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protocols::simple_moves::MutateResidue Class Reference

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

#include <MutateResidue.hh>

Inheritance diagram for protocols::simple_moves::MutateResidue:
Inheritance graph
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Public Member Functions

 MutateResidue ()
 default ctor More...
 
 MutateResidue (MutateResidue const &dm)
 copy ctor More...
 
 MutateResidue (core::Size const target, std::string const &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
 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
 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...
 
void set_break_disulfide_bonds (bool const setting)
 Set whether disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else. More...
 
bool break_disulfide_bonds () const
 Get whether disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else. 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...
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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 Member Functions

void make_mutation (core::pose::Pose &, core::Size)
 Actually make a mutation at a position, based on the current configuration of this mover. More...
 
void break_a_disulfide (core::pose::Pose &pose, core::Size const rosetta_target) const
 Given that position X is involved in a disulfide bond, break the disulfide between the residue at position X and its partner. More...
 

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_ = false
 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_ = false
 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_ = false
 If true, updates polymer-dependent atoms. More...
 
bool break_disulfide_bonds_ = true
 If true, ensure that disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else. 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 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

Constructor & Destructor Documentation

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

default ctor

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

copy ctor

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

Mutate a single residue to a new amino acid.

new_res is three letter code in capital letters, example PHE

Parameters
targetThe residue index to mutate
new_resThe 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 )
overridevirtual
void protocols::simple_moves::MutateResidue::break_a_disulfide ( core::pose::Pose pose,
core::Size const  rosetta_target 
) const
private
bool protocols::simple_moves::MutateResidue::break_disulfide_bonds ( ) const
inline

Get whether disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else.

True by default. If false, the other cysteine will still think that it is disulfide-bonded to something, and scoring will fail.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References break_disulfide_bonds_.

Referenced by make_mutation(), and parse_my_tag().

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 
)
private
std::string protocols::simple_moves::MutateResidue::mover_name ( )
static
void protocols::simple_moves::MutateResidue::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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 break_disulfide_bonds(), mutate_self_, core::select::residue_selector::parse_residue_selector(), set_break_disulfide_bonds(), 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
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_break_disulfide_bonds ( bool const  setting)

Set whether disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else.

True by default. If false, the other cysteine will still think that it is disulfide-bonded to something, and scoring will fail.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References break_disulfide_bonds_.

Referenced by parse_my_tag().

void protocols::simple_moves::MutateResidue::set_preserve_atom_coords ( bool const  val)
inline
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(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), and parse_my_tag().

void protocols::simple_moves::MutateResidue::set_res_name ( core::chemical::AA const &  aa)
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 protocols::kinematic_closure::ClosureProblem::mutate_residues(), 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 protocols::tcr::match_template_and_target_sequence(), and 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::break_disulfide_bonds_ = true
private

If true, ensure that disulfide bonds are properly broken when mutating from a disulfide-bonded cysteine to anything else.

True by default. If false, the other cysteine will still think that it is disulfide-bonded to something, and scoring will fail.

Referenced by break_disulfide_bonds(), and set_break_disulfide_bonds().

bool protocols::simple_moves::MutateResidue::mutate_self_ = false
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_ = false
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.

In Rosetta residue numbering, PDB numbering, or ReferencePose numbering.

Referenced by set_target(), and target().

bool protocols::simple_moves::MutateResidue::update_polymer_dependent_ = false
private

If true, updates polymer-dependent atoms.

false by default.

Referenced by set_update_polymer_dependent(), and update_polymer_dependent().


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