Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::ligand_docking::Translate Class Reference

#include <Translate.hh>

Inheritance diagram for protocols::ligand_docking::Translate:
Inheritance graph
[legend]
Collaboration diagram for protocols::ligand_docking::Translate:
Collaboration graph
[legend]

Public Member Functions

 Translate ()
 
 Translate (Translate_info translate_info)
 
virtual ~Translate ()
 
 Translate (Translate const &that)
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data_map, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
void apply (core::pose::Pose &pose)
 
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)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void translate_ligand (utility::pointer::owning_ptr< core::grid::CartGrid< int > > const &grid, core::Size const jump_id, core::pose::Pose &pose)
 
void translate_ligand (core::Size const jump_id, core::pose::Pose &pose, core::Size const &residue_id)
 
void uniform_translate_ligand (const utility::pointer::owning_ptr< core::grid::CartGrid< int > > &grid, const core::Size jump_id, core::pose::Pose &pose)
 
void gaussian_translate_ligand (const utility::pointer::owning_ptr< core::grid::CartGrid< int > > &grid, const core::Size jump_id, core::pose::Pose &pose)
 

Private Attributes

Translate_info translate_info_
 
utility::pointer::owning_ptr
< core::grid::CartGrid< int > > 
grid_
 
utility::vector1< core::Sizechain_ids_to_exclude_
 
std::vector< core::Sizetag_along_jumps_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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 ( )

Referenced by clone(), and fresh_instance().

protocols::ligand_docking::Translate::Translate ( Translate_info  translate_info)
protocols::ligand_docking::Translate::~Translate ( )
virtual
protocols::ligand_docking::Translate::Translate ( Translate const &  that)

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 pose)
virtual
protocols::moves::MoverOP protocols::ligand_docking::Translate::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

References Translate().

protocols::moves::MoverOP protocols::ligand_docking::Translate::fresh_instance ( ) const
virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

References Translate().

void protocols::ligand_docking::Translate::gaussian_translate_ligand ( const utility::pointer::owning_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
virtual

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

Implements protocols::moves::Mover.

void protocols::ligand_docking::Translate::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data_map,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
)
virtual
void protocols::ligand_docking::Translate::translate_ligand ( utility::pointer::owning_ptr< core::grid::CartGrid< int > > const &  grid,
core::Size const  jump_id,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::Translate::translate_ligand ( 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::owning_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
utility::pointer::owning_ptr<core::grid::CartGrid<int> > protocols::ligand_docking::Translate::grid_
private
std::vector<core::Size> protocols::ligand_docking::Translate::tag_along_jumps_
private
Translate_info protocols::ligand_docking::Translate::translate_info_
private

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