An encapsulation of helical 3D symmetry. More...

#include <symmetry.h>

Inheritance diagram for EMAN::HSym:

Collaboration diagram for EMAN::HSym:

[legend]

Public Member Functions
	HSym ()

virtual	~HSym ()

virtual string	get_name () const
	Return HSym::NAME. More...

virtual string	get_desc () const
	Get a description. More...

virtual TypeDict	get_param_types () const
	Get a dictionary containing the permissable parameters of this class Of all the symmetries, helical has the most options. More...

virtual Dict	get_delimiters (const bool inc_mirror=false) const
	Get the altitude and phi angle of the d symmetry, which depends on nysm. More...

virtual Transform	get_sym (const int n) const
	Provides access to the complete set of rotational and translational symmetry operations associated with helical symmetry. More...

virtual int	get_nsym () const
	For symmetries in general this function is supposed to return the number of unique symmetric operations that can be applied for the given Symmetry3D object. More...

virtual int	get_max_csym () const
	Gets the maximum cylcic symmetry exhibited by this object. More...

virtual bool	is_h_sym () const
	Determines whether or not this Symmetry3D is the helical type - returns true. More...

virtual bool	is_in_asym_unit (const float &altitude, const float &azimuth, const bool inc_mirror) const
	A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters. More...

virtual vector< Vec3f >	get_asym_unit_points (bool inc_mirror=false) const

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...

Public Member Functions inherited from EMAN::Symmetry3D
	Symmetry3D ()

virtual	~Symmetry3D ()

virtual float	get_az_alignment_offset () const
	This functionality is only relevant to platonic symmetries. More...

virtual bool	is_platonic_sym () const
	A function that is used to determine if this is a platonic symmetry object This function is only virtually overidden by the PlatonicSym 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...

virtual bool	is_tet_sym () const
	A function that is used to determine if this is the tetrahedral symmetry object This function is only virtually overidden by the TetSym 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 = "h"
	The name of this class - used to access it from factories etc. Should be "h". More...

Private Member Functions
	HSym (const HSym &)
	Disallow copy construction. More...

HSym &	operator= (const HSym &)
	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::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::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...

Detailed Description

An encapsulation of helical 3D symmetry.

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

Date: Feb 2008

Definition at line 446 of file symmetry.h.

Constructor & Destructor Documentation

◆ HSym() [1/2]

EMAN::HSym::HSym ( )

inline

Definition at line 449 of file symmetry.h.

449{};

Referenced by NEW().

◆ ~HSym()

virtual EMAN::HSym::~HSym ( )

inlinevirtual

Definition at line 450 of file symmetry.h.

450{};

◆ HSym() [2/2]

EMAN::HSym::HSym ( const HSym & )

private

Disallow copy construction.

Member Function Documentation

◆ get_asym_unit_points()

vector< Vec3f > HSym::get_asym_unit_points ( bool inc_mirror = false ) const

virtual

Parameters

inc_mirror whether 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.

Implements EMAN::Symmetry3D.

Definition at line 1608 of file symmetry.cpp.

{
        vector<Vec3f> ret;
 
        Dict delim = get_delimiters(inc_mirror);
        int nsym = params.set_default("nsym",1);
        float az = -(float)delim["az_max"];
 
 
        bool tracing_arcs = false;
 
 
        if ( !tracing_arcs) {
                Vec3f a(0,-1,0);
                ret.push_back(a);
 
                if ( nsym > 2 ) {
                        Dict d("type","eman");
                        d["phi"] = 0.0f;
                        d["alt"] = 0.0f;
                        d["az"] = az;
                        Vec3f b = Transform(d)*a;
                        ret.push_back(b);
                }
                else
                {
                        ret.push_back(Vec3f(1,0,0));
 
                        ret.push_back(Vec3f(0,1,0));
 
                        if ( nsym == 1 ) {
                                ret.push_back(Vec3f(-1,0,0));
                                ret.push_back(a);
                        }
                }
        }
        return ret;
 
}

References get_delimiters(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

◆ get_asym_unit_triangles()

vector< vector< Vec3f > > HSym::get_asym_unit_triangles ( bool inc_mirror ) const

virtual

Get triangles that precisely occlude the projection area of the default asymmetric unit.

This is used for collision detection in Symmetry3D::reduce

Parameters

inc_mirror whether to include the mirror portion of the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1602 of file symmetry.cpp.

                                                               {
 
        vector<vector<Vec3f> > ret;
        return ret;
}

◆ get_delimiters()

Dict HSym::get_delimiters ( const bool inc_mirror = false ) const

virtual

Get the altitude and phi angle of the d symmetry, which depends on nysm.

The "alt_max" is always 90 The "alt_min" 90-maxtilt The "az_max" is always 360/nsym degrees Helical symmetry argument is the only symmetry not to act on the inc_mirror argument. The current policy is the orientation generator using this symmetry should make its own accomodation for the inclusion of mirror orientations if the symmetry is helical (hence the presence of the is_h_sym function in the Symmetry3D class).

Parameters

inc_mirror this parameter is not specifically acted upon in this class

Returns: a dictionary containing the keys "alt_max" and "az_max" and "alt_min"

Exceptions

InvalidValueException if nsym is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 1567 of file symmetry.cpp.

                                          {
        Dict returnDict;
 
        // Get the parameters of interest
        int nsym = params.set_default("nsym",0);
        if ( nsym <= 0 ) throw InvalidValueException(nsym,"Error, you must specify a positive non zero nsym");
 
        float maxtilt = params.set_default("maxtilt",90.0f);
 
        returnDict["alt_max"] = 90.0f;
 
        returnDict["alt_min"] = 90.0f - maxtilt;
 
        returnDict["az_max"] = 360.0f;
 
        return returnDict;
}

References InvalidValueException, EMAN::FactoryBase::params, and EMAN::Dict::set_default().

Referenced by get_asym_unit_points(), and is_in_asym_unit().

◆ get_desc()

virtual string EMAN::HSym::get_desc ( ) const

inlinevirtual

Get a description.

Returns: a clear desciption of this class

Implements EMAN::FactoryBase.

Definition at line 468 of file symmetry.h.

468{ return "Helical symmetry, with support for N-start, pitch and limited tilt range. Specify as H[nsym]:[nstart]:[daz]:[tz in pix](:[maxtilt])"; }

◆ get_max_csym()

virtual int EMAN::HSym::get_max_csym ( ) const

inlinevirtual

Gets the maximum cylcic symmetry exhibited by this object.

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

Returns: nsym - this is the symmetry of the helix

Implements EMAN::Symmetry3D.

Definition at line 530 of file symmetry.h.

530{ return (int)params["nstart"]; } // may not be

References EMAN::FactoryBase::params.

◆ get_name()

virtual string EMAN::HSym::get_name ( ) const

inlinevirtual

Return HSym::NAME.

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 463 of file symmetry.h.

463{ return NAME; }

EMAN::HSym::NAME

static const string NAME

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

Definition: symmetry.h:533

References NAME.

◆ get_nsym()

virtual int EMAN::HSym::get_nsym ( ) const

inlinevirtual

For symmetries in general this function is supposed to return the number of unique symmetric operations that can be applied for the given Symmetry3D object.

For helical symmetries this is provided by the user as a parameter when setting up the helical symmetry. Generally a multiple of nstart.

Returns: the number of symmetric rotations that can be applied without going beyond 360 degrees

Exceptions

InvalidValueException if d_az (as stored internally in parms) is less than or equal to zero

Implements EMAN::Symmetry3D.

Definition at line 519 of file symmetry.h.

519{ return (int)params["nsym"]; };

References EMAN::FactoryBase::params.

◆ get_param_types()

virtual TypeDict EMAN::HSym::get_param_types ( ) const

inlinevirtual

Get a dictionary containing the permissable parameters of this class Of all the symmetries, helical has the most options.

This is because different approaches have to taken in regard to defining an asymmetric unit and to returning the set of rotational and translational symmetry operations

Returns: a dictionary containing the permissable parameters of this class

Implements EMAN::FactoryBase.

Definition at line 476 of file symmetry.h.

                {
                        TypeDict d;
                        d.put("nsym", EMObject::INT, "The number of asymmetric units to generate. This could be infinite for helical symmetry. Normally a multiple of nstart.");
                        d.put("nstart", EMObject::INT, "The Cn symmetry of a single Z-slice of the helix.");
                        d.put("tz", EMObject::FLOAT, "The translational distance (along z) between successive identical subunits in angstroms (default A/pix is 1)");
                        d.put("daz", EMObject::FLOAT, "The rotational angle (about z) between successive identical subunits in degrees");
                        d.put("apix", EMObject::FLOAT, "Angstroms per pixel, default is 1.0, used only for tz");
                        d.put("maxtilt", EMObject::FLOAT, "When generating projections, normally only 'side views' are created (3-D Z along Y in 2-D). This is the maximum out of plane tilt in degrees.");
                        return d;
                }

References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

◆ get_sym()

Transform HSym::get_sym ( const int n ) const

virtual

Provides access to the complete set of rotational and translational symmetry operations associated with helical symmetry.

This symmetry operations are generated in a straightforward way from the parameters of this class, specifically the return Transform object has an azimuth of n times the "d_az" (as specified in the parameters of this class), and has a post translation of "tz" in the z direction.

Parameters

n	the helical symmetry operation number.

Returns: a transform containing the correct rotational and translational symmetry operation.

Implements EMAN::Symmetry3D.

Definition at line 1648 of file symmetry.cpp.

{
        int nstart=params["nstart"];
        //int nsym=params["nsym"];
        float apix = params.set_default("apix",1.0f);
        float daz= params["daz"];
        float tz=params["tz"];
        float dz=tz/apix;
        Dict d("type","eman");
 
        // courtesy of Phil Baldwin
        //d["az"] = (n%nsym) * 360.0f / nsym;
        //d["az"]=(((int) n/hsym)%nstart)*360.f/nstart+(n%hsym)*daz;
        //d["az"] = n * daz;
        int ii=(n+1)/2;
        if (n>1 && n%2==0) ii*=-1; // extend to both directions 
        d["az"]=(ii%nstart)*(360.0/nstart)+floor(float(ii)/nstart)*daz; // corrected by steve, 7/21/11. No dependency on nsym
        d["alt"] = 0.0f;
        d["phi"] = 0.0f;
        Transform ret(d);
        ret.set_trans(0,0,(ii/nstart)*dz);
        return ret;
}

References EMAN::FactoryBase::params, EMAN::Dict::set_default(), and EMAN::Transform::set_trans().

◆ is_h_sym()

virtual bool EMAN::HSym::is_h_sym ( ) const

inlinevirtual

Determines whether or not this Symmetry3D is the helical type - returns true.

Returns: true - indicating that this is a helical symmetry object

Reimplemented from EMAN::Symmetry3D.

Definition at line 538 of file symmetry.h.

538{ return true; }

◆ is_in_asym_unit()

bool HSym::is_in_asym_unit	(	const float &	altitude,
		const float &	azimuth,
		const bool	inc_mirror = `false`
	)		const

virtual

A function to be used when generating orientations over portion of the unit sphere defined by parameters returned by get_delimiters.

In platonic symmetry altitude and azimuth alone are not enough to correctly demarcate the asymmetric unit. See the get_delimiters comments.

Parameters

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

Returns: true or false, depending on whether or not the orientation is within the asymmetric unit

Implements EMAN::Symmetry3D.

Definition at line 1585 of file symmetry.cpp.

{
        Dict d = get_delimiters(inc_mirror);
        float alt_max = d["alt_max"];
        float alt_min = d["alt_min"];
 
        if (inc_mirror) {
                float e = params.set_default("maxtilt",90.0f);
                alt_min -= e;
        }
 
        float az_max = d["az_max"];
 
        if ( altitude >=alt_min && altitude <= alt_max && azimuth <= az_max && azimuth >= 0 ) return true;
        return false;
}

References get_delimiters(), EMAN::FactoryBase::params, and EMAN::Dict::set_default().

◆ NEW()

static Symmetry3D * EMAN::HSym::NEW ( )

inlinestatic

Factory support function NEW.

Returns: a newly instantiated class of this type

Definition at line 455 of file symmetry.h.

                {
                        return new HSym();
                }

References HSym().

◆ operator=()

HSym & EMAN::HSym::operator= ( const HSym & )

private

Disallow assignment.

Member Data Documentation

◆ NAME

const string HSym::NAME = "h"

static

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

Definition at line 533 of file symmetry.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ HSym() [1/2]

◆ ~HSym()

◆ HSym() [2/2]

Member Function Documentation

◆ get_asym_unit_points()

◆ get_asym_unit_triangles()

◆ get_delimiters()

◆ get_desc()

◆ get_max_csym()

◆ get_name()

◆ get_nsym()

◆ get_param_types()

◆ get_sym()

◆ is_h_sym()

◆ is_in_asym_unit()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME