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Rosetta
2020.11
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Rigid-body random translate/rotate around centroid of downstream side of a jump. More...
#include <RigidBodyMover.hh>
Public Types | |
typedef ThermodynamicMover | parent |
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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 | |
RigidBodyMover () | |
RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c) | |
RigidBodyMover (RigidBodyMover const &src) | |
~RigidBodyMover () override | |
void | rot_center (core::Vector const &rot_center_in) |
Manual override of rotation center. More... | |
void | apply (core::pose::Pose &pose) override=0 |
Main Method. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
void | show (std::ostream &output=std::cout) const override |
Outputs details about the Mover, including current settings. More... | |
bool | preserve_detailed_balance () const override |
Return true if detailed balance is being preserved (i.e. no branch angle optimization). More... | |
void | set_preserve_detailed_balance (bool) override |
set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More... | |
utility::vector1 < core::id::TorsionID_Range > | torsion_id_ranges (core::pose::Pose &pose) override |
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 () |
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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... | |
core::Real | last_proposal_density_ratio () override |
Return the proposal density ratio for last apply method. 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... | |
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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, 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... | |
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 | 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 | 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... | |
Protected Attributes | |
int | rb_jump_ |
Direction | dir_ |
direction of folding (n-term to c-term) More... | |
core::Vector | rot_center_ |
center of rotation More... | |
bool | freeze_ |
Additional Inherited Members | |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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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... | |
Rigid-body random translate/rotate around centroid of downstream side of a jump.
We operate on a single jump rather than e.g. a randomly selected jump from the mobile jumps in a MoveMap. If you want a random choice among jumps, put multiple RigidBodyMovers into a RandomMover (which will give you more control, anyway).
protocols::rigid::RigidBodyMover::RigidBodyMover | ( | ) |
References protocols::rigid::c2n, dir_, protocols::rigid::n2c, and protocols::rigid::random.
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default |
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overridedefault |
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overridepure virtual |
Main Method.
Implements protocols::moves::Mover.
Implemented in protocols::rigid::RigidBodyDofSeqPerturbMover, protocols::rigid::RigidBodyDofPerturbMover, protocols::rigid::RigidBodyDofRandomTransMover, protocols::rigid::RigidBodyDofSeqTransMover, protocols::rigid::RigidBodyDofTransMover, protocols::rigid::RigidBodyDofSeqRandomizeMover, protocols::rigid::RigidBodyDofRandomizeMover, protocols::rigid::UniformSphereTransMover, protocols::rigid::RigidBodyTransMover, protocols::rigid::RigidBodyTiltMover, protocols::rigid::RigidBodyDeterministicSpinMover, protocols::rigid::RigidBodySpinMover, protocols::rigid::RigidBodyRandomizeMover, protocols::rigid::RigidBodyPerturbNoCenterMover, protocols::rigid::RigidBodyPerturbRandomJumpMover, protocols::rigid::RigidBodyPerturbMover, protocols::enzdes::PredesignPerturbMover, and protocols::topology_broker::RigidBodyRandomTMHMover.
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inline |
References freeze_.
Referenced by protocols::ligand_docking::move_ligand_to_desired_centroid(), and protocols::ligand_docking::Translate::uniform_translate_ligand().
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::rigid::RigidBodyDofSeqPerturbMover, protocols::rigid::RigidBodyDofPerturbMover, protocols::rigid::RigidBodyDofRandomTransMover, protocols::rigid::RigidBodyDofSeqTransMover, protocols::rigid::RigidBodyDofTransMover, protocols::rigid::RigidBodyDofSeqRandomizeMover, protocols::rigid::RigidBodyDofRandomizeMover, protocols::rigid::UniformSphereTransMover, protocols::rigid::RigidBodyTransMover, protocols::rigid::RigidBodyTiltMover, protocols::rigid::RigidBodyDeterministicSpinMover, protocols::rigid::RigidBodySpinMover, protocols::rigid::RigidBodyRandomizeMover, protocols::rigid::RigidBodyPerturbNoCenterMover, protocols::rigid::RigidBodyPerturbRandomJumpMover, protocols::rigid::RigidBodyPerturbMover, and protocols::topology_broker::RigidBodyRandomTMHMover.
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inlineoverridevirtual |
Return true if detailed balance is being preserved (i.e. no branch angle optimization).
Implements protocols::canonical_sampling::ThermodynamicMover.
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inline |
References rb_jump_.
Referenced by protocols::rigid::RigidBodyTransMover::centroid_axis(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::rigid::RigidBodyTiltMover::parse_my_tag(), protocols::rigid::RigidBodyTransMover::parse_my_tag(), show(), and protocols::ligand_docking::Translate::uniform_translate_ligand().
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inline |
References rb_jump_.
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inline |
Manual override of rotation center.
References rot_center_.
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inlineoverridevirtual |
set whether detailed balance is preserved (i.e. no branch angle optimization during moves)
Implements protocols::canonical_sampling::ThermodynamicMover.
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overridevirtual |
Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::rigid::RigidBodyRandomizeMover, and protocols::rigid::RigidBodyPerturbMover.
References rb_jump().
Referenced by protocols::rigid::RigidBodyPerturbMover::show(), and protocols::rigid::RigidBodyRandomizeMover::show().
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overridevirtual |
get the TorsionIDs perturbed by the mover during moves, along with their ranges
Implements protocols::canonical_sampling::ThermodynamicMover.
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inline |
References freeze_.
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protected |
direction of folding (n-term to c-term)
Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyPerturbNoCenterMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), RigidBodyMover(), and protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover().
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protected |
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protected |
Referenced by protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyPerturbNoCenterMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), rb_jump(), protocols::rigid::RigidBodyDofPerturbMover::RigidBodyDofPerturbMover(), protocols::rigid::RigidBodyDofRandomizeMover::RigidBodyDofRandomizeMover(), protocols::rigid::RigidBodyDofTransMover::RigidBodyDofTransMover(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), and protocols::rigid::RigidBodyTiltMover::tilt().
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protected |
center of rotation
Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::RigidBodyDeterministicSpinMover(), protocols::rigid::RigidBodyRandomizeMover::RigidBodyRandomizeMover(), rot_center(), and protocols::rigid::RigidBodySpinMover::rot_center().