#include <SymDockingHiRes.hh>
Public Member Functions | |
| SymDockingHiRes () | |
| SymDockingHiRes (core::scoring::ScoreFunctionOP scorefxn_in, core::scoring::ScoreFunctionOP scorefxn_pack_in) | |
| moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| ~SymDockingHiRes () override | |
| void | set_default (core::pose::Pose &pose) |
| void | set_move_map (core::kinematics::MoveMapOP movemap_in) |
| void | set_min_type (std::string min_type_in) |
| void | set_repack (bool repack_switch) |
| void | set_protocol (core::pose::Pose &pose) |
| void | set_dock_min_protocol () |
| main entrance for normal rigid-body minimization More... | |
| void | set_dock_mcm_protocol (core::pose::Pose &pose) |
| main entrance to do monte carlo minimization More... | |
| void | set_dock_ppk_protocol (core::pose::Pose &pose) |
| define the prepacking protocol More... | |
| moves::MonteCarloOP | get_mc () |
| void | design (bool const des) |
| bool | design () const |
| void | apply (core::pose::Pose &pose) override |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | task_factory (core::pack::task::TaskFactoryOP task) |
| core::pack::task::TaskFactoryOP & | task_factory () |
 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 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 void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. 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... | |
Private Types | |
| typedef core::Real | Real |
| typedef core::conformation::symmetry::SymmetricConformation | SymmetricConformation |
| typedef core::conformation::symmetry::SymmetryInfo | SymmetryInfo |
Private Member Functions | |
| void | setup_packing (core::pose::Pose &pose) |
| utility function to set up packer options for internal task factory More... | |
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 |
| 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... | |
Member Typedef Documentation
◆ Real
|
private |
◆ SymmetricConformation
|
private |
◆ SymmetryInfo
|
private |
Constructor & Destructor Documentation
◆ SymDockingHiRes() [1/2]
| protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes | ( | ) |
◆ SymDockingHiRes() [2/2]
| protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes | ( | core::scoring::ScoreFunctionOP | scorefxn_in, |
| core::scoring::ScoreFunctionOP | scorefxn_pack_in | ||
| ) |
References design_, init_task_factory_, and protocols::moves::Mover::type().
◆ ~SymDockingHiRes()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
decides what to call according to options
Implements protocols::moves::Mover.
References protocols::relax::FastRelax::apply(), docking_highres_protocol_mover_, protocols::relax::RelaxProtocolBase::max_iter(), mc_, scorefxn_, set_default(), and protocols::symmetric_docking::TR().
◆ clone()
|
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.
◆ design() [1/2]
| bool protocols::symmetric_docking::SymDockingHiRes::design | ( | ) | const |
References design_.
◆ design() [2/2]
| void protocols::symmetric_docking::SymDockingHiRes::design | ( | bool const | des | ) |
References design_.
◆ get_mc()
| moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::get_mc | ( | ) |
References mc_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ set_default()
| void protocols::symmetric_docking::SymDockingHiRes::set_default | ( | core::pose::Pose & | pose | ) |
References bb_, chi_, core::pose::symmetry::make_symmetric_movemap(), mc_, min_tolerance_, min_type_, movemap_, nb_list_, repack_period_, repack_switch_, rot_magnitude_, rtmin_, scmin_, scorefxn_, set_protocol(), setup_packing(), temperature_, and trans_magnitude_.
Referenced by apply().
◆ set_dock_mcm_protocol()
| void protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol | ( | core::pose::Pose & | pose | ) |
main entrance to do monte carlo minimization
one cycle of repack and minimization before relax Old:a total of 1 cycle of monte-carlo minimization will be carried out if the minimized structure can pass the filter after the first and fifth cycle. Then it is rigid-body minimized to a stringent tolerance.
- Remarks
- References: docking_mcm_protocol from docking_minimize.cc
- pose_docking_monte_carlo_minimize from pose_docking.cc
References core::pose::Pose::conformation(), docking_highres_protocol_mover_, core::pose::symmetry::is_symmetric(), mc_, min_tolerance_, min_type_, movemap_, nb_list_, repack_period_, repack_switch_, rot_magnitude_, scmin_, scorefxn_, scorefxn_pack_, tf_, protocols::symmetric_docking::TR(), and trans_magnitude_.
Referenced by set_protocol().
◆ set_dock_min_protocol()
| void protocols::symmetric_docking::SymDockingHiRes::set_dock_min_protocol | ( | ) |
main entrance for normal rigid-body minimization
retrieve the structure in the low array and do the normal minimization by calling using a min_mover to optimize the score accourding to the scorefunction that has been set
- Remarks
- References: docking_minimize_trial from docking_minimize.cc
- pose_docking_minimize_trial from pose_docking.cc
References docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, scorefxn_, and protocols::symmetric_docking::TR().
Referenced by set_protocol().
◆ set_dock_ppk_protocol()
| void protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol | ( | core::pose::Pose & | pose | ) |
define the prepacking protocol
References core::pose::Pose::conformation(), docking_highres_protocol_mover_, core::pose::symmetry::is_symmetric(), scmin_, scorefxn_pack_, tf_, and protocols::symmetric_docking::TR().
Referenced by set_protocol().
◆ set_min_type()
| void protocols::symmetric_docking::SymDockingHiRes::set_min_type | ( | std::string | min_type_in | ) |
References min_type_.
◆ set_move_map()
| void protocols::symmetric_docking::SymDockingHiRes::set_move_map | ( | core::kinematics::MoveMapOP | movemap_in | ) |
References movemap_.
◆ set_protocol()
| void protocols::symmetric_docking::SymDockingHiRes::set_protocol | ( | core::pose::Pose & | pose | ) |
References set_dock_mcm_protocol(), set_dock_min_protocol(), and set_dock_ppk_protocol().
Referenced by set_default().
◆ set_repack()
| void protocols::symmetric_docking::SymDockingHiRes::set_repack | ( | bool | repack_switch | ) |
References repack_switch_.
◆ setup_packing()
|
private |
utility function to set up packer options for internal task factory
References design_, init_task_factory_, core::pack::dunbrack::load_unboundrot(), tf_, and protocols::symmetric_docking::TR().
Referenced by set_default().
◆ task_factory() [1/2]
| core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockingHiRes::task_factory | ( | ) |
References init_task_factory_.
◆ task_factory() [2/2]
| void protocols::symmetric_docking::SymDockingHiRes::task_factory | ( | core::pack::task::TaskFactoryOP | task | ) |
References init_task_factory_.
Member Data Documentation
◆ bb_
|
private |
Referenced by set_default().
◆ chi_
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private |
Referenced by set_default().
◆ design_
|
private |
Referenced by design(), setup_packing(), and SymDockingHiRes().
◆ docking_highres_protocol_mover_
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private |
Referenced by apply(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_dock_ppk_protocol().
◆ init_task_factory_
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private |
task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory
Referenced by setup_packing(), SymDockingHiRes(), and task_factory().
◆ mc_
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private |
Referenced by apply(), get_mc(), set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().
◆ min_mover_
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private |
◆ min_tolerance_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().
◆ min_type_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_min_type().
◆ movemap_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_move_map().
◆ nb_list_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().
◆ pack_interface_repack_
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private |
◆ pack_rottrial_
|
private |
◆ repack_period_
|
private |
Referenced by set_default(), and set_dock_mcm_protocol().
◆ repack_switch_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), and set_repack().
◆ rot_magnitude_
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private |
Referenced by set_default(), and set_dock_mcm_protocol().
◆ rtmin_
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private |
Referenced by set_default().
◆ scmin_
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private |
Referenced by set_default(), set_dock_mcm_protocol(), and set_dock_ppk_protocol().
◆ scorefxn_
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private |
Referenced by apply(), set_default(), set_dock_mcm_protocol(), set_dock_min_protocol(), and SymDockingHiRes().
◆ scorefxn_pack_
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private |
Referenced by set_dock_mcm_protocol(), set_dock_ppk_protocol(), and SymDockingHiRes().
◆ temperature_
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private |
Referenced by set_default().
◆ tf_
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private |
tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below
Referenced by set_dock_mcm_protocol(), set_dock_ppk_protocol(), and setup_packing().
◆ trans_magnitude_
|
private |
Referenced by set_default(), and set_dock_mcm_protocol().
The documentation for this class was generated from the following files:
- src/protocols/symmetric_docking/SymDockingHiRes.hh
- src/protocols/symmetric_docking/SymDockingHiRes.cc
