Package org.rcsb.cif.schema.core

Class GeomTorsion

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.GeomTorsion
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class GeomTorsion
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items used to specify the torsion angles in the structural model as derived from the atomic sites.

  • Constructor Details

  • Method Details

    • getDistances

      public FloatColumn getDistances()
      Distances between sites 1 - 2, 2 - 3 and 3 - 4.
      Returns:
      FloatColumn

    • getId

      public StrColumn getId()
      An identifier for the torsion angle that is unique within its loop.
      Returns:
      StrColumn

    • getPublFlag

      public StrColumn getPublFlag()
      Code signals if the torsion angle is required for publication.
      Returns:
      StrColumn

    • getSiteSymmetry1

      public StrColumn getSiteSymmetry1()
      The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'pqr'. These numbers are combined to form the code 'n pqr' or n_pqr. The character string n_pqr is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. p, q and r refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (p,q,r) by the relations p = 5 + x q = 5 + y r = 5 + z
      Returns:
      StrColumn

    • getSiteSymmetry2

      public StrColumn getSiteSymmetry2()
      The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'pqr'. These numbers are combined to form the code 'n pqr' or n_pqr. The character string n_pqr is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. p, q and r refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (p,q,r) by the relations p = 5 + x q = 5 + y r = 5 + z
      Returns:
      StrColumn

    • getSiteSymmetry3

      public StrColumn getSiteSymmetry3()
      The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'pqr'. These numbers are combined to form the code 'n pqr' or n_pqr. The character string n_pqr is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. p, q and r refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (p,q,r) by the relations p = 5 + x q = 5 + y r = 5 + z
      Returns:
      StrColumn

    • getSiteSymmetry4

      public StrColumn getSiteSymmetry4()
      The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'pqr'. These numbers are combined to form the code 'n pqr' or n_pqr. The character string n_pqr is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. p, q and r refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (p,q,r) by the relations p = 5 + x q = 5 + y r = 5 + z
      Returns:
      StrColumn

    • getValue

      public FloatColumn getValue()
      Angle defined by the sites identified by _geom_torsion.id. The torsion-angle definition should be that of Klyne and Prelog. The vector direction *_label_2 to *_label_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
      Returns:
      FloatColumn

    • getAngle

      public FloatColumn getAngle()
      Angle defined by the sites identified by _geom_torsion.id. The torsion-angle definition should be that of Klyne and Prelog. The vector direction *_label_2 to *_label_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
      Returns:
      FloatColumn

    • getValueEsd

      public FloatColumn getValueEsd()
      Standard Uncertainty of the torsion angle.
      Returns:
      FloatColumn

    • getAngleSu

      public FloatColumn getAngleSu()
      Standard Uncertainty of the torsion angle.
      Returns:
      FloatColumn

    • getAtomSiteId1

      public StrColumn getAtomSiteId1()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteLabel1

      public StrColumn getAtomSiteLabel1()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteId2

      public StrColumn getAtomSiteId2()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteLabel2

      public StrColumn getAtomSiteLabel2()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteId3

      public StrColumn getAtomSiteId3()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteLabel3

      public StrColumn getAtomSiteLabel3()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteId4

      public StrColumn getAtomSiteId4()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn

    • getAtomSiteLabel4

      public StrColumn getAtomSiteLabel4()
      This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
      Returns:
      StrColumn