Used for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma).
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#include <openbabel/generic.h>
List of all members.
Public Types |
enum | LatticeType {
Undefined,
Triclinic,
Monoclinic,
Orthorhombic,
Tetragonal,
Rhombohedral,
Hexagonal,
Cubic
} |
Public Member Functions |
| OBUnitCell () |
| OBUnitCell (const OBUnitCell &) |
virtual OBGenericData * | Clone (OBBase *) const |
| ~OBUnitCell () |
OBUnitCell & | operator= (const OBUnitCell &) |
void | SetData (const double a, const double b, const double c, const double alpha, const double beta, const double gamma) |
void | SetData (const vector3 v1, const vector3 v2, const vector3 v3) |
void | SetData (const matrix3x3 m) |
void | SetOffset (const vector3 v1) |
void | SetSpaceGroup (const SpaceGroup *sg) |
void | SetSpaceGroup (const std::string sg) |
void | SetSpaceGroup (const int sg) |
void | SetLatticeType (const LatticeType lt) |
void | FillUnitCell (OBMol *) |
double | GetA () |
double | GetA () const |
double | GetB () |
double | GetB () const |
double | GetC () |
double | GetC () const |
double | GetAlpha () |
double | GetAlpha () const |
double | GetBeta () |
double | GetBeta () const |
double | GetGamma () |
double | GetGamma () const |
vector3 | GetOffset () |
vector3 | GetOffset () const |
const SpaceGroup * | GetSpaceGroup () |
const SpaceGroup * | GetSpaceGroup () const |
const std::string | GetSpaceGroupName () |
const std::string | GetSpaceGroupName () const |
LatticeType | GetLatticeType (int spacegroup) |
LatticeType | GetLatticeType (int spacegroup) const |
LatticeType | GetLatticeType () |
LatticeType | GetLatticeType () const |
std::vector< vector3 > | GetCellVectors () |
std::vector< vector3 > | GetCellVectors () const |
matrix3x3 | GetCellMatrix () |
matrix3x3 | GetCellMatrix () const |
matrix3x3 | GetOrthoMatrix () |
matrix3x3 | GetOrthoMatrix () const |
matrix3x3 | GetOrientationMatrix () |
matrix3x3 | GetOrientationMatrix () const |
matrix3x3 | GetFractionalMatrix () |
matrix3x3 | GetFractionalMatrix () const |
vector3 | FractionalToCartesian (vector3 frac) |
vector3 | FractionalToCartesian (vector3 frac) const |
vector3 | CartesianToFractional (vector3 cart) |
vector3 | CartesianToFractional (vector3 cart) const |
vector3 | WrapCartesianCoordinate (vector3 cart) |
vector3 | WrapCartesianCoordinate (vector3 cart) const |
vector3 | WrapFractionalCoordinate (vector3 frac) |
vector3 | WrapFractionalCoordinate (vector3 frac) const |
int | GetSpaceGroupNumber (std::string name="") |
int | GetSpaceGroupNumber (std::string name="") const |
double | GetCellVolume () |
double | GetCellVolume () const |
void | SetAttribute (const std::string &v) |
void | SetOrigin (const DataOrigin s) |
virtual const std::string & | GetAttribute () const |
unsigned int | GetDataType () const |
virtual const std::string & | GetValue () const |
virtual DataOrigin | GetOrigin () const |
Protected Attributes |
matrix3x3 | _mOrtho |
matrix3x3 | _mOrient |
vector3 | _offset |
std::string | _spaceGroupName |
const SpaceGroup * | _spaceGroup |
LatticeType | _lattice |
std::string | _attr |
unsigned int | _type |
DataOrigin | _source |
Detailed Description
Used for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma).
Member Enumeration Documentation
- Enumerator:
Undefined |
|
Triclinic |
|
Monoclinic |
|
Orthorhombic |
|
Tetragonal |
|
Rhombohedral |
also called trigonal
|
Hexagonal |
|
Cubic |
|
Constructor & Destructor Documentation
Member Function Documentation
void SetData |
( |
const double |
a, |
|
|
const double |
b, |
|
|
const double |
c, |
|
|
const double |
alpha, |
|
|
const double |
beta, |
|
|
const double |
gamma | |
|
) |
| | |
void SetOffset |
( |
const vector3 |
v1 |
) |
|
Set the offset to the origin to v1
.
void SetSpaceGroup |
( |
const SpaceGroup * |
sg |
) |
[inline] |
void SetSpaceGroup |
( |
const std::string |
sg |
) |
[inline] |
Set the space group symbol for this unit cell. Does not create an OBSymmetryData entry or attempt to convert between different symbol notations
void SetSpaceGroup |
( |
const int |
sg |
) |
[inline] |
Set the space group for this unit cell. Each spacegroup-symbol has a numeric equivalent which is easier to use to convert between notations. Does not create an OBSymmetryData entry or attempt to convert between different symbol notations
Set the Bravais lattice type for this unit cell.
void FillUnitCell |
( |
OBMol * |
mol |
) |
|
Duplicate symmetry-unique atoms to fill out the unit cell of the molecule, based on the known space group
double GetAlpha |
( |
|
) |
const |
double GetGamma |
( |
|
) |
const |
- Returns:
- any offset in the origin of the periodic boundaries
const SpaceGroup* GetSpaceGroup |
( |
|
) |
const [inline] |
const std::string GetSpaceGroupName |
( |
|
) |
[inline] |
- Returns:
- the text representation of the space group for this unit cell
const std::string GetSpaceGroupName |
( |
|
) |
const [inline] |
- Returns:
- lattice type (based on the
spacegroup
)
std::vector<vector3> GetCellVectors |
( |
|
) |
|
- Returns:
- v1, v2, v3 cell vectors
vector< vector3 > GetCellVectors |
( |
|
) |
const |
Wraps cartesian coordinate to fall within the unit cell.
- Parameters:
-
| cart | Vector of cartesian coordinates |
- Returns:
- Cartesian coordinates within cell boundaries.
int GetSpaceGroupNumber |
( |
std::string |
name = "" |
) |
|
- Returns:
- The numeric value of the given spacegroup
int GetSpaceGroupNumber |
( |
std::string |
name = "" |
) |
const |
- Returns:
- The cell volume (in Angstroms^3)
double GetCellVolume |
( |
|
) |
const |
void SetAttribute |
( |
const std::string & |
v |
) |
[inline, inherited] |
Set the attribute (key), which can be used to retrieve this data.
Referenced by OBGastChrg::AssignPartialCharges(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().
void SetOrigin |
( |
const DataOrigin |
s |
) |
[inline, inherited] |
Set the origin of this data, which can be used to filter the data.
Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().
virtual const std::string& GetAttribute |
( |
|
) |
const [inline, virtual, inherited] |
unsigned int GetDataType |
( |
|
) |
const [inline, inherited] |
virtual const std::string& GetValue |
( |
|
) |
const [inline, virtual, inherited] |
virtual DataOrigin GetOrigin |
( |
|
) |
const [inline, virtual, inherited] |
Member Data Documentation
Referenced by OBUnitCell::CartesianToFractional(), OBUnitCell::FractionalToCartesian(), OBUnitCell::GetA(), OBUnitCell::GetAlpha(), OBUnitCell::GetB(), OBUnitCell::GetBeta(), OBUnitCell::GetC(), OBUnitCell::GetCellMatrix(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetGamma(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().
std::string _attr [protected, inherited] |
unsigned int _type [protected, inherited] |
The documentation for this class was generated from the following files: