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protocols::membrane::AqueousPoreFinder Class Reference

Compute the center, major axis and minor axis of an ellipsoidal aqueous pore. More...

#include <AqueousPoreFinder.hh>

Inheritance diagram for protocols::membrane::AqueousPoreFinder:
Inheritance graph
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Public Member Functions

 AqueousPoreFinder ()
 Default constructor. More...
 
 AqueousPoreFinder (AqueousPoreFinder const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~AqueousPoreFinder () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Apply the mover. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
numeric::MathMatrix< core::Realget_dummy_rotation_matrix () const
 Return a rotation matrix that results in no rotation. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
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 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 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...
 

Static Public Member Functions

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...
 

Private Types

typedef utility::vector1
< numeric::CubicPolynomial > 
piecewise_poly
 

Private Member Functions

core::Real find_max_z (utility::vector1< numeric::xyzVector< core::Real > > coords) const
 
core::Real find_min_z (utility::vector1< numeric::xyzVector< core::Real > > coords) const
 
core::Real get_rotation_angle (numeric::linear_algebra::EllipseParametersOP ellipse) const
 
utility::vector1
< numeric::CubicPolynomial > 
generate_piecewise_cubic_poly_func (utility::vector1< core::Real > ellipse_locations, utility::vector1< core::Real > ellipse_parameters, core::Real const min_value, core::Real const max_value) const
 
numeric::CubicPolynomial generate_cubic_polynomial_func (core::Real const start_coord, core::Real const start_value, core::Real const start_deriv, core::Real const end_coord, core::Real const end_value, core::Real const end_deriv) const
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
distribute_coords_into_bins (utility::vector1< numeric::xyzVector< core::Real > > aqueous_coords, core::Real const binsize) const
 
core::conformation::membrane::AqueousPoreParametersOP construct_aqueous_pore (core::Real const z_axis_buffer, core::Real const ellipse_radius_buffer, utility::vector1< core::Real > ellipse_locations, utility::vector1< numeric::linear_algebra::EllipseParametersOP > ellipse_parameters) const
 TODO: need a sub-function to construct this long polynomal. More...
 

Private Attributes

core::Real tolerance_
 

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
 
- 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

Compute the center, major axis and minor axis of an ellipsoidal aqueous pore.

Member Typedef Documentation

typedef utility::vector1< numeric::CubicPolynomial > protocols::membrane::AqueousPoreFinder::piecewise_poly
private

Constructor & Destructor Documentation

protocols::membrane::AqueousPoreFinder::AqueousPoreFinder ( )

Default constructor.

Referenced by clone().

protocols::membrane::AqueousPoreFinder::AqueousPoreFinder ( AqueousPoreFinder const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::membrane::AqueousPoreFinder::~AqueousPoreFinder ( )
override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::membrane::AqueousPoreFinder::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::membrane::AqueousPoreFinder::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References AqueousPoreFinder().

core::conformation::membrane::AqueousPoreParametersOP protocols::membrane::AqueousPoreFinder::construct_aqueous_pore ( core::Real const  z_axis_buffer,
core::Real const  ellipse_radius_buffer,
utility::vector1< core::Real ellipse_locations,
utility::vector1< numeric::linear_algebra::EllipseParametersOP >  ellipse_parameters 
) const
private

TODO: need a sub-function to construct this long polynomal.

References generate_piecewise_cubic_poly_func(), and get_rotation_angle().

Referenced by apply().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > protocols::membrane::AqueousPoreFinder::distribute_coords_into_bins ( utility::vector1< numeric::xyzVector< core::Real > >  aqueous_coords,
core::Real const  binsize 
) const
private

References find_max_z(), and find_min_z().

Referenced by apply().

core::Real protocols::membrane::AqueousPoreFinder::find_max_z ( utility::vector1< numeric::xyzVector< core::Real > >  coords) const
private
core::Real protocols::membrane::AqueousPoreFinder::find_min_z ( utility::vector1< numeric::xyzVector< core::Real > >  coords) const
private
protocols::moves::MoverOP protocols::membrane::AqueousPoreFinder::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

numeric::CubicPolynomial protocols::membrane::AqueousPoreFinder::generate_cubic_polynomial_func ( core::Real const  start_coord,
core::Real const  start_value,
core::Real const  start_deriv,
core::Real const  end_coord,
core::Real const  end_value,
core::Real const  end_deriv 
) const
private
utility::vector1< numeric::CubicPolynomial > protocols::membrane::AqueousPoreFinder::generate_piecewise_cubic_poly_func ( utility::vector1< core::Real ellipse_locations,
utility::vector1< core::Real ellipse_parameters,
core::Real const  min_value,
core::Real const  max_value 
) const
private
numeric::MathMatrix< core::Real > protocols::membrane::AqueousPoreFinder::get_dummy_rotation_matrix ( ) const

Return a rotation matrix that results in no rotation.

: Return a rotation matrix that results in no rotation

std::string protocols::membrane::AqueousPoreFinder::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::membrane::AqueousPoreFinder::get_rotation_angle ( numeric::linear_algebra::EllipseParametersOP  ellipse) const
private

Referenced by construct_aqueous_pore().

std::string protocols::membrane::AqueousPoreFinder::mover_name ( )
static
void protocols::membrane::AqueousPoreFinder::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References tolerance_.

void protocols::membrane::AqueousPoreFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::membrane::AqueousPoreFinder::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

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

Member Data Documentation

core::Real protocols::membrane::AqueousPoreFinder::tolerance_
private

Referenced by apply(), and parse_my_tag().


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