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protocols::simple_moves::ShearMover Class Reference

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified. More...

#include <BackboneMover.hh>

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Public Member Functions

 ShearMover ()
 
 ShearMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)
 Constructs a ShearMover shearmover = ShearMover( movemap , kT , n_moves ) More...
 
 ~ShearMover ()
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void setup_list (core::pose::Pose &pose)
 
virtual void set_angles (core::Real angle_in)
 
virtual bool make_move (core::pose::Pose &pose)
 
virtual void test_move (core::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 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...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 get the DOF_IDs perturbed by the mover during moves, along with their ranges More...
 
- Public Member Functions inherited from protocols::simple_moves::BackboneMover
 BackboneMover ()
 
 BackboneMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)
 
 ~BackboneMover ()
 
virtual void apply (core::pose::Pose &)
 virtual functions that get overridden or called from the inheriting classes More...
 
void clear ()
 
bool check_rama ()
 
void temperature (core::Real const temperature_in)
 Properties set/get functions. More...
 
core::Real temperature () const
 
void nmoves (core::Size const nmoves_in)
 
core::Size nmoves () const
 
core::kinematics::MoveMapCOP movemap () const
 
void movemap (core::kinematics::MoveMapOP new_movemap)
 
void angle_max (core::Real const angle)
 Sets the maximum angle of perturbation, independent of secondary structure. More...
 
void angle_max (char const type, core::Real const angle)
 Sets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...
 
void angle_max (std::map< char, core::Real > angle_max_in)
 Sets the max angle of perturbation, for secondary structures 'H', 'E', and 'L'. More...
 
core::Real get_angle_max (char const type) const
 Gets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...
 
core::Real new_phi ()
 
core::Real new_psi ()
 
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
void set_preserve_detailed_balance (bool preserve_detailed_balance)
 set whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 
virtual ~ThermodynamicMover ()
 
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 More...
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback executed after the Metropolis criterion is evaluated More...
 
virtual core::Real last_proposal_density_ratio ()
 callback for proposal density ratio of 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 More...
 
virtual bool is_multi_trial ()
 determine whether the move performs multiple trials on a single apply More...
 
virtual core::Real last_inner_score_temperature_delta ()
 get change in internal score/temperature for last apply method of multiple trial movers More...
 
virtual
protocols::canonical_sampling::MetropolisHastingsMoverAP 
metropolis_hastings_mover ()
 get the MetropolisHastingsMover for multiple trial movers More...
 
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 set the MetropolisHastingsMover for multiple trial movers 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)
 
Moveroperator= (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
 
void type (const std::string &type_in)
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Additional Inherited Members

- Public Types inherited from protocols::simple_moves::BackboneMover
typedef core::Real Real
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::BackboneMover
core::kinematics::MoveMapOP movemap_
 
core::Real temperature_
 controls bias w/which uphill moves are accepted More...
 
Size nmoves_
 number of positions at which to make moves More...
 
std::map< char, core::Realangle_max_
 max allowed angle-change as a function of ss type More...
 
int num_
 
int resnum_
 
int tries_
 
core::Real big_angle_
 
core::Real small_angle_
 
utility::vector1< std::pair
< int, core::Real > > 
pos_list_
 
utility::vector1< intalready_moved_
 
core::Real old_phi_
 
core::Real new_phi_
 
core::Real old_psi_
 
core::Real new_psi_
 
core::Real old_rama_score_
 
core::Real new_rama_score_
 
bool preserve_detailed_balance_
 

Detailed Description

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods: ShearMover.apply

Constructor & Destructor Documentation

protocols::simple_moves::ShearMover::ShearMover ( )
protocols::simple_moves::ShearMover::ShearMover ( core::kinematics::MoveMapOP  movemap_in,
core::Real  temperature_in,
core::Size  nmoves_in 
)

Constructs a ShearMover shearmover = ShearMover( movemap , kT , n_moves )

MoveMap movemap /object storing BB torsion movability Real (float) kT /used in rama Metropolis Criterion Size (int) n_moves /the number of perturbations for one move

References protocols::moves::Mover::type().

protocols::simple_moves::ShearMover::~ShearMover ( )

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::ShearMover::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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::moves::Mover.

utility::vector1< core::id::DOF_ID_Range > protocols::simple_moves::ShearMover::dof_id_ranges ( core::pose::Pose pose)
virtual
std::string protocols::simple_moves::ShearMover::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::BackboneMover.

bool protocols::simple_moves::ShearMover::make_move ( core::pose::Pose pose)
virtual
void protocols::simple_moves::ShearMover::set_angles ( core::Real  angle_in)
virtual
void protocols::simple_moves::ShearMover::setup_list ( core::pose::Pose pose)
virtual
void protocols::simple_moves::ShearMover::test_move ( core::pose::Pose pose)
virtual

: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying

Reimplemented from protocols::moves::Mover.

utility::vector1< core::id::TorsionID_Range > protocols::simple_moves::ShearMover::torsion_id_ranges ( core::pose::Pose pose)
virtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.


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