Compute the center, major axis and minor axis of an ellipsoidal aqueous pore. More...
#include <AqueousPoreFinder.hh>
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 | update_mp_geo_pore (core::pose::Pose &pose, core::conformation::membrane::AqueousPoreParametersOP aqueous_pore) |
| void | show (std::ostream &output=std::cout) const override |
| Show the contents of the Mover. More... | |
| numeric::MathMatrix< core::Real > | get_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 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... | |
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
◆ piecewise_poly
|
private |
Constructor & Destructor Documentation
◆ AqueousPoreFinder() [1/2]
| protocols::membrane::AqueousPoreFinder::AqueousPoreFinder | ( | ) |
Default constructor.
Referenced by clone().
◆ AqueousPoreFinder() [2/2]
| protocols::membrane::AqueousPoreFinder::AqueousPoreFinder | ( | AqueousPoreFinder const & | src | ) |
Copy constructor (not needed unless you need deep copies)
Copy constructor.
◆ ~AqueousPoreFinder()
|
override |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ apply()
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overridevirtual |
Apply the mover.
Implements protocols::moves::Mover.
References core::conformation::Residue::aa(), core::chemical::aa_gly, core::conformation::Residue::atom(), protocols::frag_picker::CA, protocols::frag_picker::CB, core::pose::Pose::conformation(), construct_aqueous_pore(), distribute_coords_into_bins(), protocols::abinitio::filename(), find_max_z(), find_min_z(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Conformation::membrane_info(), core::pose::Pose::membrane_info(), core::pose::nres_protein(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), tolerance_, protocols::TR(), update_mp_geo_pore(), and core::conformation::Atom::xyz().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
References AqueousPoreFinder().
◆ construct_aqueous_pore()
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private |
TODO: need a sub-function to construct this long polynomal.
References generate_piecewise_cubic_poly_func(), and get_rotation_angle().
Referenced by apply().
◆ distribute_coords_into_bins()
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private |
References find_max_z(), and find_min_z().
Referenced by apply().
◆ find_max_z()
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private |
References protocols::simple_filters::coords().
Referenced by apply(), and distribute_coords_into_bins().
◆ find_min_z()
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private |
References protocols::simple_filters::coords().
Referenced by apply(), and distribute_coords_into_bins().
◆ fresh_instance()
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overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ generate_cubic_polynomial_func()
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private |
Referenced by generate_piecewise_cubic_poly_func().
◆ generate_piecewise_cubic_poly_func()
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private |
References generate_cubic_polynomial_func().
Referenced by construct_aqueous_pore().
◆ get_dummy_rotation_matrix()
| 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
◆ get_name()
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_rotation_angle()
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private |
Referenced by construct_aqueous_pore().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::membrane::AqueousPoreFinderCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References tolerance_.
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::membrane::AqueousPoreFinderCreator::provide_xml_schema().
◆ show()
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overridevirtual |
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by protocols::membrane::operator<<().
◆ update_mp_geo_pore()
| void protocols::membrane::AqueousPoreFinder::update_mp_geo_pore | ( | core::pose::Pose & | pose, |
| core::conformation::membrane::AqueousPoreParametersOP | aqueous_pore | ||
| ) |
References core::pose::Pose::conformation(), and core::conformation::Conformation::membrane_info().
Referenced by apply().
Member Data Documentation
◆ tolerance_
|
private |
Referenced by apply(), and parse_my_tag().
The documentation for this class was generated from the following files:
- src/protocols/membrane/AqueousPoreFinder.hh
- src/protocols/membrane/AqueousPoreFinder.cc
