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Rosetta
2021.16
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Rosetta
2021.16
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a particular gaussian mover from the original paper More...
#include <BBGaussianMover.hh>
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_Range > | torsion_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_Range > | dof_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 Strings & | info () |
| 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< Real > | Vector |
| typedef numeric::xyzVector< Real > | xyzVector |
| typedef utility::vector1 < xyzVector > | VdRdPhi |
| typedef utility::vector1< VdRdPhi > | VMatrix |
| typedef utility::vector1< Vector > | Matrix |
| 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_ |
a particular gaussian mover from the original paper
| protocols::simple_moves::BBG8T3AMover::BBG8T3AMover | ( | ) |
References protocols::simple_moves::BBGaussianMover::movemap(), protocols::simple_moves::BBGaussianMover::resize(), and protocols::moves::Mover::type().
Referenced by clone().
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overridedefault |
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overridevirtual |
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_.
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overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::simple_moves::BBGaussianMover.
1.8.7