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Rosetta
2020.50
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#include <EllipsoidalRandomizationMover.hh>
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 |
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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... | |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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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... | |
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.
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().
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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().
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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.
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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().
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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 | ) |
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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().
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Referenced by get_a_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().
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Referenced by calculate_plane_axes(), EllipsoidalRandomizationMover(), and set_default().
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Referenced by get_b_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().
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Referenced by apply(), get_c_axis(), point_on_ellipsoid(), recalculate_z_coordinate(), and set_default().
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Referenced by calculate_axes(), calculate_geometry(), get_nbr_atom_centroid(), and set_default().
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Referenced by calculate_plane_axes(), get_nbr_atom_non_ellipsoid_centroid(), inward_normal_to_plane(), and set_default().
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Referenced by apply(), calculate_geometry(), calculate_plane_axes(), get_spin_center(), inward_normal_to_plane(), and set_default().
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Referenced by calculate_geometry(), get_normal_to_plane(), and set_default().
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Referenced by get_partner_residue_start_stop(), set_default(), set_foldtree(), and set_partners().
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Referenced by calculate_geometry(), get_random_point_on_ellipsoid(), and set_default().
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Referenced by apply(), EllipsoidalRandomizationMover(), get_interface_residues(), set_default(), and show().
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Referenced by apply(), calculate_geometry(), get_slide_axis(), set_default(), and show().