ObjCryst::SpaceGroup Class Reference
The crystallographic space group, and the cell choice. More...
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 AsymmetricUnit & | GetAsymUnit () 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. | |
| const std::vector < SpaceGroup::TRx > & | 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 RefinableObjClock & | GetClockSpaceGroup () 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 REAL sf_re=0, const REAL sf_im=0) 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. | |
| 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). | |
| std::vector< SMx > | mvSym |
| Store floating-point matrices for faster use. | |
| std::vector< TRx > | mvTrans |
| Store floating-point translation vectors for faster use. | |
Classes | |
| struct | SMx |
| Struct to store rot+trans matrix. More... | |
| struct | TRx |
| Struct to store trans matrix. More... | |
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.
Definition at line 104 of file SpaceGroup.h.
Constructor & Destructor Documentation
| ObjCryst::SpaceGroup::SpaceGroup | ( | ) |
Default Constructor (initializes in P1).
You can use later SpaceGroup::ChangeSpaceGroup() to set the spacegroup.
Definition at line 193 of file SpaceGroup.cpp.
| 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.
Definition at line 198 of file SpaceGroup.cpp.
Member Function Documentation
| 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.
Definition at line 221 of file SpaceGroup.cpp.
| int ObjCryst::SpaceGroup::GetNbTranslationVectors | ( | ) | const |
Number of translation vectors (1 for 'P' cells, 2 for 'I', 4 for 'F',etc.
.)
Definition at line 240 of file SpaceGroup.cpp.
| const std::vector< SpaceGroup::TRx > & 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] $](form_31.png)
for a 'P' Cell, ![$ \left[ \begin {array}{ccc} 0 & 0 & 0 \\ \frac{1}{2} & \frac{1}{2} & \frac{1}{2} \\ \end{array} \right] $](form_32.png)
for a 'I' cell, and ![$ \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] $](form_33.png)
for a 'F' cell,etc...
Definition at line 245 of file SpaceGroup.cpp.
| 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,
Definition at line 251 of file SpaceGroup.cpp.
| 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
Definition at line 344 of file SpaceGroup.cpp.
| void ObjCryst::SpaceGroup::Print | ( | ) | const |
Prints a description of the spacegroup (symbol, properties).
Definition at line 359 of file SpaceGroup.cpp.
| 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.
Definition at line 398 of file SpaceGroup.cpp.
| CrystMatrix_REAL ObjCryst::SpaceGroup::GetAllEquivRefl | ( | const REAL | h, | |
| const REAL | k, | |||
| const REAL | l, | |||
| const bool | excludeFriedelMate = false, |
|||
| const bool | forceFriedelLaw = false, |
|||
| const REAL | sf_re = 0, |
|||
| const REAL | sf_im = 0 | |||
| ) | const |
Get the list of all equivalent reflections.
- Returns:
- a matrix with 5 columns for h,k,l,Re(F),Im(F) and as many rows as there are reflections (the input reflection is included), with the associated structure factor, from the structure factor of the input reflection.
- 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 sf_re,sf_im,: the real & imaginary part of the structure factor of the original reflection
Definition at line 428 of file SpaceGroup.cpp.
| 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
Definition at line 476 of file SpaceGroup.cpp.
| 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.
Definition at line 487 of file SpaceGroup.cpp.
Member Data Documentation
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.
Definition at line 271 of file SpaceGroup.h.
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/
Definition at line 279 of file SpaceGroup.h.
bool ObjCryst::SpaceGroup::mHasInversionCenter [private] |
bool ObjCryst::SpaceGroup::mIsInversionCenterAtOrigin [private] |
The documentation for this class was generated from the following files:
