Main Page | Namespace List | Class Hierarchy | Alphabetical List | Class List | File List | Namespace Members | Class Members | File Members | Related Pages

ObjCryst::SpaceGroup Class Reference

The crystallographic space group, and the cell choice. More...

Collaboration diagram for ObjCryst::SpaceGroup:

Collaboration graph
[legend]
List of all members.

Public Member Functions

 SpaceGroup ()
 Default Constructor (initializes in P1).

 SpaceGroup (const string &spgId)
 Constructor with a specified spacegroup symbol or number.

 ~SpaceGroup ()
 Destructor.

void ChangeSpaceGroup (const string &spgId)
 Change the Spacegroup.

const string & GetName () const
 Get the name of this spacegroup (its name, as supplied initially by the calling program or user).

bool IsInAsymmetricUnit (const REAL x, const REAL y, const REAL z) const
 Test if a given scatterer at (x,y,z) is in the asymmetric unit.

void ChangeToAsymmetricUnit (REAL x, REAL y, REAL z) const
 Move (x,y,z) coordinates to their equivalent in the asym unit.

const AsymmetricUnitGetAsymUnit () const
 Get the AsymmetricUnit for this spacegroup.

int GetSpaceGroupNumber () const
 Id number of the spacegroup.

bool IsCentrosymmetric () const
 Is the crystal centrosymmetric ?

int GetNbTranslationVectors () const
 Number of translation vectors (1 for 'P' cells, 2 for 'I', 4 for 'F',etc..).

CrystMatrix_REAL GetTranslationVectors () const
 Return all Translation Vectors, as a 3 columns-array.

CrystMatrix_REAL GetAllSymmetrics (const REAL x, const REAL y, const REAL z, const bool noCenter=false, const bool noTransl=false, const bool noIdentical=false) const
 Get all equivalent positions of a (xyz) position.

int GetNbSymmetrics (const bool noCenter=false, const bool noTransl=false) const
 Return the number of equivalent positions in the spacegroup, ie the multilicity of the general position.

void Print () const
 Prints a description of the spacegroup (symbol, properties).

bool HasInversionCenter () const
 Is centrosymmetric ?

bool IsInversionCenterAtOrigin () const
 Is the center of symmetry at the origin ?

const cctbx::sgtbx::space_group & GetCCTbxSpg () const
 Get the underlying cctbx Spacegroup object.

const RefinableObjClockGetClockSpaceGroup () const
 Get the SpaceGroup Clock (corresponding to the time of the initialization of the SpaceGroup).

unsigned int GetUniqueAxis () const
 Which is the unique axis (for monoclinic space groups ).

char GetExtension () const
 Extension to space group symbol ('1','2':origin choice ; 'R','H'=rhomboedral/hexagonal).

unsigned int AreReflEquiv (const REAL h1, const REAL k1, const REAL l1, const REAL h2, const REAL k2, const REAL l2) const
 Are these reflections equivalent ?

CrystMatrix_REAL GetAllEquivRefl (const REAL h, const REAL k, const REAL l, const bool excludeFriedelMate=false, const bool forceFriedelLaw=false) const
 Get the list of all equivalent reflections.

bool IsReflSystematicAbsent (const REAL h, const REAL k, const REAL l) const
 Is the reflection systematically absent ?

bool IsReflCentric (const REAL h, const REAL k, const REAL l) const
 Is the reflection centric ?

unsigned int GetExpectedIntensityFactor (const REAL h, const REAL k, const REAL l) const
 Get the "expected intensity factor" for a given reflection.


Private Member Functions

void InitSpaceGroup (const string &spgId)
 Init the spaceGroup object from its name.


Private Attributes

string mId
 Spacegroup's name ( 'I422', 'D2^8','230') Maybe we should only store the Hermann-Mauguin symbol, rather than storing the string which was initially given by the user/program for the initialization.

cctbx::sgtbx::space_group * mpCCTbxSpaceGroup
 SgOps structure for this spacegroup. (Symmetry operations).

bool mHasInversionCenter
 Is spacegroup centrosymmetric ?

bool mIsInversionCenterAtOrigin
 Is center of symmetry at the origin ?

AsymmetricUnit mAsymmetricUnit
 The spacegroup asymmetric unit.

RefinableObjClock mClock
 The Spacegroup clock.

unsigned int mUniqueAxisId
 Unique axis number (0=a,1=b,2=c).

unsigned long mNbSym
 Number of symmetry operations (excluding center, and translations).

unsigned long mNbTrans
 Number of lattice translations, including (0,0,0).

unsigned long mSpgNumber
 SpaceGroup Number.

char mExtension
 Extension to space group symbol (1,2:origin choice ; R,H=rhomboedral/hexagonal).


Detailed Description

The crystallographic space group, and the cell choice.

This class includes functions to get basic information about the symmetries, as well as getting all symmetrics for a given position in a unit cell.

This class included a pointer to a function calculating the "geometrical structure factor" (ie the sum of sin() and cos() for all symetrics, as could be found in the old version of the (red) International Tables), which was used to speed up computation of structure factors by using pre-factorised formulas. This is not used anymore, since methods can be used to speed up computations.

This class uses R. Grosse-Kunstleve 'SgLite' package, which is part of the Pymol package : http://pymol.sourceforge.net/

Warning:
: the interface of the class will somewhat change when switching from sgLite to cctbx (http://cctbx.sourceforge.net). Particularly functions Spacegroup::GetSgOps() and Spacegroup::GetHM_as_Hall() will be removed.


Constructor & Destructor Documentation

ObjCryst::SpaceGroup::SpaceGroup  ) 
 

Default Constructor (initializes in P1).

You can use later SpaceGroup::ChangeSpaceGroup() to set the spacegroup.

ObjCryst::SpaceGroup::SpaceGroup const string &  spgId  ) 
 

Constructor with a specified spacegroup symbol or number.

Parameters:
spgId The space group identifier, either an Hermann-Maugin, or Hall, or Schonflies symbol.

ObjCryst::SpaceGroup::~SpaceGroup  ) 
 

Destructor.


Member Function Documentation

unsigned int ObjCryst::SpaceGroup::AreReflEquiv const REAL  h1,
const REAL  k1,
const REAL  l1,
const REAL  h2,
const REAL  k2,
const REAL  l2
const
 

Are these reflections equivalent ?

Returns:
1 if they are equivalent, 2 if they are Friedel/Bijvoet mates, and else 0.

void ObjCryst::SpaceGroup::ChangeSpaceGroup const string &  spgId  ) 
 

Change the Spacegroup.

void ObjCryst::SpaceGroup::ChangeToAsymmetricUnit REAL  x,
REAL  y,
REAL  z
const
 

Move (x,y,z) coordinates to their equivalent in the asym unit.

Warning:
Not implemented yet.
Todo:
SpaceGroup::IsInAsymmetricUnit()

CrystMatrix_REAL ObjCryst::SpaceGroup::GetAllEquivRefl const REAL  h,
const REAL  k,
const REAL  l,
const bool  excludeFriedelMate = false,
const bool  forceFriedelLaw = false
const
 

Get the list of all equivalent reflections.

Returns:
a matrix with 3 columns for h,k,l, and as many rows as there are reflections (the input reflection is included).
Parameters:
excludeFriedelMate if true, then Friedel mates of reflections will not be listed, even if there is a center of symmetry.
forceFriedelLaw if true, a center of symmetry will be added (to force considering Friedel mates as equivalent). This as no effect if excludeFriedelMate=true

CrystMatrix_REAL ObjCryst::SpaceGroup::GetAllSymmetrics const REAL  x,
const REAL  y,
const REAL  z,
const bool  noCenter = false,
const bool  noTransl = false,
const bool  noIdentical = false
const
 

Get all equivalent positions of a (xyz) position.

Parameters:
x,y,z fractional coordinates of the position
noCenter if set to 'false' (the default), then the center of symmetry (if any) is used to generate ALL positions. If 'true', then only one half of equivalent positions are generated. This has no influence if the group is not centrosymmetric. (note Not generating symmetrical positions from center of symmetry is useful to speed up computation of structure factor, but is a bit tricky if the inversion is not at the origin. This is taken into account)
noTransl if set to 'false' (the default), then translation are taken into account to generate all atom positions. This affect only body or face(s)-centered spacegroups.
noIdentical if set to true, then atom in special positions will only return the distinct atomic positions. Currently two atoms are considered distinct if the difference for all of their fractionnal coordinates is less than 1e-5
Returns:
a 3-column (x,y,z) matrix with as many rows as symmetric atoms
Warning:
'special' positions are not taken into account. (ie an atom in special position will return duplicate entries. This may be corrected automatically later.) You can use the 'noIdentical' option for that,

const AsymmetricUnit& ObjCryst::SpaceGroup::GetAsymUnit  )  const
 

Get the AsymmetricUnit for this spacegroup.

const cctbx::sgtbx::space_group& ObjCryst::SpaceGroup::GetCCTbxSpg  )  const
 

Get the underlying cctbx Spacegroup object.

const RefinableObjClock& ObjCryst::SpaceGroup::GetClockSpaceGroup  )  const
 

Get the SpaceGroup Clock (corresponding to the time of the initialization of the SpaceGroup).

unsigned int ObjCryst::SpaceGroup::GetExpectedIntensityFactor const REAL  h,
const REAL  k,
const REAL  l
const
 

Get the "expected intensity factor" for a given reflection.

This is the number of times the reflection is identical to the reflections deduced by the symmetry operators, under all distinct pure rotationnal symmetry operations of the space group.

This is used for the probability distribution of reflection intensities.

See:

  • Stewart & Karle, Acta. Cryst 132 (1976), 1005
  • Wilson, Acta Cryst 3 (1950), 258

char ObjCryst::SpaceGroup::GetExtension  )  const
 

Extension to space group symbol ('1','2':origin choice ; 'R','H'=rhomboedral/hexagonal).

const string& ObjCryst::SpaceGroup::GetName  )  const
 

Get the name of this spacegroup (its name, as supplied initially by the calling program or user).

int ObjCryst::SpaceGroup::GetNbSymmetrics const bool  noCenter = false,
const bool  noTransl = false
const
 

Return the number of equivalent positions in the spacegroup, ie the multilicity of the general position.

Parameters:
noCenter if 'true', do not take into account the center of symmetry
noTransl if 'true', do not take into account translations

int ObjCryst::SpaceGroup::GetNbTranslationVectors  )  const
 

Number of translation vectors (1 for 'P' cells, 2 for 'I', 4 for 'F',etc..).

int ObjCryst::SpaceGroup::GetSpaceGroupNumber  )  const
 

Id number of the spacegroup.

CrystMatrix_REAL ObjCryst::SpaceGroup::GetTranslationVectors  )  const
 

Return all Translation Vectors, as a 3 columns-array.

The first vector is always [0,0,0]

Returns:
$ \left[ \begin {array}{ccc} 0 & 0 & 0 \end{array} \right] $ for a 'P' Cell, $ \left[ \begin {array}{ccc} 0 & 0 & 0 \\ \frac{1}{2} & \frac{1}{2} & \frac{1}{2} \\ \end{array} \right] $ for a 'I' cell, and $ \left[ \begin {array}{ccc} 0 & 0 & 0 \\ \frac{1}{2} & \frac{1}{2} & 0 \\ \frac{1}{2} & 0 & \frac{1}{2} \\ 0 & \frac{1}{2} & \frac{1}{2} \\ \end{array} \right] $ for a 'F' cell,etc...

unsigned int ObjCryst::SpaceGroup::GetUniqueAxis  )  const
 

Which is the unique axis (for monoclinic space groups ).

bool ObjCryst::SpaceGroup::HasInversionCenter  )  const
 

Is centrosymmetric ?

void ObjCryst::SpaceGroup::InitSpaceGroup const string &  spgId  )  [private]
 

Init the spaceGroup object from its name.

Initialize the SgOps & HM_as_Hall structures (SgLite), and set the function pointers to the functions used to compute the geometrical structure factors.

bool ObjCryst::SpaceGroup::IsCentrosymmetric  )  const
 

Is the crystal centrosymmetric ?

bool ObjCryst::SpaceGroup::IsInAsymmetricUnit const REAL  x,
const REAL  y,
const REAL  z
const
 

Test if a given scatterer at (x,y,z) is in the asymmetric unit.

bool ObjCryst::SpaceGroup::IsInversionCenterAtOrigin  )  const
 

Is the center of symmetry at the origin ?

bool ObjCryst::SpaceGroup::IsReflCentric const REAL  h,
const REAL  k,
const REAL  l
const
 

Is the reflection centric ?

bool ObjCryst::SpaceGroup::IsReflSystematicAbsent const REAL  h,
const REAL  k,
const REAL  l
const
 

Is the reflection systematically absent ?

void ObjCryst::SpaceGroup::Print  )  const
 

Prints a description of the spacegroup (symbol, properties).

Todo:


Member Data Documentation

AsymmetricUnit ObjCryst::SpaceGroup::mAsymmetricUnit [private]
 

The spacegroup asymmetric unit.

RefinableObjClock ObjCryst::SpaceGroup::mClock [private]
 

The Spacegroup clock.

char ObjCryst::SpaceGroup::mExtension [private]
 

Extension to space group symbol (1,2:origin choice ; R,H=rhomboedral/hexagonal).

bool ObjCryst::SpaceGroup::mHasInversionCenter [private]
 

Is spacegroup centrosymmetric ?

string ObjCryst::SpaceGroup::mId [private]
 

Spacegroup's name ( 'I422', 'D2^8','230') Maybe we should only store the Hermann-Mauguin symbol, rather than storing the string which was initially given by the user/program for the initialization.

bool ObjCryst::SpaceGroup::mIsInversionCenterAtOrigin [private]
 

Is center of symmetry at the origin ?

unsigned long ObjCryst::SpaceGroup::mNbSym [private]
 

Number of symmetry operations (excluding center, and translations).

unsigned long ObjCryst::SpaceGroup::mNbTrans [private]
 

Number of lattice translations, including (0,0,0).

cctbx::sgtbx::space_group* ObjCryst::SpaceGroup::mpCCTbxSpaceGroup [private]
 

SgOps structure for this spacegroup. (Symmetry operations).

See sglite subdirectory for more information. This is (c) R. Gross-Kunstleve, part of PyMol software http://pymol.sourceforge.net/

unsigned long ObjCryst::SpaceGroup::mSpgNumber [private]
 

SpaceGroup Number.

unsigned int ObjCryst::SpaceGroup::mUniqueAxisId [private]
 

Unique axis number (0=a,1=b,2=c).


The documentation for this class was generated from the following file:
Generated on Tue Nov 14 15:05:24 2006 for ObjCryst++ by doxygen 1.3.6