EMAN2
|
An encapsulation of tetrahedral symmetry Doctor Phil has this to say about tetrahedral symmetry: " Each Platonic Solid has 2E symmetry elements. More...
#include <symmetry.h>
Public Member Functions | |
TetrahedralSym () | |
Constructor calls PlatonicSym::init. More... | |
virtual | ~TetrahedralSym () |
virtual string | get_name () const |
Return TetrahedralSym::NAME. More... | |
virtual string | get_desc () const |
Get a description. More... | |
virtual int | get_max_csym () const |
Gets the maximum symmetry of this object. More... | |
virtual Transform | get_sym (const int n) const |
This function provides access to the unique rotational symmetries of a tetrahedron. More... | |
virtual bool | is_in_asym_unit (const float &altitude, const float &azimuth, const bool inc_mirror) const |
In tetrahedral symmetry special consideration must be taken when generating orientations in the asymmetric unit. More... | |
virtual int | get_nsym () const |
Gets the total number of unique roational symmetry operations associated with this symmetry For tetrahedral symmetry symmetry, this is 12. More... | |
virtual float | get_az_alignment_offset () const |
Get the azimuth alignment offset required to ensure that orientations align correctly with symmetric axes of the tetrahedron. More... | |
virtual vector< Vec3f > | get_asym_unit_points (bool inc_mirror=false) const |
virtual bool | is_tet_sym () const |
A function that is used to determine if this is the tetrahedral symmetry object. More... | |
Public Member Functions inherited from EMAN::PlatonicSym | |
PlatonicSym () | |
virtual | ~PlatonicSym () |
virtual TypeDict | get_param_types () const |
Get a dictionary containing the permissable parameters of this class Platonic symmetries actually have no parameters. More... | |
virtual Dict | get_delimiters (const bool inc_mirror=false) const |
Returns the range of altitude and azimuth angles which encompass the asymmetric unit of the Platonic symmetry (and more). More... | |
virtual bool | is_platonic_sym () const |
Determines whether or not this Symmetry3D is the platonic type - returns true. More... | |
Public Member Functions inherited from EMAN::Symmetry3D | |
Symmetry3D () | |
virtual | ~Symmetry3D () |
virtual bool | is_h_sym () const |
A function that is used to determine if this is a Helical symmetry object This function is only virtually overidden by the HSym symmetry, which returns true, not false. More... | |
virtual bool | is_c_sym () const |
A function that is used to determine if this is a c symmetry object This function is only virtually overidden by the CSym object, which returns true. More... | |
virtual bool | is_d_sym () const |
A function that is used to determine if this is a d symmetry object This function is only virtually overidden by the DSym object, which returns true. More... | |
vector< Transform > | gen_orientations (const string &generatorname="eman", const Dict &parms=Dict()) |
Ask the Symmetry3D object to generate a set of orientations in its asymmetric unit using an OrientationGenerator constructed from the given parameters (using a Factory). More... | |
virtual Transform | reduce (const Transform &t3d, int n=0) const |
A function that will reduce an orientation, as characterized by Euler anges, into a specific asymmetric unit. More... | |
virtual int | in_which_asym_unit (const Transform &t3d) const |
A function that will determine in which asymmetric unit a given orientation resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function. More... | |
virtual int | point_in_which_asym_unit (const Vec3f &v) const |
A function that will determine in which asymmetric unit a given vector resides The asymmetric unit 'number' will depend entirely on the order in which different symmetry operations are return by the Symmetry3D::get_sym function The vector is a point. More... | |
virtual vector< Transform > | get_touching_au_transforms (bool inc_mirror=true) const |
Gets a vector of Transform objects that define the set of asymmetric units that touch the default asymmetric unit. More... | |
virtual vector< Transform > | get_syms () const |
Public Member Functions inherited from EMAN::FactoryBase | |
FactoryBase () | |
virtual | ~FactoryBase () |
Dict | get_params () const |
get a copy of the parameters of this class More... | |
void | set_params (const Dict &new_params) |
Set new parameters. More... | |
void | set_param (const string key, const EMObject val) |
void | insert_params (const Dict &new_params) |
Insert parameters. More... | |
Dict | copy_relevant_params (const FactoryBase *const that) const |
Static Public Member Functions | |
static Symmetry3D * | NEW () |
Factory support function NEW. More... | |
Static Public Member Functions inherited from EMAN::Symmetry3D | |
static vector< Transform > | get_symmetries (const string &symmetry) |
Static Public Attributes | |
static const string | NAME = "tet" |
The name of this class - used to access it from factories etc. Should be "tet". More... | |
Private Member Functions | |
TetrahedralSym (const TetrahedralSym &) | |
Disallow copy construction. More... | |
TetrahedralSym & | operator= (const TetrahedralSym &) |
Disallow assignment. More... | |
Additional Inherited Members | |
Public Types inherited from EMAN::Symmetry3D | |
typedef vector< vector< Vec3f > >::const_iterator | cit |
typedef vector< vector< Vec3f > >::iterator | ncit |
Protected Member Functions inherited from EMAN::PlatonicSym | |
void | init () |
Init - Called to initialize platonic_params, should be called in the constructor of all Platonic solids that derive from this. More... | |
float | platonic_alt_lower_bound (const float &azimuth, const float &alpha) const |
Returns the lower bound of the asymmetric unit, as dependent on azimuth, and on alpha - alpha is alt_max for icos and oct, but may be alt_max/2.0 for tet depending on mirror symmetry etc. More... | |
virtual vector< vector< Vec3f > > | get_asym_unit_triangles (bool inc_mirror) const |
Get triangles that precisely occlude the projection area of the default asymmetric unit. More... | |
Protected Member Functions inherited from EMAN::Symmetry3D | |
void | cache_au_planes () const |
Establish the asymmetric unit planes cache. More... | |
void | delete_au_planes () |
Clear the asymmetric unit planes cache. More... | |
Protected Attributes inherited from EMAN::PlatonicSym | |
Dict | platonic_params |
A dictionary that stores important angles, in radians. More... | |
Protected Attributes inherited from EMAN::Symmetry3D | |
float ** | cached_au_planes |
The asymmetric unit planes are cached to provide a great speed up the point_in_which_asym_unit function, which is called by reduce and by in_which_asym_unit. More... | |
int | cache_size |
Have to remember the cache size. More... | |
int | num_triangles |
This is stores the number of triangles returned by get_asym_unit_triangles(true) More... | |
vector< vector< Vec3f > > | au_sym_triangles |
This cache is of size cache_size. More... | |
Protected Attributes inherited from EMAN::FactoryBase | |
Dict | params |
This is the dictionary the stores the parameters of the object. More... | |
An encapsulation of tetrahedral symmetry Doctor Phil has this to say about tetrahedral symmetry: " Each Platonic Solid has 2E symmetry elements.
The tetrahedron has n=m=3; F=4, E=6=nF/2, V=4=nF/m. It is composed of four triangles."
Definition at line 675 of file symmetry.h.
|
inline |
Constructor calls PlatonicSym::init.
Definition at line 680 of file symmetry.h.
References EMAN::PlatonicSym::init().
Referenced by NEW().
|
inlinevirtual |
Definition at line 681 of file symmetry.h.
|
private |
Disallow copy construction.
|
virtual |
inc_mirror | whether or not to include the mirror portion of the asymmetric unit |
Reimplemented from EMAN::PlatonicSym.
Definition at line 2031 of file symmetry.cpp.
References get_az_alignment_offset(), EMAN::Vec3< Type >::normalize(), and EMAN::PlatonicSym::platonic_params.
|
virtual |
Get the azimuth alignment offset required to ensure that orientations align correctly with symmetric axes of the tetrahedron.
This offset is directly related to the way the symmetric operations are generated by get_sym. All orientations generated as a result of using the delimiters supplied by this class should by offset by this azimuth to ensure proper alignment with tetrahedral objects in EMAN2
Reimplemented from EMAN::Symmetry3D.
Definition at line 1977 of file symmetry.cpp.
Referenced by get_asym_unit_points().
|
inlinevirtual |
Get a description.
Implements EMAN::FactoryBase.
Definition at line 700 of file symmetry.h.
|
inlinevirtual |
Gets the maximum symmetry of this object.
This is used by OrientationGenerators, and is probably not something a general user would utilize.
Implements EMAN::Symmetry3D.
Definition at line 706 of file symmetry.h.
|
inlinevirtual |
Return TetrahedralSym::NAME.
Implements EMAN::FactoryBase.
Definition at line 694 of file symmetry.h.
References NAME.
|
inlinevirtual |
Gets the total number of unique roational symmetry operations associated with this symmetry For tetrahedral symmetry symmetry, this is 12.
Implements EMAN::Symmetry3D.
Definition at line 736 of file symmetry.h.
|
virtual |
This function provides access to the unique rotational symmetries of a tetrahedron.
In this implementation, the tetrahedral symmetry group has a face along the z-axis. In all, there are 12 (accessed by get_nysm) unique rotational symmetric operations for the tetrahedron. In the terminology defined Append A (titled Symmetry Elements) in the manuscript Baldwin and Penczek, 2007. The Transform Class in SPARX and EMAN2. JSB 157(250-261), Doctor Phil has this to say: "B^3=A^3=1; BABA=1; implies A^2=BAB, ABA=B^2 , AB^2A = B^2AB^2 and 12 words with at most a single A 1 B BB A BA AB BBA BAB ABB BBAB BABB BBABB at most one A is necessary"
n | the symmetric operation number |
Implements EMAN::Symmetry3D.
Definition at line 2006 of file symmetry.cpp.
References EMAN::EMConsts::rad2deg.
|
virtual |
In tetrahedral symmetry special consideration must be taken when generating orientations in the asymmetric unit.
This function is a specialization of the functionality in PlatonicSym::is_in_asym_unit
altitude | the EMAN style altitude of the 3D orientation in degrees |
azimuth | the EMAN style azimuth of the 3D orientation in degrees |
inc_mirror | whether or not to include orientations if they are in the mirror portion of the asymmetric unit |
Reimplemented from EMAN::PlatonicSym.
Definition at line 1979 of file symmetry.cpp.
References EMAN::EMConsts::deg2rad, EMAN::PlatonicSym::get_delimiters(), EMAN::Util::get_min(), EMAN::PlatonicSym::platonic_alt_lower_bound(), and EMAN::PlatonicSym::platonic_params.
|
inlinevirtual |
A function that is used to determine if this is the tetrahedral symmetry object.
Reimplemented from EMAN::Symmetry3D.
Definition at line 758 of file symmetry.h.
|
inlinestatic |
Factory support function NEW.
Definition at line 686 of file symmetry.h.
References TetrahedralSym().
|
private |
Disallow assignment.
|
static |
The name of this class - used to access it from factories etc. Should be "tet".
Definition at line 747 of file symmetry.h.
Referenced by get_name().