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protocols::docking::DockMinMover Class Reference

#include <DockMinMover.hh>

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

 DockMinMover ()
 Default constructor. More...
 
 DockMinMover (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments. The first is the DockJumps, the second is a scorefunction to use for minimization. More...
 
 DockMinMover (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, moves::MonteCarloOP mc)
 
 DockMinMover (DockJumps const movable_jumps, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, std::string min_type, core::Real min_tolerance, bool nb_list, moves::MonteCarloOP mc)
 Constructor with seven arguments. The first is the DockJumps, the second is a movemap, the third is a scorefunction, the fourth is the minimization type (as a string), the fifth is the tolerance, the sixth is a boolean for the nb_list and the seventh is a MonteCarloOP. More...
 
 ~DockMinMover () override
 
void set_default ()
 Sets up the default values for the obejct including the movemap and minimization type. More...
 
void set_min_type (std::string min_type)
 setters for member variables More...
 
void set_min_tolerance (core::Real min_tolerance)
 
void apply (core::pose::Pose &) override
 Main Method. More...
 
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 Attributes

core::kinematics::MoveMapOP movemap_
 
std::string min_type_
 
core::Real min_tolerance_
 
bool nb_list_
 
moves::MonteCarloOP mc_
 
moves::TrialMoverOP minimize_trial_
 

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::DockMinMover::DockMinMover ( )
protocols::docking::DockMinMover::DockMinMover ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionOP  scorefxn 
)

Constructor with two arguments. The first is the DockJumps, the second is a scorefunction to use for minimization.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and set_default().

protocols::docking::DockMinMover::DockMinMover ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionOP  scorefxn,
moves::MonteCarloOP  mc 
)
protocols::docking::DockMinMover::DockMinMover ( DockJumps const  movable_jumps,
core::kinematics::MoveMapOP  movemap,
core::scoring::ScoreFunctionOP  scorefxn,
std::string  min_type,
core::Real  min_tolerance,
bool  nb_list,
moves::MonteCarloOP  mc 
)

Constructor with seven arguments. The first is the DockJumps, the second is a movemap, the third is a scorefunction, the fourth is the minimization type (as a string), the fifth is the tolerance, the sixth is a boolean for the nb_list and the seventh is a MonteCarloOP.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, and nb_list_.

protocols::docking::DockMinMover::~DockMinMover ( )
overridedefault

Member Function Documentation

void protocols::docking::DockMinMover::apply ( core::pose::Pose )
overridevirtual
std::string protocols::docking::DockMinMover::get_name ( ) const
overridevirtual

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

Implements protocols::docking::DockingHighRes.

References mover_name().

std::string protocols::docking::DockMinMover::mover_name ( )
static
void protocols::docking::DockMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::DockMinMover::set_default ( )

Sets up the default values for the obejct including the movemap and minimization type.

References min_tolerance_, min_type_, protocols::docking::DockingHighRes::movable_jumps(), movemap_, and nb_list_.

Referenced by DockMinMover().

void protocols::docking::DockMinMover::set_min_tolerance ( core::Real  min_tolerance)
inline

References min_tolerance_.

void protocols::docking::DockMinMover::set_min_type ( std::string  min_type)
inline

setters for member variables

References min_type_.

Member Data Documentation

moves::MonteCarloOP protocols::docking::DockMinMover::mc_
private

Referenced by apply(), and DockMinMover().

core::Real protocols::docking::DockMinMover::min_tolerance_
private
std::string protocols::docking::DockMinMover::min_type_
private
moves::TrialMoverOP protocols::docking::DockMinMover::minimize_trial_
private

Referenced by apply(), and DockMinMover().

core::kinematics::MoveMapOP protocols::docking::DockMinMover::movemap_
private

Referenced by DockMinMover(), and set_default().

bool protocols::docking::DockMinMover::nb_list_
private

Referenced by DockMinMover(), and set_default().


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