Public Member Functions | List of all members
protocols::simple_moves::BBG8T3AMover Class Reference

a particular gaussian mover from the original paper More...

#include <BBGaussianMover.hh>

Inheritance diagram for protocols::simple_moves::BBG8T3AMover:
Inheritance graph

Public Member Functions

protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 BBG8T3AMover ()
 ~BBG8T3AMover () override
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::simple_moves::BBGaussianMover
 BBGaussianMover ()
 BBGaussianMover (core::Size, core::Size, core::Size)
 ~BBGaussianMover () override
void apply (Pose &pose) override
 Main Method. More...
void init ()
void resize (core::Size, core::Size, core::Size)
void factorA (Real const fA)
void factorB (Real const fB)
void get_G ()
void get_A ()
Real get_L_prime ()
Real get_L_move (Pose &)
void get_VdRdPhi (Pose const &)
core::kinematics::MoveMapCOP movemap (core::pose::Pose const &) const
 Generates the movemap used by this mover for the given pose. More...
void movemap (core::kinematics::MoveMapCOP new_movemap)
void movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)
 The movemap_factory will be used to generate a movemap, if an explcit one hasn't already been set. More...
void update_counting_last_PDR (Real)
Real last_proposal_density_ratio () override
 get the ratio of proposal densities for the last move More...
bool preserve_detailed_balance () const override
 get whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
void set_preserve_detailed_balance (bool preserve_detailed_balance) override
 set whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
utility::vector1< core::id::TorsionID_Rangetorsion_id_ranges (core::pose::Pose &) override
 dummy More...
void init_kic_loop (core::Size looplength, core::kinematics::MoveMapCOP mm)
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 Default constructor. More...
 ~ThermodynamicMover () override
 Default destructor. More...
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 Callback executed before any Monte Carlo trials are attempted. More...
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after the Metropolis criterion is evaluated. More...
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after all Monte Carlo trials are completed. More...
virtual bool is_multi_trial ()
 Return true if the move performs multiple trials on each apply. More...
virtual core::Real last_inner_score_delta_over_temperature ()
 If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...
virtual protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover ()
 If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...
virtual utility::vector1< core::id::DOF_ID_Rangedof_id_ranges (core::pose::Pose &pose)
 Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. 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...
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
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 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Additional Inherited Members

- Public Types inherited from protocols::simple_moves::BBGaussianMover
typedef core::Real Real
typedef core::Size Size
typedef core::pose::Pose Pose
typedef core::pose::PoseOP PoseOP
typedef core::pose::PoseCOP PoseCOP
typedef core::conformation::Residue Residue
typedef utility::vector1< RealVector
typedef numeric::xyzVector< RealxyzVector
typedef utility::vector1< xyzVectorVdRdPhi
typedef utility::vector1< VdRdPhiVMatrix
typedef utility::vector1< VectorMatrix
- 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::simple_moves::BBGaussianMover
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...
- Protected Member Functions inherited from protocols::simple_moves::BBGaussianMover
void setup_list (Pose const &)
xyzVector get_dRdPhi (xyzVector const &r1, xyzVector const &r2, xyzVector const &r)
xyzVector get_dRdTheta (xyzVector const &r1, xyzVector const &r2, xyzVector const &r3, xyzVector const &r)
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
Real cholesky_fw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)
Real cholesky_bw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)
void pivot_range_randomly (Pose &, core::Size, core::Size)
 randomly rotate the dih angle in this range for avoiding the fixed ends 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::simple_moves::BBGaussianMover
core::Size n_end_atom_
core::Size n_dof_angle_
core::Size n_pert_res_
core::Size resnum_
utility::vector1< std::pair< core::Size, Size > > available_seg_list_
utility::vector1< std::pair< core::Size, std::string > > end_atom_list_
Matrix matrix_G
Matrix matrix_A
VMatrix matrix_dRdPhi
Real last_proposal_density_ratio_
bool preserve_detailed_balance_
core::kinematics::MoveMapCOP movemap_
core::select::movemap::MoveMapFactoryCOP movemap_factory_
Vector dphi_
Real factorA_
Real factorB_
core::Size N_auto_all
core::Size N_auto_small
bool use_all_pivot_res_
bool auto_adjust_factorA_
bool fix_short_segment_
bool shrink_frag_ends_

Detailed Description

a particular gaussian mover from the original paper

using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end

Constructor & Destructor Documentation

◆ BBG8T3AMover()

protocols::simple_moves::BBG8T3AMover::BBG8T3AMover ( )

◆ ~BBG8T3AMover()

protocols::simple_moves::BBG8T3AMover::~BBG8T3AMover ( )

Member Function Documentation

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::BBG8T3AMover::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::simple_moves::BBGaussianMover.

References BBG8T3AMover(), protocols::simple_moves::BBGaussianMover::factorA_, protocols::simple_moves::BBGaussianMover::factorB_, and protocols::simple_moves::BBGaussianMover::movemap_.

◆ get_name()

std::string protocols::simple_moves::BBG8T3AMover::get_name ( ) const

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

Reimplemented from protocols::simple_moves::BBGaussianMover.

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