Package org.rcsb.cif.schema.mm

Class ChemicalConnAtom

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.ChemicalConnAtom
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ChemicalConnAtom
extends DelegatingCategory
Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (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. 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 that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • 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()
      The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure.
      Returns:
      FloatColumn

    • getDisplayY

      public FloatColumn getDisplayY()
      The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure.
      Returns:
      FloatColumn

    • getNCA

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

    • getNH

      public IntColumn getNH()
      The 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 is 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. Within an ATOM_SITE list, this number must match one of the _atom_site.chemical_conn_number values.
      Returns:
      IntColumn

    • getTypeSymbol

      public StrColumn getTypeSymbol()
      This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
      Returns:
      StrColumn