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protocols::simple_moves::BBConRotMover Class Reference

#include <BBConRotMover.hh>

Inheritance diagram for protocols::simple_moves::BBConRotMover:
Inheritance graph
[legend]

Public Types

typedef numeric::xyzMatrix
< core::Real
xyzMatrix
 
- Public Types inherited from protocols::simple_moves::BBGaussianMover
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< RealVector
 
typedef numeric::xyzVector< RealxyzVector
 
typedef utility::vector1
< xyzVector
VdRdPhi
 
typedef utility::vector1< VdRdPhiVMatrix
 
typedef utility::vector1< VectorMatrix
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 BBConRotMover ()
 
 ~BBConRotMover () override
 
void apply (Pose &) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void factorA (core::Real const fA)
 
void factorB (core::Real const fB)
 
void factorC (core::Real const fC)
 
- Public Member Functions inherited from protocols::simple_moves::BBGaussianMover
 BBGaussianMover ()
 
 BBGaussianMover (core::Size, core::Size, core::Size)
 
 ~BBGaussianMover () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (Pose &pose) override
 Main Method. More...
 
void init ()
 
void resize (core::Size, core::Size, core::Size)
 
void factorA (Real const fA)
 
void factorB (Real const fB)
 
void get_G ()
 
void get_A ()
 
Real get_L_prime ()
 
Real get_L_move (Pose &)
 
void get_VdRdPhi (Pose const &)
 
core::kinematics::MoveMapCOP movemap (core::pose::Pose const &) const
 Generates the movemap used by this mover for the given pose. More...
 
void movemap (core::kinematics::MoveMapCOP new_movemap)
 
void movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)
 The movemap_factory will be used to generate a movemap, if an explcit one hasn't already been set. More...
 
void update_counting_last_PDR (Real)
 
Real last_proposal_density_ratio () override
 get the ratio of proposal densities for the last move More...
 
bool preserve_detailed_balance () const override
 get whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
void set_preserve_detailed_balance (bool preserve_detailed_balance) override
 set whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &) override
 dummy More...
 
void init_kic_loop (core::Size looplength, core::kinematics::MoveMapCOP mm)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 Default constructor. More...
 
 ~ThermodynamicMover () override
 Default destructor. More...
 
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 Callback executed before any Monte Carlo trials are attempted. More...
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after the Metropolis criterion is evaluated. More...
 
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after all Monte Carlo trials are completed. More...
 
virtual bool is_multi_trial ()
 Return true if the move performs multiple trials on each apply. More...
 
virtual core::Real last_inner_score_delta_over_temperature ()
 If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...
 
virtual
protocols::canonical_sampling::MetropolisHastingsMoverAP 
metropolis_hastings_mover ()
 If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...
 
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Protected Member Functions

bool make_move (Pose &)
 
void get_VdRdPhi (Pose const &)
 
void get_G ()
 
void get_A ()
 
Real get_L_move (Pose &)
 
Real get_L_prime ()
 
- Protected Member Functions inherited from protocols::simple_moves::BBGaussianMover
void setup_list (Pose const &)
 
xyzVector get_dRdPhi (xyzVector const &r1, xyzVector const &r2, xyzVector const &r)
 
xyzVector get_dRdTheta (xyzVector const &r1, xyzVector const &r2, xyzVector const &r3, xyzVector const &r)
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
Real cholesky_fw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)
 
Real cholesky_bw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)
 
void pivot_range_randomly (Pose &, core::Size, core::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...
 

Private Member Functions

void get_xyz (xyzVector const &a, xyzVector const &b, xyzVector const &c, xyzVector &d, Real distance, Real theta, Real phi)
 get xyz of d, given reference atoms a,b,c (a-b-c-d) and distance of c-d bond angle theta of d-c-b dihedral angle phi of d-c-b-a More...
 
Real calc_jacobian_cartesians (xyzVector const &, xyzVector const &, xyzVector const &, xyzVector const &, xyzVector const &)
 
bool get_determinant (core::Real a[5][5], int n, core::Real &det)
 
bool closure (xyzVector &r0, xyzVector &r1, xyzVector &r2, xyzVector &r3, xyzVector &r4, xyzVector &r5, xyzVector &r6, xyzVector &p1, xyzVector &p2, xyzVector &p3, Real const theta1_old, Real const theta2_old, Real const theta3_old, Real const theta4_old, Real const alpha1_old, Real const alpha2_old, Real const alpha3_old, Real &theta1, Real &theta2, Real &theta3, Real &theta4, Real &alpha1, Real &alpha2, Real &alpha3)
 

Private Attributes

Vector dphi
 
Vector oldphi
 
Real factorA_
 
Real factorB_
 
Real factorC_
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::simple_moves::BBGaussianMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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 Attributes inherited from protocols::simple_moves::BBGaussianMover
core::Size n_end_atom_
 
core::Size n_dof_angle_
 
core::Size n_pert_res_
 
core::Size resnum_
 
utility::vector1< std::pair
< core::Size, Size > > 
available_seg_list_
 
utility::vector1< std::pair
< core::Size, std::string > > 
end_atom_list_
 
Matrix matrix_G
 
Matrix matrix_A
 
VMatrix matrix_dRdPhi
 
Real last_proposal_density_ratio_
 
bool preserve_detailed_balance_
 
core::kinematics::MoveMapCOP movemap_
 
core::select::movemap::MoveMapFactoryCOP movemap_factory_
 
Vector dphi_
 
Real factorA_
 
Real factorB_
 
core::Size N_auto_all
 
core::Size N_auto_small
 
bool use_all_pivot_res_
 
bool auto_adjust_factorA_
 
bool fix_short_segment_
 
bool shrink_frag_ends_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::BBConRotMover::BBConRotMover ( )
protocols::simple_moves::BBConRotMover::~BBConRotMover ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::BBConRotMover::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References make_move(), and protocols::simple_moves::TR().

core::Real protocols::simple_moves::BBConRotMover::calc_jacobian_cartesians ( xyzVector const &  v6,
xyzVector const &  v7,
xyzVector const &  v8,
xyzVector const &  v9,
xyzVector const &  v10 
)
private
bool protocols::simple_moves::BBConRotMover::closure ( xyzVector r0,
xyzVector r1,
xyzVector r2,
xyzVector r3,
xyzVector r4,
xyzVector r5,
xyzVector r6,
xyzVector p1,
xyzVector p2,
xyzVector p3,
Real const  theta1_old,
Real const  theta2_old,
Real const  theta3_old,
Real const  theta4_old,
Real const  alpha1_old,
Real const  alpha2_old,
Real const  alpha3_old,
Real theta1,
Real theta2,
Real theta3,
Real theta4,
Real alpha1,
Real alpha2,
Real alpha3 
)
private
void protocols::simple_moves::BBConRotMover::factorA ( core::Real const  fA)
void protocols::simple_moves::BBConRotMover::factorB ( core::Real const  fB)
void protocols::simple_moves::BBConRotMover::factorC ( core::Real const  fC)
void protocols::simple_moves::BBConRotMover::get_A ( )
protected
bool protocols::simple_moves::BBConRotMover::get_determinant ( core::Real  a[5][5],
int  n,
core::Real det 
)
private
void protocols::simple_moves::BBConRotMover::get_G ( )
protected
core::Real protocols::simple_moves::BBConRotMover::get_L_move ( Pose segment)
protected
core::Real protocols::simple_moves::BBConRotMover::get_L_prime ( )
protected
std::string protocols::simple_moves::BBConRotMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::simple_moves::BBConRotMover::get_VdRdPhi ( Pose const &  segment)
protected
void protocols::simple_moves::BBConRotMover::get_xyz ( xyzVector const &  a,
xyzVector const &  b,
xyzVector const &  c,
xyzVector d,
Real  distance,
Real  theta,
Real  phi 
)
private

get xyz of d, given reference atoms a,b,c (a-b-c-d) and distance of c-d bond angle theta of d-c-b dihedral angle phi of d-c-b-a

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by closure().

bool protocols::simple_moves::BBConRotMover::make_move ( Pose pose)
protected

Member Data Documentation

Vector protocols::simple_moves::BBConRotMover::dphi
private

Referenced by get_L_move(), and get_L_prime().

Real protocols::simple_moves::BBConRotMover::factorA_
private

Referenced by BBConRotMover(), and get_A().

Real protocols::simple_moves::BBConRotMover::factorB_
private

Referenced by BBConRotMover(), and get_A().

Real protocols::simple_moves::BBConRotMover::factorC_
private
Vector protocols::simple_moves::BBConRotMover::oldphi
private

Referenced by get_L_move(), and make_move().


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