Package org.rcsb.cif.model.generated

Class ChemicalConnAtom

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class ChemicalConnAtom
extends BaseCategory
    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 Detail

      • ChemicalConnAtom

        public ChemicalConnAtom​(String name,
                        int rowCount,
                        Object[] encodedColumns)

      • ChemicalConnAtom

        public ChemicalConnAtom​(String name)

    • Method Detail

      • 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