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protocols::docking::DockingHighResLegacy Class Reference

this mover does the high resolution refinement stage of the RosettaDock algorithm More...

#include <DockingHighResLegacy.hh>

Inheritance diagram for protocols::docking::DockingHighResLegacy:
Inheritance graph
[legend]

Public Member Functions

 DockingHighResLegacy ()
 
 DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 
 DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 
 DockingHighResLegacy (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 
 ~DockingHighResLegacy () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
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)
 
virtual void set_task_factory (core::pack::task::TaskFactoryOP task)
 
void define_loops (core::pose::Pose const &pose, loops::LoopsOP loop_set, Real &interface_dist)
 
void set_trans_magnitude (core::Real trans_magnitude)
 
void set_rot_magnitude (core::Real rot_magnitude)
 
void set_rt_min (bool rt_min)
 
bool rt_min ()
 
void set_sc_min (bool sc_min)
 
bool sc_min ()
 
moves::MonteCarloOP get_mc ()
 
core::Real get_trans_magnitude ()
 
core::Real get_rot_magnitude ()
 
void apply (core::pose::Pose &pose) override
 
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)
 main entrance to prepacking for docking More...
 
void design (bool const des)
 
bool design () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::docking::DockingHighRes
 DockingHighRes ()
 Default constructor. More...
 
 DockingHighRes (core::Size const rb_jump)
 Constructor with one argument - the jump number to dock over. More...
 
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...
 
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 
 DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 
 DockingHighRes (DockingHighRes const &old_instance)
 
 ~DockingHighRes () override
 
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
 
void set_ignore_default_task (bool ignore_default_task)
 
bool ignore_default_task ()
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)
 
DockJumpsmovable_jumps ()
 
DockJumps const & movable_jumps () const
 
void set_movable_jumps (DockJumps movable_jumps)
 
core::pack::task::TaskFactoryCOP task_factory ()
 
void set_sc_min (bool sc_min)
 
void set_rt_min (bool rt_min)
 
void set_partners (std::string partners)
 
std::string get_partners () const
 
void set_interface_definition_task_operation (protocols::simple_task_operations::InterfaceTaskOperationOP interface_definition)
 
void set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)
 
void add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)
 
utility::vector1
< core::pack::task::operation::TaskOperationOP
get_additional_task_operarations ()
 
bool sc_min ()
 
bool rt_min ()
 
std::string partners ()
 
core::scoring::ScoreFunctionOP scorefxn () const
 
core::scoring::ScoreFunctionOP scorefxn_pack () const
 
- 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

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::kinematics::MoveMapOP movemap_
 
moves::SequenceMoverOP docking_highres_protocol_mover_
 
moves::MonteCarloOP mc_
 
core::Real trans_magnitude_
 
core::Real rot_magnitude_
 
bool chi_
 
bool bb_
 
bool repack_switch_
 
bool design_
 
bool rt_min_
 
bool sc_min_
 
core::pack::task::TaskFactoryOP init_task_factory_
 
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
 
- Protected Member Functions inherited from protocols::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP tf2 ()
 
- 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...
 

Detailed Description

this mover does the high resolution refinement stage of the RosettaDock algorithm

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( )
protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( int  rb_jump,
core::scoring::ScoreFunctionOP  scorefxn 
)
protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( int  rb_jump,
core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::ScoreFunctionOP  scorefxn_pack 
)
protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::ScoreFunctionOP  scorefxn_pack 
)
protocols::docking::DockingHighResLegacy::~DockingHighResLegacy ( )
overridedefault

Member Function Documentation

void protocols::docking::DockingHighResLegacy::apply ( core::pose::Pose pose)
overridevirtual

decides what to call according to options

Implements protocols::docking::DockingHighRes.

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

protocols::moves::MoverOP protocols::docking::DockingHighResLegacy::clone ( ) const
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.

void protocols::docking::DockingHighResLegacy::define_loops ( core::pose::Pose const &  pose,
loops::LoopsOP  loop_set,
Real interface_dist 
)
void protocols::docking::DockingHighResLegacy::design ( bool const  des)
bool protocols::docking::DockingHighResLegacy::design ( ) const

References design_.

moves::MonteCarloOP protocols::docking::DockingHighResLegacy::get_mc ( )

References mc_.

std::string protocols::docking::DockingHighResLegacy::get_name ( ) const
overridevirtual

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

Implements protocols::docking::DockingHighRes.

References mover_name().

core::Real protocols::docking::DockingHighResLegacy::get_rot_magnitude ( )
inline

References rot_magnitude_.

core::Real protocols::docking::DockingHighResLegacy::get_trans_magnitude ( )
inline

References trans_magnitude_.

std::string protocols::docking::DockingHighResLegacy::mover_name ( )
static
void protocols::docking::DockingHighResLegacy::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
bool protocols::docking::DockingHighResLegacy::rt_min ( )
inline
bool protocols::docking::DockingHighResLegacy::sc_min ( )
inline
void protocols::docking::DockingHighResLegacy::set_default ( core::pose::Pose pose)
void protocols::docking::DockingHighResLegacy::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.

Remarks
References: docking_mcm_protocol from docking_minimize.cc
pose_docking_monte_carlo_minimize from pose_docking.cc
Author
Sid Chaudhury May 28 2009

References define_loops(), docking_highres_protocol_mover_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::moves::Mover::get_input_pose(), init_task_factory_, mc_, min_tolerance_, min_type_, protocols::docking::DockingHighRes::movable_jumps(), movemap_, nb_list_, protocols::rigid::partner_downstream, repack_period_, repack_switch_, rot_magnitude_, rt_min(), sc_min(), protocols::docking::DockingHighRes::scorefxn(), protocols::docking::DockingHighRes::scorefxn_pack(), set_task_factory(), core::pose::Pose::size(), protocols::docking::DockingHighRes::task_factory(), protocols::docking::TR(), and trans_magnitude_.

Referenced by set_protocol().

void protocols::docking::DockingHighResLegacy::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
Author
Monica Berrondo June 14 2007

References docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and protocols::docking::TR().

Referenced by set_protocol().

void protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol ( core::pose::Pose pose)

main entrance to prepacking for docking

does a full repack of all sidechains for each partner after moving them away by 500A, then it brings them back together

Remarks
References: pose_docking_prepack_protocol from pose_docking.cc
Author
Sid Chaudhury October 3 2008

References docking_highres_protocol_mover_, protocols::docking::DockingHighRes::movable_jumps(), rt_min(), sc_min(), protocols::docking::DockingHighRes::scorefxn_pack(), protocols::docking::DockingHighRes::task_factory(), and protocols::docking::TR().

void protocols::docking::DockingHighResLegacy::set_min_type ( std::string  min_type_in)

References min_type_.

void protocols::docking::DockingHighResLegacy::set_move_map ( core::kinematics::MoveMapOP  movemap_in)

References movemap_.

void protocols::docking::DockingHighResLegacy::set_protocol ( core::pose::Pose pose)
void protocols::docking::DockingHighResLegacy::set_repack ( bool  repack_switch)

References repack_switch_.

void protocols::docking::DockingHighResLegacy::set_rot_magnitude ( core::Real  rot_magnitude)

References rot_magnitude_.

Referenced by set_default().

void protocols::docking::DockingHighResLegacy::set_rt_min ( bool  rt_min)
inline

References rt_min(), and rt_min_.

void protocols::docking::DockingHighResLegacy::set_sc_min ( bool  sc_min)
inline

References sc_min(), and sc_min_.

void protocols::docking::DockingHighResLegacy::set_task_factory ( core::pack::task::TaskFactoryOP  task)
virtual
void protocols::docking::DockingHighResLegacy::set_trans_magnitude ( core::Real  trans_magnitude)

References trans_magnitude_.

Referenced by set_default().

void protocols::docking::DockingHighResLegacy::setup_packing ( core::pose::Pose pose)
private

Member Data Documentation

bool protocols::docking::DockingHighResLegacy::bb_
private

Referenced by set_default().

bool protocols::docking::DockingHighResLegacy::chi_
private

Referenced by set_default().

bool protocols::docking::DockingHighResLegacy::design_
private
moves::SequenceMoverOP protocols::docking::DockingHighResLegacy::docking_highres_protocol_mover_
private
core::pack::task::TaskFactoryOP protocols::docking::DockingHighResLegacy::init_task_factory_
private
moves::MonteCarloOP protocols::docking::DockingHighResLegacy::mc_
private
core::Real protocols::docking::DockingHighResLegacy::min_tolerance_
private
std::string protocols::docking::DockingHighResLegacy::min_type_
private
core::kinematics::MoveMapOP protocols::docking::DockingHighResLegacy::movemap_
private
bool protocols::docking::DockingHighResLegacy::nb_list_
private
core::Size protocols::docking::DockingHighResLegacy::repack_period_
private
bool protocols::docking::DockingHighResLegacy::repack_switch_
private
core::Real protocols::docking::DockingHighResLegacy::rot_magnitude_
private
bool protocols::docking::DockingHighResLegacy::rt_min_
private

Referenced by rt_min(), and set_rt_min().

bool protocols::docking::DockingHighResLegacy::sc_min_
private

Referenced by sc_min(), and set_sc_min().

core::Real protocols::docking::DockingHighResLegacy::temperature_
private

Referenced by set_default().

core::Real protocols::docking::DockingHighResLegacy::trans_magnitude_
private

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