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protocols::minimization_packing::PertMinMover Class Reference

Random perturbation, followed by minimization. More...

#include <PertMinMover.hh>

Inheritance diagram for protocols::minimization_packing::PertMinMover:
Inheritance graph
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Public Member Functions

 PertMinMover ()
 
 PertMinMover (PertMinMover const &src)
 
 ~PertMinMover () override
 
core::Real pert_size () const
 
bool uniform () const
 
bool sc_only () const
 
core::select::residue_selector::ResidueSelectorCOP residues () const
 
core::scoring::ScoreFunctionCOP scorefxn () const
 
core::select::movemap::MoveMapFactoryCOP movemap () const
 
void pert_size (core::Real setting)
 
void uniform (bool setting)
 
void sc_only (bool setting)
 
void residues (core::select::residue_selector::ResidueSelectorCOP setting)
 
void scorefxn (core::scoring::ScoreFunctionCOP setting)
 
void movemap_factory (core::select::movemap::MoveMapFactoryCOP setting)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void pert (core::pose::Pose &pose, utility::vector1< bool > const &resi) const
 
void min (core::pose::Pose &pose) const
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme 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 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 Attributes

core::Real pert_size_
 The size of the random perturbation. More...
 
bool uniform_
 Do a uniform perturbation (default is Gaussian) More...
 
bool sc_only_
 Don't perturb the backbone coordinates. More...
 
core::select::residue_selector::ResidueSelectorCOP residues_
 Only perturb the selected residues. More...
 
core::scoring::ScoreFunctionCOP scorefxn_
 the score function to use in minimization More...
 
core::select::movemap::MoveMapFactoryCOP movemap_factory_
 The movemap factory to be used in minimization. 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

Random perturbation, followed by minimization.

Constructor & Destructor Documentation

protocols::minimization_packing::PertMinMover::PertMinMover ( )
protocols::minimization_packing::PertMinMover::PertMinMover ( PertMinMover const &  src)
default
protocols::minimization_packing::PertMinMover::~PertMinMover ( )
overridedefault

Member Function Documentation

void protocols::minimization_packing::PertMinMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::minimization_packing::PertMinMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::minimization_packing::PertMinMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::minimization_packing::PertMinMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::minimization_packing::PertMinMover::min ( core::pose::Pose pose) const
core::select::movemap::MoveMapFactoryCOP protocols::minimization_packing::PertMinMover::movemap ( ) const
inline

References movemap_factory_.

void protocols::minimization_packing::PertMinMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP  setting)
inline

References movemap_factory_.

Referenced by parse_my_tag().

std::string protocols::minimization_packing::PertMinMover::mover_name ( )
static
void protocols::minimization_packing::PertMinMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::minimization_packing::PertMinMover::pert ( core::pose::Pose pose,
utility::vector1< bool > const &  resi 
) const
core::Real protocols::minimization_packing::PertMinMover::pert_size ( ) const
inline

References pert_size_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::pert_size ( core::Real  setting)
inline

References pert_size_.

void protocols::minimization_packing::PertMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::select::residue_selector::ResidueSelectorCOP protocols::minimization_packing::PertMinMover::residues ( ) const
inline

References residues_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::residues ( core::select::residue_selector::ResidueSelectorCOP  setting)
inline

References residues_.

bool protocols::minimization_packing::PertMinMover::sc_only ( ) const
inline

References sc_only_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::sc_only ( bool  setting)
inline

References sc_only_.

core::scoring::ScoreFunctionCOP protocols::minimization_packing::PertMinMover::scorefxn ( ) const
inline

References scorefxn_.

Referenced by min(), and parse_my_tag().

void protocols::minimization_packing::PertMinMover::scorefxn ( core::scoring::ScoreFunctionCOP  setting)
inline

References scorefxn_.

void protocols::minimization_packing::PertMinMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by protocols::minimization_packing::operator<<().

bool protocols::minimization_packing::PertMinMover::uniform ( ) const
inline

References uniform_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::uniform ( bool  setting)
inline

References uniform_.

Member Data Documentation

core::select::movemap::MoveMapFactoryCOP protocols::minimization_packing::PertMinMover::movemap_factory_
private

The movemap factory to be used in minimization.

Referenced by min(), movemap(), and movemap_factory().

core::Real protocols::minimization_packing::PertMinMover::pert_size_
private

The size of the random perturbation.

Referenced by pert(), and pert_size().

core::select::residue_selector::ResidueSelectorCOP protocols::minimization_packing::PertMinMover::residues_
private

Only perturb the selected residues.

Referenced by apply(), and residues().

bool protocols::minimization_packing::PertMinMover::sc_only_
private

Don't perturb the backbone coordinates.

Referenced by pert(), and sc_only().

core::scoring::ScoreFunctionCOP protocols::minimization_packing::PertMinMover::scorefxn_
private

the score function to use in minimization

Referenced by apply(), and scorefxn().

bool protocols::minimization_packing::PertMinMover::uniform_
private

Do a uniform perturbation (default is Gaussian)

Referenced by pert(), and uniform().


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