class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions More...
#include <SidechainMoverBase.hh>
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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::Size > | packed_residues_ |
| utility::vector1< bool > | residue_packed_ |
| bool | preserve_detailed_balance_ |
| bool | change_chi_without_replacing_residue_ |
| utility::vector1< core::Real > | last_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
◆ ChiVector
| typedef utility::vector1< core::Real > protocols::simple_moves::sidechain_moves::SidechainMoverBase::ChiVector |
Constructor & Destructor Documentation
◆ SidechainMoverBase() [1/3]
| protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase | ( | ) |
default constructor
References init_from_options(), and set_defaults().
◆ SidechainMoverBase() [2/3]
| 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().
◆ SidechainMoverBase() [3/3]
| protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase | ( | SidechainMoverBase const & | mover | ) |
References task_, and task_factory_.
◆ ~SidechainMoverBase()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
apply a sidechain move to a Pose object
Implements protocols::moves::Mover.
References change_chi_without_replacing_residue(), have_mutated_residue(), init_task(), make_move(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), and suggest_residue_number().
◆ change_chi_without_replacing_residue()
| 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().
◆ compute_proposal_density()
|
pure virtual |
◆ dof_id_ranges()
|
overridevirtual |
get the DOF_IDs perturbed by the mover during moves, along with their ranges
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), core::chemical::rna::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), init_task(), core::chemical::ResidueTypeBase::name3(), packed_residues_, core::pose::Pose::residue_type(), task_, and core::id::DOF_ID::valid().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ have_mutated_residue()
|
inlinevirtual |
return true if your last move has mutated residue — make sure the residue is replaced entirely
Referenced by apply().
◆ idealize_sidechains()
| void protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains | ( | core::pose::Pose & | pose | ) |
idealize sidechains that might be altered
all sidechains that might be changed are replaced with ideal coordinates that have the original chi angles
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), init_task(), core::chemical::ResidueType::nchi(), packed_residues_, core::pack::task::ResidueLevelTask::preserve_c_beta(), 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().
◆ init_from_options()
|
private |
References set_task_factory().
Referenced by SidechainMoverBase().
◆ init_task()
| 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().
◆ initialize_simulation()
|
overridevirtual |
Callback executed before any Monte Carlo trials are attempted.
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
References idealize_sidechains(), and init_task().
◆ 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_.
◆ make_chi_move()
|
pure virtual |
◆ make_move()
|
virtual |
References compute_proposal_density(), last_proposal_density_ratio_, make_chi_move(), and preserve_detailed_balance_.
Referenced by apply().
◆ packed_residues()
| 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_.
◆ parse_my_tag()
|
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_.
◆ preserve_detailed_balance()
|
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().
◆ residue_packed()
| 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_.
◆ rotamer_library()
| pack::dunbrack::RotamerLibrary const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library | ( | ) | const |
get the rotamer library
References rotamer_library_.
◆ set_change_chi_without_replacing_residue()
| 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().
◆ set_defaults()
|
private |
References change_chi_without_replacing_residue_, and last_proposal_density_ratio_.
Referenced by SidechainMoverBase().
◆ set_preserve_detailed_balance()
|
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().
◆ set_task()
| void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task | ( | core::pack::task::PackerTaskCOP | task | ) |
set the task
References core::chemical::aa_pro, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), packed_residues_, residue_packed_, task(), and task_.
Referenced by init_task().
◆ set_task_factory()
| 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().
◆ suggest_residue_number()
|
virtual |
References core::conformation::Residue::name1(), packed_residues_, core::pose::Pose::residue(), and core::scoring::rg.
Referenced by apply().
◆ task()
| pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task | ( | ) | const |
◆ task_factory()
| pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory | ( | ) | const |
◆ torsion_id_ranges()
|
overridevirtual |
get the TorsionIDs perturbed by the mover during moves, along with their ranges
Implements protocols::canonical_sampling::ThermodynamicMover.
Member Data Documentation
◆ change_chi_without_replacing_residue_
|
private |
◆ last_chi_angles_
|
private |
◆ last_nchi_
|
private |
◆ last_proposal_density_ratio_
|
private |
Referenced by last_proposal_density_ratio(), make_move(), and set_defaults().
◆ packed_residues_
|
private |
Referenced by dof_id_ranges(), idealize_sidechains(), packed_residues(), set_task(), and suggest_residue_number().
◆ preserve_detailed_balance_
|
private |
Referenced by make_move(), preserve_detailed_balance(), and set_preserve_detailed_balance().
◆ residue_packed_
|
private |
Referenced by residue_packed(), and set_task().
◆ rotamer_library_
|
private |
Referenced by rotamer_library().
◆ task_
|
private |
Referenced by dof_id_ranges(), idealize_sidechains(), init_task(), set_task(), SidechainMoverBase(), and task().
◆ task_factory_
|
private |
Referenced by init_task(), parse_my_tag(), set_task_factory(), SidechainMoverBase(), and task_factory().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/sidechain_moves/SidechainMoverBase.hh
- src/protocols/simple_moves/sidechain_moves/SidechainMoverBase.cc
