Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover Class Reference

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

#include <JumpRotamerSidechainMover.hh>

Public Types

typedef
PerturbRotamerSidechainMover 
Parent
 
- Public Types inherited from protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
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 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::stringStrings
 

Public Member Functions

 JumpRotamerSidechainMover ()
 default constructor More...
 
 JumpRotamerSidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 JumpRotamerSidechainMover (JumpRotamerSidechainMover const &mover)
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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 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...
 
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...
 
- Public Member Functions inherited from protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
 PerturbRotamerSidechainMover ()
 default constructor More...
 
 PerturbRotamerSidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 PerturbRotamerSidechainMover (PerturbRotamerSidechainMover const &mover)
 
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 are attempted. 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 ()
 Default constructor. More...
 
virtual ~ThermodynamicMover ()
 Default destructor. 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_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
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...
 
- 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
 
void set_type (std::string const &setting)
 
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
 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
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Protected Member Functions

void set_defaults ()
 
void compute_tempered_rotamer_probabilities (RotamerList const &, core::Real temperature, utility::vector1< core::Real > &prob, core::Real &normalize) const
 
void compute_rotdensities (RotamerList const &, ChiVector const &new_chi, core::Real &rot_density) const
 
- Protected Member Functions inherited from protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
void set_defaults ()
 
- 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...
 

Private Attributes

bool sample_rotwells_unif_
 

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...
 

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::JumpRotamerSidechainMover::JumpRotamerSidechainMover ( )

default constructor

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

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

constructor with user provided rotamer library

References set_defaults().

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

References set_defaults().

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::clone ( ) const
virtual

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::sidechain_moves::PerturbRotamerSidechainMover.

Real protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::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::JumpRotamerSidechainMover::compute_rotdensities ( RotamerList const &  rotamers,
ChiVector const &  new_chi,
core::Real rot_density 
) const
protected
void protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_tempered_rotamer_probabilities ( RotamerList const &  rotamers,
core::Real  temperature,
utility::vector1< core::Real > &  prob,
core::Real normalize 
) const
protected
std::string protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

void protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::make_chi_move ( core::conformation::Residue const &  residue,
ChiVector const &  old_chi,
ChiVector new_chi 
)
virtual
void protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::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::PerturbRotamerSidechainMover.

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

Member Data Documentation

bool protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::sample_rotwells_unif_
private

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