A mover to mutate a single residue. More...
#include <MutateResidue.hh>
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 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 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
◆ parent
Constructor & Destructor Documentation
◆ MutateResidue() [1/5]
| protocols::simple_moves::MutateResidue::MutateResidue | ( | ) |
default ctor
◆ MutateResidue() [2/5]
|
default |
copy ctor
◆ MutateResidue() [3/5]
| 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
-
target The residue index to mutate new_res The name of the replacement residue
References set_target(), and target().
◆ MutateResidue() [4/5]
| protocols::simple_moves::MutateResidue::MutateResidue | ( | core::Size const | target, |
| int | new_res | ||
| ) |
References set_target(), and target().
◆ MutateResidue() [5/5]
| protocols::simple_moves::MutateResidue::MutateResidue | ( | core::Size const | target, |
| core::chemical::AA const | aa | ||
| ) |
References set_target(), and target().
◆ ~MutateResidue()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
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::denovo_design::movers::FastDesign::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), protocols::denovo_design::construct_poly_ala_pose(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine().
◆ break_a_disulfide()
|
private |
Given that position X is involved in a disulfide bond, break the disulfide between the residue at position X and its partner.
References core::chemical::ResidueTypeBase::base_name(), core::conformation::break_disulfide(), core::pose::Pose::conformation(), core::conformation::get_disulf_partner(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::residue_type(), and protocols::simple_moves::TR().
Referenced by make_mutation().
◆ break_disulfide_bonds()
|
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.
References break_disulfide_bonds_.
Referenced by make_mutation(), and parse_my_tag().
◆ clone()
|
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.
◆ fresh_instance()
|
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()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ make_mutation()
|
private |
Actually make a mutation at a position, based on the current configuration of this mover.
References core::chemical::ResidueTypeBase::base_name(), break_a_disulfide(), break_disulfide_bonds(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::get_disulf_partner(), core::pose::get_restype_for_pose(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueTypeBase::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().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::simple_moves::MutateResidueCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
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().
◆ preserve_atom_coords()
|
inline |
Get whether the mover should try to preserve atoms' xyz coordinates or not.
References preserve_atom_coords_.
Referenced by make_mutation().
◆ provide_xml_schema()
|
static |
◆ res_name()
|
inline |
Get the residue to mutate to.
This is the full name, not the three-letter code.
References res_name_.
◆ set_break_disulfide_bonds()
| 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.
References break_disulfide_bonds_.
Referenced by parse_my_tag().
◆ set_preserve_atom_coords()
|
inline |
Set whether the mover should try to preserve atoms' xyz coordinates or not.
References preserve_atom_coords_, and protocols::hybridization::val.
Referenced by protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), and parse_my_tag().
◆ set_res_name() [1/2]
| void protocols::simple_moves::MutateResidue::set_res_name | ( | core::chemical::AA const & | aa | ) |
References protocols::cluster::calibur::aa, core::chemical::name_from_aa(), and res_name_.
◆ set_res_name() [2/2]
|
inline |
Set the residue to mutate to.
This is the full name, not the three-letter code.
References res_name_.
Referenced by make_mutation(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), and parse_my_tag().
◆ set_selector()
| void protocols::simple_moves::MutateResidue::set_selector | ( | core::select::residue_selector::ResidueSelectorCOP | selector_in | ) |
◆ set_target() [1/2]
| 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_.
◆ set_target() [2/2]
|
inline |
Set this mover's target residue index.
References target_.
Referenced by protocols::kinematic_closure::ClosureProblem::mutate_residues(), MutateResidue(), and parse_my_tag().
◆ set_update_polymer_dependent()
|
inline |
Set whether this mover updates polymer-dependent atoms in the residue that it mutates.
References update_polymer_dependent_.
Referenced by parse_my_tag().
◆ target()
|
inline |
Get this mover's target residue index.
References target_.
Referenced by apply(), and MutateResidue().
◆ update_polymer_dependent()
|
inline |
Set whether this mover updates polymer-dependent atoms in the residue that it mutates.
References update_polymer_dependent_.
Referenced by make_mutation(), and parse_my_tag().
Member Data Documentation
◆ break_disulfide_bonds_
|
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().
◆ 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().
◆ 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().
◆ 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().
◆ selector_
|
private |
gets a residue selector
Referenced by apply(), and set_selector().
◆ target_
|
private |
The index of the residue to mutate.
In Rosetta residue numbering, PDB numbering, or ReferencePose numbering.
Referenced by set_target(), and target().
◆ update_polymer_dependent_
|
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:
- src/protocols/simple_moves/MutateResidue.hh
- src/protocols/simple_moves/MutateResidue.cc
