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Rosetta
2020.50
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#include <DockingLowResEnsemble.hh>
Public Member Functions | |
DockingLowResEnsemble () | |
Default constructor. More... | |
~DockingLowResEnsemble () override | |
DockingLowResEnsemble (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps) | |
Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More... | |
void | ensemble_defaults () |
protocols::moves::MoverOP | clone () const override |
Return a clone of the Mover object. More... | |
core::Size | get_current_conformer_ensemble1 () override |
core::Size | get_current_conformer_ensemble2 () override |
void | show (std::ostream &out=std::cout) const override |
void | set_ensemble1 (DockingEnsembleOP ensemble1) |
void | set_ensemble2 (DockingEnsembleOP ensemble2) |
void | lowres_inner_cycle (core::pose::Pose &pose) override |
void | adaptive_inner_cycle (core::pose::Pose &pose) |
void | try_all_conformers (core::pose::Pose &pose) |
void | initialize_movers () |
void | calc_ensemble_accept_rate_ () |
void | reset_ensemble_trial_counters () |
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DockingLowRes () | |
Default constructor. More... | |
~DockingLowRes () override | |
DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1) | |
Constructor with two arguments. The first is scorefunction to be used for docking, the second is the jump to dock over. More... | |
DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps) | |
Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More... | |
void | set_default () |
Assigns default values to primitive members. More... | |
void | set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn) |
void | sync_magnitudes_with_flags () |
void | sync_objects_with_flags () |
Instantiates non-primitive members based on the value of the primitive members. More... | |
moves::MonteCarloOP | get_mc () |
void | apply (core::pose::Pose &pose) override |
Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
void | rigid_body_trial (core::pose::Pose &pose) |
Perform a cycle of rigid-body Monte Carlo moves. More... | |
core::Real | get_trans_magnitude () |
Option getters - added by SSRB. More... | |
core::Real | get_rot_magnitude () |
core::Real | get_accept_rate () |
core::Size | get_inner_cycles () |
core::Size | get_outer_cycles () |
core::Real | get_temperature () |
protocols::moves::TrialMoverOP | get_rb_trial () |
protocols::moves::SequenceMoverOP | get_rb_seq () |
protocols::rigid::RigidBodyPerturbNoCenterMoverOP | get_rb_mover () |
DockJumps | get_movable_jumps () |
core::scoring::ScoreFunctionCOP | get_scorefxn () |
protocols::moves::PyMOLMoverOP | get_pymol_mover () |
bool | get_view_in_pymol () |
void | set_inner_cycles (core::Size inner_cycles) |
void | set_outer_cycles (core::Size outer_cycles) |
void | set_trans_magnitude (core::Real trans_magnitude) |
void | set_rot_magnitude (core::Real rot_magnitude) |
void | set_rb_trial (protocols::moves::TrialMoverOP rb_trial_in) |
void | reset_rb_trial_counters () |
void | calc_accept_rate () |
void | pymol_color_change (core::pose::Pose &pose) |
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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 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 |
virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
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 core::Real | last_proposal_density_ratio () |
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... | |
Protected Member Functions | |
void | finalize_setup (core::pose::Pose &pose) override |
Performs the portion of setup of non-primitive members that requires a pose - called on apply. More... | |
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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... | |
Private Member Functions | |
void | ensemble1_trial (core::pose::Pose &pose) |
void | ensemble2_trial (core::pose::Pose &pose) |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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bool | flags_and_objects_are_in_sync_ |
bool | first_apply_with_current_setup_ |
protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble | ( | ) |
Default constructor.
References protocols::moves::Mover::type().
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overridedefault |
protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble | ( | core::scoring::ScoreFunctionCOP | scorefxn, |
DockJumps const | movable_jumps | ||
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Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps.
References protocols::moves::Mover::type().
void protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle | ( | core::pose::Pose & | pose | ) |
References accept_rate_ens1_, accept_rate_ens2_, protocols::docking::DockingLowRes::calc_accept_rate(), calc_ensemble_accept_rate_(), ens1_trial_wt_, ens2_trial_wt_, ensemble1_trial(), ensemble2_trial(), protocols::docking::DockingLowRes::get_accept_rate(), protocols::docking::DockingLowRes::get_inner_cycles(), protocols::docking::DockingLowRes::get_mc(), initialize_movers(), rb_trial_wt_, reset_ensemble_trial_counters(), protocols::docking::DockingLowRes::reset_rb_trial_counters(), core::scoring::rg, protocols::docking::DockingLowRes::rigid_body_trial(), and protocols::docking::TR().
Referenced by lowres_inner_cycle().
void protocols::docking::DockingLowResEnsemble::calc_ensemble_accept_rate_ | ( | ) |
References accept_rate_ens1_, accept_rate_ens2_, num_accepted_ens1_, num_accepted_ens2_, num_trials_ens1_, and num_trials_ens2_.
Referenced by adaptive_inner_cycle().
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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::docking::DockingLowRes.
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private |
References current_conformer_ensemble1_, ensemble1_mover_, ensemble1_trial_, protocols::docking::DockingLowRes::get_view_in_pymol(), num_accepted_ens1_, num_trials_ens1_, protocols::docking::DockingLowRes::pymol_color_change(), and protocols::docking::TR().
Referenced by adaptive_inner_cycle(), and try_all_conformers().
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References current_conformer_ensemble2_, ensemble2_mover_, ensemble2_trial_, protocols::docking::DockingLowRes::get_view_in_pymol(), num_accepted_ens2_, num_trials_ens2_, protocols::docking::DockingLowRes::pymol_color_change(), and protocols::docking::TR().
Referenced by adaptive_inner_cycle(), and try_all_conformers().
void protocols::docking::DockingLowResEnsemble::ensemble_defaults | ( | ) |
References current_conformer_ensemble1_, current_conformer_ensemble2_, current_outer_cycle_, ens1_trial_wt_, ens2_trial_wt_, rb_trial_wt_, reset_ensemble_trial_counters(), protocols::docking::DockingLowRes::set_inner_cycles(), and protocols::docking::DockingLowRes::set_outer_cycles().
Referenced by finalize_setup().
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overrideprotectedvirtual |
Performs the portion of setup of non-primitive members that requires a pose - called on apply.
Reimplemented from protocols::docking::DockingLowRes.
References ensemble1_mover_, ensemble1_seq_, ensemble2_mover_, ensemble2_seq_, ensemble_defaults(), protocols::docking::DockingLowRes::finalize_setup(), protocols::docking::DockingLowRes::get_pymol_mover(), and protocols::docking::DockingLowRes::get_view_in_pymol().
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overridevirtual |
Reimplemented from protocols::docking::DockingLowRes.
References current_conformer_ensemble1_.
Referenced by lowres_inner_cycle().
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overridevirtual |
Reimplemented from protocols::docking::DockingLowRes.
References current_conformer_ensemble2_.
Referenced by lowres_inner_cycle().
void protocols::docking::DockingLowResEnsemble::initialize_movers | ( | ) |
References protocols::moves::accept_reject, ensemble1_seq_, ensemble1_trial_, ensemble2_seq_, ensemble2_trial_, protocols::docking::DockingLowRes::get_mc(), protocols::docking::DockingLowRes::get_rb_mover(), protocols::docking::DockingLowRes::get_rb_seq(), protocols::docking::DockingLowRes::get_rot_magnitude(), protocols::docking::DockingLowRes::get_trans_magnitude(), and protocols::docking::DockingLowRes::set_rb_trial().
Referenced by adaptive_inner_cycle(), and try_all_conformers().
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overridevirtual |
Reimplemented from protocols::docking::DockingLowRes.
References accept_rate_ens1_, accept_rate_ens2_, adaptive_inner_cycle(), current_outer_cycle_, ens1_trial_wt_, ens2_trial_wt_, ensemble1_mover_, ensemble2_mover_, get_current_conformer_ensemble1(), get_current_conformer_ensemble2(), and try_all_conformers().
void protocols::docking::DockingLowResEnsemble::reset_ensemble_trial_counters | ( | ) |
References accept_rate_ens1_, accept_rate_ens2_, num_accepted_ens1_, num_accepted_ens2_, num_trials_ens1_, and num_trials_ens2_.
Referenced by adaptive_inner_cycle(), and ensemble_defaults().
void protocols::docking::DockingLowResEnsemble::set_ensemble1 | ( | DockingEnsembleOP | ensemble1 | ) |
References ensemble1_mover_.
Referenced by protocols::docking::DockingProtocol::finalize_setup().
void protocols::docking::DockingLowResEnsemble::set_ensemble2 | ( | DockingEnsembleOP | ensemble2 | ) |
References ensemble2_mover_.
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overridevirtual |
Show the complete setup of the docking protocol
Reimplemented from protocols::docking::DockingLowRes.
References ensemble1_mover_, ensemble2_mover_, and protocols::docking::DockingLowRes::show().
void protocols::docking::DockingLowResEnsemble::try_all_conformers | ( | core::pose::Pose & | pose | ) |
References ensemble1_mover_, ensemble1_trial(), ensemble2_mover_, ensemble2_trial(), protocols::docking::DockingLowRes::get_mc(), and initialize_movers().
Referenced by lowres_inner_cycle().
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Referenced by ensemble1_trial(), ensemble_defaults(), and get_current_conformer_ensemble1().
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Referenced by ensemble2_trial(), ensemble_defaults(), and get_current_conformer_ensemble2().
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Referenced by ensemble_defaults(), and lowres_inner_cycle().
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Referenced by adaptive_inner_cycle(), ensemble_defaults(), and lowres_inner_cycle().
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Referenced by adaptive_inner_cycle(), ensemble_defaults(), and lowres_inner_cycle().
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Referenced by ensemble1_trial(), finalize_setup(), lowres_inner_cycle(), set_ensemble1(), show(), and try_all_conformers().
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Referenced by finalize_setup(), and initialize_movers().
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Referenced by ensemble1_trial(), and initialize_movers().
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Referenced by ensemble2_trial(), finalize_setup(), lowres_inner_cycle(), set_ensemble2(), show(), and try_all_conformers().
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Referenced by finalize_setup(), and initialize_movers().
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Referenced by ensemble2_trial(), and initialize_movers().
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Referenced by calc_ensemble_accept_rate_(), ensemble1_trial(), and reset_ensemble_trial_counters().
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Referenced by calc_ensemble_accept_rate_(), ensemble2_trial(), and reset_ensemble_trial_counters().
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Referenced by calc_ensemble_accept_rate_(), ensemble1_trial(), and reset_ensemble_trial_counters().
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Referenced by calc_ensemble_accept_rate_(), ensemble2_trial(), and reset_ensemble_trial_counters().
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Referenced by adaptive_inner_cycle(), and ensemble_defaults().