Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::docking::EllipsoidalRandomizationMover Class Reference

#include <EllipsoidalRandomizationMover.hh>

Public Member Functions

 EllipsoidalRandomizationMover ()
 Default constructor. More...
 EllipsoidalRandomizationMover (EllipsoidalRandomizationMover const &object_to_copy)
 Copy constructor. More...
 EllipsoidalRandomizationMover (core::Size, bool)
 Constructor with arguments. More...
EllipsoidalRandomizationMoveroperator= (EllipsoidalRandomizationMover const &object_to_copy)
 Assignment operator. More...
 ~EllipsoidalRandomizationMover ()
 Destructor. More...
void set_default ()
 Sets up the default values for the object including the movemap and minimization type. More...
void init_from_options ()
 Initializes data members from options. More...
void apply (core::pose::Pose &)
 Applies EllipsoidalRandomizationMover mover. More...
virtual std::string get_name () const
 Returns mover name. More...
virtual void show (std::ostream &output=std::cout) const
 Generates string representation of EllipsoidalRandomizationMover. More...
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
std::pair< numeric::xyzMatrix
< core::Real >, Vector
calculate_geometry (core::pose::Pose &)
 Defines geometry required for docking move. More...
numeric::xyzMatrix< core::Realcalculate_axes (core::pose::Pose &)
 Calculates ellipsoid axes from atomic coordinates. More...
Real single_beta_sample (double, double)
 Returns a sample from a beta distribution. More...
Vector point_on_ellipsoid (numeric::xyzMatrix< core::Real >)
 Selects a random point on ellipsoid surface. More...
Real recalculate_z_coordinate (Vector)
 Calculates 3rd coordinate of a point on ellipsoid surface given first 2 coordinates. More...
Vector normal_to_ellipsoid (Vector)
 Calculates normal vector to a point on ellipsoid. More...
numeric::xyzMatrix< core::Realget_rotation_matrix (Vector, Vector)
 Calculates a rotation matrix to superimpose source vector to target vector. More...
utility::vector1< core::Sizeget_partner_residue_start_stop (core::pose::Pose &, bool)
 Identifies first and last residues of a docking partner. More...
void set_foldtree (core::pose::Pose &)
 Sets pose fold tree based on -partners flag. More...
utility::vector1< boolget_interface_residues (core::pose::Pose &, core::Real)
 Identifies residues at interface of docking partners. More...
utility::vector1< Vectorcalculate_plane_axes (core::pose::Pose &)
 Calculates two vectors defining a plane at the docking interface. More...
Vector inward_normal_to_plane (utility::vector1< Vector >)
 Calculates normal vector from a plane at the docking interface. More...
void copy_data (EllipsoidalRandomizationMover object_to_copy_to, EllipsoidalRandomizationMover object_to_copy_from)
 Copies data members from one object to another. More...
void set_partners (std::string const &)
 Set the partners_ string. More...
Vector get_slide_axis () const
 Get the axis for sliding partners into contact. More...
Vector get_spin_center () const
 Get the point about which to spin the docking partner. More...
Vector get_c_alpha_centroid () const
Vector get_c_alpha_non_ellipsoid_centroid () const
core::Real get_a_axis () const
core::Real get_b_axis () const
core::Real get_c_axis () const
Vector get_random_point_on_ellipsoid () const
Vector get_normal_to_plane () const
- 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)
virtual void parse_my_tag (TagCOP tag, basic::datacache::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...
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

Private Attributes

Vector c_alpha_centroid_
Vector c_alpha_plane_centroid_
Vector c_alpha_non_ellipsoid_centroid_
Vector slide_axis_
core::Real a_axis_
core::Real b_axis_
core::Real c_axis_
Vector random_point_on_ellipsoid_
Vector normal_to_plane_
core::Size rb_jump_
bool ellipsoid_is_first_partner_
std::string partners_

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 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

This mover approximates one docking partner as an ellipsoid and docks the other partner along a random normal to said ellipsoid; sliding the partners into contact is necessary to complete this docking move.

Constructor & Destructor Documentation

protocols::docking::EllipsoidalRandomizationMover::EllipsoidalRandomizationMover ( )

Default constructor.

References init_from_options(), and set_default().

Referenced by clone(), and fresh_instance().

protocols::docking::EllipsoidalRandomizationMover::EllipsoidalRandomizationMover ( EllipsoidalRandomizationMover const &  object_to_copy)

Copy constructor.

References copy_data().

protocols::docking::EllipsoidalRandomizationMover::EllipsoidalRandomizationMover ( core::Size  rb_jump,
bool  ellipsoid_is_first_partner 

Constructor with arguments.

References ellipsoid_is_first_partner_, init_from_options(), rb_jump_, and set_default().

protocols::docking::EllipsoidalRandomizationMover::~EllipsoidalRandomizationMover ( )


Member Function Documentation

void protocols::docking::EllipsoidalRandomizationMover::apply ( core::pose::Pose pose)
numeric::xyzMatrix< Real > protocols::docking::EllipsoidalRandomizationMover::calculate_axes ( core::pose::Pose pose_in)
std::pair< numeric::xyzMatrix< core::Real >, Vector > protocols::docking::EllipsoidalRandomizationMover::calculate_geometry ( core::pose::Pose pose)
utility::vector1< Vector > protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes ( core::pose::Pose pose_in)
protocols::moves::MoverOP protocols::docking::EllipsoidalRandomizationMover::clone ( ) const

Return a clone of the Mover object.

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 EllipsoidalRandomizationMover().

void protocols::docking::EllipsoidalRandomizationMover::copy_data ( EllipsoidalRandomizationMover  object_to_copy_to,
EllipsoidalRandomizationMover  object_to_copy_from 
protocols::moves::MoverOP protocols::docking::EllipsoidalRandomizationMover::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

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 EllipsoidalRandomizationMover().

core::Real protocols::docking::EllipsoidalRandomizationMover::get_a_axis ( ) const

References a_axis_.

core::Real protocols::docking::EllipsoidalRandomizationMover::get_b_axis ( ) const

References b_axis_.

Vector protocols::docking::EllipsoidalRandomizationMover::get_c_alpha_centroid ( ) const

References c_alpha_centroid_.

Vector protocols::docking::EllipsoidalRandomizationMover::get_c_alpha_non_ellipsoid_centroid ( ) const
core::Real protocols::docking::EllipsoidalRandomizationMover::get_c_axis ( ) const

References c_axis_.

utility::vector1< bool > protocols::docking::EllipsoidalRandomizationMover::get_interface_residues ( core::pose::Pose pose_in,
core::Real  interface_distance_cutoff 
std::string protocols::docking::EllipsoidalRandomizationMover::get_name ( ) const

Returns mover name.

Implements protocols::moves::Mover.

Vector protocols::docking::EllipsoidalRandomizationMover::get_normal_to_plane ( ) const

References normal_to_plane_.

utility::vector1< core::Size > protocols::docking::EllipsoidalRandomizationMover::get_partner_residue_start_stop ( core::pose::Pose pose_in,
bool  first_partner 

Identifies first and last residues of a docking partner.

References partners_, core::pose::Pose::pdb_info(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by calculate_axes(), and calculate_plane_axes().

Vector protocols::docking::EllipsoidalRandomizationMover::get_random_point_on_ellipsoid ( ) const
numeric::xyzMatrix< core::Real > protocols::docking::EllipsoidalRandomizationMover::get_rotation_matrix ( Vector  target_vector,
Vector  source_vector 
Vector protocols::docking::EllipsoidalRandomizationMover::get_slide_axis ( ) const

Get the axis for sliding partners into contact.

References slide_axis_.

Referenced by protocols::docking::DockingInitialPerturbation::apply_body().

Vector protocols::docking::EllipsoidalRandomizationMover::get_spin_center ( ) const

Get the point about which to spin the docking partner.

References c_alpha_plane_centroid_.

Referenced by protocols::docking::DockingInitialPerturbation::apply_body().

void protocols::docking::EllipsoidalRandomizationMover::init_from_options ( )

Initializes data members from options.

References ellipsoid_is_first_partner_, option, set_partners(), and user.

Referenced by EllipsoidalRandomizationMover().

Vector protocols::docking::EllipsoidalRandomizationMover::inward_normal_to_plane ( utility::vector1< Vector two_plane_vectors)

Calculates normal vector from a plane at the docking interface.

References c_alpha_non_ellipsoid_centroid_, c_alpha_plane_centroid_, numeric::xyzVector< class >::length(), and numeric::xyzVector< class >::normalize_any().

Referenced by calculate_geometry().

Vector protocols::docking::EllipsoidalRandomizationMover::normal_to_ellipsoid ( Vector  ellipsoid_point)
EllipsoidalRandomizationMover & protocols::docking::EllipsoidalRandomizationMover::operator= ( EllipsoidalRandomizationMover const &  object_to_copy)

Assignment operator.

References copy_data(), and protocols::moves::Mover::operator=().

Vector protocols::docking::EllipsoidalRandomizationMover::point_on_ellipsoid ( numeric::xyzMatrix< core::Real axes)
Real protocols::docking::EllipsoidalRandomizationMover::recalculate_z_coordinate ( Vector  perturbed_ellipsoid_point)

Calculates 3rd coordinate of a point on ellipsoid surface given first 2 coordinates.

References a_axis_, b_axis_, c_axis_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by normal_to_ellipsoid().

void protocols::docking::EllipsoidalRandomizationMover::set_default ( )
void protocols::docking::EllipsoidalRandomizationMover::set_foldtree ( core::pose::Pose pose_in)

Sets pose fold tree based on -partners flag.

References partners_, and protocols::docking::setup_foldtree().

Referenced by get_interface_residues().

void protocols::docking::EllipsoidalRandomizationMover::set_partners ( std::string const &  partners)

Set the partners_ string.

References partners_.

Referenced by init_from_options().

void protocols::docking::EllipsoidalRandomizationMover::show ( std::ostream &  output = std::cout) const

Generates string representation of EllipsoidalRandomizationMover.

Reimplemented from protocols::moves::Mover.

References rb_jump_, protocols::moves::Mover::show(), and slide_axis_.

Referenced by protocols::docking::operator<<().

Real protocols::docking::EllipsoidalRandomizationMover::single_beta_sample ( double  alpha_param,
double  beta_param 

Returns a sample from a beta distribution.

Referenced by point_on_ellipsoid().

Member Data Documentation

core::Real protocols::docking::EllipsoidalRandomizationMover::a_axis_
core::Real protocols::docking::EllipsoidalRandomizationMover::b_axis_
Vector protocols::docking::EllipsoidalRandomizationMover::c_alpha_centroid_
Vector protocols::docking::EllipsoidalRandomizationMover::c_alpha_non_ellipsoid_centroid_
Vector protocols::docking::EllipsoidalRandomizationMover::c_alpha_plane_centroid_
core::Real protocols::docking::EllipsoidalRandomizationMover::c_axis_
bool protocols::docking::EllipsoidalRandomizationMover::ellipsoid_is_first_partner_
Vector protocols::docking::EllipsoidalRandomizationMover::normal_to_plane_
std::string protocols::docking::EllipsoidalRandomizationMover::partners_
Vector protocols::docking::EllipsoidalRandomizationMover::random_point_on_ellipsoid_
core::Size protocols::docking::EllipsoidalRandomizationMover::rb_jump_
Vector protocols::docking::EllipsoidalRandomizationMover::slide_axis_

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