Package org.rcsb.cif.schema.core

Class ChemicalConnAtom

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.ChemicalConnAtom
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ChemicalConnAtom
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items which describe the 2D chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. In particular, the chemical_conn_atom data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide they must also contain symmetry-generated atoms, so as to describe a complete chemical entity.

  • Constructor Details

  • Method Details

    • getCharge

      public IntColumn getCharge()
      The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
      Returns:
      IntColumn

    • getDisplayX

      public FloatColumn getDisplayX()
      Cartesian coordinate (x) of the atom site in a chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal.
      Returns:
      FloatColumn

    • getDisplayY

      public FloatColumn getDisplayY()
      Cartesian coordinate (y) of the atom site in a chemical diagram. The coordinate origin is at the lower left corner, the y axis is vertical.
      Returns:
      FloatColumn

    • getNCA

      public IntColumn getNCA()
      Total number of connected atoms excluding terminal hydrogen atoms.
      Returns:
      IntColumn

    • getNH

      public IntColumn getNH()
      Total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the atom_site list. This number will be the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the atom_site list.
      Returns:
      IntColumn

    • getNumber

      public IntColumn getNumber()
      The chemical sequence number to be associated with this atom.
      Returns:
      IntColumn

    • getTypeSymbol

      public StrColumn getTypeSymbol()
      A code identifying the atom type.
      Returns:
      StrColumn