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protocols::relax::RangeRelaxMover Class Reference

#include <RangeRelaxMover.hh>

Inheritance diagram for protocols::relax::RangeRelaxMover:
Inheritance graph
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Public Member Functions

 RangeRelaxMover ()
 Constructors ///. More...
 
 RangeRelaxMover (core::Size center_resnumber)
 Custom Constructor. More...
 
 RangeRelaxMover (RangeRelaxMover const &src)
 Copy Constructor. More...
 
RangeRelaxMoveroperator= (RangeRelaxMover const &src)
 Assignment Operator. More...
 
 ~RangeRelaxMover () override
 Destructor. More...
 
std::string get_name () const override
 Rosetta Scripts Methods ///. More...
 
void apply (Pose &pose) override
 Run RangeRelax. More...
 
void add_membrane_again (bool yesno)
 Run AddMembraneMover before? More...
 
void optimize_membrane (bool yesno)
 Optimize membrane. More...
 
void idealize (bool yesno)
 Idealize pose after run? More...
 
void set_angle_max (core::Real angle_max)
 Set maximum dihedral angle perturbation. More...
 
void set_nmoves (std::string nmoves)
 Set number of moves, can be "nres" or a number. More...
 
void set_scorefunction (core::scoring::ScoreFunctionOP sfxn)
 Use scorefunction. More...
 
void set_native (core::pose::PoseOP pose)
 Set native. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Member Functions

void register_options ()
 Setup Methods ///. More...
 
void set_defaults ()
 Set default values. More...
 
void init_from_cmd ()
 Initialize from commandline. More...
 
core::kinematics::FoldTree finalize_setup (Pose &pose)
 Finalize setup. More...
 
void constrain_to_reference (Pose &pose, Pose &ref_pose)
 Create constraints to reference pose. More...
 
void repack_sequence_window (Pose &pose, protocols::moves::MonteCarloOP mc)
 Repack in a sequence window. More...
 
utility::vector1< boolget_window_repack_residues (Pose &pose, core::SSize center1, core::SSize center2, core::SSize halfrange)
 Initialize from commandline. More...
 
void repack_spherical_range (Pose &pose, protocols::moves::MonteCarloOP mc)
 Repack in spherical range. More...
 
utility::vector1< boolget_spherical_repack_residues (Pose &pose, core::Real inner_radius, core::Real outer_radius)
 Initialize from commandline. More...
 
void repack_all (Pose &pose, protocols::moves::MonteCarloOP mc)
 Repack all residues again. More...
 
void idealize_pose (Pose &pose, core::optimization::MinimizerOptions minopts, core::optimization::AtomTreeMinimizer atm)
 Idealize pose. More...
 
void print_score (Pose &pose)
 Print score to cout. More...
 

Private Attributes

core::pose::PoseOP native_
 Native. More...
 
core::Size center_resnumber_
 Center residue number. More...
 
core::Real angle_max_
 Maximum allowed dihedral angle change for Small and ShearMover. More...
 
std::string moves_
 Number of moves Small and ShearMover can make. More...
 
core::Size nmoves_
 
core::kinematics::MoveMapOP movemap_
 Movemap for Small and ShearMover. More...
 
core::scoring::ScoreFunctionOP sfxn_
 Scorefxn for scoring. More...
 
core::scoring::ScoreFunctionOP sfxn_nocst_
 Scorefunction without constraints. More...
 
std::string cst_file_
 constraint filename More...
 
core::Real cst_weight_
 constraint weight More...
 
bool cst_to_start_
 constrain to starting coordinates More...
 
bool cst_to_native_
 constrain to native More...
 
bool addmem_
 Add Membrane to native? More...
 
bool optmem_
 Optimize membrane for protein? More...
 
bool repack_again_
 Additional round of repack which packs all residues simultaneously. More...
 
core::Size cycles_
 Cycles for repacking and minimization. More...
 
core::Size min_cycles_
 Cycles within the Minimizer. More...
 
bool spherical_wave_
 Relax in centric wave pattern. More...
 
bool idealize_
 Idealize decoy after run? More...
 

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
 
- 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...
 

Constructor & Destructor Documentation

protocols::relax::RangeRelaxMover::RangeRelaxMover ( )

Constructors ///.

Default Constructor

Defaults: dih angle_max = 0.1, nmoves = "nres", movemap = bb and all chi

Default Constructor

Defaults: dih angle_max = 1, nmoves = nres, movemap = bb and all chi

References init_from_cmd(), register_options(), and set_defaults().

Referenced by operator=().

protocols::relax::RangeRelaxMover::RangeRelaxMover ( core::Size  center_resnumber)

Custom Constructor.

Takes the center residue to start relaxing from

References center_resnumber_, init_from_cmd(), register_options(), and set_defaults().

protocols::relax::RangeRelaxMover::RangeRelaxMover ( RangeRelaxMover const &  src)
default

Copy Constructor.

Create a deep copy of this mover

protocols::relax::RangeRelaxMover::~RangeRelaxMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::relax::RangeRelaxMover::add_membrane_again ( bool  yesno)

Run AddMembraneMover before?

Run AddMembraneMover again?

If you want to keep your anchor point for MEM, then pick no This is only needed for the native, not the pose itself

If you want to keep your anchor point for MEM, then pick no

References addmem_.

void protocols::relax::RangeRelaxMover::apply ( Pose pose)
overridevirtual
void protocols::relax::RangeRelaxMover::constrain_to_reference ( Pose pose,
Pose ref_pose 
)
private
core::kinematics::FoldTree protocols::relax::RangeRelaxMover::finalize_setup ( Pose pose)
private
std::string protocols::relax::RangeRelaxMover::get_name ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Mover Methods /// Get the name of this Mover (RangeRelaxMover)

Create a Clone of this mover Get the name of this Mover (RangeRelaxMover)

Implements protocols::moves::Mover.

utility::vector1< bool > protocols::relax::RangeRelaxMover::get_spherical_repack_residues ( Pose pose,
core::Real  inner_radius,
core::Real  outer_radius 
)
private
utility::vector1< bool > protocols::relax::RangeRelaxMover::get_window_repack_residues ( Pose pose,
core::SSize  center1,
core::SSize  center2,
core::SSize  halfrange 
)
private

Initialize from commandline.

References core::pose::Pose::size(), and protocols::relax::TR().

Referenced by repack_sequence_window().

void protocols::relax::RangeRelaxMover::idealize ( bool  yesno)

Idealize pose after run?

Might lead to better decoy but takes longer

References idealize_.

void protocols::relax::RangeRelaxMover::idealize_pose ( Pose pose,
core::optimization::MinimizerOptions  minopts,
core::optimization::AtomTreeMinimizer  atm 
)
private
void protocols::relax::RangeRelaxMover::init_from_cmd ( )
private
RangeRelaxMover & protocols::relax::RangeRelaxMover::operator= ( RangeRelaxMover const &  src)

Assignment Operator.

References RangeRelaxMover().

void protocols::relax::RangeRelaxMover::optimize_membrane ( bool  yesno)

Optimize membrane.

References optmem_.

void protocols::relax::RangeRelaxMover::print_score ( Pose pose)
private
void protocols::relax::RangeRelaxMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line

Referenced by RangeRelaxMover().

void protocols::relax::RangeRelaxMover::repack_all ( Pose pose,
protocols::moves::MonteCarloOP  mc 
)
private
void protocols::relax::RangeRelaxMover::repack_sequence_window ( Pose pose,
protocols::moves::MonteCarloOP  mc 
)
private
void protocols::relax::RangeRelaxMover::repack_spherical_range ( Pose pose,
protocols::moves::MonteCarloOP  mc 
)
private
void protocols::relax::RangeRelaxMover::set_angle_max ( core::Real  angle_max)

Set maximum dihedral angle perturbation.

References angle_max_.

void protocols::relax::RangeRelaxMover::set_defaults ( )
private
void protocols::relax::RangeRelaxMover::set_native ( core::pose::PoseOP  pose)

Set native.

References native_.

void protocols::relax::RangeRelaxMover::set_nmoves ( std::string  nmoves)

Set number of moves, can be "nres" or a number.

References moves_.

void protocols::relax::RangeRelaxMover::set_scorefunction ( core::scoring::ScoreFunctionOP  sfxn)

Use scorefunction.

Use membrane scorefunction.

References sfxn_, and sfxn_nocst_.

Member Data Documentation

bool protocols::relax::RangeRelaxMover::addmem_
private

Add Membrane to native?

Referenced by add_membrane_again(), finalize_setup(), init_from_cmd(), and set_defaults().

core::Real protocols::relax::RangeRelaxMover::angle_max_
private

Maximum allowed dihedral angle change for Small and ShearMover.

Referenced by apply(), init_from_cmd(), set_angle_max(), and set_defaults().

core::Size protocols::relax::RangeRelaxMover::center_resnumber_
private
std::string protocols::relax::RangeRelaxMover::cst_file_
private

constraint filename

Referenced by finalize_setup(), init_from_cmd(), and set_defaults().

bool protocols::relax::RangeRelaxMover::cst_to_native_
private

constrain to native

Referenced by finalize_setup(), init_from_cmd(), and set_defaults().

bool protocols::relax::RangeRelaxMover::cst_to_start_
private

constrain to starting coordinates

Referenced by apply(), finalize_setup(), init_from_cmd(), and set_defaults().

core::Real protocols::relax::RangeRelaxMover::cst_weight_
private

constraint weight

Referenced by finalize_setup(), init_from_cmd(), and set_defaults().

core::Size protocols::relax::RangeRelaxMover::cycles_
private

Cycles for repacking and minimization.

Referenced by apply(), init_from_cmd(), and set_defaults().

bool protocols::relax::RangeRelaxMover::idealize_
private

Idealize decoy after run?

Referenced by apply(), idealize(), init_from_cmd(), and set_defaults().

core::Size protocols::relax::RangeRelaxMover::min_cycles_
private

Cycles within the Minimizer.

Referenced by apply(), init_from_cmd(), and set_defaults().

core::kinematics::MoveMapOP protocols::relax::RangeRelaxMover::movemap_
private

Movemap for Small and ShearMover.

Referenced by apply(), idealize_pose(), and set_defaults().

std::string protocols::relax::RangeRelaxMover::moves_
private

Number of moves Small and ShearMover can make.

moves_ is a string and can take 'nres' as well as a number nmoves_ is the actual number that is taken after conversion

Referenced by finalize_setup(), init_from_cmd(), set_defaults(), and set_nmoves().

core::pose::PoseOP protocols::relax::RangeRelaxMover::native_
private
core::Size protocols::relax::RangeRelaxMover::nmoves_
private

Referenced by apply(), and finalize_setup().

bool protocols::relax::RangeRelaxMover::optmem_
private

Optimize membrane for protein?

Referenced by apply(), init_from_cmd(), optimize_membrane(), and set_defaults().

bool protocols::relax::RangeRelaxMover::repack_again_
private

Additional round of repack which packs all residues simultaneously.

Referenced by apply(), init_from_cmd(), and set_defaults().

core::scoring::ScoreFunctionOP protocols::relax::RangeRelaxMover::sfxn_
private
core::scoring::ScoreFunctionOP protocols::relax::RangeRelaxMover::sfxn_nocst_
private

Scorefunction without constraints.

Referenced by constrain_to_reference(), finalize_setup(), set_defaults(), and set_scorefunction().

bool protocols::relax::RangeRelaxMover::spherical_wave_
private

Relax in centric wave pattern.

Referenced by apply(), init_from_cmd(), and set_defaults().


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