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protocols::simple_moves::BBGaussianMover Class Referenceabstract

the basic class for implementing Gaussian Perturbation of bb More...

#include <BBGaussianMover.hh>

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Public Types

typedef core::Vector Vector
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef core::pose::PoseCOP PoseCOP
 
typedef core::conformation::Residue Residue
 
typedef utility::vector1< VectorVdRdPhi
 
typedef utility::vector1< VdRdPhiVMatrix
 
typedef utility::vector1
< utility::vector1< Real > > 
Matrix
 
typedef numeric::xyzMatrix< RealxyzMatrix
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 BBGaussianMover (Size, Size, Size)
 
 ~BBGaussianMover ()
 
core::kinematics::MoveMapCOP movemap ()
 
void movemap (core::kinematics::MoveMapCOP new_movemap)
 
Real last_proposal_density_ratio () const
 get the ratio of proposal densities for the last move 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 ()
 
virtual void apply (Pose &)=0
 
std::string const & type () const
 
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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
 
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
 this function informs 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
 this function informs 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...
 
virtual 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). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

void setup_list (Pose const &)
 
Vector get_dRdPhi (Vector const &r1, Vector const &r2, Vector const &r)
 
Vector get_dRdTheta (Vector const &r1, Vector const &r2, Vector const &r3, Vector const &r)
 
virtual void get_VdRdPhi (Pose const &)=0
 
virtual void get_G ()=0
 
virtual void get_A ()=0
 
virtual Real get_L_move (Pose &)=0
 
virtual Real get_L_prime ()=0
 
Real cholesky_fw (Matrix &, Size, utility::vector1< Real > &, utility::vector1< Real > &, Size from=1, Size to=0, Real scale=1.0)
 
Real cholesky_bw (Matrix &, Size, utility::vector1< Real > &, utility::vector1< Real > &, Size from=1, Size to=0, Real scale=1.0)
 
void pivot_range_randomly (Pose &, Size, Size)
 randomly rotate the dih angle in this range for avoiding the fixed ends 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

Size n_end_atom_
 
Size n_dof_angle_
 
Size n_pert_res_
 
Size resnum_
 
utility::vector1< std::pair
< Size, Size > > 
available_seg_list_
 
Matrix matrix_G
 
Matrix matrix_A
 
VMatrix matrix_dRdPhi
 
Real last_proposal_density_ratio_
 
core::kinematics::MoveMapCOP movemap_
 

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 

Detailed Description

the basic class for implementing Gaussian Perturbation of bb

Note
"Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space" "The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158." Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: "pivot" update the bb conformation, or followed by a chainclosure method (BBConRot)

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::BBGaussianMover::BBGaussianMover ( Size  n_end_atom,
Size  n_dof_angle,
Size  n_pert_res 
)
protocols::simple_moves::BBGaussianMover::~BBGaussianMover ( )

Member Function Documentation

core::Real protocols::simple_moves::BBGaussianMover::cholesky_bw ( Matrix a,
Size  n,
utility::vector1< Real > &  dphi,
utility::vector1< Real > &  delta,
Size  from = 1,
Size  to = 0,
Real  scale = 1.0 
)
protected
core::Real protocols::simple_moves::BBGaussianMover::cholesky_fw ( Matrix a,
Size  n,
utility::vector1< Real > &  delta,
utility::vector1< Real > &  dphi,
Size  from = 1,
Size  to = 0,
Real  scale = 1.0 
)
protected
virtual void protocols::simple_moves::BBGaussianMover::get_A ( )
protectedpure virtual
Vector protocols::simple_moves::BBGaussianMover::get_dRdPhi ( Vector const &  r1,
Vector const &  r2,
Vector const &  r 
)
inlineprotected
Vector protocols::simple_moves::BBGaussianMover::get_dRdTheta ( Vector const &  r1,
Vector const &  r2,
Vector const &  r3,
Vector const &  r 
)
inlineprotected
virtual void protocols::simple_moves::BBGaussianMover::get_G ( )
protectedpure virtual
virtual Real protocols::simple_moves::BBGaussianMover::get_L_move ( Pose )
protectedpure virtual
virtual Real protocols::simple_moves::BBGaussianMover::get_L_prime ( )
protectedpure virtual
virtual void protocols::simple_moves::BBGaussianMover::get_VdRdPhi ( Pose const &  )
protectedpure virtual
core::Real protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio ( ) const

get the ratio of proposal densities for the last move

References last_proposal_density_ratio_.

core::kinematics::MoveMapCOP protocols::simple_moves::BBGaussianMover::movemap ( )
void protocols::simple_moves::BBGaussianMover::movemap ( core::kinematics::MoveMapCOP  new_movemap)

References available_seg_list_, and movemap_.

void protocols::simple_moves::BBGaussianMover::pivot_range_randomly ( Pose pose,
Size  i,
Size  to 
)
protected
void protocols::simple_moves::BBGaussianMover::setup_list ( Pose const &  pose)
protected

Member Data Documentation

utility::vector1< std::pair<Size,Size> > protocols::simple_moves::BBGaussianMover::available_seg_list_
protected
Real protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio_
protected
Matrix protocols::simple_moves::BBGaussianMover::matrix_A
protected
VMatrix protocols::simple_moves::BBGaussianMover::matrix_dRdPhi
protected
Matrix protocols::simple_moves::BBGaussianMover::matrix_G
protected
core::kinematics::MoveMapCOP protocols::simple_moves::BBGaussianMover::movemap_
protected
Size protocols::simple_moves::BBGaussianMover::n_dof_angle_
protected
Size protocols::simple_moves::BBGaussianMover::n_end_atom_
protected
Size protocols::simple_moves::BBGaussianMover::n_pert_res_
protected
Size protocols::simple_moves::BBGaussianMover::resnum_
protected

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