Package org.rcsb.cif.schema.core

Class Cell

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.Cell
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Cell
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items used to describe the parameters of the crystal unit cell and their measurement.

  • Constructor Details

  • Method Details

    • getAtomicMass

      public FloatColumn getAtomicMass()
      Atomic mass of the contents of the unit cell. This calculated from the atom sites present in the ATOM_TYPE list, rather than the ATOM_SITE lists of atoms in the refined model.
      Returns:
      FloatColumn

    • getFormulaUnitsZ

      public IntColumn getFormulaUnitsZ()
      The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum.
      Returns:
      IntColumn

    • getMetricTensor

      public FloatColumn getMetricTensor()
      The direct space (covariant) metric tensor used to transform vectors and coordinates from real (direct) to reciprocal space.
      Returns:
      FloatColumn

    • getOrthogonalMatrix

      public FloatColumn getOrthogonalMatrix()
      Orthogonal matrix of the crystal unit cell. Definition uses Rollet's axial assignments with cell vectors a,b,c aligned with orthogonal axes X,Y,Z so that c||Z and b in plane YZ.
      Returns:
      FloatColumn

    • getVolume

      public FloatColumn getVolume()
      Volume of the crystal unit cell.
      Returns:
      FloatColumn

    • getAngleAlpha

      public FloatColumn getAngleAlpha()
      The angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleBeta

      public FloatColumn getAngleBeta()
      The angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleGamma

      public FloatColumn getAngleGamma()
      The angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getLengthA

      public FloatColumn getLengthA()
      The length of each cell axis.
      Returns:
      FloatColumn

    • getLengthB

      public FloatColumn getLengthB()
      The length of each cell axis.
      Returns:
      FloatColumn

    • getLengthC

      public FloatColumn getLengthC()
      The length of each cell axis.
      Returns:
      FloatColumn

    • getConvertUijToBetaij

      public FloatColumn getConvertUijToBetaij()
      The reciprocal space matrix for converting the U(ij) matrix of atomic displacement parameters to a dimensionless beta(IJ) matrix. The adp factor in a structure factor expression: t = exp -2pi**2 ( U11 h h a* a* + ...... 2 U23 k l b* c* ) t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* ) = exp - ( beta11 h h + ............ 2 beta23 k l ) The conversion of the U or B matrices to the beta matrix beta = C U C = C B C /8pi**2 where C is conversion matrix defined here.
      Returns:
      FloatColumn

    • getConvertUisoToUij

      public FloatColumn getConvertUisoToUij()
      The reciprocal space matrix for converting the isotropic Uiso atomic displacement parameter to the anisotropic matrix Uij. | 1 cos(gamma*) cos(beta*) | U[i,j] = Uiso * | cos(gamma*) 1 cos(alpha*) | | cos(beta*) cos(alpha*) 1 |
      Returns:
      FloatColumn

    • getReciprocalMetricTensor

      public FloatColumn getReciprocalMetricTensor()
      The reciprocal (contravariant) metric tensor used to transform vectors and coordinates from reciprocal space to real (direct) space.
      Returns:
      FloatColumn

    • getReciprocalOrthogonalMatrix

      public FloatColumn getReciprocalOrthogonalMatrix()
      Orthogonal matrix of the reciprocal space. The matrix may be used to transform the non-orthogonal vector h = (h,k,l) into the orthogonal indices p = (p,q,r) M h = p
      Returns:
      FloatColumn

    • getReciprocalAngleAlpha

      public FloatColumn getReciprocalAngleAlpha()
      Reciprocal of the angle between _cell.length_b and _cell.length_c. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
      Returns:
      FloatColumn

    • getReciprocalAngleBeta

      public FloatColumn getReciprocalAngleBeta()
      Reciprocal of the angle between _cell.length_a and _cell.length_c. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
      Returns:
      FloatColumn

    • getReciprocalAngleGamma

      public FloatColumn getReciprocalAngleGamma()
      Reciprocal of the angle between _cell.length_a and _cell.length_b. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
      Returns:
      FloatColumn

    • getReciprocalLengthA

      public FloatColumn getReciprocalLengthA()
      Reciprocal of the _cell.length_a.
      Returns:
      FloatColumn

    • getReciprocalLengthB

      public FloatColumn getReciprocalLengthB()
      Reciprocal of the _cell.length_b.
      Returns:
      FloatColumn

    • getReciprocalLengthC

      public FloatColumn getReciprocalLengthC()
      Reciprocal of the _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalVectorA

      public FloatColumn getReciprocalVectorA()
      Reciprocal of the _cell.vector_a.
      Returns:
      FloatColumn

    • getReciprocalVectorB

      public FloatColumn getReciprocalVectorB()
      Reciprocal of the _cell.vector_b.
      Returns:
      FloatColumn

    • getReciprocalVectorC

      public FloatColumn getReciprocalVectorC()
      Reciprocal of the _cell.vector_c.
      Returns:
      FloatColumn

    • getVectorA

      public FloatColumn getVectorA()
      The cell vector along the x axis.
      Returns:
      FloatColumn

    • getVectorB

      public FloatColumn getVectorB()
      The cell vector along the y axis.
      Returns:
      FloatColumn

    • getVectorC

      public FloatColumn getVectorC()
      The cell vector along the z axis.
      Returns:
      FloatColumn

    • getDetails

      public StrColumn getDetails()
      Description of special aspects of the cell choice, noting possible alternative settings.
      Returns:
      StrColumn

    • getSpecialDetails

      public StrColumn getSpecialDetails()
      Description of special aspects of the cell choice, noting possible alternative settings.
      Returns:
      StrColumn

    • getVolumeEsd

      public FloatColumn getVolumeEsd()
      Standard uncertainty of the volume of the crystal unit cell.
      Returns:
      FloatColumn

    • getVolumeSu

      public FloatColumn getVolumeSu()
      Standard uncertainty of the volume of the crystal unit cell.
      Returns:
      FloatColumn

    • getAngleAlphaEsd

      public FloatColumn getAngleAlphaEsd()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleAlphaSu

      public FloatColumn getAngleAlphaSu()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getBetaSu

      public FloatColumn getBetaSu()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleBetaEsd

      public FloatColumn getAngleBetaEsd()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleBetaSu

      public FloatColumn getAngleBetaSu()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getGammaSu

      public FloatColumn getGammaSu()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleGammaEsd

      public FloatColumn getAngleGammaEsd()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getAngleGammaSu

      public FloatColumn getAngleGammaSu()
      Standard uncertainty of the angle between the bounding cell axes.
      Returns:
      FloatColumn

    • getLengthAEsd

      public FloatColumn getLengthAEsd()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getLengthASu

      public FloatColumn getLengthASu()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getLengthBEsd

      public FloatColumn getLengthBEsd()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getLengthBSu

      public FloatColumn getLengthBSu()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getLengthCEsd

      public FloatColumn getLengthCEsd()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getLengthCSu

      public FloatColumn getLengthCSu()
      Standard uncertainty of the length of each cell axis.
      Returns:
      FloatColumn

    • getReciprocalAngleAlphaEsd

      public FloatColumn getReciprocalAngleAlphaEsd()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_b and _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalAngleAlphaSu

      public FloatColumn getReciprocalAngleAlphaSu()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_b and _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalAngleBetaEsd

      public FloatColumn getReciprocalAngleBetaEsd()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_a and _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalAngleBetaSu

      public FloatColumn getReciprocalAngleBetaSu()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_a and _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalAngleGammaEsd

      public FloatColumn getReciprocalAngleGammaEsd()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_a and _cell.length_b.
      Returns:
      FloatColumn

    • getReciprocalAngleGammaSu

      public FloatColumn getReciprocalAngleGammaSu()
      Standard Uncertainty of the Reciprocal of the angle between _cell.length_a and _cell.length_b.
      Returns:
      FloatColumn

    • getReciprocalLengthAEsd

      public FloatColumn getReciprocalLengthAEsd()
      Standard Uncertainty of the reciprocal of the _cell.length_a.
      Returns:
      FloatColumn

    • getReciprocalLengthASu

      public FloatColumn getReciprocalLengthASu()
      Standard Uncertainty of the reciprocal of the _cell.length_a.
      Returns:
      FloatColumn

    • getReciprocalLengthBEsd

      public FloatColumn getReciprocalLengthBEsd()
      Standard Uncertainty of the reciprocal of the _cell.length_b.
      Returns:
      FloatColumn

    • getReciprocalLengthBSu

      public FloatColumn getReciprocalLengthBSu()
      Standard Uncertainty of the reciprocal of the _cell.length_b.
      Returns:
      FloatColumn

    • getReciprocalLengthCEsd

      public FloatColumn getReciprocalLengthCEsd()
      Standard Uncertainty of the reciprocal of the _cell.length_c.
      Returns:
      FloatColumn

    • getReciprocalLengthCSu

      public FloatColumn getReciprocalLengthCSu()
      Standard Uncertainty of the reciprocal of the _cell.length_c.
      Returns:
      FloatColumn