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Rosetta Protocols
2014.16.56682
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Rosetta Protocols
2014.16.56682
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#include <RigidBodyMover.hh>
Public Types | |
| typedef RigidBodySpinMover | parent |
 Public Types inherited from protocols::rigid::RigidBodySpinMover | |
| typedef RigidBodyMover | parent |
| Public Types inherited from protocols::rigid::RigidBodyMover | |
| typedef ThermodynamicMover | parent |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| RigidBodyDeterministicSpinMover () | |
| RigidBodyDeterministicSpinMover (int const rb_jump_in, core::Vector spin_axis, core::Vector rotation_center, float angle_magnitude) | |
| constructor with arguments spin axis is initialized to 0 then calculated during apply() if spin_axis is not already set More... | |
| RigidBodyDeterministicSpinMover (RigidBodyDeterministicSpinMover const &src) | |
| ~RigidBodyDeterministicSpinMover () | |
| void | angle_magnitude (float angle_magnitude) |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::rigid::RigidBodySpinMover | |
| RigidBodySpinMover () | |
| RigidBodySpinMover (int const rb_jump_in) | |
| constructor with arguments spin axis is initialized to 0 and then calculated during apply() More... | |
| RigidBodySpinMover (RigidBodySpinMover const &src) | |
| ~RigidBodySpinMover () | |
| void | spin_axis (core::Vector spin_axis_in) |
| void | rot_center (core::Vector const rot_center_in) |
| Public Member Functions inherited from protocols::rigid::RigidBodyMover | |
| RigidBodyMover () | |
| RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c) | |
| RigidBodyMover (RigidBodyMover const &src) | |
| virtual | ~RigidBodyMover () |
| void | rot_center (core::Vector const rot_center_in) |
| Manual override of rotation center. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual bool | preserve_detailed_balance () const |
| Return true if detailed balance is being preserved (i.e. no branch angle optimization). More... | |
| virtual void | set_preserve_detailed_balance (bool) |
| set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More... | |
| virtual utility::vector1 < core::id::TorsionID_Range > | torsion_id_ranges (core::pose::Pose &pose) |
| get the TorsionIDs perturbed by the mover during moves, along with their ranges More... | |
| int | rb_jump () const |
| void | rb_jump (int jump_id) |
| void | unfreeze () |
| void | freeze () |
| Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover | |
| ThermodynamicMover () | |
| Default constructor. More... | |
| virtual | ~ThermodynamicMover () |
| Default destructor. More... | |
| virtual void | initialize_simulation (core::pose::Pose &pose, MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) |
| Callback executed before any Monte Carlo trials are attempted. More... | |
| virtual void | observe_after_metropolis (MetropolisHastingsMover const &metropolis_hastings_mover) |
| Callback executed after the Metropolis criterion is evaluated. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| Return the proposal density ratio for last apply method. More... | |
| virtual void | finalize_simulation (core::pose::Pose &pose, 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_temperature_delta () |
| If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More... | |
| virtual MetropolisHastingsMoverAP | metropolis_hastings_mover () |
| If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More... | |
| virtual void | set_metropolis_hastings_mover (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 | ~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) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| std::string const & | type () const |
| 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 MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| 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 Strings & | info () |
| 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... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Attributes | |
| float | angle_magnitude_ |
Additional Inherited Members | |
| 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::rigid::RigidBodySpinMover | |
| core::Vector | spin_axis_ |
| bool | update_spin_axis_ |
| Protected Attributes inherited from protocols::rigid::RigidBodyMover | |
| int | rb_jump_ |
| Direction | dir_ |
| direction of folding (n-term to c-term) More... | |
| core::Vector | rot_center_ |
| center of rotation More... | |
| bool | freeze_ |
| protocols::rigid::RigidBodyDeterministicSpinMover::RigidBodyDeterministicSpinMover | ( | ) |
References angle_magnitude_, and protocols::moves::Mover::type().
| protocols::rigid::RigidBodyDeterministicSpinMover::RigidBodyDeterministicSpinMover | ( | int const | rb_jump_in, |
| core::Vector | spin_axis, | ||
| core::Vector | rotation_center, | ||
| float | angle_magnitude | ||
| ) |
constructor with arguments spin axis is initialized to 0 then calculated during apply() if spin_axis is not already set
constructor with arguments takes a complete set of arguments needed for apply
References angle_magnitude(), angle_magnitude_, protocols::rigid::RigidBodySpinMover::rot_center(), protocols::rigid::RigidBodyMover::rot_center_, protocols::rigid::RigidBodySpinMover::spin_axis(), protocols::rigid::RigidBodySpinMover::spin_axis_, protocols::moves::Mover::type(), and protocols::rigid::RigidBodySpinMover::update_spin_axis_.
| protocols::rigid::RigidBodyDeterministicSpinMover::RigidBodyDeterministicSpinMover | ( | RigidBodyDeterministicSpinMover const & | src | ) |
| protocols::rigid::RigidBodyDeterministicSpinMover::~RigidBodyDeterministicSpinMover | ( | ) |
| void protocols::rigid::RigidBodyDeterministicSpinMover::angle_magnitude | ( | float | angle_magnitude | ) |
References angle_magnitude_.
Referenced by RigidBodyDeterministicSpinMover().
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virtual |
Reimplemented from protocols::rigid::RigidBodySpinMover.
References angle_magnitude_, protocols::geometry::centroids_by_jump(), core::pose::Pose::conformation(), protocols::rigid::RigidBodyMover::dir_, core::conformation::Conformation::downstream_jump_stub(), core::pose::Pose::jump(), protocols::rigid::RigidBodyMover::rb_jump_, protocols::rigid::RigidBodyMover::rot_center_, core::kinematics::Jump::rotation_by_axis(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rb_center(), protocols::rigid::RigidBodySpinMover::spin_axis_, protocols::rigid::TRBM, protocols::rigid::RigidBodySpinMover::update_spin_axis_, core::conformation::Conformation::upstream_jump_stub(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().
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virtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::rigid::RigidBodySpinMover.
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private |
Referenced by angle_magnitude(), apply(), and RigidBodyDeterministicSpinMover().
1.8.7