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protocols::symmetric_docking::SymDockingHiRes Class Reference

#include <SymDockingHiRes.hh>

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

Public Member Functions

 SymDockingHiRes ()
 SymDockingHiRes (core::scoring::ScoreFunctionOP scorefxn_in, core::scoring::ScoreFunctionOP scorefxn_pack_in)
moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual ~SymDockingHiRes ()
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
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 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 ~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)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
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 void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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 Stringsinfo ()
 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 Types

typedef core::Real Real

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_
simple_moves::symmetry::SymMinMoverOP min_mover_
moves::SequenceMoverOP docking_highres_protocol_mover_
moves::MonteCarloOP mc_
simple_moves::symmetry::SymPackRotamersMoverOP pack_interface_repack_
simple_moves::symmetry::SymRotamerTrialsMoverOP 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::TagPtr TagPtr
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. 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...

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes ( )
protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes ( core::scoring::ScoreFunctionOP  scorefxn_in,
core::scoring::ScoreFunctionOP  scorefxn_pack_in 
protocols::symmetric_docking::SymDockingHiRes::~SymDockingHiRes ( )

Member Function Documentation

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

docking high resolution apply function

decides what to call according to options

Implements protocols::moves::Mover.

References docking_highres_protocol_mover_, mc_, set_default(), and protocols::symmetric_docking::TR().

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

clone has to be overridden only if clone invocation is expected.

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.

References SymDockingHiRes().

void protocols::symmetric_docking::SymDockingHiRes::design ( bool const  des)

References design_.

bool protocols::symmetric_docking::SymDockingHiRes::design ( ) const

References design_.

moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::get_mc ( )

References mc_.

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

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::symmetric_docking::SymDockingHiRes::set_default ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol ( core::pose::Pose pose)

main entrance to do monte carlo minimization


a total of 50 cycles 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
Sid Chaudhury May 28 2009, modified for symmetric docking by Ingemar Andre
Last Modified: April 30 2008

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_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), tf_, protocols::symmetric_docking::TR(), and trans_magnitude_.

Referenced by set_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
Last Modified: October 15 2007

References docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, scorefxn_, and protocols::symmetric_docking::TR().

Referenced by set_protocol().

void protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockingHiRes::set_min_type ( std::string  min_type_in)

References min_type_.

void protocols::symmetric_docking::SymDockingHiRes::set_move_map ( core::kinematics::MoveMapOP  movemap_in)

References movemap_.

void protocols::symmetric_docking::SymDockingHiRes::set_protocol ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockingHiRes::set_repack ( bool  repack_switch)

References repack_switch_.

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().

void protocols::symmetric_docking::SymDockingHiRes::task_factory ( core::pack::task::TaskFactoryOP  task)

References init_task_factory_.

core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockingHiRes::task_factory ( )

References init_task_factory_.

Member Data Documentation

bool protocols::symmetric_docking::SymDockingHiRes::bb_

Referenced by set_default().

bool protocols::symmetric_docking::SymDockingHiRes::chi_

Referenced by set_default().

bool protocols::symmetric_docking::SymDockingHiRes::design_
moves::SequenceMoverOP protocols::symmetric_docking::SymDockingHiRes::docking_highres_protocol_mover_
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().

moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::mc_
simple_moves::symmetry::SymMinMoverOP protocols::symmetric_docking::SymDockingHiRes::min_mover_
core::Real protocols::symmetric_docking::SymDockingHiRes::min_tolerance_
std::string protocols::symmetric_docking::SymDockingHiRes::min_type_
core::kinematics::MoveMapOP protocols::symmetric_docking::SymDockingHiRes::movemap_
bool protocols::symmetric_docking::SymDockingHiRes::nb_list_
simple_moves::symmetry::SymPackRotamersMoverOP protocols::symmetric_docking::SymDockingHiRes::pack_interface_repack_
simple_moves::symmetry::SymRotamerTrialsMoverOP protocols::symmetric_docking::SymDockingHiRes::pack_rottrial_
core::Size protocols::symmetric_docking::SymDockingHiRes::repack_period_
bool protocols::symmetric_docking::SymDockingHiRes::repack_switch_
core::Real protocols::symmetric_docking::SymDockingHiRes::rot_magnitude_
bool protocols::symmetric_docking::SymDockingHiRes::rtmin_

Referenced by set_default().

bool protocols::symmetric_docking::SymDockingHiRes::scmin_
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockingHiRes::scorefxn_
core::scoring::ScoreFunctionCOP protocols::symmetric_docking::SymDockingHiRes::scorefxn_pack_
core::Real protocols::symmetric_docking::SymDockingHiRes::temperature_

Referenced by set_default().

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().

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

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