Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::membrane::ddG::MembraneDDGMover Class Reference

Mutate Residue, Repack within pack_radius and compute ddG score of mutation. More...

#include <MembraneDDGMover.hh>

Public Member Functions

 MembraneDDGMover ()
 Constructors ///. More...
 
 MembraneDDGMover (Real pack_radius_in, ScoreFunctionOP sfxn_in, utility::vector1< MutationOP > mutations_in)
 Custom Constructor. More...
 
 MembraneDDGMover (MembraneDDGMover const &src)
 Copy Constructor. More...
 
MembraneDDGMoveroperator= (MembraneDDGMover const &src)
 Assignment Operator. More...
 
 ~MembraneDDGMover ()
 Destructor. More...
 
virtual protocols::moves::MoverOP clone () const
 Rosetta Scripts Methods ///. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Create a Fresh Instance of this Mover. 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 &)
 Pase Rosetta Scripts Options for this Mover. More...
 
virtual std::string get_name () const
 Mover Methods ///. More...
 
virtual void apply (Pose &pose)
 Compute ddG Scores for Membranes. More...
 
- 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...
 

Private Member Functions

core::Real compute_ddG_score (Pose &pose, AA aa, Size position, core::Real native_score)
 Compute ddG Score. More...
 
utility::vector1< char > designed_amino_acids ()
 List of AAs to test. More...
 
std::set< Sizeget_residue_neighbors (Pose &pose, core::Size position, core::Real radius)
 Access Neighbors within Radius. More...
 

Private Attributes

Real pack_radius_
 
ScoreFunctionOP sfxn_
 
utility::vector1< MutationOPmutations_
 

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
protocols::filters::Filters_map 
Filters_map
 
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::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

Mutate Residue, Repack within pack_radius and compute ddG score of mutation.

Constructor & Destructor Documentation

protocols::membrane::ddG::MembraneDDGMover::MembraneDDGMover ( )

Constructors ///.

Default Constructor

Construct a defauilt version of this mover: pack_radius = 0.0, membrane env smooth sfxn

Default Constructor (private)

Construct a defauilt version of this mover: pack_radius = 0.0, membrane env smooth sfxn, and no mutations

References core::scoring::ScoreFunctionFactory::create_score_function(), and sfxn_.

Referenced by clone(), fresh_instance(), and operator=().

protocols::membrane::ddG::MembraneDDGMover::MembraneDDGMover ( Real  pack_radius_in,
ScoreFunctionOP  sfxn_in,
utility::vector1< MutationOP mutations_in 
)

Custom Constructor.

Specify a pack radius, scorefunction to use, etc.

Create a ddG task given a pack radius, score funciton, and list of mutations

protocols::membrane::ddG::MembraneDDGMover::MembraneDDGMover ( MembraneDDGMover const &  src)

Copy Constructor.

Create a deep copy of this object

protocols::membrane::ddG::MembraneDDGMover::~MembraneDDGMover ( )

Destructor.

Member Function Documentation

void protocols::membrane::ddG::MembraneDDGMover::apply ( Pose pose)
virtual

Compute ddG Scores for Membranes.

Implements protocols::moves::Mover.

References compute_ddG_score(), mutations_, and protocols::TR.

protocols::moves::MoverOP protocols::membrane::ddG::MembraneDDGMover::clone ( ) const
virtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

References MembraneDDGMover().

core::Real protocols::membrane::ddG::MembraneDDGMover::compute_ddG_score ( Pose pose,
AA  aa,
Size  position,
core::Real  native_score 
)
private

Compute ddG Score.

Compute ddG from a copy of the native pose, native score and provided resfile. Doing this PyRosetta Style - thanks to Evan Baugh's Mutate.py for instructions

References get_residue_neighbors(), core::pose::Pose::is_fullatom(), neighbors, pack_radius_, sfxn_, and utility_exit_with_message.

Referenced by apply().

utility::vector1< char > protocols::membrane::ddG::MembraneDDGMover::designed_amino_acids ( )
private

List of AAs to test.

Return a vector 1 of characters representing the 20 AAs to substitute. This is possibly too specific to my current task as well

protocols::moves::MoverOP protocols::membrane::ddG::MembraneDDGMover::fresh_instance ( ) const
virtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

References MembraneDDGMover().

std::string protocols::membrane::ddG::MembraneDDGMover::get_name ( ) const
virtual

Mover Methods ///.

Get the name of this Mover (MembraneDDGMover)

Implements protocols::moves::Mover.

std::set< Size > protocols::membrane::ddG::MembraneDDGMover::get_residue_neighbors ( Pose pose,
core::Size  position,
core::Real  radius 
)
private
MembraneDDGMover & protocols::membrane::ddG::MembraneDDGMover::operator= ( MembraneDDGMover const &  src)

Assignment Operator.

Create a deep copy of this object overloading the assignment operator

References MembraneDDGMover().

void protocols::membrane::ddG::MembraneDDGMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

Member Data Documentation

utility::vector1< MutationOP > protocols::membrane::ddG::MembraneDDGMover::mutations_
private

Referenced by apply().

Real protocols::membrane::ddG::MembraneDDGMover::pack_radius_
private

Referenced by compute_ddG_score().

ScoreFunctionOP protocols::membrane::ddG::MembraneDDGMover::sfxn_
private

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