Rosetta 3.4
Public Member Functions
protocols::docking::DockingHighResLegacy Class Reference

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

#include <DockingHighResLegacy.hh>

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List of all members.

Public Member Functions

 DockingHighResLegacy ()
 DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionCOP scorefxn)
 DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreFunctionCOP scorefxn_pack)
 DockingHighResLegacy (DockJumps const movable_jumps, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreFunctionCOP scorefxn_pack)
 ~DockingHighResLegacy ()
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
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)
moves::MonteCarloOP get_mc ()
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_dock_min_protocol ()
 main entrance for normal rigid-body minimization
void set_dock_mcm_protocol (core::pose::Pose &pose)
 main entrance to do monte carlo minimization
void set_dock_ppk_protocol (core::pose::Pose &pose)
 main entrance to prepacking for docking
void design (bool const des)
bool design () const

Detailed Description

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


Constructor & Destructor Documentation

protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( )

References protocols::moves::Mover::type().

Referenced by clone().

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

Member Function Documentation

void protocols::docking::DockingHighResLegacy::apply ( core::pose::Pose pose) [virtual]

docking high resolution apply function

Detailed:
decides what to call according to options

Implements protocols::docking::DockingHighRes.

References set_default(), and protocols::TR().

protocols::moves::MoverOP protocols::docking::DockingHighResLegacy::clone ( ) const [virtual]

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 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 
)
bool protocols::docking::DockingHighResLegacy::design ( ) const
void protocols::docking::DockingHighResLegacy::design ( bool const  des)
moves::MonteCarloOP protocols::docking::DockingHighResLegacy::get_mc ( )
std::string protocols::docking::DockingHighResLegacy::get_name ( ) const [virtual]

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

Implements protocols::docking::DockingHighRes.

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

dock_mcm_protocol

Detailed:
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
Authors:
Sid Chaudhury May 28 2009
Last Modified: April 30 2008

References protocols::moves::MoverContainer::add_mover(), clone(), define_loops(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::moves::Mover::get_input_pose(), protocols::docking::DockingHighRes::movable_jumps(), protocols::rigid::partner_downstream, protocols::docking::DockingHighRes::rt_min(), protocols::docking::DockingHighRes::sc_min(), protocols::docking::DockingHighRes::scorefxn(), protocols::docking::DockingHighRes::scorefxn_pack(), set_task_factory(), protocols::docking::DockingHighRes::task_factory(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by set_protocol().

void protocols::docking::DockingHighResLegacy::set_dock_min_protocol ( )

main entrance for normal rigid-body minimization

minimize_trial

Detailed:
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
Authors:
Monica Berrondo June 14 2007
Last Modified: October 15 2007

References protocols::moves::MoverContainer::add_mover(), 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

dock_ppk_protocol

Detailed:
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
Authors:
Sid Chaudhury October 3 2008
Last Modified: October 3 2008

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

void protocols::docking::DockingHighResLegacy::set_min_type ( std::string  min_type_in)
void protocols::docking::DockingHighResLegacy::set_move_map ( core::kinematics::MoveMapOP  movemap_in)
void protocols::docking::DockingHighResLegacy::set_protocol ( core::pose::Pose pose)
void protocols::docking::DockingHighResLegacy::set_repack ( bool  repack_switch)
void protocols::docking::DockingHighResLegacy::set_task_factory ( core::pack::task::TaskFactoryOP  task) [virtual]

Reimplemented from protocols::docking::DockingHighRes.

Referenced by set_dock_mcm_protocol().


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