Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | List of all members
protocols::normalmode::CartesianNormalModeMover Class Reference

#include <NormalModeRelaxMover.hh>

Public Member Functions

 CartesianNormalModeMover (core::pose::Pose const &, core::scoring::ScoreFunctionCOP sfxn, std::string const relaxmode)
 CartesianNormalModeMover (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP mm, std::string const mode="CA", Real const distcut=10.0, std::string const relaxmode="min")
 ~CartesianNormalModeMover ()
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual void gen_coord_constraint (pose::Pose &pose, utility::vector1< Vector > const &excrd)
 Pure virtual functions inside NMmover. More...
virtual void set_default_minoption ()
- Public Member Functions inherited from protocols::normalmode::NormalModeRelaxMover
 NormalModeRelaxMover ()
 ~NormalModeRelaxMover ()
virtual protocols::moves::MoverOP fresh_instance () const
 Virtual functions from Mover. More...
virtual void set_movemap (core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap)
void set_harmonic_constants (Real const k_uniform)
 Common options. More...
void set_harmonic_constants (Real const k_connected, Real const k_segment, Real const k_long)
void invert_direction ()
void set_extrapolate_scale (Real const scale)
void set_cst_sdev (Real const cst_sdev)
void set_mode (utility::vector1< Size > const mode_using, utility::vector1< Real > const mode_scales)
void set_mode (Size const i_mode)
void set_cartesian_minimize (bool const value)
void set_random_mode (Size const nmode, std::string const select_option="probabilistic", Real const importance_portion=1.0)
void set_minoption (optimization::MinimizerOptionsCOP minoption)
void refresh_normalmode ()
protocols::normalmode::NormalMode NM ()
Real cst_sdev ()
Real get_dynamic_scale ()
- 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
void set_type (std::string const &setting)
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 void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Member Functions

utility::vector1< Vectorextrapolate_mode (pose::Pose const &pose)
Real get_RMSD (utility::vector1< Vector > const excrd, pose::Pose const &pose)

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::stringStrings
- 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...
- 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...
- Protected Attributes inherited from protocols::normalmode::NormalModeRelaxMover
Real direction_
Real moving_distance_
Real cst_sdev_
bool refresh_normalmode_
bool cartesian_minimize_
optimization::MinimizerOptionsCOP minoption_
Real scale_dynamic_
std::string relaxmode_
utility::vector1< Sizemode_using_
utility::vector1< Realmode_scale_
core::kinematics::MoveMapOP mm_
core::scoring::ScoreFunctionOP sfxn_
core::scoring::ScoreFunctionOP sfxn_cen_
protocols::normalmode::NormalMode NM_

Constructor & Destructor Documentation

protocols::normalmode::CartesianNormalModeMover::CartesianNormalModeMover ( core::pose::Pose const &  ,
core::scoring::ScoreFunctionCOP  sfxn,
std::string const  relaxmode 
protocols::normalmode::CartesianNormalModeMover::CartesianNormalModeMover ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  sfxn,
core::kinematics::MoveMapCOP  mm,
std::string const  mode = "CA",
Real const  distcut = 10.0,
std::string const  relaxmode = "min" 
protocols::normalmode::CartesianNormalModeMover::~CartesianNormalModeMover ( )

Member Function Documentation

void protocols::normalmode::CartesianNormalModeMover::apply ( core::pose::Pose pose)
virtual protocols::moves::MoverOP protocols::normalmode::CartesianNormalModeMover::clone ( ) const

Return a clone of the Mover object.

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.

utility::vector1< Vector > protocols::normalmode::CartesianNormalModeMover::extrapolate_mode ( pose::Pose const &  pose)
void protocols::normalmode::CartesianNormalModeMover::gen_coord_constraint ( pose::Pose pose,
utility::vector1< Vector > const &  excrd 
virtual std::string protocols::normalmode::CartesianNormalModeMover::get_name ( ) const

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

Implements protocols::moves::Mover.

Real protocols::normalmode::CartesianNormalModeMover::get_RMSD ( utility::vector1< Vector > const  excrd,
pose::Pose const &  pose 
void protocols::normalmode::CartesianNormalModeMover::set_default_minoption ( )

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