EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions
EMAN::IcosahedralSym Class Reference

An encapsulation of icosahedral symmetry Doctor Phil has this to say about icosahedral symmetry: "Each Platonic Solid has 2E symmetry elements. More...

#include <symmetry.h>

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List of all members.

Public Member Functions

 IcosahedralSym ()
 Constructor calls PlatonicSym::init.
virtual ~IcosahedralSym ()
virtual string get_name () const
 Return IcosahedralSym::NAME.
virtual string get_desc () const
 Get a description.
virtual int get_max_csym () const
 Gets the maximum symmetry of this object.
virtual Transform get_sym (const int n) const
 This function provides access to the unique rotational symmetries of an icosahedron.
virtual int get_nsym () const
 Gets the total number of unique rotational symmetry operations associated with this symmetry For icosahedral symmetry, this is 60.
virtual float get_az_alignment_offset () const
 Get the azimuth alignment offset required to ensure that orientations align correctly with symmetric axes of the icosahedron.

Static Public Member Functions

static Symmetry3DNEW ()
 Factory support function NEW.

Static Public Attributes

static const string NAME = "icos"
 The name of this class - used to access it from factories etc. Should be "icos".

Private Member Functions

 IcosahedralSym (const IcosahedralSym &)
 Disallow copy construction.
IcosahedralSymoperator= (const IcosahedralSym &)
 Disallow assignment.

Detailed Description

An encapsulation of icosahedral symmetry Doctor Phil has this to say about icosahedral symmetry: "Each Platonic Solid has 2E symmetry elements.

An icosahedron has m=5, n=3, F=20 E=30=nF/2, V=12=nF/m,since vertices shared by 5 triangles It is composed of 20 triangles. E=3*20/2 A dodecahedron has m=3, n=5 F=12 E=30 V=20 It is composed of 12 pentagons. E=5*12/2; V= 5*12/3, since vertices shared by 3 pentagons"

Author:
David Woolford (based on previous work by Phil Baldwin and Steve Ludtke)
Date:
Feb 2008

Definition at line 855 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::IcosahedralSym::IcosahedralSym ( ) [inline]

Constructor calls PlatonicSym::init.

Definition at line 860 of file symmetry.h.

References EMAN::PlatonicSym::init().

Referenced by NEW().

{init(); }
virtual EMAN::IcosahedralSym::~IcosahedralSym ( ) [inline, virtual]

Definition at line 861 of file symmetry.h.

{ }
EMAN::IcosahedralSym::IcosahedralSym ( const IcosahedralSym ) [private]

Disallow copy construction.


Member Function Documentation

float IcosahedralSym::get_az_alignment_offset ( ) const [virtual]

Get the azimuth alignment offset required to ensure that orientations align correctly with symmetric axes of the icosahedron.

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 1785 of file symmetry.cpp.

Referenced by get_sym().

{ return 234.0; } // This offset positions a 3 fold axis on the positive x axis
virtual string EMAN::IcosahedralSym::get_desc ( ) const [inline, virtual]

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 879 of file symmetry.h.

{ return "Icosahedral symmetry support"; }
virtual int EMAN::IcosahedralSym::get_max_csym ( ) const [inline, virtual]

Gets the maximum symmetry of this object.

This is used by OrientationGenerators, and is probably not something a general user would utilize.

Returns:
for icosahedral symmetry, this number is 5

Implements EMAN::Symmetry3D.

Definition at line 885 of file symmetry.h.

{ return 5; }// 5 is the greatest symmetry
virtual string EMAN::IcosahedralSym::get_name ( ) const [inline, virtual]

Return IcosahedralSym::NAME.

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 874 of file symmetry.h.

References NAME.

{ return NAME; };
virtual int EMAN::IcosahedralSym::get_nsym ( ) const [inline, virtual]

Gets the total number of unique rotational symmetry operations associated with this symmetry For icosahedral symmetry, this is 60.

Returns:
60

Implements EMAN::Symmetry3D.

Definition at line 899 of file symmetry.h.

{ return 60; };
Transform IcosahedralSym::get_sym ( const int  n) const [virtual]

This function provides access to the unique rotational symmetries of an icosahedron.

We have placed the icosahedral symmetry group with a face along the z-axis. In all, there are 60 (accessed by get_nysm) unique rotational symmetric operations for the icosahedron.

Parameters:
nthe symmetric operation number.
Returns:
a transform containing the correct rotational symmetry operation.

Implements EMAN::Symmetry3D.

Definition at line 1787 of file symmetry.cpp.

References get_az_alignment_offset().

{
        // These rotations courtesy of Phil Baldwin
        static double  lvl0=0.; //  there is one pentagon on top; five-fold along z
        static double  lvl1= 63.4349; // that is atan(2)  // there are 5 pentagons with centers at this height (angle)
        static double  lvl2=116.5651; //that is 180-lvl1  // there are 5 pentagons with centers at this height (angle)
        static double lvl3=180.0;

        static double ICOS[180] = { // This is with a pentagon normal to z
                0,lvl0,0,    0,lvl0,288,   0,lvl0,216,   0,lvl0,144,  0,lvl0,72,
  0,lvl1,36,   0,lvl1,324,   0,lvl1,252,   0,lvl1,180,  0,lvl1,108,
  72,lvl1,36,  72,lvl1,324,  72,lvl1,252,  72,lvl1,180,  72,lvl1,108,
  144,lvl1,36, 144,lvl1,324, 144,lvl1,252, 144,lvl1,180, 144,lvl1,108,
  216,lvl1,36, 216,lvl1,324, 216,lvl1,252, 216,lvl1,180, 216,lvl1,108,
  288,lvl1,36, 288,lvl1,324, 288,lvl1,252, 288,lvl1,180, 288,lvl1,108,
  36,lvl2,0,   36,lvl2,288,  36,lvl2,216,  36,lvl2,144,  36,lvl2,72,
  108,lvl2,0,  108,lvl2,288, 108,lvl2,216, 108,lvl2,144, 108,lvl2,72,
  180,lvl2,0,  180,lvl2,288, 180,lvl2,216, 180,lvl2,144, 180,lvl2,72,
  252,lvl2,0,  252,lvl2,288, 252,lvl2,216, 252,lvl2,144, 252,lvl2,72,
  324,lvl2,0,  324,lvl2,288, 324,lvl2,216, 324,lvl2,144, 324,lvl2,72,
  0,lvl3,0,    0,lvl3,288,   0,lvl3,216,   0,lvl3,144,   0,lvl3,72
        };

        int idx = n % 60;
        Dict d("type","eman");
//      Transform3D ret;
        if (get_az_alignment_offset() == 234.0) {
                d["az"] =(float)ICOS[idx * 3 ]+90;
                d["alt"] = (float)ICOS[idx * 3 + 1];
                d["phi"] = (float)ICOS[idx * 3 + 2]-90;
//              ret.set_rotation((float)ICOS[idx * 3 ]+90,(float)ICOS[idx * 3 + 1], (float)ICOS[idx * 3 + 2]-90);
        }
        else {
                d["az"] =(float)(float)ICOS[idx * 3 ];
                d["alt"] = (float)ICOS[idx * 3 + 1];
                d["phi"] = (float)ICOS[idx * 3 + 2];
//              ret.set_rotation((float)ICOS[idx * 3 ],(float)ICOS[idx * 3 + 1], (float)ICOS[idx * 3 + 2]);
        }

//      ret.set_rotation((float)ICOS[idx * 3 ],(float)ICOS[idx * 3 + 1], (float)ICOS[idx * 3 + 2]);
//      if ( get_az_alignment_offset() != 0 ) {
//              Transform3D t(get_az_alignment_offset(),0,0);
//              ret = t*ret;
//      }
        return Transform(d);

}
static Symmetry3D* EMAN::IcosahedralSym::NEW ( ) [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 866 of file symmetry.h.

References IcosahedralSym().

                {
                        return new IcosahedralSym();
                }
IcosahedralSym& EMAN::IcosahedralSym::operator= ( const IcosahedralSym ) [private]

Disallow assignment.


Member Data Documentation

const string IcosahedralSym::NAME = "icos" [static]

The name of this class - used to access it from factories etc. Should be "icos".

Definition at line 910 of file symmetry.h.

Referenced by EMAN::PlatonicSym::get_delimiters(), and get_name().


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