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

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

#include <SidechainMover.hh>

Public Member Functions

 SidechainMover ()
 default constructor More...
 
 SidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 SidechainMover (SidechainMover const &mover)
 
 ~SidechainMover ()
 
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...
 
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...
 
core::conformation::ResidueOP make_move (core::conformation::ResidueOP res)
 
bool task_initialized ()
 
void apply (core::pose::Pose &pose)
 apply a sidechain move to a Pose object More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
core::Real proposal_density (core::conformation::Residue const &proposed_residue, core::Size const proposed_resnum, core::chemical::ResidueType const &initial_residue_type, utility::vector1< core::Real > const &initial_chi_angles) const
 
void test_move (core::pose::Pose &)
 test the backrub move 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...
 
core::Real prob_uniform () const
 get the probability of uniformly sampling chi angles More...
 
void set_prob_uniform (core::Real prob_uniform)
 set the probability of uniformly sampling chi angles 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 preserve_detailed_balance)
 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 const change_chi_without_replacing_residue)
 perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. 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...
 
core::Real prob_withinrot () const
 get the probability of sampling within the same rotamer More...
 
void set_prob_withinrot (core::Real prob_withinrot)
 set the probability of sampling within the same rotamer More...
 
core::Real prob_random_pert_current () const
 
void set_prob_random_pert_current (core::Real prob_pert)
 
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...
 
core::Size next_resnum () const
 get the next residue to be changed, 0 means a random will be chosen More...
 
void next_resnum (core::Size resnum)
 set the next residue to be changed, 0 means a random will be chosen More...
 
core::Size last_nchi () const
 get the number of chi angles sampled in the last move More...
 
bool last_mutation () const
 get whether the last move mutated the residue More...
 
bool last_uniform () const
 get whether the last move used uniform chi sampling More...
 
bool last_withinrot () const
 get whether the last move sampled within the same rotamer More...
 
virtual core::Real last_proposal_density_ratio ()
 get the ratio of proposal densities for the last move More...
 
void update_type ()
 update string describing the move type More...
 
void set_sampling_temperature (core::Real temp)
 set temperature for bias sampling at dunbrack distribution More...
 
core::Real sampling_temperature ()
 
- 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
 
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 Attributes

core::Real temperature0_
 
core::Real sampling_temperature_
 

Private Member Functions

void make_rotwell_jump (utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &rotamer_sample_data)
 
void preturb_rot_and_dunbrack_eval (core::conformation::ResidueOP input_residue)
 
void perturb_rot_within_well (utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &rotamer_sample_data, utility::vector1< core::Real > const &previous_chi_angles)
 
bool dunbrack_accept (numeric::random::RandomGenerator &Rand, core::conformation::Residue &res, utility::vector1< core::Real > const &previous_chi_angles, utility::vector1< core::Real > const &new_chi_angles)
 
void perturb_chi (numeric::random::RandomGenerator &Rand, core::Real max_deviation, utility::vector1< core::Real > &current_chi, utility::vector1< core::Real > &new_chi)
 

Private Attributes

core::pack::dunbrack::RotamerLibrary
const & 
rotamer_library_
 
core::pack::task::TaskFactoryCOP task_factory_
 
core::pack::task::PackerTaskCOP task_
 
core::pose::PoseOP pose_
 
utility::vector1< core::Sizepacked_residues_
 
utility::vector1< boolresidue_packed_
 
core::Real prob_uniform_
 
core::Real prob_withinrot_
 
core::Real prob_random_pert_to_current_
 
bool preserve_detailed_balance_
 
bool accept_according_to_dunbrack_
 
bool sample_rotwells_unif_
 
bool change_chi_without_replacing_residue_
 
core::Size next_resnum_
 
utility::vector1< core::Reallast_chi_angles_
 
core::Size last_nchi_
 
bool last_mutation_
 
bool last_uniform_
 
bool last_withinrot_
 
bool last_pertrot_
 
core::Real last_proposal_density_ratio_
 
bool task_initialized_
 
core::pack::dunbrack::RotamerLibraryScratchSpaceOP scratch_
 

Additional Inherited Members

- 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
 
- 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...
 

Detailed Description

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

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMover::SidechainMover ( )

default constructor

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

constructor with user provided rotamer library

protocols::simple_moves::sidechain_moves::SidechainMover::SidechainMover ( SidechainMover const &  mover)
protocols::simple_moves::sidechain_moves::SidechainMover::~SidechainMover ( )

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMover::apply ( core::pose::Pose pose)
virtual
bool protocols::simple_moves::sidechain_moves::SidechainMover::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.

References change_chi_without_replacing_residue_.

Referenced by apply(), parse_my_tag(), and set_change_chi_without_replacing_residue().

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMover::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::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

utility::vector1< core::id::DOF_ID_Range > protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges ( core::pose::Pose pose)
virtual
bool protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept ( numeric::random::RandomGenerator Rand,
core::conformation::Residue res,
utility::vector1< core::Real > const &  previous_chi_angles,
utility::vector1< core::Real > const &  new_chi_angles 
)
private
std::string protocols::simple_moves::sidechain_moves::SidechainMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

void protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains ( core::pose::Pose pose)

idealize sidechains that might be altered

Detailed:
all sidechains that might be changed are replaced with ideal coordinates that have the original chi angles

References core::pose::Pose::chi(), core::pose::Pose::conformation(), init_task(), packed_residues_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_chi(), and task_.

Referenced by initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMover::init_task ( core::pose::Pose const &  pose)

initialize the packer task if necessary

Detailed:
Check to make sure that a packer task exists and matches the numer of residues in the given pose. If that isn't the case, create a new one with the task factory. Exits with an error if no task factory exists.

References pose_, set_task(), task_, task_factory_, core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), apply(), dof_id_ranges(), and idealize_sidechains().

void protocols::simple_moves::sidechain_moves::SidechainMover::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
virtual
bool protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation ( ) const

get whether the last move mutated the residue

References last_mutation_.

core::Size protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi ( ) const

get the number of chi angles sampled in the last move

References last_nchi_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio ( )
virtual
bool protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform ( ) const

get whether the last move used uniform chi sampling

References last_uniform_.

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot ( ) const

get whether the last move sampled within the same rotamer

References last_withinrot_.

core::conformation::ResidueOP protocols::simple_moves::sidechain_moves::SidechainMover::make_move ( core::conformation::ResidueOP  res)
void protocols::simple_moves::sidechain_moves::SidechainMover::make_rotwell_jump ( utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &  rotamer_sample_data)
private
core::Size protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum ( ) const

get the next residue to be changed, 0 means a random will be chosen

References next_resnum_.

void protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum ( core::Size  resnum)

set the next residue to be changed, 0 means a random will be chosen

References next_resnum_, residue_packed_, and runtime_assert.

utility::vector1< core::Size > const & protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues ( ) const

get the residues that can be changed by this mover

References packed_residues_.

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::apply().

void protocols::simple_moves::sidechain_moves::SidechainMover::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::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

References change_chi_without_replacing_residue(), end, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), preserve_detailed_balance(), prob_random_pert_current(), prob_uniform(), prob_withinrot(), core::pack::task::TaskFactory::push_back(), set_change_chi_without_replacing_residue(), set_preserve_detailed_balance(), set_prob_random_pert_current(), set_prob_uniform(), set_prob_withinrot(), utility::string_split(), and task_factory_.

void protocols::simple_moves::sidechain_moves::SidechainMover::perturb_chi ( numeric::random::RandomGenerator Rand,
core::Real  max_deviation,
utility::vector1< core::Real > &  current_chi,
utility::vector1< core::Real > &  new_chi 
)
private
void protocols::simple_moves::sidechain_moves::SidechainMover::perturb_rot_within_well ( utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &  rotamer_sample_data,
utility::vector1< core::Real > const &  previous_chi_angles 
)
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance ( ) const
virtual

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_preserve_detailed_balance().

void protocols::simple_moves::sidechain_moves::SidechainMover::preturb_rot_and_dunbrack_eval ( core::conformation::ResidueOP  input_residue)
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_current ( ) const
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform ( ) const

get the probability of uniformly sampling chi angles

References prob_uniform_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_prob_uniform().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot ( ) const

get the probability of sampling within the same rotamer

References prob_withinrot_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_prob_withinrot().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density ( core::conformation::Residue const &  proposed_residue,
core::Size const  proposed_resnum,
core::chemical::ResidueType const &  initial_residue_type,
utility::vector1< core::Real > const &  initial_chi_angles 
) const
utility::vector1< bool > const & protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed ( ) const

get a vector indicating whether each residue can be packed

References residue_packed_.

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

get the rotamer library

References rotamer_library_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature ( )
inline

References sampling_temperature_.

void protocols::simple_moves::sidechain_moves::SidechainMover::set_change_chi_without_replacing_residue ( bool const  change_chi_without_replacing_residue)

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

References change_chi_without_replacing_residue(), and change_chi_without_replacing_residue_.

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_preserve_detailed_balance ( bool  preserve_detailed_balance)
virtual

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance(), and preserve_detailed_balance_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_random_pert_current ( core::Real  prob_pert)
void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform ( core::Real  prob_uniform)
void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_withinrot ( core::Real  prob_withinrot)

set the probability of sampling within the same rotamer

References prob_withinrot(), and prob_withinrot_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_sampling_temperature ( core::Real  temp)
inline

set temperature for bias sampling at dunbrack distribution

References sampling_temperature_.

void protocols::simple_moves::sidechain_moves::SidechainMover::set_task ( core::pack::task::PackerTaskCOP  task)
void protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory ( core::pack::task::TaskFactoryCOP  task_factory)
core::pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMover::task ( ) const

get the packer task

References task_.

Referenced by set_task().

core::pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_factory ( ) const

get the task factory

References task_factory_.

Referenced by set_task_factory().

bool protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized ( )

References task_initialized_.

void protocols::simple_moves::sidechain_moves::SidechainMover::test_move ( core::pose::Pose )
virtual

test the backrub move

Detailed:

Reimplemented from protocols::moves::Mover.

utility::vector1< core::id::TorsionID_Range > protocols::simple_moves::sidechain_moves::SidechainMover::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.

void protocols::simple_moves::sidechain_moves::SidechainMover::update_type ( )

update string describing the move type

Detailed:
All move types are prefixed with "sc". Sections are divided by underscores. The next section indicates whether a mutation was made ("mut") or not ("chi"). The last section indicates wehter chi sampling was uniform ("unif"), used Dunbrack rotamer statistics ("rot"), or whether no chi angles existed in the placed residue ("none").

References last_mutation_, last_nchi_, last_pertrot_, last_uniform_, last_withinrot_, protocols::motifs::mt, and protocols::moves::Mover::type().

Referenced by make_move().

Member Data Documentation

bool protocols::simple_moves::sidechain_moves::SidechainMover::accept_according_to_dunbrack_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::change_chi_without_replacing_residue_
private
utility::vector1<core::Real> protocols::simple_moves::sidechain_moves::SidechainMover::last_chi_angles_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation_
private
core::Size protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi_
private

Referenced by last_nchi(), make_move(), and update_type().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_pertrot_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot_
private
core::Size protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum_
private

Referenced by apply(), and next_resnum().

utility::vector1<core::Size> protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues_
private
core::pose::PoseOP protocols::simple_moves::sidechain_moves::SidechainMover::pose_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_to_current_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot_
private
utility::vector1<bool> protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed_
private
core::pack::dunbrack::RotamerLibrary const& protocols::simple_moves::sidechain_moves::SidechainMover::rotamer_library_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::sample_rotwells_unif_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature_
protected
core::pack::dunbrack::RotamerLibraryScratchSpaceOP protocols::simple_moves::sidechain_moves::SidechainMover::scratch_
private

Referenced by dunbrack_accept(), and SidechainMover().

core::pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_
private
core::pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_factory_
private
bool protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized_
private

Referenced by task_initialized().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::temperature0_
protected

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