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

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>

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List of all members.

Public Member Functions

 TetrahedralSym ()
 Constructor calls PlatonicSym::init.
virtual ~TetrahedralSym ()
virtual string get_name () const
 Return TetrahedralSym::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 a tetrahedron.
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.
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.
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.
virtual vector< Vec3fget_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.

Static Public Member Functions

static Symmetry3DNEW ()
 Factory support function NEW.

Static Public Attributes

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

Private Member Functions

 TetrahedralSym (const TetrahedralSym &)
 Disallow copy construction.
TetrahedralSymoperator= (const TetrahedralSym &)
 Disallow assignment.

Detailed Description

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."

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

Definition at line 675 of file symmetry.h.


Constructor & Destructor Documentation

EMAN::TetrahedralSym::TetrahedralSym ( ) [inline]

Constructor calls PlatonicSym::init.

Definition at line 680 of file symmetry.h.

References EMAN::PlatonicSym::init().

Referenced by NEW().

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

Definition at line 681 of file symmetry.h.

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

Disallow copy construction.


Member Function Documentation

vector< Vec3f > TetrahedralSym::get_asym_unit_points ( bool  inc_mirror = false) const [virtual]
Parameters:
inc_mirrorwhether or not to include the mirror portion of the asymmetric unit
Returns:
a cyclic set of points which can be connected using great arcs on the unit sphere to demarcate the asymmetric unit. The last should may be connected to the first.

Reimplemented from EMAN::PlatonicSym.

Definition at line 2006 of file symmetry.cpp.

References b, get_az_alignment_offset(), EMAN::Vec3< Type >::normalize(), EMAN::PlatonicSym::platonic_params, and t.

{
        vector<Vec3f> ret;

        Vec3f b = Vec3f(0,0,1);
        ret.push_back(b);
        float theta_c_on_two = (float)platonic_params["theta_c_on_two"]; // already in radians
        float theta_c = 2*theta_c_on_two;

        Vec3f c_on_two = Vec3f(0,-sin(theta_c_on_two),cos(theta_c_on_two));
        Vec3f c = Vec3f(0,-sin(theta_c),cos(theta_c));
        ret.push_back(c_on_two);
        float cap_sig = platonic_params["az_max"];
        if ( inc_mirror ) {
                Vec3f a = Vec3f(sin(theta_c)*sin(cap_sig),-sin(theta_c)*cos(cap_sig),cos(theta_c));

                Vec3f f = a+b+c;
                f.normalize();

                ret.push_back(f);
        }

        Vec3f a_on_two = Vec3f(sin(theta_c_on_two)*sin(cap_sig),-sin(theta_c_on_two)*cos(cap_sig),cos(theta_c_on_two));
        ret.push_back(a_on_two);


        if ( get_az_alignment_offset() != 0 ) {
                Dict d("type","eman");
                d["az"] = get_az_alignment_offset();
                d["phi"] = 0.0f;
                d["alt"] = 0.0f;
                Transform t(d);
                for (vector<Vec3f>::iterator it = ret.begin(); it != ret.end(); ++it )
                {
                        *it = (*it)*t;
                }
        }

        return ret;
}
float TetrahedralSym::get_az_alignment_offset ( ) const [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 1943 of file symmetry.cpp.

Referenced by get_asym_unit_points().

{ return  0.0; }
virtual string EMAN::TetrahedralSym::get_desc ( ) const [inline, virtual]

Get a description.

Returns:
a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 700 of file symmetry.h.

{ return "Tetrahedral symmetry support"; }
virtual int EMAN::TetrahedralSym::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 tetrahedral symmetry, this number is 3

Implements EMAN::Symmetry3D.

Definition at line 706 of file symmetry.h.

{ return 3; }
virtual string EMAN::TetrahedralSym::get_name ( ) const [inline, virtual]

Return TetrahedralSym::NAME.

Returns:
the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 694 of file symmetry.h.

References NAME.

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

Gets the total number of unique roational symmetry operations associated with this symmetry For tetrahedral symmetry symmetry, this is 12.

Returns:
12

Implements EMAN::Symmetry3D.

Definition at line 736 of file symmetry.h.

{ return 12; };
Transform TetrahedralSym::get_sym ( const int  n) const [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"

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

Implements EMAN::Symmetry3D.

Definition at line 1978 of file symmetry.cpp.

{
        // These rotations courtesy of Phil Baldwin
         // It has n=m=3; F=4, E=6=nF/2, V=4=nF/m
        static double lvl0=0;         // There is a face along z
        static double lvl1=109.4712;  //  that is acos(-1/3)  // There  are 3 faces at this angle

        static double TET[36] = {// This is with the face along z
                0,lvl0,0,   0,lvl0,120,    0,lvl0,240,
  0,lvl1,60,   0,lvl1,180,    0,lvl1,300,
  120,lvl1,60, 120,lvl1,180,  120,lvl1,300,
  240,lvl1,60, 240,lvl1,180,  240,lvl1,300
        };
        //
        int idx = n % 12;
//      Transform3D ret;
//      ret.set_rotation((float)TET[idx * 3 ],(float)TET[idx * 3 + 1], (float)TET[idx * 3 + 2] );
//      return ret;

        Dict d("type","eman");
        d["az"] = (float)TET[idx * 3 ];
        d["alt"] = (float)TET[idx * 3 + 1];
        d["phi"] = (float)TET[idx * 3 + 2];
        return Transform(d);

}
bool TetrahedralSym::is_in_asym_unit ( const float &  altitude,
const float &  azimuth,
const bool  inc_mirror 
) const [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

Parameters:
altitudethe EMAN style altitude of the 3D orientation in degrees
azimuththe EMAN style azimuth of the 3D orientation in degrees
inc_mirrorwhether or not to include orientations if they are in the mirror portion of the asymmetric unit
Returns:
true or false, depending on whether or not the orientation is within the asymmetric unit

Reimplemented from EMAN::PlatonicSym.

Definition at line 1945 of file symmetry.cpp.

References EMAN::EMConsts::deg2rad, EMAN::PlatonicSym::get_delimiters(), EMAN::PlatonicSym::platonic_alt_lower_bound(), and EMAN::PlatonicSym::platonic_params.

{
        Dict d = get_delimiters(inc_mirror);
        float alt_max = d["alt_max"];
        float az_max = d["az_max"];

        if ( altitude >= 0 &&  altitude <= alt_max && azimuth <= az_max && azimuth >= 0) {
                // convert azimuth to radians
                float tmpaz = (float)(EMConsts::deg2rad * azimuth);

                float cap_sig = platonic_params["az_max"];
                float alt_max = platonic_params["alt_max"];
                if ( tmpaz > ( cap_sig/2.0f ) )tmpaz = cap_sig - tmpaz;

                float lower_alt_bound = platonic_alt_lower_bound(tmpaz, alt_max );

                // convert altitude to radians
                float tmpalt = (float)(EMConsts::deg2rad * altitude);
                if ( lower_alt_bound > tmpalt ) {
                        if ( !inc_mirror ) {
                                float upper_alt_bound = platonic_alt_lower_bound( tmpaz, alt_max/2.0f);
                                // you could change the "<" to a ">" here to get the other mirror part of the asym unit
                                if ( upper_alt_bound < tmpalt ) return false;
                                else return true;
                        }
                        else return true;
                }
                return false;
        }
        else return false;
}
virtual bool EMAN::TetrahedralSym::is_tet_sym ( ) const [inline, virtual]

A function that is used to determine if this is the tetrahedral symmetry object.

Returns:
true - indicating that this is not a tetrahedral symmetry object

Reimplemented from EMAN::Symmetry3D.

Definition at line 758 of file symmetry.h.

{ return true; }
static Symmetry3D* EMAN::TetrahedralSym::NEW ( ) [inline, static]

Factory support function NEW.

Returns:
a newly instantiated class of this type

Definition at line 686 of file symmetry.h.

References TetrahedralSym().

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

Disallow assignment.


Member Data Documentation

const string TetrahedralSym::NAME = "tet" [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().


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