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protocols::carbohydrates::TautomerizeAnomerMover Class Reference

A Mover class for tautomerizing from one anomer to another at a reducing end. More...

#include <TautomerizeAnomerMover.hh>

Inheritance diagram for protocols::carbohydrates::TautomerizeAnomerMover:
Inheritance graph
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Public Member Functions

 TautomerizeAnomerMover ()
 Default constructor. More...
 
 TautomerizeAnomerMover (TautomerizeAnomerMover const &object_to_copy)
 Copy constructor. More...
 
 TautomerizeAnomerMover (core::select::residue_selector::ResidueSelectorCOP selector)
 Constructor with ResidueSelector input option. More...
 
TautomerizeAnomerMoveroperator= (TautomerizeAnomerMover const &object_to_copy)
 
 ~TautomerizeAnomerMover () override=default
 
void show (std::ostream &output=std::cout) const override
 Generate string representation of TautomerizeAnomerMover for debugging purposes. More...
 
std::string get_name () const override
 Return the name of the Mover. 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 (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &input_pose) override
 Apply the corresponding move to <input_pose>. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
core::select::residue_selector::ResidueSelectorCOP selector () const
 Get the current ResidueSelector. More...
 
void selector (core::select::residue_selector::ResidueSelectorCOP new_selector)
 Set the ResidueSelector. 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 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 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...
 

Static Public Member Functions

static void register_options ()
 Register options with the option system. More...
 
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 Member Functions

void init ()
 
void copy_data (TautomerizeAnomerMover &object_to_copy_to, TautomerizeAnomerMover const &object_to_copy_from)
 
void setup_movable_reducing_ends (core::pose::Pose const &pose)
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
utility::vector1< core::uintmovable_reducing_ends_
 

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 class for tautomerizing from one anomer to another at a reducing end.

This carbohydrate-specific Mover randomly selects a free reducing end (not a glycoside) and inverts the stereochemistry, swapping alpha anomers for beta and beta for alpha. (This could be considered an extremely limited design case; however, reducing ends readily tautomerize in solution, in contrast to other cases, in which residues do not readily mutate into others!) It is generally not certain which form is preferred (if any) in sugar-binding proteins, and crystal structures sometimes arbitrarily assign one anomer over another when fitting density, so this Mover can assure that each anomer is sampled. If a ResidueSelector is set, the Mover will select from the subset at random; it will not guarantee tautomerization of every Residue in the subset.

Note
This Mover assumes that, any time a new saccharide .params file is added to the Rosetta database, its anomer is also added.

Constructor & Destructor Documentation

protocols::carbohydrates::TautomerizeAnomerMover::TautomerizeAnomerMover ( )

Default constructor.

References init().

protocols::carbohydrates::TautomerizeAnomerMover::TautomerizeAnomerMover ( TautomerizeAnomerMover const &  object_to_copy)

Copy constructor.

References copy_data().

protocols::carbohydrates::TautomerizeAnomerMover::TautomerizeAnomerMover ( core::select::residue_selector::ResidueSelectorCOP  selector)

Constructor with ResidueSelector input option.

References init().

protocols::carbohydrates::TautomerizeAnomerMover::~TautomerizeAnomerMover ( )
overridedefault

Member Function Documentation

void protocols::carbohydrates::TautomerizeAnomerMover::apply ( core::pose::Pose input_pose)
overridevirtual
protocols::moves::MoverOP protocols::carbohydrates::TautomerizeAnomerMover::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.

void protocols::carbohydrates::TautomerizeAnomerMover::copy_data ( TautomerizeAnomerMover object_to_copy_to,
TautomerizeAnomerMover const &  object_to_copy_from 
)
private
protocols::moves::MoverOP protocols::carbohydrates::TautomerizeAnomerMover::fresh_instance ( ) const
overridevirtual

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::carbohydrates::TautomerizeAnomerMover::get_name ( ) const
overridevirtual

Return the name of the Mover.

Implements protocols::moves::Mover.

References mover_name().

Referenced by apply().

void protocols::carbohydrates::TautomerizeAnomerMover::init ( void  )
private
static std::string protocols::carbohydrates::TautomerizeAnomerMover::mover_name ( )
inlinestatic
bool protocols::carbohydrates::TautomerizeAnomerMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns
true

Reimplemented from protocols::moves::Mover.

TautomerizeAnomerMover & protocols::carbohydrates::TautomerizeAnomerMover::operator= ( TautomerizeAnomerMover const &  object_to_copy)

References copy_data().

void protocols::carbohydrates::TautomerizeAnomerMover::parse_my_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 core::select::residue_selector::parse_residue_selector(), and selector_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::carbohydrates::TautomerizeAnomerMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::carbohydrates::TautomerizeAnomerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::carbohydrates::TautomerizeAnomerMover::register_options ( )
static

Register options with the option system.

References protocols::moves::Mover::register_options().

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::TautomerizeAnomerMover::selector ( ) const
inline

Get the current ResidueSelector.

References selector_.

void protocols::carbohydrates::TautomerizeAnomerMover::selector ( core::select::residue_selector::ResidueSelectorCOP  new_selector)
inline

Set the ResidueSelector.

References selector_.

void protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends ( core::pose::Pose const &  pose)
private
void protocols::carbohydrates::TautomerizeAnomerMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Generate string representation of TautomerizeAnomerMover for debugging purposes.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by apply(), and protocols::carbohydrates::operator<<().

Member Data Documentation

utility::vector1< core::uint > protocols::carbohydrates::TautomerizeAnomerMover::movable_reducing_ends_
private
core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::TautomerizeAnomerMover::selector_
private

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