Rosetta 3.4
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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>

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List of all members.

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 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.
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
protocols::moves::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).
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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.

Detailed Description

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


Member Typedef Documentation

Reimplemented from protocols::moves::Mover.


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 core::chemical::aa_cys, core::chemical::aa_gly, core::chemical::aa_pro, 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_, core::pack::pack_rotamers(), protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), core::pack::symmetric_pack_rotamers(), 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]

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.

Implements protocols::simple_moves::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::RepackMinimize::fresh_instance ( ) const [inline, virtual]

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).

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::TagPtr const  tag,
protocols::moves::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::protein_interface_design::movers::TR().


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