Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_moves::sidechain_moves::SidechainMCMover Class Reference

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

#include <SidechainMCMover.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMCMover:
Inheritance graph
[legend]

Public Member Functions

 SidechainMCMover ()
 default constructor More...
 
 SidechainMCMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 ~SidechainMCMover () override
 
void show_counters (std::ostream &out)
 
void setup (core::scoring::ScoreFunctionCOP sfxn)
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &pose) override
 apply a sidechain move to a Pose object More...
 
void set_ntrials (core::Size ntrial)
 
core::Size ntrials ()
 
void set_temperature (core::Real temp)
 
core::Real temperature ()
 
void set_inherit_scorefxn_temperature (bool inherit_scorefxn_temperature)
 
bool inherit_scorefxn_temperature () const
 
void set_scorefunction (core::scoring::ScoreFunction const &sfxn)
 
core::scoring::ScoreFunctionCOP scorefunction ()
 
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...
 
core::Real last_proposal_density_ratio () override
 Return the proposal density ratio for last apply method. More...
 
bool is_multi_trial () override
 Return true if the move performs multiple trials on each apply. More...
 
core::Real last_inner_score_delta_over_temperature () override
 If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...
 
protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover () override
 If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...
 
void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover) override
 If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::simple_moves::sidechain_moves::SidechainMover
 SidechainMover ()
 default constructor More...
 
 SidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library More...
 
 SidechainMover (SidechainMover const &mover)
 
 ~SidechainMover () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
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...
 
core::conformation::ResidueOP make_move (core::conformation::ResidueOP res, core::pose::Pose const &pose)
 
bool task_initialized ()
 
void apply (core::pose::Pose &pose) override
 apply a sidechain move to a Pose object 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 &) override
 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 override
 get whether detailed balance is preserved (i.e. proposal density ratio calculated) More...
 
void set_preserve_detailed_balance (bool preserve_detailed_balance) 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 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...
 
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...
 
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...
 
core::Real last_proposal_density_ratio () override
 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 ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
- 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 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...
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::simple_moves::sidechain_moves::SidechainMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

bool pass_metropolis (core::Real delta_energy, core::Real last_proposal_density_ratio)
 
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

utility::vector1
< core::conformation::ResidueOP
current_
 
utility::vector1
< core::conformation::ResidueOP
previous_
 
utility::vector1
< core::conformation::ResidueOP
best_
 
core::Real temperature_
 
core::Size ntrials_
 
core::Real best_energy_
 
core::Real current_energy_
 
core::scoring::ScoreFunctionOP sfxn_
 
bool inherit_scorefxn_temperature_
 
core::pack::interaction_graph::SimpleInteractionGraphOP ig_
 
core::Real accepts_
 
core::Real current_ntrial_
 
core::Real score_pre_apply_
 
core::Real score_post_apply_
 
protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover_
 

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 std::list< std::string > Strings
 
- 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::sidechain_moves::SidechainMover
core::Real temperature0_
 
core::Real sampling_temperature_
 

Detailed Description

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

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMCMover::SidechainMCMover ( )

default constructor

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

constructor with user provided rotamer library

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

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMCMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMCMover::clone ( ) const
overridevirtual

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.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMCMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::simple_moves::sidechain_moves::SidechainMCMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::simple_moves::sidechain_moves::SidechainMCMover::inherit_scorefxn_temperature ( ) const
inline
void protocols::simple_moves::sidechain_moves::SidechainMCMover::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
overridevirtual
bool protocols::simple_moves::sidechain_moves::SidechainMCMover::is_multi_trial ( )
inlineoverridevirtual
core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::last_inner_score_delta_over_temperature ( )
inlineoverridevirtual

If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply().

See also
is_multi_trial()

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References score_post_apply_, score_pre_apply_, and temperature_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::last_proposal_density_ratio ( )
inlineoverridevirtual

Return the proposal density ratio for last apply method.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Referenced by pass_metropolis().

protocols::canonical_sampling::MetropolisHastingsMoverAP protocols::simple_moves::sidechain_moves::SidechainMCMover::metropolis_hastings_mover ( )
inlineoverridevirtual

If this is a multi-trial move, return the MetropolisHastingsMover being used internally.

See also
is_multi_trial()

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References metropolis_hastings_mover_.

Referenced by apply(), and set_metropolis_hastings_mover().

std::string protocols::simple_moves::sidechain_moves::SidechainMCMover::mover_name ( )
static
core::Size protocols::simple_moves::sidechain_moves::SidechainMCMover::ntrials ( )
inline

References ntrials_.

void protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
bool protocols::simple_moves::sidechain_moves::SidechainMCMover::pass_metropolis ( core::Real  delta_energy,
core::Real  last_proposal_density_ratio 
)
private
void protocols::simple_moves::sidechain_moves::SidechainMCMover::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::SidechainMCMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::scoring::ScoreFunctionCOP protocols::simple_moves::sidechain_moves::SidechainMCMover::scorefunction ( )
inline

References sfxn_.

void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_inherit_scorefxn_temperature ( bool  inherit_scorefxn_temperature)
inline
void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_metropolis_hastings_mover ( protocols::canonical_sampling::MetropolisHastingsMoverAP  metropolis_hastings_mover)
inlineoverridevirtual

If this is a multi-trial move, set the MetropolisHastingsMover to be used internally.

See also
is_multi_trial()

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References metropolis_hastings_mover(), and metropolis_hastings_mover_.

void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_ntrials ( core::Size  ntrial)
inline

References ntrials_.

void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_scorefunction ( core::scoring::ScoreFunction const &  sfxn)
inline
void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_temperature ( core::Real  temp)
inline

References temperature_.

Referenced by apply(), and initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::setup ( core::scoring::ScoreFunctionCOP  sfxn)

References ig_, and set_scorefunction().

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::show_counters ( std::ostream &  out)

References accepts_, and current_ntrial_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::temperature ( )
inline

References temperature_.

Member Data Documentation

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::accepts_
private

Referenced by pass_metropolis(), and show_counters().

utility::vector1< core::conformation::ResidueOP > protocols::simple_moves::sidechain_moves::SidechainMCMover::best_
private

Referenced by apply().

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::best_energy_
private

Referenced by apply().

utility::vector1< core::conformation::ResidueOP > protocols::simple_moves::sidechain_moves::SidechainMCMover::current_
private

Referenced by apply().

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::current_energy_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::current_ntrial_
private

Referenced by pass_metropolis(), and show_counters().

core::pack::interaction_graph::SimpleInteractionGraphOP protocols::simple_moves::sidechain_moves::SidechainMCMover::ig_
private

Referenced by apply(), and setup().

bool protocols::simple_moves::sidechain_moves::SidechainMCMover::inherit_scorefxn_temperature_
private
protocols::canonical_sampling::MetropolisHastingsMoverAP protocols::simple_moves::sidechain_moves::SidechainMCMover::metropolis_hastings_mover_
private
core::Size protocols::simple_moves::sidechain_moves::SidechainMCMover::ntrials_
private
utility::vector1< core::conformation::ResidueOP > protocols::simple_moves::sidechain_moves::SidechainMCMover::previous_
private

Referenced by apply().

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::score_post_apply_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::score_pre_apply_
private
core::scoring::ScoreFunctionOP protocols::simple_moves::sidechain_moves::SidechainMCMover::sfxn_
private
core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::temperature_
private

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