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protocols::normalmode::NormalModeRelaxMover Class Reference

#include <NormalModeRelaxMover.hh>

Inheritance diagram for protocols::normalmode::NormalModeRelaxMover:
Inheritance graph
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Public Member Functions

 NormalModeRelaxMover ()
 
 NormalModeRelaxMover (core::scoring::ScoreFunctionCOP sfxn, bool const cartesian)
 
 NormalModeRelaxMover (core::scoring::ScoreFunctionCOP sfxn, bool cartesian, core::kinematics::MoveMapCOP mm, std::string const relaxmode, core::Real const distcut)
 
 ~NormalModeRelaxMover () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void apply_on_pose (core::pose::Pose &pose, core::kinematics::MoveMapOP movemap)
 
protocols::moves::MoverOP fresh_instance () const override
 Virtual functions from Mover. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_default ()
 
void set_harmonic_constants (core::Real const k_uniform)
 Setters. More...
 
void set_harmonic_constants (core::Real const k_connected, core::Real const k_segment, core::Real const k_long)
 
void invert_direction ()
 
void set_extrapolate_scale (core::Real const scale)
 
void set_cst_sdev (core::Real const cst_sdev)
 
void set_cartesian_minimize (bool const value)
 
void set_minoption (core::optimization::MinimizerOptionsCOP minoption)
 
void set_relaxmode (std::string const mode)
 
void set_mode (utility::vector1< core::Size > const mode_using, utility::vector1< core::Real > const mode_scales)
 
void set_mode (core::Size const i_mode)
 
void set_random_mode (std::string const select_option="probabilistic", core::Real const importance_portion=1.0)
 
void refresh_normalmode ()
 
protocols::normalmode::NormalMode
const 
NM () const
 
core::Real cst_sdev () const
 
core::Real get_dynamic_scale () const
 
std::string relaxmode () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::pose::PoseOP get_additional_output () override
 used by the job distributor and MultiplePoseMover (MPM) to return as many of the potential poses as possible. More...
 
- 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 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...
 
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...
 
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
 
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 Member Functions

virtual void initialize_NM_for_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap const &movemap)
 
void gen_coord_constraint (core::pose::Pose &pose, utility::vector1< core::Vector > const &excrd) const
 
void set_default_minoption ()
 
utility::vector1< core::Vectorextrapolate_mode_on_crd (core::pose::Pose const &pose) const
 
core::pose::Pose extrapolate_mode_on_pose (core::pose::Pose const &pose) const
 
core::Real get_RMSD (utility::vector1< core::Vector > const excrd, core::pose::Pose const &pose) const
 

Private Attributes

core::Size nmodes_ = 5
 
bool mix_modes_ = false
 
bool cartesian_ = true
 
core::Real pertscale_ = 1.0
 
bool randomselect_ = false
 
core::Real selection_kT_ = 1e6
 
bool centroid_ = false
 
core::Size nsample_ = 5
 
core::Real moving_distance_ = 1.0
 
bool refresh_normalmode_ = true
 
core::Real direction_ = 1.0
 
core::Real cst_sdev_ = 1.0
 
bool cartesian_minimize_ = false
 
bool dump_silent_ = false
 
std::string outsilent_
 
utility::vector1
< core::pose::PoseOP
output_pose_OPs_
 
std::string relaxmode_
 
core::optimization::MinimizerOptionsCOP minoption_
 
utility::vector1< core::Sizemode_using_
 
utility::vector1< core::Realmode_scale_
 
core::select::movemap::MoveMapFactoryCOP mmf_
 
core::kinematics::MoveMapOP mm_
 
core::scoring::ScoreFunctionOP sfxn_
 
core::scoring::ScoreFunctionOP sfxn_cen_
 
protocols::normalmode::NormalMode NM_
 
core::Real scale_dynamic_
 
utility::vector1< core::Realdtor_
 

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::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::normalmode::NormalModeRelaxMover::NormalModeRelaxMover ( )
protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover ( core::scoring::ScoreFunctionCOP  sfxn,
bool const  cartesian 
)
protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover ( core::scoring::ScoreFunctionCOP  sfxn,
bool  cartesian,
core::kinematics::MoveMapCOP  mm,
std::string const  relaxmode,
core::Real const  distcut 
)
protocols::normalmode::NormalModeRelaxMover::~NormalModeRelaxMover ( )
overridedefault

Member Function Documentation

void protocols::normalmode::NormalModeRelaxMover::apply ( core::pose::Pose )
overridevirtual
void protocols::normalmode::NormalModeRelaxMover::apply_on_pose ( core::pose::Pose pose,
core::kinematics::MoveMapOP  movemap 
)
protocols::moves::MoverOP protocols::normalmode::NormalModeRelaxMover::clone ( ) const
inlineoverridevirtual

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.

Referenced by fresh_instance().

core::Real protocols::normalmode::NormalModeRelaxMover::cst_sdev ( ) const
inline

References cst_sdev_.

Referenced by gen_coord_constraint(), and set_cst_sdev().

utility::vector1< Vector > protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd ( core::pose::Pose const &  pose) const
private
pose::Pose protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose ( core::pose::Pose const &  pose) const
private
protocols::moves::MoverOP protocols::normalmode::NormalModeRelaxMover::fresh_instance ( ) const
inlineoverridevirtual

Virtual functions from Mover.

Reimplemented from protocols::moves::Mover.

References clone().

void protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint ( core::pose::Pose pose,
utility::vector1< core::Vector > const &  excrd 
) const
private
core::pose::PoseOP protocols::normalmode::NormalModeRelaxMover::get_additional_output ( )
overridevirtual

used by the job distributor and MultiplePoseMover (MPM) to return as many of the potential poses as possible.

normal mode relaxed poses are remembered as PoseOPs in a score-sorted fashion. Each time this is called, the best is removed from memory and returned until no more remain. Assumes randomselect_/order of output_pose_OPs_ isn't changed between calls because this would not be reflected in how addnl poses are retrived (sorting/shuffling is done only once)

Reimplemented from protocols::moves::Mover.

References centroid_, core::chemical::element::F, output_pose_OPs_, sfxn_, sfxn_cen_, and protocols::TR().

core::Real protocols::normalmode::NormalModeRelaxMover::get_dynamic_scale ( ) const
inline

References scale_dynamic_.

std::string protocols::normalmode::NormalModeRelaxMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Real protocols::normalmode::NormalModeRelaxMover::get_RMSD ( utility::vector1< core::Vector > const  excrd,
core::pose::Pose const &  pose 
) const
private
void protocols::normalmode::NormalModeRelaxMover::initialize_NM_for_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap const &  movemap 
)
privatevirtual
void protocols::normalmode::NormalModeRelaxMover::invert_direction ( )
inline

References direction_.

std::string protocols::normalmode::NormalModeRelaxMover::mover_name ( )
static
protocols::normalmode::NormalMode const protocols::normalmode::NormalModeRelaxMover::NM ( ) const
inline
void protocols::normalmode::NormalModeRelaxMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References cartesian_, cartesian_minimize_, centroid_, dump_silent_, mix_modes_, mmf_, NM_, nmodes_, nsample_, outsilent_, protocols::rosetta_scripts::parse_movemap_factory_legacy(), pertscale_, randomselect_, relaxmode_, selection_kT_, set_harmonic_constants(), sfxn_, sfxn_cen_, and protocols::normalmode::NormalMode::torsion().

void protocols::normalmode::NormalModeRelaxMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::normalmode::NormalModeRelaxMover::refresh_normalmode ( )
inline

References refresh_normalmode_.

std::string protocols::normalmode::NormalModeRelaxMover::relaxmode ( ) const
inline

References relaxmode_.

Referenced by NormalModeRelaxMover().

void protocols::normalmode::NormalModeRelaxMover::set_cartesian_minimize ( bool const  value)
inline

References cartesian_minimize_.

void protocols::normalmode::NormalModeRelaxMover::set_cst_sdev ( core::Real const  cst_sdev)
inline

References cst_sdev(), and cst_sdev_.

void protocols::normalmode::NormalModeRelaxMover::set_default ( )
void protocols::normalmode::NormalModeRelaxMover::set_default_minoption ( )
private
void protocols::normalmode::NormalModeRelaxMover::set_extrapolate_scale ( core::Real const  scale)
inline

References moving_distance_.

Referenced by apply().

void protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants ( core::Real const  k_uniform)
void protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants ( core::Real const  k_connected,
core::Real const  k_segment,
core::Real const  k_long 
)
void protocols::normalmode::NormalModeRelaxMover::set_minoption ( core::optimization::MinimizerOptionsCOP  minoption)
inline

References minoption_.

void protocols::normalmode::NormalModeRelaxMover::set_mode ( utility::vector1< core::Size > const  mode_using,
utility::vector1< core::Real > const  mode_scales 
)

References mode_scale_, mode_using_, NM(), and protocols::TR().

Referenced by apply().

void protocols::normalmode::NormalModeRelaxMover::set_mode ( core::Size const  i_mode)

References mode_scale_, and mode_using_.

void protocols::normalmode::NormalModeRelaxMover::set_random_mode ( std::string const  select_option = "probabilistic",
core::Real const  importance_portion = 1.0 
)
void protocols::normalmode::NormalModeRelaxMover::set_relaxmode ( std::string const  mode)
inline

References relaxmode_.

Member Data Documentation

bool protocols::normalmode::NormalModeRelaxMover::cartesian_ = true
private
bool protocols::normalmode::NormalModeRelaxMover::cartesian_minimize_ = false
private
bool protocols::normalmode::NormalModeRelaxMover::centroid_ = false
private
core::Real protocols::normalmode::NormalModeRelaxMover::cst_sdev_ = 1.0
private

Referenced by cst_sdev(), and set_cst_sdev().

core::Real protocols::normalmode::NormalModeRelaxMover::direction_ = 1.0
private
utility::vector1< core::Real > protocols::normalmode::NormalModeRelaxMover::dtor_
mutableprivate
bool protocols::normalmode::NormalModeRelaxMover::dump_silent_ = false
private

Referenced by apply(), and parse_my_tag().

core::optimization::MinimizerOptionsCOP protocols::normalmode::NormalModeRelaxMover::minoption_
private
bool protocols::normalmode::NormalModeRelaxMover::mix_modes_ = false
private

Referenced by apply(), and parse_my_tag().

core::kinematics::MoveMapOP protocols::normalmode::NormalModeRelaxMover::mm_
private

Referenced by apply(), and NormalModeRelaxMover().

core::select::movemap::MoveMapFactoryCOP protocols::normalmode::NormalModeRelaxMover::mmf_
private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Real > protocols::normalmode::NormalModeRelaxMover::mode_scale_
private
utility::vector1< core::Size > protocols::normalmode::NormalModeRelaxMover::mode_using_
private
core::Real protocols::normalmode::NormalModeRelaxMover::moving_distance_ = 1.0
private
protocols::normalmode::NormalMode protocols::normalmode::NormalModeRelaxMover::NM_
private
core::Size protocols::normalmode::NormalModeRelaxMover::nmodes_ = 5
private
core::Size protocols::normalmode::NormalModeRelaxMover::nsample_ = 5
private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::pose::PoseOP > protocols::normalmode::NormalModeRelaxMover::output_pose_OPs_
private

Referenced by apply(), and get_additional_output().

std::string protocols::normalmode::NormalModeRelaxMover::outsilent_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::normalmode::NormalModeRelaxMover::pertscale_ = 1.0
private

Referenced by apply(), and parse_my_tag().

bool protocols::normalmode::NormalModeRelaxMover::randomselect_ = false
private

Referenced by apply(), and parse_my_tag().

bool protocols::normalmode::NormalModeRelaxMover::refresh_normalmode_ = true
private
std::string protocols::normalmode::NormalModeRelaxMover::relaxmode_
private
core::Real protocols::normalmode::NormalModeRelaxMover::scale_dynamic_
mutableprivate
core::Real protocols::normalmode::NormalModeRelaxMover::selection_kT_ = 1e6
private

Referenced by parse_my_tag().

core::scoring::ScoreFunctionOP protocols::normalmode::NormalModeRelaxMover::sfxn_
private
core::scoring::ScoreFunctionOP protocols::normalmode::NormalModeRelaxMover::sfxn_cen_
private

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