Rosetta Protocols  2014.35
Public Types | Public Member Functions | List of all members
protocols::protein_interface_design::movers::RepackMinimize Class Reference

One round of design/repacking followed by interface sc/bb and rigid-body minimization. More...

#include <RepackMinimize.hh>

Public Types

typedef core::pose::Pose Pose
 
typedef core::Real Real
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 RepackMinimize ()
 
 RepackMinimize (ScoreFunctionCOP scorefxn_repack, ScoreFunctionCOP scorefxn_minimize, utility::vector1< core::Size > const target_residues, bool const repack_partner1=false, bool const repack_partner2=true, core::Real const interface_distance_cutoff=8.0, bool const repack_non_ala=true)
 
virtual ~RepackMinimize ()
 
void apply (Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
- Public Member Functions inherited from protocols::simple_moves::DesignRepackMover
 DesignRepackMover ()
 
 DesignRepackMover (std::string const name)
 
void setup_packer_and_movemap (core::pose::Pose const &pose)
 
void min_rb (utility::vector1< bool > const min_rb)
 
void min_rb (bool const min_rb)
 in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...
 
utility::vector1< bool > const & min_rb () const
 
bool min_rb_set () const
 
void min_sc (utility::vector1< bool > const &min_sc)
 
utility::vector1< bool > const & min_sc () const
 
bool min_sc_set () const
 
void min_bb (utility::vector1< bool > const &min_bb)
 
utility::vector1< bool > const & min_bb () const
 
bool min_bb_set () const
 
bool optimize_foldtree () const
 
void optimize_foldtree (bool const opt)
 
void prevent_repacking (utility::vector1< core::Size > const p)
 
utility::vector1< core::Size >
const & 
prevent_repacking () const
 
void restrict_to_repacking (utility::vector1< core::Size > const p)
 
utility::vector1< core::Size >
const & 
restrict_to_repacking () const
 
void design (bool const des)
 
bool design () const
 
void set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
 
core::scoring::ScoreFunctionOP scorefxn_repack () const
 
core::scoring::ScoreFunctionOP scorefxn_minimize () const
 
core::pack::task::PackerTaskCOP task () const
 
core::pack::task::PackerTaskOPtask ()
 
void clear_task ()
 after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...
 
void clear_task_factory ()
 
void use_preset_task (bool const bt)
 
bool use_preset_task () const
 
void task_factory (core::pack::task::TaskFactoryOP p)
 
core::pack::task::TaskFactoryOPtask_factory ()
 
core::pack::task::TaskFactoryOP task_factory () const
 
virtual ~DesignRepackMover ()
 
- 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)
 
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...
 
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...
 

Additional Inherited Members

- 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...
 
- Protected Attributes inherited from protocols::simple_moves::DesignRepackMover
core::scoring::ScoreFunctionOP scorefxn_repack_
 
core::scoring::ScoreFunctionOP scorefxn_minimize_
 
bool repack_partner1_
 
bool repack_partner2_
 
bool design_partner1_
 
bool design_partner2_
 
utility::vector1< boolmin_sc_
 
utility::vector1< boolcurr_min_sc_
 
utility::vector1< boolmin_rb_
 
utility::vector1< boolmin_bb_
 
utility::vector1< boolcurr_min_bb_
 
utility::vector1< boolcurr_min_rb_
 
bool min_rb_set_
 
bool min_sc_set_
 
bool min_bb_set_
 
utility::vector1< core::Sizetarget_residues_
 
core::Real interface_distance_cutoff_
 
bool repack_non_ala_
 
bool optimize_foldtree_
 
bool automatic_repacking_definition_
 
core::pack::task::PackerTaskOP task_
 
bool use_preset_task_
 
utility::vector1< boolallowed_aas_
 
utility::vector1< core::Sizeprevent_repacking_
 
utility::vector1< core::Sizerestrict_to_repacking_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool symmetry_
 

Detailed Description

One round of design/repacking followed by interface sc/bb and rigid-body minimization.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize ( )
protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize ( ScoreFunctionCOP  scorefxn_repack,
ScoreFunctionCOP  scorefxn_minimize,
utility::vector1< core::Size > const  target_residues,
bool const  repack_partner1 = false,
bool const  repack_partner2 = true,
core::Real const  interface_distance_cutoff = 8.0,
bool const  repack_non_ala = true 
)
protocols::protein_interface_design::movers::RepackMinimize::~RepackMinimize ( )
virtual

Member Function Documentation

void protocols::protein_interface_design::movers::RepackMinimize::apply ( pose::Pose pose)
virtual

designs interface residues and minimizes the pose. If minimization parameters have not been set by the user the default minimization behaviour is as follows:

  • minimize bb/sc for all residues that are repacked.
  • minimize bb/sc of residues that are +-1 from target residues
  • minimize bb for all residues (minimizing over only interface residues causes large motions during minimization)
  • minimize rb jump Note that some confusion may arise from the use of repack1_ and repack2_ The behaviour of these variables is such that if they're false, then the relevant partner is not designed but may be repacked. Turning off design_ precludes design across the whole system only allowing repack. At one point the names should be rethought...

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::simple_moves::DesignRepackMover::allowed_aas_, protocols::simple_moves::DesignRepackMover::curr_min_bb_, protocols::simple_moves::DesignRepackMover::curr_min_rb_, protocols::simple_moves::DesignRepackMover::curr_min_sc_, MinimizeInterface(), protocols::simple_moves::DesignRepackMover::optimize_foldtree_, protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::DesignRepackMover::symmetry_, SymMinimizeInterface(), protocols::simple_moves::DesignRepackMover::target_residues_, protocols::simple_moves::DesignRepackMover::task_, and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::RepackMinimize::clone ( ) const
virtual

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.

Implements protocols::simple_moves::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::RepackMinimize::fresh_instance ( ) const
inlinevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::RepackMinimize::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::RepackMinimizeCreator::mover_name().

void protocols::protein_interface_design::movers::RepackMinimize::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::simple_moves::DesignRepackMover::parse_my_tag(), and protocols::protein_interface_design::movers::TR.


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