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protocols::docking::DockingHighRes Class Referenceabstract

#include <DockingHighRes.hh>

Inheritance diagram for protocols::docking::DockingHighRes:
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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)
 
virtual ~DockingHighRes ()
 
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
 
core::pack::task::TaskFactoryCOP task_factory ()
 
virtual void apply (core::pose::Pose &pose)=0
 
virtual std::string get_name () const =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)
 
void set_interface_definition_task_operation (protocols::toolbox::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 ~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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, 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
 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...
 
virtual 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

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...
 

Private Types

typedef core::Real Real
 

Private Member Functions

void init (DockJumps const movable_jumps)
 

Private Attributes

bool sc_min_
 
bool rt_min_
 
std::string partners_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP scorefxn_pack_
 
DockJumps movable_jumps_
 
core::pack::task::TaskFactoryOP tf_
 
protocols::docking::DockTaskFactoryOP tf2_
 
bool ignore_default_task_
 

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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::docking::DockingHighRes::DockingHighRes ( )
protocols::docking::DockingHighRes::DockingHighRes ( core::Size const  rb_jump)

Constructor with one argument - the jump number to dock over.

References core::scoring::ScoreFunctionFactory::create_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)
protocols::docking::DockingHighRes::~DockingHighRes ( )
virtual

Member Function Documentation

void protocols::docking::DockingHighRes::add_additional_task_operaration ( core::pack::task::operation::TaskOperationOP  task_operation)

References tf2_.

virtual void protocols::docking::DockingHighRes::apply ( core::pose::Pose pose)
pure virtual
utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingHighRes::get_additional_task_operarations ( )

References tf2_.

virtual std::string protocols::docking::DockingHighRes::get_name ( ) const
pure virtual
bool protocols::docking::DockingHighRes::ignore_default_task ( )
void protocols::docking::DockingHighRes::init ( DockJumps const  movable_jumps)
private
DockJumps& protocols::docking::DockingHighRes::movable_jumps ( )
inline
DockJumps const& protocols::docking::DockingHighRes::movable_jumps ( ) const
inline

References movable_jumps_.

std::string protocols::docking::DockingHighRes::partners ( )
inline
bool protocols::docking::DockingHighRes::rt_min ( )
inline
bool protocols::docking::DockingHighRes::sc_min ( )
inline
core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn ( ) const
core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn_pack ( ) const
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)
void protocols::docking::DockingHighRes::set_interface_definition_task_operation ( protocols::toolbox::task_operations::InterfaceTaskOperationOP  interface_definition)

References tf2_.

void protocols::docking::DockingHighRes::set_partners ( std::string  partners)
inline
void protocols::docking::DockingHighRes::set_rt_min ( bool  rt_min)
inline
void protocols::docking::DockingHighRes::set_sc_min ( bool  sc_min)
inline
void protocols::docking::DockingHighRes::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
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)
core::pack::task::TaskFactoryCOP protocols::docking::DockingHighRes::task_factory ( )
protocols::docking::DockTaskFactoryOP protocols::docking::DockingHighRes::tf2 ( )
protected

Member Data Documentation

bool protocols::docking::DockingHighRes::ignore_default_task_
private
DockJumps protocols::docking::DockingHighRes::movable_jumps_
private

Referenced by DockingHighRes(), init(), and movable_jumps().

std::string protocols::docking::DockingHighRes::partners_
private
bool protocols::docking::DockingHighRes::rt_min_
private
bool protocols::docking::DockingHighRes::sc_min_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn_pack_
private
protocols::docking::DockTaskFactoryOP protocols::docking::DockingHighRes::tf2_
private
core::pack::task::TaskFactoryOP protocols::docking::DockingHighRes::tf_
private

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