Rosetta 3.4
Public Types | Public Member Functions
protocols::simple_moves::ConsensusDesignMover Class Reference

This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed. More...

#include <ConsensusDesignMover.hh>

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List of all members.

Public Types

typedef core::Size Size
typedef core::pose::Pose Pose
typedef protocols::moves::MoverOP MoverOP

Public Member Functions

 ConsensusDesignMover ()
 ConsensusDesignMover (core::pack::task::PackerTaskCOP ptask, core::scoring::ScoreFunctionCOP sfxn)
 ~ConsensusDesignMover ()
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).
virtual void apply (core::pose::Pose &pose)
void set_sasa_cutoff (core::Real cutoff)
void set_invert_task (bool setting)
void set_use_seqprof_constraints (bool setting)
core::pack::task::PackerTaskCOP create_consensus_design_task (core::pose::Pose const &pose)
core::scoring::constraints::ConstraintCOPs create_sequence_profile_constraints (core::pose::Pose const &pose, core::pack::task::PackerTask const &task) const
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data_map, 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

This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed.


Member Typedef Documentation

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

protocols::simple_moves::ConsensusDesignMover::ConsensusDesignMover ( )

Referenced by clone(), and fresh_instance().

protocols::simple_moves::ConsensusDesignMover::ConsensusDesignMover ( core::pack::task::PackerTaskCOP  ptask,
core::scoring::ScoreFunctionCOP  sfxn 
)
protocols::simple_moves::ConsensusDesignMover::~ConsensusDesignMover ( )

Member Function Documentation

void protocols::simple_moves::ConsensusDesignMover::apply ( core::pose::Pose pose) [virtual]

this mover is allowed to touch all residues specified as designable in the passed in task, resp. if the invert_task_ variable is set to true, all residues specified as non-packable in the task if no task is passed in, all residues will be considered legit

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraints(), protocols::simple_moves::PackRotamersMover::apply(), create_consensus_design_task(), create_sequence_profile_constraints(), core::scoring::getScoreFunction(), core::pose::Pose::remove_constraints(), and core::scoring::res_type_constraint.

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply().

protocols::moves::MoverOP protocols::simple_moves::ConsensusDesignMover::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 ConsensusDesignMover().

core::pack::task::PackerTaskCOP protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task ( core::pose::Pose const &  pose)
core::scoring::constraints::ConstraintCOPs protocols::simple_moves::ConsensusDesignMover::create_sequence_profile_constraints ( core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  task 
) const
protocols::moves::MoverOP protocols::simple_moves::ConsensusDesignMover::fresh_instance ( ) const [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.

Reimplemented from protocols::moves::Mover.

References ConsensusDesignMover().

std::string protocols::simple_moves::ConsensusDesignMover::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::simple_moves::ConsensusDesignMover::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::moves::Mover.

References protocols::moves::DataMap::get(), and protocols::rosetta_scripts::parse_task_operations().

void protocols::simple_moves::ConsensusDesignMover::set_invert_task ( bool  setting) [inline]
void protocols::simple_moves::ConsensusDesignMover::set_sasa_cutoff ( core::Real  cutoff) [inline]
void protocols::simple_moves::ConsensusDesignMover::set_use_seqprof_constraints ( bool  setting) [inline]

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