|
Rosetta 3.5
|
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 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 () | |
| virtual void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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 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 |
| virtual 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... | |
| 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 |
| get whether detailed balance is preserved (i.e. proposal density ratio calculated) More... | |
| void | set_preserve_detailed_balance (bool setting) |
| set whether detailed balance is preserved (i.e. proposal density ratio calculated) More... | |
| bool | change_chi_without_replacing_residue () const |
| perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More... | |
| void | set_change_chi_without_replacing_residue (bool setting) |
| perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More... | |
| virtual bool | have_mutated_residue () const |
| return true if your last move has mutated residue — make sure the residue is replaced entirely More... | |
| virtual utility::vector1 < core::id::TorsionID_Range > | torsion_id_ranges (core::pose::Pose &pose) |
| get the TorsionIDs perturbed by the mover during moves, along with their ranges More... | |
| virtual utility::vector1 < core::id::DOF_ID_Range > | dof_id_ranges (core::pose::Pose &pose) |
| get the DOF_IDs perturbed by the mover during moves, along with their ranges More... | |
| utility::vector1< core::Size > const & | packed_residues () const |
| get the residues that can be changed by this mover More... | |
| utility::vector1< bool > const & | residue_packed () const |
| get a vector indicating whether each residue can be packed More... | |
| virtual core::Real | last_proposal_density_ratio () |
| get the ratio of proposal densities for the last move More... | |
Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover | |
| ThermodynamicMover () | |
| virtual | ~ThermodynamicMover () |
| 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 More... | |
| virtual bool | is_multi_trial () |
| determine whether the move performs multiple trials on a single apply More... | |
| virtual core::Real | last_inner_score_temperature_delta () |
| get change in internal score/temperature for last apply method of multiple trial movers More... | |
| virtual protocols::canonical_sampling::MetropolisHastingsMoverAP | metropolis_hastings_mover () |
| get the MetropolisHastingsMover for multiple trial movers More... | |
| virtual void | set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover) |
| set the MetropolisHastingsMover for multiple trial movers 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) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| std::string const & | type () const |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| void | set_current_tag (std::string const &new_tag) |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| void | type (const std::string &type_in) |
| virtual MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual bool | reinitialize_for_each_job () const |
| this function informs 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 |
| this function informs 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 |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Member Functions | |
| void | set_defaults () |
| void | init_from_options () |
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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... | |
class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
Definition at line 48 of file SidechainMoverBase.hh.
| typedef utility::vector1< core::Real > protocols::simple_moves::sidechain_moves::SidechainMoverBase::ChiVector |
Definition at line 52 of file SidechainMoverBase.hh.
| protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase | ( | ) |
default constructor
Definition at line 77 of file SidechainMoverBase.cc.
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
Definition at line 84 of file SidechainMoverBase.cc.
References init_from_options(), and set_defaults().
| protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase | ( | SidechainMoverBase const & | mover) |
Definition at line 93 of file SidechainMoverBase.cc.
References task_, and task_factory_.
| protocols::simple_moves::sidechain_moves::SidechainMoverBase::~SidechainMoverBase | ( | ) |
Definition at line 111 of file SidechainMoverBase.cc.
|
virtual |
apply a sidechain move to a Pose object
Implements protocols::moves::Mover.
Definition at line 202 of file SidechainMoverBase.cc.
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().
| 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.
Definition at line 389 of file SidechainMoverBase.cc.
References change_chi_without_replacing_residue_.
Referenced by apply(), parse_my_tag(), and set_change_chi_without_replacing_residue().
|
pure virtual |
|
virtual |
get the DOF_IDs perturbed by the mover during moves, along with their ranges
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
Definition at line 405 of file SidechainMoverBase.cc.
References core::id::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), init_task(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::nchi(), packed_residues_, core::pose::Pose::residue_type(), and task_.
|
virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.
Definition at line 285 of file SidechainMoverBase.cc.
|
inlinevirtual |
return true if your last move has mutated residue — make sure the residue is replaced entirely
Definition at line 152 of file SidechainMoverBase.hh.
Referenced by apply().
| void protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains | ( | core::pose::Pose & | pose) |
idealize sidechains that might be altered
Definition at line 293 of file SidechainMoverBase.cc.
References core::chemical::aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), 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().
|
private |
Definition at line 153 of file SidechainMoverBase.cc.
References core::pack::task::TaskFactory::push_back(), and 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
Definition at line 171 of file SidechainMoverBase.cc.
References set_task(), task_, task_factory_, and core::pose::Pose::total_residue().
Referenced by apply(), dof_id_ranges(), idealize_sidechains(), and initialize_simulation().
|
virtual |
callback executed before any Monte Carlo trials
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
Definition at line 183 of file SidechainMoverBase.cc.
References idealize_sidechains(), and init_task().
|
virtual |
get the ratio of proposal densities for the last move
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
Definition at line 453 of file SidechainMoverBase.cc.
References last_proposal_density_ratio_.
|
pure virtual |
|
virtual |
Definition at line 227 of file SidechainMoverBase.cc.
References compute_proposal_density(), protocols::comparative_modeling::features::E, last_proposal_density_ratio_, make_chi_move(), preserve_detailed_balance_, and protocols::simple_moves::tr().
Referenced by apply().
| utility::vector1< Size > const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues | ( | ) | const |
get the residues that can be changed by this mover
Definition at line 444 of file SidechainMoverBase.cc.
References packed_residues_.
|
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::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.
Definition at line 114 of file SidechainMoverBase.cc.
References change_chi_without_replacing_residue(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), preserve_detailed_balance(), set_change_chi_without_replacing_residue(), set_preserve_detailed_balance(), and task_factory_.
|
virtual |
get whether detailed balance is preserved (i.e. proposal density ratio calculated)
Implements protocols::canonical_sampling::ThermodynamicMover.
Definition at line 377 of file SidechainMoverBase.cc.
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
Definition at line 449 of file SidechainMoverBase.cc.
References residue_packed_.
| pack::dunbrack::RotamerLibrary const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library | ( | ) | const |
get the rotamer library
Definition at line 330 of file SidechainMoverBase.cc.
References rotamer_library_.
Referenced by protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list().
| 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.
Definition at line 394 of file SidechainMoverBase.cc.
References change_chi_without_replacing_residue(), and change_chi_without_replacing_residue_.
Referenced by parse_my_tag().
|
private |
Definition at line 147 of file SidechainMoverBase.cc.
References change_chi_without_replacing_residue_, and last_proposal_density_ratio_.
Referenced by SidechainMoverBase().
|
virtual |
set whether detailed balance is preserved (i.e. proposal density ratio calculated)
Implements protocols::canonical_sampling::ThermodynamicMover.
Definition at line 382 of file SidechainMoverBase.cc.
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
Definition at line 350 of file SidechainMoverBase.cc.
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
Definition at line 340 of file SidechainMoverBase.cc.
References task_factory(), and task_factory_.
Referenced by init_from_options().
|
virtual |
Definition at line 192 of file SidechainMoverBase.cc.
References core::conformation::Residue::name1(), packed_residues_, core::pose::Pose::residue(), and protocols::simple_moves::RG().
Referenced by apply().
| pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task | ( | ) | const |
get the packer task
Definition at line 345 of file SidechainMoverBase.cc.
References task_.
Referenced by set_task().
| pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory | ( | ) | const |
get the task factory
Definition at line 335 of file SidechainMoverBase.cc.
References task_factory_.
Referenced by set_task_factory().
|
virtual |
get the TorsionIDs perturbed by the mover during moves, along with their ranges
Implements protocols::canonical_sampling::ThermodynamicMover.
Definition at line 400 of file SidechainMoverBase.cc.
|
private |
Definition at line 200 of file SidechainMoverBase.hh.
Referenced by change_chi_without_replacing_residue(), set_change_chi_without_replacing_residue(), and set_defaults().
|
private |
Definition at line 202 of file SidechainMoverBase.hh.
|
private |
Definition at line 203 of file SidechainMoverBase.hh.
|
private |
Definition at line 205 of file SidechainMoverBase.hh.
Referenced by last_proposal_density_ratio(), make_move(), and set_defaults().
|
private |
Definition at line 196 of file SidechainMoverBase.hh.
Referenced by dof_id_ranges(), idealize_sidechains(), packed_residues(), set_task(), and suggest_residue_number().
|
private |
Definition at line 199 of file SidechainMoverBase.hh.
Referenced by make_move(), preserve_detailed_balance(), and set_preserve_detailed_balance().
|
private |
Definition at line 197 of file SidechainMoverBase.hh.
Referenced by residue_packed(), and set_task().
|
private |
Definition at line 193 of file SidechainMoverBase.hh.
Referenced by rotamer_library().
|
private |
Definition at line 195 of file SidechainMoverBase.hh.
Referenced by dof_id_ranges(), idealize_sidechains(), init_task(), set_task(), SidechainMoverBase(), and task().
|
private |
Definition at line 194 of file SidechainMoverBase.hh.
Referenced by init_task(), parse_my_tag(), set_task_factory(), SidechainMoverBase(), and task_factory().
1.8.4