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protocols::ligand_docking::Translate Class Reference

#include <Translate.hh>

Inheritance diagram for protocols::ligand_docking::Translate:
Inheritance graph
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Public Member Functions

 Translate ()
 
 Translate (Translate_info translate_info)
 
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 (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
core::Size get_chain_id (core::pose::Pose const &pose)
 
void add_excluded_chains (std::set< core::Size >::const_iterator begin, std::set< core::Size >::const_iterator end)
 
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 Member Functions

void translate_ligand (utility::pointer::shared_ptr< core::grid::CartGrid< int > > const &grid, core::Size const jump_id, core::pose::Pose &pose)
 
void translate_ligand (qsar::scoring_grid::GridSetCOP grid_set, core::Size const jump_id, core::pose::Pose &pose, core::Size const &residue_id)
 
void uniform_translate_ligand (const utility::pointer::shared_ptr< core::grid::CartGrid< int > > &grid, const core::Size jump_id, core::pose::Pose &pose)
 
void gaussian_translate_ligand (const utility::pointer::shared_ptr< core::grid::CartGrid< int > > &grid, const core::Size jump_id, core::pose::Pose &pose)
 

Private Attributes

protocols::qsar::scoring_grid::GridSetCOP grid_set_prototype_
 
Translate_info translate_info_
 
utility::pointer::shared_ptr
< core::grid::CartGrid< int > > 
grid_
 
utility::vector1< core::Sizechain_ids_to_exclude_
 
utility::vector1< std::string > tag_along_chains_
 

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::ligand_docking::Translate::Translate ( )
protocols::ligand_docking::Translate::Translate ( Translate_info  translate_info)

Member Function Documentation

void protocols::ligand_docking::Translate::add_excluded_chains ( std::set< core::Size >::const_iterator  begin,
std::set< core::Size >::const_iterator  end 
)
void protocols::ligand_docking::Translate::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::ligand_docking::Translate::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::ligand_docking::Translate::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.

void protocols::ligand_docking::Translate::gaussian_translate_ligand ( const utility::pointer::shared_ptr< core::grid::CartGrid< int > > &  grid,
const core::Size  jump_id,
core::pose::Pose pose 
)
private
core::Size protocols::ligand_docking::Translate::get_chain_id ( core::pose::Pose const &  pose)
std::string protocols::ligand_docking::Translate::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::ligand_docking::Translate::mover_name ( )
static
void protocols::ligand_docking::Translate::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data_map 
)
overridevirtual
void protocols::ligand_docking::Translate::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::ligand_docking::Translate::translate_ligand ( utility::pointer::shared_ptr< core::grid::CartGrid< int > > const &  grid,
core::Size const  jump_id,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::Translate::translate_ligand ( qsar::scoring_grid::GridSetCOP  grid_set,
core::Size const  jump_id,
core::pose::Pose pose,
core::Size const &  residue_id 
)
private
void protocols::ligand_docking::Translate::uniform_translate_ligand ( const utility::pointer::shared_ptr< core::grid::CartGrid< int > > &  grid,
const core::Size  jump_id,
core::pose::Pose pose 
)
private

Member Data Documentation

utility::vector1<core::Size> protocols::ligand_docking::Translate::chain_ids_to_exclude_
private

Referenced by add_excluded_chains(), and apply().

utility::pointer::shared_ptr<core::grid::CartGrid<int> > protocols::ligand_docking::Translate::grid_
private
protocols::qsar::scoring_grid::GridSetCOP protocols::ligand_docking::Translate::grid_set_prototype_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<std::string> protocols::ligand_docking::Translate::tag_along_chains_
private
Translate_info protocols::ligand_docking::Translate::translate_info_
private

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