Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::carbohydrates::GlycanTreeMinMover Class Reference

A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector. More...

#include <GlycanTreeMinMover.hh>

Inheritance diagram for protocols::carbohydrates::GlycanTreeMinMover:
Inheritance graph
[legend]

Public Member Functions

 GlycanTreeMinMover ()
 Constructors ///. More...
 
 GlycanTreeMinMover (core::select::residue_selector::ResidueSelectorCOP selector, bool min_rings=false, bool min_bb=true, bool min_chi=true)
 
 GlycanTreeMinMover (GlycanTreeMinMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~GlycanTreeMinMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 
void set_min_rings (bool min_rings)
 Minimize Rings? Default False. More...
 
void set_min_chi (bool min_chi)
 Minimize Chi? Default True. More...
 
void set_min_bb (bool min_bb)
 Minimize BB? Default True. More...
 
void set_minmover (protocols::minimization_packing::MinMoverCOP min_mover)
 Set a pre-configured MinMover for this class. Will OVERRIDE movemap settings. More...
 
std::string get_name () const override
 Get the name of the Mover. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Rosetta Scripts Support ///. More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme 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 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 std::string class_name ()
 Show the contents of the Mover. More...
 
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

bool min_rings_ = false
 
bool min_bb_ = true
 
bool min_chi_ = true
 
core::select::residue_selector::ResidueSelectorCOP selector_ = nullptr
 
protocols::minimization_packing::MinMoverOP min_mover_ = nullptr
 

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 class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector.

Supports Symmetry

Constructor & Destructor Documentation

protocols::carbohydrates::GlycanTreeMinMover::GlycanTreeMinMover ( )

Constructors ///.

Default constructor

protocols::carbohydrates::GlycanTreeMinMover::GlycanTreeMinMover ( core::select::residue_selector::ResidueSelectorCOP  selector,
bool  min_rings = false,
bool  min_bb = true,
bool  min_chi = true 
)

References selector_.

protocols::carbohydrates::GlycanTreeMinMover::GlycanTreeMinMover ( GlycanTreeMinMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References min_mover_, selector_, and set_minmover().

protocols::carbohydrates::GlycanTreeMinMover::~GlycanTreeMinMover ( )
overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::carbohydrates::GlycanTreeMinMover::apply ( core::pose::Pose pose)
overridevirtual
std::string protocols::carbohydrates::GlycanTreeMinMover::class_name ( )
static

Show the contents of the Mover.

Referenced by get_name(), and protocols::carbohydrates::GlycanTreeMinMoverCreator::keyname().

protocols::moves::MoverOP protocols::carbohydrates::GlycanTreeMinMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::carbohydrates::GlycanTreeMinMover::fresh_instance ( ) const
overridevirtual

Rosetta Scripts Support ///.

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::carbohydrates::GlycanTreeMinMover::get_name ( ) const
overridevirtual

Get the name of the Mover.

Implements protocols::moves::Mover.

References class_name().

Referenced by provide_authorship_info_for_unpublished().

bool protocols::carbohydrates::GlycanTreeMinMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns
true

Reimplemented from protocols::moves::Mover.

void protocols::carbohydrates::GlycanTreeMinMover::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 min_bb_, min_chi_, min_rings_, core::select::residue_selector::parse_residue_selector(), and selector_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::carbohydrates::GlycanTreeMinMover::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 get_name().

void protocols::carbohydrates::GlycanTreeMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::carbohydrates::GlycanTreeMinMover::set_min_bb ( bool  min_bb)

Minimize BB? Default True.

References min_bb_.

void protocols::carbohydrates::GlycanTreeMinMover::set_min_chi ( bool  min_chi)

Minimize Chi? Default True.

References min_chi_.

void protocols::carbohydrates::GlycanTreeMinMover::set_min_rings ( bool  min_rings)

Minimize Rings? Default False.

References min_rings_.

void protocols::carbohydrates::GlycanTreeMinMover::set_minmover ( protocols::minimization_packing::MinMoverCOP  min_mover)

Set a pre-configured MinMover for this class. Will OVERRIDE movemap settings.

References min_mover_.

Referenced by GlycanTreeMinMover().

void protocols::carbohydrates::GlycanTreeMinMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector_.

Member Data Documentation

bool protocols::carbohydrates::GlycanTreeMinMover::min_bb_ = true
private

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

bool protocols::carbohydrates::GlycanTreeMinMover::min_chi_ = true
private

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

protocols::minimization_packing::MinMoverOP protocols::carbohydrates::GlycanTreeMinMover::min_mover_ = nullptr
private
bool protocols::carbohydrates::GlycanTreeMinMover::min_rings_ = false
private

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

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::GlycanTreeMinMover::selector_ = nullptr
private

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