Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::surface_docking::SurfaceDockingProtocol Class Reference

#include <SurfaceDockingProtocol.hh>

Public Member Functions

 SurfaceDockingProtocol ()
 Default constructor. More...
 
 SurfaceDockingProtocol (SurfaceDockingProtocol const &src)
 Copy constructor. More...
 
 ~SurfaceDockingProtocol ()
 
void show (std::ostream &ouput=std::cout) const
 Register options with the option system. More...
 
virtual std::string get_name () const
 Insertion operator (overloaded so that SurfaceDockingProtocol can be "printed" in Pyrosetta). More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual void apply (core::pose::Pose &pose)
 Apply the corresponding move to the pose. More...
 
- 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
 
void set_type (std::string const &setting)
 
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)
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void init ()
 
void copy_data (SurfaceDockingProtocol object_to_copy_to, SurfaceDockingProtocol object_to_copy_from)
 
bool valid_surface_pose (core::pose::Pose const &pose)
 
void calc_secondary_structure (core::pose::Pose &pose)
 
void calc_secondary_structure_with_surface (core::pose::Pose const &pose)
 
void set_secondary_structure (core::pose::Pose &pose)
 
void initialize_surface_energies (core::pose::Pose &pose, Size first_protein_residue)
 
void set_surface_parameters (core::pose::Pose &pose)
 
void setup_movers (core::pose::Pose const &pose, Size const first_protein_residue)
 
void setup_abinitio ()
 
void setup_slide_movers (core::pose::Pose const &pose)
 
void split_protein_surface_poses (core::pose::Pose const &pose, core::pose::Pose &surface, core::pose::Pose &protein)
 
void merge_protein_surface_poses (core::pose::Pose &pose, core::pose::Pose const &surface, core::pose::Pose const &protein)
 
core::pack::task::PackerTaskOP create_surface_packer_task (core::pose::Pose const &pose, Size const first_protein_residue)
 

Private Attributes

core::scoring::ScoreFunctionOP score_sidechain_pack_
 
std::string sec_struct_
 
protocols::surface_docking::SurfaceParametersOP surface_parameters_
 
simple_moves::SwitchResidueTypeSetMoverOP to_centroid_
 
simple_moves::SwitchResidueTypeSetMoverOP to_full_atom_
 
SurfaceOrientMoverOP surface_orient_
 
protocols::abinitio::ClassicAbinitioOP abinitio_
 
protocols::surface_docking::CentroidRelaxMoverOP centroid_relax_
 
protocols::simple_moves::PackRotamersMoverOP pack_rotamers_fullatom_
 
protocols::rigid::RigidBodyTransMoverOP slide_away_from_surface_
 
protocols::docking::FaDockingSlideIntoContactOP slide_into_surface_
 
protocols::surface_docking::FullatomRelaxMoverOP fullatom_relax_
 
protocols::rigid::RigidBodyTransMoverOP position_above_surface_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 
- 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::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol ( )

Default constructor.

References init().

Referenced by clone(), and fresh_instance().

protocols::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol ( SurfaceDockingProtocol const &  src)

Copy constructor.

References copy_data().

protocols::surface_docking::SurfaceDockingProtocol::~SurfaceDockingProtocol ( )

Member Function Documentation

void protocols::surface_docking::SurfaceDockingProtocol::apply ( core::pose::Pose pose)
virtual
void protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure ( core::pose::Pose pose)
private
void protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure_with_surface ( core::pose::Pose const &  pose)
private
protocols::moves::MoverOP protocols::surface_docking::SurfaceDockingProtocol::clone ( ) const
virtual

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.

References SurfaceDockingProtocol().

void protocols::surface_docking::SurfaceDockingProtocol::copy_data ( SurfaceDockingProtocol  object_to_copy_to,
SurfaceDockingProtocol  object_to_copy_from 
)
private
core::pack::task::PackerTaskOP protocols::surface_docking::SurfaceDockingProtocol::create_surface_packer_task ( core::pose::Pose const &  pose,
Size const  first_protein_residue 
)
private
protocols::moves::MoverOP protocols::surface_docking::SurfaceDockingProtocol::fresh_instance ( ) const
virtual

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.

References SurfaceDockingProtocol().

std::string protocols::surface_docking::SurfaceDockingProtocol::get_name ( ) const
virtual

Insertion operator (overloaded so that SurfaceDockingProtocol can be "printed" in Pyrosetta).

Assignment operator Return the name of the Mover.

Implements protocols::moves::Mover.

void protocols::surface_docking::SurfaceDockingProtocol::init ( void  )
private
void protocols::surface_docking::SurfaceDockingProtocol::initialize_surface_energies ( core::pose::Pose pose,
Size  first_protein_residue 
)
private
void protocols::surface_docking::SurfaceDockingProtocol::merge_protein_surface_poses ( core::pose::Pose pose,
core::pose::Pose const &  surface,
core::pose::Pose const &  protein 
)
private
void protocols::surface_docking::SurfaceDockingProtocol::set_secondary_structure ( core::pose::Pose pose)
private
void protocols::surface_docking::SurfaceDockingProtocol::set_surface_parameters ( core::pose::Pose pose)
private

References surface_parameters_.

Referenced by apply().

void protocols::surface_docking::SurfaceDockingProtocol::setup_abinitio ( )
private
void protocols::surface_docking::SurfaceDockingProtocol::setup_movers ( core::pose::Pose const &  pose,
Size const  first_protein_residue 
)
private
void protocols::surface_docking::SurfaceDockingProtocol::setup_slide_movers ( core::pose::Pose const &  pose)
private
void protocols::surface_docking::SurfaceDockingProtocol::show ( std::ostream &  ouput = std::cout) const
virtual

Register options with the option system.

Generate string representation of SurfaceDockingProtocol for debugging purposes

Reimplemented from protocols::moves::Mover.

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

void protocols::surface_docking::SurfaceDockingProtocol::split_protein_surface_poses ( core::pose::Pose const &  pose,
core::pose::Pose surface,
core::pose::Pose protein 
)
private
bool protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose ( core::pose::Pose const &  pose)
private

Member Data Documentation

protocols::abinitio::ClassicAbinitioOP protocols::surface_docking::SurfaceDockingProtocol::abinitio_
private

Referenced by apply(), copy_data(), init(), and setup_abinitio().

protocols::surface_docking::CentroidRelaxMoverOP protocols::surface_docking::SurfaceDockingProtocol::centroid_relax_
private

Referenced by apply(), copy_data(), init(), and setup_movers().

protocols::surface_docking::FullatomRelaxMoverOP protocols::surface_docking::SurfaceDockingProtocol::fullatom_relax_
private

Referenced by apply(), copy_data(), init(), and setup_movers().

protocols::simple_moves::PackRotamersMoverOP protocols::surface_docking::SurfaceDockingProtocol::pack_rotamers_fullatom_
private

Referenced by apply(), copy_data(), init(), and setup_movers().

protocols::rigid::RigidBodyTransMoverOP protocols::surface_docking::SurfaceDockingProtocol::position_above_surface_
private

Referenced by apply(), and setup_slide_movers().

core::scoring::ScoreFunctionOP protocols::surface_docking::SurfaceDockingProtocol::score_sidechain_pack_
private

Referenced by copy_data(), init(), and setup_movers().

std::string protocols::surface_docking::SurfaceDockingProtocol::sec_struct_
private
protocols::rigid::RigidBodyTransMoverOP protocols::surface_docking::SurfaceDockingProtocol::slide_away_from_surface_
private

Referenced by copy_data(), init(), and setup_slide_movers().

protocols::docking::FaDockingSlideIntoContactOP protocols::surface_docking::SurfaceDockingProtocol::slide_into_surface_
private
SurfaceOrientMoverOP protocols::surface_docking::SurfaceDockingProtocol::surface_orient_
private

Referenced by apply(), copy_data(), init(), and setup_movers().

protocols::surface_docking::SurfaceParametersOP protocols::surface_docking::SurfaceDockingProtocol::surface_parameters_
private
simple_moves::SwitchResidueTypeSetMoverOP protocols::surface_docking::SurfaceDockingProtocol::to_centroid_
private

Referenced by apply(), copy_data(), init(), and setup_movers().

simple_moves::SwitchResidueTypeSetMoverOP protocols::surface_docking::SurfaceDockingProtocol::to_full_atom_
private

Referenced by apply(), copy_data(), init(), and setup_movers().


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