Rosetta Protocols  2014.35
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::docking::DockingHighResLegacy Class Reference

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

#include <DockingHighResLegacy.hh>

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 ()
protocols::moves::MoverOP clone () const
 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 ()
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 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
- 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)
virtual ~DockingHighRes ()
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
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)
void set_interface_definition_task_operation (protocols::toolbox::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)
< 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 ~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
void set_type (std::string const &setting)
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 (TagCOP tag, basic::datacache::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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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::stringStrings
- 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::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 ( )

Member Function Documentation

void protocols::docking::DockingHighResLegacy::apply ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::docking::DockingHighResLegacy::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.

References DockingHighResLegacy().

Referenced by set_dock_mcm_protocol().

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)

References design_.

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

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

Implements protocols::docking::DockingHighRes.

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

References rot_magnitude_.

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

References trans_magnitude_.

bool protocols::docking::DockingHighResLegacy::rt_min ( )
bool protocols::docking::DockingHighResLegacy::sc_min ( )
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.
References: docking_mcm_protocol from
pose_docking_monte_carlo_minimize from
Sid Chaudhury May 28 2009
Last Modified: April 30 2008

References protocols::moves::MoverContainer::add_mover(), clone(), define_loops(), docking_highres_protocol_mover_, exit, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::moves::Mover::get_input_pose(), init_task_factory_, initial_repack, mc_, min_tolerance_, min_type_, minimization_threshold, protocols::docking::DockingHighRes::movable_jumps(), movemap_, nb_list_, option, protocols::rigid::partner_downstream, repack_period_, repack_switch_, rot_magnitude_, rt_min(), rtmin, sc_min(), protocols::docking::DockingHighRes::scorefxn(), protocols::docking::DockingHighRes::scorefxn_pack(), set_task_factory(), protocols::docking::DockingHighRes::task_factory(), protocols::simple_moves::PackRotamersMover::task_factory(), core::pose::Pose::total_residue(), protocols::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
References: docking_minimize_trial from
pose_docking_minimize_trial from
Monica Berrondo June 14 2007
Last Modified: October 15 2007

References protocols::moves::MoverContainer::add_mover(), docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and protocols::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
References: pose_docking_prepack_protocol from
Sid Chaudhury October 3 2008
Last Modified: October 3 2008

References protocols::moves::MoverContainer::add_mover(), begin, docking_highres_protocol_mover_, protocols::docking::DockingHighRes::movable_jumps(), rt_min(), sc_min(), protocols::docking::DockingHighRes::scorefxn_pack(), protocols::docking::DockingHighRes::task_factory(), protocols::TR, and trans_magnitude.

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)

References rt_min(), and rt_min_.

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

References sc_min(), and sc_min_.

void protocols::docking::DockingHighResLegacy::set_task_factory ( core::pack::task::TaskFactoryOP  task)
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)

Member Data Documentation

bool protocols::docking::DockingHighResLegacy::bb_

Referenced by set_default().

bool protocols::docking::DockingHighResLegacy::chi_

Referenced by set_default().

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

Referenced by rt_min(), and set_rt_min().

bool protocols::docking::DockingHighResLegacy::sc_min_

Referenced by sc_min(), and set_sc_min().

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

Referenced by set_default().

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

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