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protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover Class Reference

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions More...

#include <PerturbRotamerSidechainMover.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover:
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Collaboration diagram for protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover:
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Public Types

typedef SidechainMoverBase Parent
 
typedef utility::vector1
< core::pack::dunbrack::DunbrackRotamerSampleData
RotamerList
 
- Public Types inherited from protocols::simple_moves::sidechain_moves::SidechainMoverBase
typedef utility::vector1
< core::Real
ChiVector
 

Public Member Functions

 PerturbRotamerSidechainMover ()
 default constructor More...
 
 PerturbRotamerSidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 PerturbRotamerSidechainMover (PerturbRotamerSidechainMover const &mover)
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
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...
 
virtual void make_chi_move (core::conformation::Residue const &residue, ChiVector const &old_chi, ChiVector &new_chi)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual core::Real compute_proposal_density (core::conformation::Residue const &new_residue, core::Size const resnum, core::chemical::ResidueType const &old_res_type, ChiVector const &old_chi) const
 all angles in degree More...
 
void set_temperature (core::Real setting)
 
core::Real temperature () const
 
void build_rotamer_list (core::conformation::Residue const &, bool filter, RotamerList &) const
 all angles in degree More...
 
void compute_rotdensities (RotamerList const &, ChiVector const &old_chi, ChiVector const &new_chi, core::Real &within_rot_density) const
 
- Public Member Functions inherited from protocols::simple_moves::sidechain_moves::SidechainMoverBase
 SidechainMoverBase ()
 default constructor More...
 
 SidechainMoverBase (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 SidechainMoverBase (SidechainMoverBase const &mover)
 
 ~SidechainMoverBase ()
 
void init_task (core::pose::Pose const &pose)
 initialize the packer task if necessary 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 More...
 
virtual
core::conformation::ResidueOP 
make_move (core::conformation::ResidueOP res)
 
virtual core::Size suggest_residue_number (core::pose::Pose const &) const
 
virtual void apply (core::pose::Pose &pose)
 apply a sidechain move to a Pose object More...
 
void idealize_sidechains (core::pose::Pose &pose)
 idealize sidechains that might be altered More...
 
core::pack::dunbrack::RotamerLibrary
const & 
rotamer_library () const
 get the rotamer library More...
 
core::pack::task::TaskFactoryCOP task_factory () const
 get the task factory More...
 
void set_task_factory (core::pack::task::TaskFactoryCOP task_factory)
 set the task factory More...
 
core::pack::task::PackerTaskCOP task () const
 get the packer task More...
 
void set_task (core::pack::task::PackerTaskCOP task)
 set the task More...
 
bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. proposal density ratio calculated) More...
 
void set_preserve_detailed_balance (bool setting)
 set whether detailed balance is preserved (i.e. proposal density ratio calculated) More...
 
bool change_chi_without_replacing_residue () const
 perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More...
 
void set_change_chi_without_replacing_residue (bool setting)
 perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More...
 
virtual bool have_mutated_residue () const
 return true if your last move has mutated residue — make sure the residue is replaced entirely 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...
 
utility::vector1< core::Size >
const & 
packed_residues () const
 get the residues that can be changed by this mover More...
 
utility::vector1< bool > const & residue_packed () const
 get a vector indicating whether each residue can be packed More...
 
virtual core::Real last_proposal_density_ratio ()
 get the ratio of proposal densities for the last move More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 
virtual ~ThermodynamicMover ()
 
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 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
 
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)
 
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
 

Protected Member Functions

void set_defaults ()
 

Private Attributes

core::Real temperature_
 

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. 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...
 

Detailed Description

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( )

default constructor

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

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( core::pack::dunbrack::RotamerLibrary const &  rotamer_library)

constructor with user provided rotamer library

References set_defaults(), and protocols::moves::Mover::type().

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( PerturbRotamerSidechainMover const &  mover)

References set_defaults().

Member Function Documentation

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list ( core::conformation::Residue const &  residue,
bool  filter,
RotamerList rotamers 
) const
protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density ( core::conformation::Residue const &  new_residue,
core::Size const  resnum,
core::chemical::ResidueType const &  old_res_type,
ChiVector const &  old_chi 
) const
virtual
void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_rotdensities ( RotamerList const &  rotamers,
ChiVector const &  old_chi,
ChiVector const &  new_chi,
core::Real within_rot_density 
) const

References temperature().

Referenced by compute_proposal_density().

std::string protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::make_chi_move ( core::conformation::Residue const &  residue,
ChiVector const &  old_chi,
ChiVector new_chi 
)
virtual
void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_defaults ( )
protected

References temperature_.

Referenced by PerturbRotamerSidechainMover().

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_temperature ( core::Real  setting)
inline

References temperature_.

core::Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature ( ) const
inline

Member Data Documentation

core::Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature_
private

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