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::minimization_packing::TaskAwareMinMover Class Reference

#include <TaskAwareMinMover.hh>

Inheritance diagram for protocols::minimization_packing::TaskAwareMinMover:
Inheritance graph
[legend]

Public Member Functions

 TaskAwareMinMover ()
 
 TaskAwareMinMover (protocols::minimization_packing::MinMoverOP minmover_in, core::pack::task::TaskFactoryCOP factory_in)
 constructor with TaskFactory More...
 
 TaskAwareMinMover (protocols::minimization_packing::MinMoverOP minmover_in, core::pack::task::PackerTaskCOP const &task_in)
 Constructor with PackerTask. The input PackerTask is cloned. More...
 
 ~TaskAwareMinMover () override
 
void apply (core::pose::Pose &pose) override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option More...
 
void chi (bool val)
 
void bb (bool val)
 
void jump (bool const j)
 
bool chi () const
 
bool bb () const
 
bool jump () const
 
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 Attributes

protocols::minimization_packing::MinMoverOP minmover_
 OP for MinMover. More...
 
core::kinematics::MoveMapCOP base_movemap_
 Default movemap to use (Will be altered by the task info). More...
 
core::pack::task::TaskFactoryCOP factory_
 OP for constant task factory for nonconstant tasks, if present. More...
 
bool chi_
 
bool bb_
 
bool jump_
 
core::pack::task::PackerTaskOP task_
 Optional: from code, a packer task may be provided directly, but it must match the size of the pose on which we will be calling apply(). 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

this class wraps MinMover, but ensures that its MoveMap always contains up-to-date information about sidechain mobility. It takes its base movemap, allows sidechain freedom at any position mobile in a Factory-generated PackerTask, and passes the new movemap to MinMover. The MinMover's MoveMap does not accumulate state over many calls to apply().

Constructor & Destructor Documentation

protocols::minimization_packing::TaskAwareMinMover::TaskAwareMinMover ( )
protocols::minimization_packing::TaskAwareMinMover::TaskAwareMinMover ( protocols::minimization_packing::MinMoverOP  minmover_in,
core::pack::task::TaskFactoryCOP  factory_in 
)

constructor with TaskFactory

References base_movemap_, minmover_, and protocols::moves::Mover::type().

protocols::minimization_packing::TaskAwareMinMover::TaskAwareMinMover ( protocols::minimization_packing::MinMoverOP  minmover_in,
core::pack::task::PackerTaskCOP const &  task_in 
)

Constructor with PackerTask. The input PackerTask is cloned.

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

References base_movemap_, minmover_, and protocols::moves::Mover::type().

protocols::minimization_packing::TaskAwareMinMover::~TaskAwareMinMover ( )
overridedefault

Member Function Documentation

void protocols::minimization_packing::TaskAwareMinMover::apply ( core::pose::Pose pose)
overridevirtual

apply will extract the movemap from your minmover, modify it to include sidechain DOFs that are packable according to some TaskFactory, run the minmover with this movemap, and revert the minmover to its original movemap.

Implements protocols::moves::Mover.

References base_movemap_, bb_, chi_, factory_, jump_, minmover_, task_, and core::pose::Pose::total_residue().

Referenced by protocols::floppy_tail::FloppyTailMover::high_res().

void protocols::minimization_packing::TaskAwareMinMover::bb ( bool  val)
inline
bool protocols::minimization_packing::TaskAwareMinMover::bb ( ) const
inline

References bb_.

void protocols::minimization_packing::TaskAwareMinMover::chi ( bool  val)
inline
bool protocols::minimization_packing::TaskAwareMinMover::chi ( ) const
inline

References chi_.

protocols::moves::MoverOP protocols::minimization_packing::TaskAwareMinMover::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.

protocols::moves::MoverOP protocols::minimization_packing::TaskAwareMinMover::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::minimization_packing::TaskAwareMinMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::minimization_packing::TaskAwareMinMover::jump ( bool const  j)
inline

References jump_.

bool protocols::minimization_packing::TaskAwareMinMover::jump ( ) const
inline

References jump_.

Referenced by parse_my_tag().

std::string protocols::minimization_packing::TaskAwareMinMover::mover_name ( )
static
void protocols::minimization_packing::TaskAwareMinMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References bb_, chi_, jump(), jump_, minmover_, core::scoring::parse_score_function(), and parse_task_operations().

void protocols::minimization_packing::TaskAwareMinMover::parse_task_operations ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual

parse "task_operations" XML option

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

References factory_, and core::pack::task::parse_task_operations().

Referenced by parse_my_tag().

void protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

core::kinematics::MoveMapCOP protocols::minimization_packing::TaskAwareMinMover::base_movemap_
private

Default movemap to use (Will be altered by the task info).

Referenced by apply(), and TaskAwareMinMover().

bool protocols::minimization_packing::TaskAwareMinMover::bb_
private

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

bool protocols::minimization_packing::TaskAwareMinMover::chi_
private

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

core::pack::task::TaskFactoryCOP protocols::minimization_packing::TaskAwareMinMover::factory_
private

OP for constant task factory for nonconstant tasks, if present.

Referenced by apply(), and parse_task_operations().

bool protocols::minimization_packing::TaskAwareMinMover::jump_
private

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

protocols::minimization_packing::MinMoverOP protocols::minimization_packing::TaskAwareMinMover::minmover_
private

OP for MinMover.

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

core::pack::task::PackerTaskOP protocols::minimization_packing::TaskAwareMinMover::task_
private

Optional: from code, a packer task may be provided directly, but it must match the size of the pose on which we will be calling apply().

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

Referenced by apply().


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