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Rosetta
2020.50
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#include <DockingHighRes.hh>
Public Member Functions | |
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) |
DockJumps & | movable_jumps () |
DockJumps const & | movable_jumps () const |
void | set_movable_jumps (DockJumps movable_jumps) |
core::pack::task::TaskFactoryCOP | task_factory () |
void | apply (core::pose::Pose &pose) override=0 |
Main Method. More... | |
std::string | get_name () const override=0 |
Each derived class must specify its name. The class name. More... | |
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 |
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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 Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Protected Member Functions | |
protocols::docking::DockTaskFactoryOP | tf2 () |
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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... | |
Private Types | |
typedef core::Real | Real |
Private Member Functions | |
void | init (DockJumps const movable_jumps) |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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protocols::docking::DockingHighRes::DockingHighRes | ( | ) |
Default constructor.
References core::scoring::get_score_function(), init(), scorefxn_, and scorefxn_pack_.
protocols::docking::DockingHighRes::DockingHighRes | ( | core::Size const | rb_jump | ) |
Constructor with one argument - the jump number to dock over.
References core::scoring::get_score_function(), init(), scorefxn_, and scorefxn_pack_.
protocols::docking::DockingHighRes::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.
References init().
protocols::docking::DockingHighRes::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.
References init().
protocols::docking::DockingHighRes::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.
References init().
protocols::docking::DockingHighRes::DockingHighRes | ( | DockingHighRes const & | old_instance | ) |
References movable_jumps_, partners_, rt_min_, sc_min_, scorefxn_, scorefxn_pack_, tf2_, and tf_.
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void protocols::docking::DockingHighRes::add_additional_task_operaration | ( | core::pack::task::operation::TaskOperationOP | task_operation | ) |
References tf2_.
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overridepure virtual |
Main Method.
Implements protocols::moves::Mover.
Implemented in protocols::docking::DockingHighResLegacy, protocols::docking::InterfaceSidechainMinMover, protocols::docking::DockMCMProtocol, protocols::docking::DockMinMover, protocols::antibody::snugdock::SnugDock, protocols::docking::SidechainMinMover, protocols::docking::DockingEnsemblePrepackProtocol, and protocols::docking::DockingPrepackProtocol.
utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingHighRes::get_additional_task_operarations | ( | ) |
References tf2_.
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overridepure virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Implemented in protocols::docking::DockingHighResLegacy, protocols::docking::InterfaceSidechainMinMover, protocols::antibody::snugdock::SnugDock, protocols::docking::DockMCMProtocol, protocols::docking::DockMinMover, protocols::docking::SidechainMinMover, protocols::docking::DockingPrepackProtocol, and protocols::docking::DockingEnsemblePrepackProtocol.
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References partners_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility().
bool protocols::docking::DockingHighRes::ignore_default_task | ( | ) |
References ignore_default_task_.
Referenced by protocols::docking::DockMCMProtocol::apply(), and set_ignore_default_task().
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References ignore_default_task_, movable_jumps(), movable_jumps_, partners_, rt_min_, sc_min_, tf2_, tf_, and protocols::moves::Mover::type().
Referenced by DockingHighRes().
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References movable_jumps_.
Referenced by protocols::docking::DockingPrepackProtocol::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::InterfaceSidechainMinMover::apply(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::finalize_setup(), init(), protocols::docking::DockingEnsemblePrepackProtocol::move_away(), protocols::docking::DockingEnsemblePrepackProtocol::move_back(), protocols::docking::DockMinMover::set_default(), protocols::docking::DockingHighResLegacy::set_default(), protocols::docking::InterfaceSidechainMinMover::set_default(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), set_movable_jumps(), and protocols::docking::DockingHighResLegacy::setup_packing().
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References movable_jumps_.
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core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn | ( | ) | const |
References scorefxn_.
Referenced by protocols::antibody::snugdock::SnugDock::apply(), protocols::docking::DockMinMover::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockMinMover::DockMinMover(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::score_and_output(), protocols::docking::DockMCMProtocol::scorefxn_docking(), protocols::docking::SidechainMinMover::set_default(), protocols::docking::DockingHighResLegacy::set_default(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_min_protocol(), and set_scorefxn().
core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn_pack | ( | ) | const |
References scorefxn_pack_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockMCMProtocol::scorefxn_packing(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), set_scorefxn_pack(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers(), and protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers().
void protocols::docking::DockingHighRes::set_additional_task_operarations | ( | utility::vector1< core::pack::task::operation::TaskOperationOP > | additional_task_operations | ) |
References tf2_.
void protocols::docking::DockingHighRes::set_ignore_default_task | ( | bool | ignore_default_task | ) |
References ignore_default_task(), and ignore_default_task_.
void protocols::docking::DockingHighRes::set_interface_definition_task_operation | ( | protocols::simple_task_operations::InterfaceTaskOperationOP | interface_definition | ) |
References tf2_.
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References movable_jumps(), and movable_jumps_.
Referenced by protocols::docking::DockingPrepackProtocol::finalize_setup().
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References partners(), and partners_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::init_from_options(), and protocols::docking::DockingPrepackProtocol::init_from_options().
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References rt_min(), and rt_min_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::init_from_options(), and protocols::docking::DockingPrepackProtocol::init_from_options().
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References sc_min(), and sc_min_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::init_from_options(), and protocols::docking::DockingPrepackProtocol::init_from_options().
void protocols::docking::DockingHighRes::set_scorefxn | ( | core::scoring::ScoreFunctionOP | scorefxn | ) |
References scorefxn(), and scorefxn_.
Referenced by protocols::docking::DockingPrepackProtocol::finalize_setup(), and protocols::docking::SidechainMinMover::SidechainMinMover().
void protocols::docking::DockingHighRes::set_scorefxn_pack | ( | core::scoring::ScoreFunctionOP | scorefxn_pack | ) |
References scorefxn_pack(), and scorefxn_pack_.
void protocols::docking::DockingHighRes::set_task_factory | ( | core::pack::task::TaskFactoryCOP | tf | ) |
References tf_.
Referenced by protocols::docking::DockTaskFactory::create_and_attach_task_factory(), and protocols::docking::SidechainMinMover::SidechainMinMover().
core::pack::task::TaskFactoryCOP protocols::docking::DockingHighRes::task_factory | ( | ) |
References tf_.
Referenced by protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers(), protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers(), and protocols::docking::SidechainMinMover::update_movemap().
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Referenced by ignore_default_task(), init(), and set_ignore_default_task().
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Referenced by DockingHighRes(), init(), movable_jumps(), and set_movable_jumps().
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Referenced by DockingHighRes(), get_partners(), init(), partners(), and set_partners().
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Referenced by DockingHighRes(), init(), rt_min(), and set_rt_min().
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Referenced by DockingHighRes(), init(), sc_min(), and set_sc_min().
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Referenced by DockingHighRes(), scorefxn(), and set_scorefxn().
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Referenced by DockingHighRes(), scorefxn_pack(), and set_scorefxn_pack().
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Referenced by DockingHighRes(), init(), set_task_factory(), and task_factory().