Package org.rcsb.cif.schema.core

Class GeomBond

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

  • Constructor Details

  • Method Details

    • getId

      public StrColumn getId()
      Unique identifier for the bond.
      Returns:
      StrColumn

    • getMultiplicity

      public IntColumn getMultiplicity()
      The number of times the given bond appears in the environment of the atoms labelled _geom_bond.atom_site_label_1. In cases where the full list of bonds is given, one of the series of equivalent bonds may be assigned the appropriate multiplicity while the others are assigned a value of 0.
      Returns:
      IntColumn

    • getPublFlag

      public StrColumn getPublFlag()
      This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles.
      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

    • getValence

      public FloatColumn getValence()
      Bond valence calculated from the bond distance.
      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

    • getDist

      public FloatColumn getDist()
      Intramolecular bond distance between the sites identified by _geom_bond.id
      Returns:
      FloatColumn

    • getDistance

      public FloatColumn getDistance()
      Intramolecular bond distance between the sites identified by _geom_bond.id
      Returns:
      FloatColumn

    • getDistEsd

      public FloatColumn getDistEsd()
      Standard Uncertainty of the intramolecular bond distance between the sites identified by _geom_bond.id
      Returns:
      FloatColumn

    • getDistanceSu

      public FloatColumn getDistanceSu()
      Standard Uncertainty of the intramolecular bond distance between the sites identified by _geom_bond.id
      Returns:
      FloatColumn