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protocols::symmetry::SetupForSymmetryMover Class Reference

#include <SetupForSymmetryMover.hh>

Inheritance diagram for protocols::symmetry::SetupForSymmetryMover:
Inheritance graph
[legend]

Public Member Functions

 SetupForSymmetryMover ()
 default constructor, reads from the global options object More...
 
 SetupForSymmetryMover (utility::options::OptionCollection const &options)
 reads from a (possibly-local) option collection object More...
 
 SetupForSymmetryMover (core::conformation::symmetry::SymmDataOP symmdata)
 
 SetupForSymmetryMover (core::conformation::symmetry::SymmDataOP symmdata, utility::options::OptionCollection const &options)
 
 SetupForSymmetryMover (std::string const &symmdef_file)
 
 SetupForSymmetryMover (std::string const &symmdef_file, utility::options::OptionCollection const &options)
 
 ~SetupForSymmetryMover () override
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. 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...
 
void slide_into_contact (bool val)
 
void set_preserve_datacache (bool const preserve_cache)
 Sets whether or not the input asymmetric pose's datacache should be copied into the new symmetric pose. More...
 
void set_keep_pdb_info_labels (bool const keep_pdb_info_labels)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void process_symmdef_file (std::string tag)
 
void set_refinable_lattice (bool setting)
 
- 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 void options_read_in_ctor (utility::options::OptionKeyList &opts)
 
- 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 make_symmetric_pose (core::pose::Pose &pose) const
 constructs a symmetric pose with a symmetric conformation and energies object. More...
 
void read_refinable_lattice (utility::options::OptionCollection const &options)
 

Private Attributes

bool slide_
 
bool cryst1_
 
bool preserve_datacache_
 
core::conformation::symmetry::SymmDataOP symmdef_
 
std::string symdef_fname_from_options_system_
 
bool refinable_lattice_was_set_
 
bool refinable_lattice_
 
bool keep_pdb_info_labels_
 
bool set_global_symmetry_at_parsetime_
 

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...
 

Constructor & Destructor Documentation

protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( )

default constructor, reads from the global options object

protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( utility::options::OptionCollection const &  options)

reads from a (possibly-local) option collection object

References read_refinable_lattice(), and symdef_fname_from_options_system_.

protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( core::conformation::symmetry::SymmDataOP  symmdata)
protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( core::conformation::symmetry::SymmDataOP  symmdata,
utility::options::OptionCollection const &  options 
)
protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( std::string const &  symmdef_file)
protocols::symmetry::SetupForSymmetryMover::SetupForSymmetryMover ( std::string const &  symmdef_file,
utility::options::OptionCollection const &  options 
)
protocols::symmetry::SetupForSymmetryMover::~SetupForSymmetryMover ( )
overridedefault

Member Function Documentation

void protocols::symmetry::SetupForSymmetryMover::apply ( core::pose::Pose )
overridevirtual
moves::MoverOP protocols::symmetry::SetupForSymmetryMover::clone ( ) const
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.

Referenced by parse_my_tag().

std::string protocols::symmetry::SetupForSymmetryMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::symmetry::SetupForSymmetryMover::make_symmetric_pose ( core::pose::Pose pose) const
private

constructs a symmetric pose with a symmetric conformation and energies object.

Calls core::pose::make_symmetric_pose(). If preserve_datacache is set, this also copies the datacache into the new symmetric pose.

Parameters
[in,out]poseInput asymmetric pose, output symmetric pose

References core::pose::Pose::data(), keep_pdb_info_labels_, core::pose::symmetry::make_symmetric_pose(), preserve_datacache_, and symmdef_.

Referenced by apply().

std::string protocols::symmetry::SetupForSymmetryMover::mover_name ( )
static
void protocols::symmetry::SetupForSymmetryMover::options_read_in_ctor ( utility::options::OptionKeyList &  opts)
static
void protocols::symmetry::SetupForSymmetryMover::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 clone(), keep_pdb_info_labels_, preserve_datacache_, process_symmdef_file(), set_global_symmetry_at_parsetime_, symdef_fname_from_options_system_, symmdef_, and protocols::symmetry::TR().

void protocols::symmetry::SetupForSymmetryMover::process_symmdef_file ( std::string  tag)

References cryst1_, and symmdef_.

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

void protocols::symmetry::SetupForSymmetryMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::symmetry::SetupForSymmetryMover::read_refinable_lattice ( utility::options::OptionCollection const &  options)
private
void protocols::symmetry::SetupForSymmetryMover::set_keep_pdb_info_labels ( bool const  keep_pdb_info_labels)

References keep_pdb_info_labels_.

void protocols::symmetry::SetupForSymmetryMover::set_preserve_datacache ( bool const  preserve_cache)

Sets whether or not the input asymmetric pose's datacache should be copied into the new symmetric pose.

Parameters
[in]preserve_cacheIf true, input pose's datacache is copied into new symmetric pose If false, input pose's datacache is cleared (default = false)

References preserve_datacache_.

void protocols::symmetry::SetupForSymmetryMover::set_refinable_lattice ( bool  setting)
void protocols::symmetry::SetupForSymmetryMover::slide_into_contact ( bool  val)
inline

Member Data Documentation

bool protocols::symmetry::SetupForSymmetryMover::cryst1_
private

Referenced by apply(), and process_symmdef_file().

bool protocols::symmetry::SetupForSymmetryMover::keep_pdb_info_labels_
private
bool protocols::symmetry::SetupForSymmetryMover::preserve_datacache_
private
bool protocols::symmetry::SetupForSymmetryMover::refinable_lattice_
private
bool protocols::symmetry::SetupForSymmetryMover::refinable_lattice_was_set_
private
bool protocols::symmetry::SetupForSymmetryMover::set_global_symmetry_at_parsetime_
private

Referenced by parse_my_tag().

bool protocols::symmetry::SetupForSymmetryMover::slide_
private

Referenced by apply(), and slide_into_contact().

std::string protocols::symmetry::SetupForSymmetryMover::symdef_fname_from_options_system_
private
core::conformation::symmetry::SymmDataOP protocols::symmetry::SetupForSymmetryMover::symmdef_
private

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