Package org.rcsb.cif.schema.core

Class ModelSite

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.ModelSite
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ModelSite
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items used to describe atomic sites and connections in the proposed atomic model.

  • Constructor Details

  • Method Details

    • getAdpEigenSystem

      public StrColumn getAdpEigenSystem()
      The set of three adp eigenvales and associated eigenvectors in the form of 4 element List. Each list has the form (val, vecX, vecY, vecZ) where the vector elements are direction cosines to the orthogonal axes X,Y,Z. The lists are sorted in descending magnitude of val. That is, the list with the largest val is first, and the smallest val is last.
      Returns:
      StrColumn

    • getAdpMatrixBeta

      public FloatColumn getAdpMatrixBeta()
      Matrix of dimensionless anisotropic atomic displacement parameters.
      Returns:
      FloatColumn

    • getCartnXyz

      public FloatColumn getCartnXyz()
      Vector of Cartesian (orthogonal angstrom) atom site coordinates.
      Returns:
      FloatColumn

    • getDisplayColour

      public StrColumn getDisplayColour()
      Display colour code assigned to this atom site. Note that the possible colours are enumerated in the colour_RGB list, and the default code is enumerated in the colour_hue list.
      Returns:
      StrColumn

    • getFractXyz

      public FloatColumn getFractXyz()
      Vector of fractional atom site coordinates.
      Returns:
      FloatColumn

    • getId

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

    • getIndex

      public IntColumn getIndex()
      Index number of an atomic site in the connected molecule.
      Returns:
      IntColumn

    • getLabel

      public StrColumn getLabel()
      Code identifies a site in the atom_site category of data.
      Returns:
      StrColumn

    • getMoleIndex

      public IntColumn getMoleIndex()
      Index number of a distinct molecules in the cell, not related by symmetry.
      Returns:
      IntColumn

    • getRadiusBond

      public FloatColumn getRadiusBond()
      Atomic radius of atom located at this site.
      Returns:
      FloatColumn

    • getRadiusContact

      public FloatColumn getRadiusContact()
      Atomic contact radius of atom specie located at this site.
      Returns:
      FloatColumn

    • getSymop

      public StrColumn getSymop()
      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

    • getTypeSymbol

      public StrColumn getTypeSymbol()
      Code to identify the atom specie(s) occupying this site.
      Returns:
      StrColumn