Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::symmetric_docking::SymDockingHiRes Class Reference

#include <SymDockingHiRes.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockingHiRes:
Inheritance graph

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::TaskFactoryOPtask_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 Stringsinfo ()
 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...

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_
core::scoring::ScoreFunctionCOP scorefxn_pack_
core::kinematics::MoveMapOP movemap_
minimization_packing::MinMoverOP min_mover_
moves::SequenceMoverOP docking_highres_protocol_mover_
moves::MonteCarloOP mc_
minimization_packing::PackRotamersMoverOP pack_interface_repack_
minimization_packing::RotamerTrialsMoverOP pack_rottrial_
core::Real trans_magnitude_
core::Real rot_magnitude_
bool chi_
bool bb_
bool repack_switch_
bool design_
bool rtmin_
bool scmin_
core::pack::task::TaskFactoryOP tf_
 tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below More...
core::pack::task::TaskFactoryOP init_task_factory_
 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 More...
core::Size repack_period_
core::Real temperature_
core::Real min_tolerance_
bool nb_list_
std::string min_type_

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

◆ SymmetricConformation

◆ SymmetryInfo

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 

◆ ~SymDockingHiRes()

protocols::symmetric_docking::SymDockingHiRes::~SymDockingHiRes ( )

Member Function Documentation

◆ apply()

void protocols::symmetric_docking::SymDockingHiRes::apply ( core::pose::Pose pose)

◆ clone()

protocols::moves::MoverOP protocols::symmetric_docking::SymDockingHiRes::clone ( ) const

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()

std::string protocols::symmetric_docking::SymDockingHiRes::get_name ( ) const

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)

◆ 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.

References: docking_mcm_protocol from
pose_docking_monte_carlo_minimize from
Oroginally: Sid Chaudhury May 28 2009, modified for symmetric docking by Ingemar Andre, SymDock2: modified by Shourya S. Roy Burman

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

References: docking_minimize_trial from
pose_docking_minimize_trial from
Monica Berrondo June 14 2007, modified for symmetric docking by Ingemar Andre

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)

◆ 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)

◆ set_repack()

void protocols::symmetric_docking::SymDockingHiRes::set_repack ( bool  repack_switch)

References repack_switch_.

◆ setup_packing()

void protocols::symmetric_docking::SymDockingHiRes::setup_packing ( core::pose::Pose pose)

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_

bool protocols::symmetric_docking::SymDockingHiRes::bb_

Referenced by set_default().

◆ chi_

bool protocols::symmetric_docking::SymDockingHiRes::chi_

Referenced by set_default().

◆ design_

bool protocols::symmetric_docking::SymDockingHiRes::design_

◆ docking_highres_protocol_mover_

moves::SequenceMoverOP protocols::symmetric_docking::SymDockingHiRes::docking_highres_protocol_mover_

◆ init_task_factory_

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockingHiRes::init_task_factory_

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_

moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::mc_

◆ min_mover_

minimization_packing::MinMoverOP protocols::symmetric_docking::SymDockingHiRes::min_mover_

◆ min_tolerance_

core::Real protocols::symmetric_docking::SymDockingHiRes::min_tolerance_

◆ min_type_

std::string protocols::symmetric_docking::SymDockingHiRes::min_type_

◆ movemap_

core::kinematics::MoveMapOP protocols::symmetric_docking::SymDockingHiRes::movemap_

◆ nb_list_

bool protocols::symmetric_docking::SymDockingHiRes::nb_list_

◆ pack_interface_repack_

minimization_packing::PackRotamersMoverOP protocols::symmetric_docking::SymDockingHiRes::pack_interface_repack_

◆ pack_rottrial_

minimization_packing::RotamerTrialsMoverOP protocols::symmetric_docking::SymDockingHiRes::pack_rottrial_

◆ repack_period_

core::Size protocols::symmetric_docking::SymDockingHiRes::repack_period_

◆ repack_switch_

bool protocols::symmetric_docking::SymDockingHiRes::repack_switch_

◆ rot_magnitude_

core::Real protocols::symmetric_docking::SymDockingHiRes::rot_magnitude_

◆ rtmin_

bool protocols::symmetric_docking::SymDockingHiRes::rtmin_

Referenced by set_default().

◆ scmin_

bool protocols::symmetric_docking::SymDockingHiRes::scmin_

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockingHiRes::scorefxn_

◆ scorefxn_pack_

core::scoring::ScoreFunctionCOP protocols::symmetric_docking::SymDockingHiRes::scorefxn_pack_

◆ temperature_

core::Real protocols::symmetric_docking::SymDockingHiRes::temperature_

Referenced by set_default().

◆ tf_

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockingHiRes::tf_

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_

core::Real protocols::symmetric_docking::SymDockingHiRes::trans_magnitude_

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