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protocols::docking::DockingPrepackProtocol Class Reference

#include <DockingPrepackProtocol.hh>

Inheritance diagram for protocols::docking::DockingPrepackProtocol:
Inheritance graph
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Public Member Functions

 DockingPrepackProtocol ()
 Default constructor. More...
 
 ~DockingPrepackProtocol () override
 
void setup_defaults ()
 Assigns default values to members. More...
 
void setup_pack_operation_movers ()
 Instantiates and configures movers used by DockingPrepackProtocol. More...
 
void apply (core::pose::Pose &) override
 Main Method. More...
 
void score_and_output (std::string filename, core::pose::Pose &)
 Scores and outputs the pose - jd2 compatible. More...
 
void set_dock_ppk (bool dock_ppk)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::docking::DockingHighRes
 DockingHighRes ()
 Default constructor. More...
 
 DockingHighRes (core::Size const rb_jump)
 Constructor with one argument - the jump number to dock over. More...
 
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...
 
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 
 DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 
 DockingHighRes (DockingHighRes const &old_instance)
 
 ~DockingHighRes () override
 
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
 
void set_ignore_default_task (bool ignore_default_task)
 
bool ignore_default_task ()
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)
 
DockJumpsmovable_jumps ()
 
DockJumps const & movable_jumps () const
 
void set_movable_jumps (DockJumps movable_jumps)
 
core::pack::task::TaskFactoryCOP task_factory ()
 
void set_sc_min (bool sc_min)
 
void set_rt_min (bool rt_min)
 
void set_partners (std::string partners)
 
std::string get_partners () const
 
void set_interface_definition_task_operation (protocols::simple_task_operations::InterfaceTaskOperationOP interface_definition)
 
void set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)
 
void add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)
 
utility::vector1
< core::pack::task::operation::TaskOperationOP
get_additional_task_operarations ()
 
bool sc_min ()
 
bool rt_min ()
 
std::string partners ()
 
core::scoring::ScoreFunctionOP scorefxn () const
 
core::scoring::ScoreFunctionOP scorefxn_pack () const
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 finalize_setup (core::pose::Pose &)
 Performs setup that requires a pose. More...
 
void register_options ()
 
void init_from_options ()
 

Private Attributes

utility::vector1
< rigid::RigidBodyTransMoverOP
trans_away_vec_
 
utility::vector1
< rigid::RigidBodyTransMoverOP
trans_back_vec_
 
core::Real trans_magnitude_
 
bool membrane_
 membrane for translating in the membrane plane More...
 
protocols::minimization_packing::RotamerTrialsMinMoverOP rtmin_mover_
 
protocols::minimization_packing::PackRotamersMoverOP prepack_full_repack_
 
SidechainMinMoverOP scmin_mover_
 
protocols::moves::SequenceMoverOP pack_operations_
 
bool dock_ppk_
 
FaDockingSlideIntoContactOP fa_dock_slide_into_contact_
 
bool movers_setup_
 

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::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP tf2 ()
 
- 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::docking::DockingPrepackProtocol::DockingPrepackProtocol ( )

Default constructor.

References init_from_options(), register_options(), and setup_defaults().

protocols::docking::DockingPrepackProtocol::~DockingPrepackProtocol ( )
overridedefault

Member Function Documentation

void protocols::docking::DockingPrepackProtocol::apply ( core::pose::Pose )
overridevirtual
void protocols::docking::DockingPrepackProtocol::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::docking::DockingPrepackProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::docking::DockingHighRes.

References mover_name().

void protocols::docking::DockingPrepackProtocol::init_from_options ( )
private
std::string protocols::docking::DockingPrepackProtocol::mover_name ( )
static
void protocols::docking::DockingPrepackProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::DockingPrepackProtocol::register_options ( )
private

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::score_and_output ( std::string  filename,
core::pose::Pose pose 
)
void protocols::docking::DockingPrepackProtocol::set_dock_ppk ( bool  dock_ppk)

References dock_ppk_.

Referenced by init_from_options().

void protocols::docking::DockingPrepackProtocol::setup_defaults ( )

Assigns default values to members.

References dock_ppk_, membrane_, movers_setup_, pack_operations_, and trans_magnitude_.

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers ( )

Member Data Documentation

bool protocols::docking::DockingPrepackProtocol::dock_ppk_
private

Referenced by apply(), set_dock_ppk(), and setup_defaults().

FaDockingSlideIntoContactOP protocols::docking::DockingPrepackProtocol::fa_dock_slide_into_contact_
private
bool protocols::docking::DockingPrepackProtocol::membrane_
private

membrane for translating in the membrane plane

Referenced by apply(), finalize_setup(), init_from_options(), and setup_defaults().

bool protocols::docking::DockingPrepackProtocol::movers_setup_
private
protocols::moves::SequenceMoverOP protocols::docking::DockingPrepackProtocol::pack_operations_
private
protocols::minimization_packing::PackRotamersMoverOP protocols::docking::DockingPrepackProtocol::prepack_full_repack_
private
protocols::minimization_packing::RotamerTrialsMinMoverOP protocols::docking::DockingPrepackProtocol::rtmin_mover_
private
SidechainMinMoverOP protocols::docking::DockingPrepackProtocol::scmin_mover_
private
utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_away_vec_
private
utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_back_vec_
private
core::Real protocols::docking::DockingPrepackProtocol::trans_magnitude_
private

Referenced by apply(), and setup_defaults().


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