◆ add_nt_seq_to_pose()

void protocols::evolution::NucleotideMutation::add_nt_seq_to_pose ( core::pose::Pose & pose )

References core::chemical::NucleotideTools::aa2randomCodon(), core::pose::add_comment(), init_sequence(), core::pose::Pose::sequence(), and protocols::evolution::TR().

Referenced by apply().

◆ apply()

void protocols::evolution::NucleotideMutation::apply ( Pose & )

overridevirtual

◆ bbnbrs() [1/2]

core::Size protocols::evolution::NucleotideMutation::bbnbrs ( ) const

inline

References bbnbrs_.

Referenced by apply(), compute_folding_energies(), and parse_my_tag().

◆ bbnbrs() [2/2]

void protocols::evolution::NucleotideMutation::bbnbrs ( core::Size const n )

inline

References bbnbrs_.

◆ cache_task() [1/2]

bool protocols::evolution::NucleotideMutation::cache_task ( ) const

References cache_task_.

◆ cache_task() [2/2]

void protocols::evolution::NucleotideMutation::cache_task ( bool cache )

References cache_task_.

◆ clone()

protocols::moves::MoverOP protocols::evolution::NucleotideMutation::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ compute_folding_energies()

void protocols::evolution::NucleotideMutation::compute_folding_energies	(	core::scoring::ScoreFunctionOP	fa_scorefxn,
		core::pose::Pose &	pose,
		utility::vector1< bool > const &	is_flexible,
		utility::vector1< bool > const &	is_mutpos,
		core::Size	bbnbrs = `1`,
		bool	flexbb = `true`
	)

References protocols::relax::FastRelax::apply(), bbnbrs(), protocols::relax::RelaxProtocolBase::cartesian(), flexbb(), protocols::relax::RelaxProtocolBase::set_movemap(), and core::pose::Pose::size().

Referenced by apply().

◆ continue_if_silent() [1/2]

bool protocols::evolution::NucleotideMutation::continue_if_silent ( ) const

inline

References continue_if_silent_.

Referenced by apply(), and parse_my_tag().

◆ continue_if_silent() [2/2]

void protocols::evolution::NucleotideMutation::continue_if_silent ( bool const c )

inline

References continue_if_silent_.

◆ find_neighbors()

void protocols::evolution::NucleotideMutation::find_neighbors	(	utility::vector1< bool > const &	is_mutated,
		core::pose::Pose const &	pose,
		utility::vector1< bool > &	is_flexible,
		core::Real const	heavyatom_distance_threshold = `6.0`
	)

References core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::electron_density::square().

Referenced by apply().

◆ flexbb() [1/2]

bool protocols::evolution::NucleotideMutation::flexbb ( ) const

inline

References flexbb_.

Referenced by apply(), compute_folding_energies(), and parse_my_tag().

◆ flexbb() [2/2]

void protocols::evolution::NucleotideMutation::flexbb ( bool const f )

inline

References flexbb_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::evolution::NucleotideMutation::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::evolution::NucleotideMutation::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ init_sequence() [1/2]

std::string protocols::evolution::NucleotideMutation::init_sequence ( ) const

inline

References init_sequence_.

Referenced by add_nt_seq_to_pose(), and parse_my_tag().

◆ init_sequence() [2/2]

void protocols::evolution::NucleotideMutation::init_sequence ( std::string const & s )

inline

References init_sequence_.

◆ mover_name()

std::string protocols::evolution::NucleotideMutation::mover_name ( )

static

Referenced by get_name(), protocols::evolution::NucleotideMutationCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::evolution::NucleotideMutation::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References bbnbrs(), cache_task_, continue_if_silent(), flexbb(), init_sequence(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn_, and task_factory().

◆ provide_xml_schema()

void protocols::evolution::NucleotideMutation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::evolution::NucleotideMutationCreator::provide_xml_schema().

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::evolution::NucleotideMutation::scorefxn ( ) const

References scorefxn_.

Referenced by apply(), and scorefxn().

◆ scorefxn() [2/2]

void protocols::evolution::NucleotideMutation::scorefxn ( core::scoring::ScoreFunctionOP sfxn )

References scorefxn(), and scorefxn_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::evolution::NucleotideMutation::task_factory ( ) const

References task_factory_.

Referenced by apply(), parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

void protocols::evolution::NucleotideMutation::task_factory ( core::pack::task::TaskFactoryOP tf )

References task_factory(), and task_factory_.

Member Data Documentation

◆ bbnbrs_

core::Size protocols::evolution::NucleotideMutation::bbnbrs_

private

Referenced by bbnbrs().

◆ cache_task_

bool protocols::evolution::NucleotideMutation::cache_task_

private

Referenced by apply(), cache_task(), and parse_my_tag().

◆ continue_if_silent_

bool protocols::evolution::NucleotideMutation::continue_if_silent_

private

Referenced by continue_if_silent().

◆ flexbb_

bool protocols::evolution::NucleotideMutation::flexbb_

private

Referenced by flexbb().

◆ init_sequence_

std::string protocols::evolution::NucleotideMutation::init_sequence_

private

Referenced by init_sequence().

◆ reference_pose_

core::pose::PoseOP protocols::evolution::NucleotideMutation::reference_pose_

private

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::evolution::NucleotideMutation::scorefxn_

private

Referenced by parse_my_tag(), and scorefxn().

◆ task_

core::pack::task::PackerTaskCOP protocols::evolution::NucleotideMutation::task_

private

Referenced by apply().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::evolution::NucleotideMutation::task_factory_

private

Referenced by task_factory().

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

src/protocols/evolution/NucleotideMutation.hh
src/protocols/evolution/NucleotideMutation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Pose

Constructor & Destructor Documentation

◆ NucleotideMutation()

◆ ~NucleotideMutation()

Member Function Documentation

◆ add_nt_seq_to_pose()

◆ apply()

◆ bbnbrs() [1/2]

◆ bbnbrs() [2/2]

◆ cache_task() [1/2]

◆ cache_task() [2/2]

◆ clone()

◆ compute_folding_energies()

◆ continue_if_silent() [1/2]

◆ continue_if_silent() [2/2]

◆ find_neighbors()

◆ flexbb() [1/2]

◆ flexbb() [2/2]

◆ fresh_instance()

◆ get_name()

◆ init_sequence() [1/2]

◆ init_sequence() [2/2]

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

◆ task_factory() [1/2]

◆ task_factory() [2/2]

Member Data Documentation

◆ bbnbrs_

◆ cache_task_

◆ continue_if_silent_

◆ flexbb_

◆ init_sequence_

◆ reference_pose_

◆ scorefxn_

◆ task_

◆ task_factory_