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protocols::simple_moves::sidechain_moves::SidechainMoverBase Class Referenceabstract

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

#include <SidechainMoverBase.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMoverBase:
Inheritance graph
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Public Types

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 std::list< std::string > Strings
 

Public Member Functions

 SidechainMoverBase ()
 default constructor More...
 
 SidechainMoverBase (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 SidechainMoverBase (SidechainMoverBase const &mover)
 
 ~SidechainMoverBase () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 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...
 
void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) override
 Callback executed before any Monte Carlo trials are attempted. More...
 
virtual
core::conformation::ResidueOP 
make_move (core::conformation::ResidueOP res)
 
virtual void make_chi_move (core::conformation::Residue const &residue, ChiVector const &old_chi, ChiVector &new_chi)=0
 
virtual core::Size suggest_residue_number (core::pose::Pose const &) const
 
void apply (core::pose::Pose &pose) override
 apply a sidechain move to a Pose object More...
 
std::string get_name () const override
 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 =0
 
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 override
 get whether detailed balance is preserved (i.e. proposal density ratio calculated) More...
 
void set_preserve_detailed_balance (bool setting) override
 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...
 
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...
 
utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose) override
 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...
 
core::Real last_proposal_density_ratio () override
 get the ratio of proposal densities for the last move More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 Default constructor. More...
 
 ~ThermodynamicMover () override
 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_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...
 
- Public Member Functions inherited from protocols::moves::Mover
 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
 
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 show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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 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...
 

Private Member Functions

void set_defaults ()
 
void init_from_options ()
 

Private Attributes

core::pack::dunbrack::RotamerLibrary
const & 
rotamer_library_
 
core::pack::task::TaskFactoryCOP task_factory_
 
core::pack::task::PackerTaskCOP task_
 
utility::vector1< core::Sizepacked_residues_
 
utility::vector1< boolresidue_packed_
 
bool preserve_detailed_balance_
 
bool change_chi_without_replacing_residue_
 
utility::vector1< core::Reallast_chi_angles_
 
core::Size last_nchi_
 
core::Real last_proposal_density_ratio_
 

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...
 
- 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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase ( )

default constructor

References init_from_options(), and set_defaults().

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

constructor with user provided rotamer library

References init_from_options(), and set_defaults().

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

References task_, and task_factory_.

protocols::simple_moves::sidechain_moves::SidechainMoverBase::~SidechainMoverBase ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply ( core::pose::Pose pose)
overridevirtual
bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::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().

virtual core::Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::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
pure virtual
utility::vector1< id::DOF_ID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges ( core::pose::Pose pose)
overridevirtual
std::string protocols::simple_moves::sidechain_moves::SidechainMoverBase::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

virtual bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue ( ) const
inlinevirtual

return true if your last move has mutated residue — make sure the residue is replaced entirely

Referenced by apply().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains ( core::pose::Pose pose)
void protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_from_options ( )
private

References set_task_factory().

Referenced by SidechainMoverBase().

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

initialize the packer task if necessary

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 set_task(), core::pose::Pose::size(), task_, and task_factory_.

Referenced by apply(), dof_id_ranges(), idealize_sidechains(), and initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
overridevirtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References idealize_sidechains(), and init_task().

Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio ( )
overridevirtual

get the ratio of proposal densities for the last move

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References last_proposal_density_ratio_.

virtual void protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_chi_move ( core::conformation::Residue const &  residue,
ChiVector const &  old_chi,
ChiVector new_chi 
)
pure virtual
conformation::ResidueOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move ( core::conformation::ResidueOP  res)
virtual
utility::vector1< core::Size > const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues ( ) const

get the residues that can be changed by this mover

References packed_residues_.

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References change_chi_without_replacing_residue(), preserve_detailed_balance(), set_change_chi_without_replacing_residue(), set_preserve_detailed_balance(), and task_factory_.

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance ( ) const
overridevirtual

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(), and set_preserve_detailed_balance().

utility::vector1< bool > const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed ( ) const

get a vector indicating whether each residue can be packed

References residue_packed_.

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

get the rotamer library

References rotamer_library_.

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.

References change_chi_without_replacing_residue(), and change_chi_without_replacing_residue_.

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_defaults ( )
private
void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance ( bool  setting)
overridevirtual

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().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task ( core::pack::task::PackerTaskCOP  task)

set the task

References core::chemical::aa_pro, packed_residues_, residue_packed_, task(), and task_.

Referenced by init_task().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory ( core::pack::task::TaskFactoryCOP  task_factory)

set the task factory

References task_factory(), and task_factory_.

Referenced by init_from_options().

core::Size protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number ( core::pose::Pose const &  pose) const
virtual
pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task ( ) const

get the packer task

References task_.

Referenced by set_task().

pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory ( ) const

get the task factory

References task_factory_.

Referenced by set_task_factory().

utility::vector1< id::TorsionID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::torsion_id_ranges ( core::pose::Pose pose)
overridevirtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

Member Data Documentation

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue_
private
utility::vector1<core::Real> protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_chi_angles_
private
core::Size protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_nchi_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio_
private
utility::vector1<core::Size> protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues_
private
bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance_
private
utility::vector1<bool> protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed_
private

Referenced by residue_packed(), and set_task().

core::pack::dunbrack::RotamerLibrary const& protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library_
private

Referenced by rotamer_library().

core::pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_
private
core::pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory_
private

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