protocols::docking::EllipsoidalRandomizationMover Class Reference

#include <EllipsoidalRandomizationMover.hh>

Inheritance diagram for protocols::docking::EllipsoidalRandomizationMover:

Public Member Functions
	EllipsoidalRandomizationMover ()
	Default constructor. More...
	EllipsoidalRandomizationMover (core::Size rb_jump, bool ellipsoid_is_first_partner, bool autofoldtree)
	Constructor with arguments. 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 &) override
	Applies EllipsoidalRandomizationMover mover. More...
std::string	get_name () const override
	Returns mover name. More...
void	show (std::ostream &output=std::cout) const override
	Generates string representation of EllipsoidalRandomizationMover. More...
protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...
std::pair< numeric::xyzMatrix < core::Real >, core::Vector >	calculate_geometry (core::pose::Pose &)
	Defines geometry required for docking move. More...
numeric::xyzMatrix< core::Real >	calculate_axes (core::pose::Pose &)
	Calculates ellipsoid axes from atomic coordinates. More...
core::Real	single_beta_sample (core::Real, core::Real)
	Returns a sample from a beta distribution. More...
core::Vector	point_on_ellipsoid (numeric::xyzMatrix< core::Real >)
	Selects a random point on ellipsoid surface. More...
core::Real	recalculate_z_coordinate (core::Vector)
	Calculates 3rd coordinate of a point on ellipsoid surface given first 2 coordinates. More...
core::Vector	normal_to_ellipsoid (core::Vector)
	Calculates normal vector to a point on ellipsoid. More...
numeric::xyzMatrix< core::Real >	get_rotation_matrix (core::Vector, core::Vector)
	Calculates a rotation matrix to superimpose source vector to target vector. More...
utility::vector1< core::Size >	get_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< bool >	get_interface_residues (core::pose::Pose &pose_in, core::Real interface_distence_cutoff, bool autofoldtree)
	Identifies residues at interface of docking partners. More...
utility::vector1< core::Vector >	calculate_plane_axes (core::pose::Pose &)
	Calculates two vectors defining a plane at the docking interface. More...
core::Vector	inward_normal_to_plane (utility::vector1< core::Vector >)
	Calculates normal vector from a plane at the docking interface. More...
void	set_partners (std::string const &)
	Set the partners_ string. More...
core::Vector	get_slide_axis () const
	Get the axis for sliding partners into contact. More...
core::Vector	get_spin_center () const
	Get the point about which to spin the docking partner. More...
core::Vector	get_nbr_atom_centroid () const
core::Vector	get_nbr_atom_non_ellipsoid_centroid () const
core::Real	get_a_axis () const
core::Real	get_b_axis () const
core::Real	get_c_axis () const
core::Vector	get_random_point_on_ellipsoid () const
core::Vector	get_normal_to_plane () const
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...
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
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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 core::Real	last_proposal_density_ratio ()
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 Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
core::Vector	nbr_atom_centroid_
core::Vector	nbr_atom_plane_centroid_
core::Vector	nbr_atom_non_ellipsoid_centroid_
core::Vector	slide_axis_
core::Real	a_axis_
core::Real	b_axis_
core::Real	c_axis_
core::Vector	random_point_on_ellipsoid_
core::Vector	normal_to_plane_
core::Size	rb_jump_
bool	ellipsoid_is_first_partner_
bool	autofoldtree_
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::string >	Strings
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().

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

Constructor with arguments.

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

Member Function Documentation

void protocols::docking::EllipsoidalRandomizationMover::apply ( core::pose::Pose &  pose )

overridevirtual

Applies EllipsoidalRandomizationMover mover.

Implements protocols::moves::Mover.

References protocols::rigid::RigidBodyTransMover::apply(), c_axis_, calculate_geometry(), core::pose::Pose::conformation(), core::pose::Pose::jump(), nbr_atom_plane_centroid_, rb_jump_, core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), slide_axis_, protocols::rigid::RigidBodyTransMover::step_size(), protocols::docking::TR(), protocols::rigid::RigidBodyTransMover::trans_axis(), and core::conformation::Conformation::upstream_jump_stub().

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

numeric::xyzMatrix< Real > protocols::docking::EllipsoidalRandomizationMover::calculate_axes

(

core::pose::Pose &

pose_in

)

Calculates ellipsoid axes from atomic coordinates.

References core::conformation::Residue::atom(), ellipsoid_is_first_partner_, get_partner_residue_start_stop(), core::conformation::Residue::is_protein(), nbr_atom_centroid_, core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by calculate_geometry().

std::pair< numeric::xyzMatrix< core::Real >, Vector > protocols::docking::EllipsoidalRandomizationMover::calculate_geometry

(

core::pose::Pose &

pose

)

Defines geometry required for docking move.

References calculate_axes(), calculate_plane_axes(), ellipsoid_is_first_partner_, get_rotation_matrix(), inward_normal_to_plane(), nbr_atom_centroid_, nbr_atom_plane_centroid_, normal_to_ellipsoid(), normal_to_plane_, point_on_ellipsoid(), random_point_on_ellipsoid_, slide_axis_, and protocols::docking::TR().

Referenced by apply().

utility::vector1< Vector > protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes

(

core::pose::Pose &

pose_in

)

Calculates two vectors defining a plane at the docking interface.

References core::conformation::Residue::atom(), autofoldtree_, ellipsoid_is_first_partner_, get_interface_residues(), get_partner_residue_start_stop(), core::conformation::Residue::is_protein(), nbr_atom_non_ellipsoid_centroid_, nbr_atom_plane_centroid_, core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), protocols::docking::TR(), and core::conformation::Atom::xyz().

Referenced by calculate_geometry().

protocols::moves::MoverOP protocols::docking::EllipsoidalRandomizationMover::clone ( ) const

overridevirtual

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.

protocols::moves::MoverOP protocols::docking::EllipsoidalRandomizationMover::fresh_instance ( ) const

overridevirtual

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.

core::Real protocols::docking::EllipsoidalRandomizationMover::get_a_axis

(

)

const

References a_axis_.

core::Real protocols::docking::EllipsoidalRandomizationMover::get_b_axis

(

)

const

References b_axis_.

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_distence_cutoff,
		bool	autofoldtree
	)

Identifies residues at interface of docking partners.

References protocols::scoring::Interface::calculate(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), protocols::scoring::Interface::is_interface(), core::kinematics::FoldTree::partition_by_jump(), rb_jump_, set_foldtree(), core::pose::Pose::size(), and core::pose::Pose::update_residue_neighbors().

Referenced by calculate_plane_axes().

std::string protocols::docking::EllipsoidalRandomizationMover::get_name ( ) const

overridevirtual

Returns mover name.

Implements protocols::moves::Mover.

Vector protocols::docking::EllipsoidalRandomizationMover::get_nbr_atom_centroid

(

)

const

References nbr_atom_centroid_.

Vector protocols::docking::EllipsoidalRandomizationMover::get_nbr_atom_non_ellipsoid_centroid

(

)

const

References nbr_atom_non_ellipsoid_centroid_.

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(), and core::pose::Pose::size().

Referenced by calculate_axes(), and calculate_plane_axes().

Vector protocols::docking::EllipsoidalRandomizationMover::get_random_point_on_ellipsoid

(

)

const

References random_point_on_ellipsoid_.

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

Calculates a rotation matrix to superimpose source vector to target vector.

Referenced by calculate_geometry().

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 nbr_atom_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_, and set_partners().

Referenced by EllipsoidalRandomizationMover().

Vector protocols::docking::EllipsoidalRandomizationMover::inward_normal_to_plane

(

utility::vector1< core::Vector >

two_plane_vectors

)

Calculates normal vector from a plane at the docking interface.

References nbr_atom_non_ellipsoid_centroid_, and nbr_atom_plane_centroid_.

Referenced by calculate_geometry().

Vector protocols::docking::EllipsoidalRandomizationMover::normal_to_ellipsoid

(

core::Vector

ellipsoid_point

)

Calculates normal vector to a point on ellipsoid.

References recalculate_z_coordinate().

Referenced by calculate_geometry().

Vector protocols::docking::EllipsoidalRandomizationMover::point_on_ellipsoid

(

numeric::xyzMatrix< core::Real >

axes

)

Selects a random point on ellipsoid surface.

References a_axis_, b_axis_, c_axis_, and single_beta_sample().

Referenced by calculate_geometry().

Real protocols::docking::EllipsoidalRandomizationMover::recalculate_z_coordinate

(

core::Vector

perturbed_ellipsoid_point

)

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

References a_axis_, b_axis_, and c_axis_.

Referenced by normal_to_ellipsoid().

void protocols::docking::EllipsoidalRandomizationMover::set_default

(

)

Sets up the default values for the object including the movemap and minimization type.

References a_axis_, autofoldtree_, b_axis_, c_axis_, ellipsoid_is_first_partner_, nbr_atom_centroid_, nbr_atom_non_ellipsoid_centroid_, nbr_atom_plane_centroid_, normal_to_plane_, partners_, random_point_on_ellipsoid_, rb_jump_, and slide_axis_.

Referenced by EllipsoidalRandomizationMover().

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

overridevirtual

Generates string representation of EllipsoidalRandomizationMover.

Reimplemented from protocols::moves::Mover.

References rb_jump_, and slide_axis_.

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

Real protocols::docking::EllipsoidalRandomizationMover::single_beta_sample	(	core::Real	alpha_param,
		core::Real	beta_param
	)

Returns a sample from a beta distribution.

Referenced by point_on_ellipsoid().

Member Data Documentation

core::Real protocols::docking::EllipsoidalRandomizationMover::a_axis_

private

Referenced by get_a_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().

bool protocols::docking::EllipsoidalRandomizationMover::autofoldtree_

private

Referenced by calculate_plane_axes(), EllipsoidalRandomizationMover(), and set_default().

core::Real protocols::docking::EllipsoidalRandomizationMover::b_axis_

private

Referenced by get_b_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().

core::Real protocols::docking::EllipsoidalRandomizationMover::c_axis_

private

Referenced by apply(), get_c_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().

bool protocols::docking::EllipsoidalRandomizationMover::ellipsoid_is_first_partner_

private

Referenced by calculate_axes(), calculate_geometry(), calculate_plane_axes(), EllipsoidalRandomizationMover(), init_from_options(), and set_default().

core::Vector protocols::docking::EllipsoidalRandomizationMover::nbr_atom_centroid_

private

Referenced by calculate_axes(), calculate_geometry(), get_nbr_atom_centroid(), and set_default().

core::Vector protocols::docking::EllipsoidalRandomizationMover::nbr_atom_non_ellipsoid_centroid_

private

Referenced by calculate_plane_axes(), get_nbr_atom_non_ellipsoid_centroid(), inward_normal_to_plane(), and set_default().

core::Vector protocols::docking::EllipsoidalRandomizationMover::nbr_atom_plane_centroid_

private

Referenced by apply(), calculate_geometry(), calculate_plane_axes(), get_spin_center(), inward_normal_to_plane(), and set_default().

core::Vector protocols::docking::EllipsoidalRandomizationMover::normal_to_plane_

private

Referenced by calculate_geometry(), get_normal_to_plane(), and set_default().

std::string protocols::docking::EllipsoidalRandomizationMover::partners_

private

Referenced by get_partner_residue_start_stop(), set_default(), set_foldtree(), and set_partners().

core::Vector protocols::docking::EllipsoidalRandomizationMover::random_point_on_ellipsoid_

private

Referenced by calculate_geometry(), get_random_point_on_ellipsoid(), and set_default().

core::Size protocols::docking::EllipsoidalRandomizationMover::rb_jump_

private

Referenced by apply(), EllipsoidalRandomizationMover(), get_interface_residues(), set_default(), and show().

core::Vector protocols::docking::EllipsoidalRandomizationMover::slide_axis_

private

Referenced by apply(), calculate_geometry(), get_slide_axis(), set_default(), and show().

---

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

• src/protocols/docking/EllipsoidalRandomizationMover.hh
• src/protocols/docking/EllipsoidalRandomizationMover.cc