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protocols::dna::DnaInterfaceMinMover Class Reference

#include <DnaInterfaceMinMover.hh>

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Public Types

typedef utility::tag::TagPtr TagPtr
 
- Public Types inherited from protocols::simple_moves::MinMover
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::optimization::MinimizerOptionsOP 
MinimizerOptionsOP
 
typedef
core::optimization::MinimizerOptionsCOP 
MinimizerOptionsCOP
 
typedef core::Real Real
 
- 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
 

Public Member Functions

 DnaInterfaceMinMover ()
 
 DnaInterfaceMinMover (DnaInterfaceMinMover const &)
 
DnaInterfaceMinMoveroperator= (DnaInterfaceMinMover const &)
 
virtual ~DnaInterfaceMinMover ()
 
 DnaInterfaceMinMover (DnaInterfaceFinderOP)
 
virtual void apply (core::pose::Pose &)
 Minimizes the DOFs of <pose_> specified in the MoveMap using the ScoreFunction. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void use_interface (DnaInterfaceFinderOP)
 
void chi (bool value)
 
void bb (bool value)
 
void reset_from_interface ()
 
virtual void parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const &)
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme More...
 
virtual moves::MoverOP clone () const
 required in the context of the parser/scripting scheme More...
 
- Public Member Functions inherited from protocols::simple_moves::MinMover
 MinMover ()
 Constructs a MinMover minmover = protocols::simple_moves::MinMover() More...
 
 MinMover (std::string const &)
 
virtual ~MinMover ()
 
 MinMover (core::kinematics::MoveMapOP movemap_in, ScoreFunctionCOP scorefxn_in, std::string const &min_type_in, Real tolerance_in, bool use_nb_list_in, bool deriv_check_in=false, bool deriv_check_verbose_in=false)
 
void parse_opts (TagPtr const, protocols::moves::DataMap &data_map, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 
void parse_chi_and_bb (TagPtr const )
 
void parse_dof_tasks (TagPtr const tag, protocols::moves::DataMap &data)
 
void parse_dof_task_type (std::string const &tag_name, core::id::DOF_Type dof_type, core::id::TorsionType torsion_type, TagPtr const tag, protocols::moves::DataMap &data)
 helper function for parse_of_tasks More...
 
virtual void parse_def_opts (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)
 
virtual MinimizerOptionsOP min_options ()
 allow non-const access to the internal minimizer options object More...
 
virtual MinimizerOptionsCOP min_options () const
 allow const access to the internal minimizer options object More...
 
virtual void movemap (core::kinematics::MoveMapCOP movemap_in)
 Sets the MoveMap to <movemap_in> determines which DOF to minimize. More...
 
virtual
core::kinematics::MoveMapCOP 
movemap () const
 
virtual void score_function (ScoreFunctionCOP scorefxn_in)
 Sets the ScoreFunction to <scorefxn_in> determines which function to minimize. More...
 
virtual void score_function (core::scoring::ScoreFunction const &scorefxn_in)
 
virtual ScoreFunctionCOP score_function () const
 
virtual void min_type (std::string min_type_in)
 
virtual void tolerance (Real tolerance_in)
 
virtual void nb_list (bool nb_list_in)
 
virtual void deriv_check (bool deriv_check_in)
 
Real tolerance () const
 
std::string min_type () const
 
bool nb_list () const
 
bool deriv_check () const
 
void cartesian (bool newval)
 
bool cartesian () 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 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)
 
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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

DnaInterfaceFinderOP interface_
 
bool chi_
 
bool bb_
 

Additional Inherited Members

- 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...
 
- Protected Member Functions inherited from protocols::simple_moves::MinMover
void apply_dof_tasks_to_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap) const
 for use with RosettaScripts current method of using TaskOperations to specify residue sets. More...
 

Member Typedef Documentation

typedef utility::tag::TagPtr protocols::dna::DnaInterfaceMinMover::TagPtr

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( )
protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceMinMover const &  src)
protocols::dna::DnaInterfaceMinMover::~DnaInterfaceMinMover ( )
virtual
protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceFinderOP  interface)

Member Function Documentation

void protocols::dna::DnaInterfaceMinMover::apply ( core::pose::Pose pose_)
virtual

Minimizes the DOFs of <pose_> specified in the MoveMap using the ScoreFunction.

example(s): minmover.apply(pose) See also: MinMover MinMover.movemap MinMover.score_function

Reimplemented from protocols::simple_moves::MinMover.

References core::scoring::ScoreFunctionFactory::create_score_function(), interface_, protocols::simple_moves::MinMover::min_options(), protocols::simple_moves::MinMover::movemap(), reset_from_interface(), and protocols::simple_moves::MinMover::score_function().

void protocols::dna::DnaInterfaceMinMover::bb ( bool  value)
inline

References bb_.

void protocols::dna::DnaInterfaceMinMover::chi ( bool  value)
inline

References chi_.

MoverOP protocols::dna::DnaInterfaceMinMover::clone ( ) const
virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::MinMover.

References DnaInterfaceMinMover().

MoverOP protocols::dna::DnaInterfaceMinMover::fresh_instance ( ) const
virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::MinMover.

References DnaInterfaceMinMover().

std::string protocols::dna::DnaInterfaceMinMover::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::MinMover.

References protocols::dna::DnaInterfaceMinMoverCreator::mover_name().

DnaInterfaceMinMover & protocols::dna::DnaInterfaceMinMover::operator= ( DnaInterfaceMinMover const &  src)

References bb_, chi_, and interface_.

void protocols::dna::DnaInterfaceMinMover::parse_my_tag ( TagPtr const  tag,
moves::DataMap datamap,
protocols::filters::Filters_map const &  ,
moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
void protocols::dna::DnaInterfaceMinMover::reset_from_interface ( )
void protocols::dna::DnaInterfaceMinMover::use_interface ( DnaInterfaceFinderOP  interface)

References interface_, and reset_from_interface().

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::dna::DnaInterfaceMinMover::bb_
private

Referenced by bb(), operator=(), and reset_from_interface().

bool protocols::dna::DnaInterfaceMinMover::chi_
private
DnaInterfaceFinderOP protocols::dna::DnaInterfaceMinMover::interface_
private

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