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protocols::simple_moves::MinMover Class Reference

A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set. More...

#include <MinMover.hh>

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Public Types

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

 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)
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::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...
 
virtual void parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...
 
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
 
virtual void apply (core::pose::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 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
 

Protected Member Functions

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...
 
- 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 std::map< std::pair
< core::id::DOF_Type,
core::id::TorsionType >
, core::pack::task::TaskFactoryOP
DOF_TaskMap
 

Private Attributes

core::kinematics::MoveMapOP movemap_
 
ScoreFunctionCOP scorefxn_
 
MinimizerOptionsOP min_options_
 
Real threshold_
 
bool cartesian_
 
DOF_TaskMap dof_tasks_
 

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...
 

Detailed Description

A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set.

Common Methods: MinMover.apply MinMover.movemap MinMover.score_function

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::MinMover::MinMover ( )

Constructs a MinMover minmover = protocols::simple_moves::MinMover()

References min_options_.

Referenced by fresh_instance().

protocols::simple_moves::MinMover::MinMover ( std::string const &  name)

References min_options_.

protocols::simple_moves::MinMover::~MinMover ( )
virtual
protocols::simple_moves::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 
)

Member Function Documentation

void protocols::simple_moves::MinMover::apply ( core::pose::Pose pose_)
virtual
void protocols::simple_moves::MinMover::apply_dof_tasks_to_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap movemap 
) const
protected

for use with RosettaScripts current method of using TaskOperations to specify residue sets.

restrict the move map by the packer task: If a residue is not designable, the backbone is fixes If a residue is not packable, the sidechain is fixed

WARNING: This is extending the abuse of using task operations for general ResidueSubsets

When TaskOperations replaced with ResidueSetOperations please change this too!

References dof_tasks_, core::id::PHI, and core::scoring::hbonds::t().

Referenced by protocols::simple_moves::symmetry::SymMinMover::apply(), and apply().

void protocols::simple_moves::MinMover::cartesian ( bool  newval)
inline

References cartesian_.

bool protocols::simple_moves::MinMover::cartesian ( ) const
inline
protocols::moves::MoverOP protocols::simple_moves::MinMover::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

Referenced by parse_def_opts().

void protocols::simple_moves::MinMover::deriv_check ( bool  deriv_check_in)
virtual
bool protocols::simple_moves::MinMover::deriv_check ( ) const

References min_options_.

protocols::moves::MoverOP protocols::simple_moves::MinMover::fresh_instance ( ) const
virtual

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References MinMover().

std::string protocols::simple_moves::MinMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References protocols::simple_moves::MinMoverCreator::mover_name().

MinimizerOptionsOP protocols::simple_moves::MinMover::min_options ( )
virtual
MinimizerOptionsCOP protocols::simple_moves::MinMover::min_options ( ) const
virtual

allow const access to the internal minimizer options object

References min_options_.

void protocols::simple_moves::MinMover::min_type ( std::string  min_type_in)
virtual
std::string protocols::simple_moves::MinMover::min_type ( ) const
virtual void protocols::simple_moves::MinMover::movemap ( core::kinematics::MoveMapCOP  movemap_in)
virtual

Sets the MoveMap to <movemap_in> determines which DOF to minimize.

example(s): minmover.movemap(movemap1) See also: MinMover MinMover.apply MinMover.score_function MoveMap

Referenced by protocols::simple_moves::operator<<().

MoveMapCOP protocols::simple_moves::MinMover::movemap ( ) const
virtual
void protocols::simple_moves::MinMover::nb_list ( bool  nb_list_in)
virtual
bool protocols::simple_moves::MinMover::nb_list ( ) const

References min_options_.

void protocols::simple_moves::MinMover::parse_chi_and_bb ( TagPtr const  tag)

References core::id::D, movemap_, and core::id::THETA.

Referenced by parse_my_tag().

void protocols::simple_moves::MinMover::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks,
protocols::moves::MoverCacheSP  cache 
)
virtual
void protocols::simple_moves::MinMover::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 protocols::simple_moves::MinMover::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

References dof_tasks_, protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

Referenced by parse_dof_tasks().

void protocols::simple_moves::MinMover::parse_dof_tasks ( TagPtr const  tag,
protocols::moves::DataMap data 
)
void protocols::simple_moves::MinMover::parse_my_tag ( TagPtr const  tag,
protocols::moves::DataMap data,
Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual
void protocols::simple_moves::MinMover::parse_opts ( TagPtr const  tag,
protocols::moves::DataMap data_map,
Filters_map const &  ,
protocols::moves::Movers_map const &  ,
Pose const &   
)
void protocols::simple_moves::MinMover::score_function ( ScoreFunctionCOP  scorefxn_in)
virtual

Sets the ScoreFunction to <scorefxn_in> determines which function to minimize.

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

References scorefxn_.

Referenced by protocols::simple_moves::operator<<().

void protocols::simple_moves::MinMover::score_function ( core::scoring::ScoreFunction const &  scorefxn_in)
virtual
ScoreFunctionCOP protocols::simple_moves::MinMover::score_function ( ) const
virtual
void protocols::simple_moves::MinMover::tolerance ( Real  tolerance_in)
virtual
Real protocols::simple_moves::MinMover::tolerance ( ) const

Member Data Documentation

bool protocols::simple_moves::MinMover::cartesian_
private

Referenced by cartesian().

DOF_TaskMap protocols::simple_moves::MinMover::dof_tasks_
private

Until ResidueSubsetOperations are implemented, RosettaScripts uses TaskOperations as a generic way to specify sets of residues, so it is necessary to have a method of controling a movemap from a set of task operations. This is not suppose to be a general interface for MinMover, so only expose it through the parse_my_tag. Another small complication is that TaskOperations must be defined in the context of a pose, so hang on to it here until the apply. In case MinMover is applied multiple times, to avoid accumulating state, reset the move map to before the task operations were applied at the end of apply.

Referenced by apply_dof_tasks_to_movemap(), and parse_dof_task_type().

MinimizerOptionsOP protocols::simple_moves::MinMover::min_options_
private
core::kinematics::MoveMapOP protocols::simple_moves::MinMover::movemap_
private
ScoreFunctionCOP protocols::simple_moves::MinMover::scorefxn_
private

Referenced by apply(), and score_function().

Real protocols::simple_moves::MinMover::threshold_
private

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