A mover to mutate a single residue. More...

#include <MutateResidue.hh>

Inheritance diagram for protocols::simple_moves::MutateResidue:

Public Member Functions
	MutateResidue ()
	default ctor More...

	MutateResidue (MutateResidue const &dm)
	copy ctor More...

	MutateResidue (core::Size const target, std::string new_res)
	Mutate a single residue to a new amino acid. More...

	MutateResidue (core::Size const target, int new_res)

	MutateResidue (core::Size const target, core::chemical::AA const aa)

	~MutateResidue () override=default

void	apply (core::pose::Pose &pose) override

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 &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	Reinitialize this protocols::moves::Mover with parameters from the specified tags. More...

void	set_target (std::string const &target_in)
	Set this mover's target residue index. More...

void	set_target (core::Size const target_in)
	Set this mover's target residue index, based on the Rosetta indexing. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set a selector if specified by the user. More...

std::string	target () const
	Get this mover's target residue index. More...

void	set_res_name (std::string const &name_in)
	Set the residue to mutate to. More...

void	set_res_name (core::chemical::AA const &aa)

void	set_update_polymer_dependent (bool const setting)
	Set whether this mover updates polymer-dependent atoms in the residue that it mutates. More...

bool	update_polymer_dependent () const
	Set whether this mover updates polymer-dependent atoms in the residue that it mutates. More...

std::string	res_name ()
	Get the residue to mutate to. More...

void	set_preserve_atom_coords (bool const val)
	Set whether the mover should try to preserve atoms' xyz coordinates or not. More...

bool	preserve_atom_coords ()
	Get whether the mover should try to preserve atoms' xyz coordinates or not. More...

void	make_mutation (core::pose::Pose &, core::Size)

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 ()

	~Mover () override

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 type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 Types
typedef protocols::moves::Mover	parent

Private Attributes
std::string	target_
	The index of the residue to mutate. More...

std::string	res_name_
	The name (full name, not three-letter code) of the residue to mutate to. More...

bool	preserve_atom_coords_
	Should the mover try to preserve the xyz coordinates of the atoms in the side-chain if the new residue has an atom name matching an atom name in the old residue? Default false. More...

bool	mutate_self_
	If true, mutates the residue to itself, ie. Ala -> Ala. This fixes some problems with TerCards being attached to residues that shouldn't have them for RotamerLinks. More...

bool	update_polymer_dependent_
	If true, updates polymer-dependent atoms. More...

core::select::residue_selector::ResidueSelectorCOP	selector_
	gets a residue selector More...

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

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

A mover to mutate a single residue.

Member Typedef Documentation

typedef protocols::moves::Mover protocols::simple_moves::MutateResidue::parent

private

Constructor & Destructor Documentation

protocols::simple_moves::MutateResidue::MutateResidue ( )

default ctor

protocols::simple_moves::MutateResidue::MutateResidue ( MutateResidue const & dm )

copy ctor

protocols::simple_moves::MutateResidue::MutateResidue	(	core::Size const	target,
		std::string	new_res
	)

Mutate a single residue to a new amino acid.

new_res is three letter code in capital letters, example PHE

Parameters

target	The residue index to mutate
new_res	The name of the replacement residue

References set_target().

protocols::simple_moves::MutateResidue::MutateResidue	(	core::Size const	target,
		int	new_res
	)

References set_target().

protocols::simple_moves::MutateResidue::MutateResidue	(	core::Size const	target,
		core::chemical::AA const	aa
	)

References set_target().

protocols::simple_moves::MutateResidue::~MutateResidue ( )

overridedefault

Member Function Documentation

void protocols::simple_moves::MutateResidue::apply ( core::pose::Pose & pose )

overridevirtual

Implements protocols::moves::Mover.

References make_mutation(), core::pose::parse_resnum(), selector_, target(), and core::pose::Pose::total_residue().

Referenced by protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::denovo_design::construct_poly_ala_pose(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), and protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala().

protocols::moves::MoverOP protocols::simple_moves::MutateResidue::clone ( ) const

inlineoverridevirtual

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.

protocols::moves::MoverOP protocols::simple_moves::MutateResidue::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.

std::string protocols::simple_moves::MutateResidue::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::simple_moves::MutateResidue::make_mutation	(	core::pose::Pose &	pose,
		core::Size	rosetta_target
	)

References core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pose::get_restype_for_pose(), core::chemical::ResidueType::mode(), mutate_self_, core::conformation::Residue::name3(), preserve_atom_coords(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only(), core::pose::Pose::replace_residue(), res_name_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), set_res_name(), core::pose::Pose::size(), protocols::simple_moves::TR(), and update_polymer_dependent().

Referenced by apply().

std::string protocols::simple_moves::MutateResidue::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::MutateResidueCreator::keyname(), and provide_xml_schema().

void protocols::simple_moves::MutateResidue::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

overridevirtual

Reinitialize this protocols::moves::Mover with parameters from the specified tags.

Parameters recognized:

target_pdb_num or target_res_num. A single target residue to form disulfides to
target_pdb_nums or target_res_nums. A list of possible target residues

Reimplemented from protocols::moves::Mover.

References mutate_self_, protocols::rosetta_scripts::parse_residue_selector(), set_preserve_atom_coords(), set_res_name(), set_selector(), set_target(), set_update_polymer_dependent(), protocols::simple_moves::TR(), and update_polymer_dependent().

bool protocols::simple_moves::MutateResidue::preserve_atom_coords ( )

inline

Get whether the mover should try to preserve atoms' xyz coordinates or not.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References preserve_atom_coords_.

Referenced by make_mutation().

void protocols::simple_moves::MutateResidue::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::MutateResidueCreator::provide_xml_schema().

std::string protocols::simple_moves::MutateResidue::res_name ( )

inline

Get the residue to mutate to.

This is the full name, not the three-letter code.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References res_name_.

void protocols::simple_moves::MutateResidue::set_preserve_atom_coords ( bool const val )

inline

Set whether the mover should try to preserve atoms' xyz coordinates or not.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References preserve_atom_coords_, and protocols::hybridization::val.

Referenced by protocols::cyclic_peptide::threefold_linker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::threefold_linker::TBMB_Helper::add_linker_symmetric(), protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), and parse_my_tag().

void protocols::simple_moves::MutateResidue::set_res_name ( std::string const & name_in )

inline

Set the residue to mutate to.

This is the full name, not the three-letter code.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References res_name_.

Referenced by make_mutation(), and parse_my_tag().

void protocols::simple_moves::MutateResidue::set_res_name ( core::chemical::AA const & aa )

References core::chemical::name_from_aa(), and res_name_.

void protocols::simple_moves::MutateResidue::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set a selector if specified by the user.

References selector_.

Referenced by parse_my_tag().

void protocols::simple_moves::MutateResidue::set_target ( std::string const & target_in )

inline

Set this mover's target residue index.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References target_.

Referenced by MutateResidue(), and parse_my_tag().

void protocols::simple_moves::MutateResidue::set_target ( core::Size const target_in )

Set this mover's target residue index, based on the Rosetta indexing.

References target_.

void protocols::simple_moves::MutateResidue::set_update_polymer_dependent ( bool const setting )

inline

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References update_polymer_dependent_.

Referenced by parse_my_tag().

std::string protocols::simple_moves::MutateResidue::target ( ) const

inline

Get this mover's target residue index.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References target_.

Referenced by apply().

bool protocols::simple_moves::MutateResidue::update_polymer_dependent ( ) const

inline

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References update_polymer_dependent_.

Referenced by make_mutation(), and parse_my_tag().

Member Data Documentation

bool protocols::simple_moves::MutateResidue::mutate_self_

private

If true, mutates the residue to itself, ie. Ala -> Ala. This fixes some problems with TerCards being attached to residues that shouldn't have them for RotamerLinks.

Referenced by make_mutation(), and parse_my_tag().

bool protocols::simple_moves::MutateResidue::preserve_atom_coords_

private

Should the mover try to preserve the xyz coordinates of the atoms in the side-chain if the new residue has an atom name matching an atom name in the old residue? Default false.

Referenced by preserve_atom_coords(), and set_preserve_atom_coords().

std::string protocols::simple_moves::MutateResidue::res_name_

private

The name (full name, not three-letter code) of the residue to mutate to.

Referenced by make_mutation(), res_name(), and set_res_name().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::MutateResidue::selector_

private

gets a residue selector

Referenced by apply(), and set_selector().

std::string protocols::simple_moves::MutateResidue::target_

private

The index of the residue to mutate.