Package org.rcsb.cif.model.generated

Class ChemCompAtom

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class ChemCompAtom
extends BaseCategory
    Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories.

    • Constructor Detail

      • ChemCompAtom

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

      • ChemCompAtom

        public ChemCompAtom​(String name)

    • Method Detail

      • getAltAtomId

        public StrColumn getAltAtomId()
        An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
        Returns:
        StrColumn

      • getAtomId

        public StrColumn getAtomId()
        The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier.
        Returns:
        StrColumn

      • 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

      • getModelCartnX

        public FloatColumn getModelCartnX()
        The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
        Returns:
        FloatColumn

      • getModelCartnXEsd

        public FloatColumn getModelCartnXEsd()
        The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_x.
        Returns:
        FloatColumn

      • getModelCartnY

        public FloatColumn getModelCartnY()
        The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
        Returns:
        FloatColumn

      • getModelCartnYEsd

        public FloatColumn getModelCartnYEsd()
        The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_y.
        Returns:
        FloatColumn

      • getModelCartnZ

        public FloatColumn getModelCartnZ()
        The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
        Returns:
        FloatColumn

      • getModelCartnZEsd

        public FloatColumn getModelCartnZEsd()
        The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_z.
        Returns:
        FloatColumn

      • getCompId

        public StrColumn getCompId()
        This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
        Returns:
        StrColumn

      • getPartialCharge

        public FloatColumn getPartialCharge()
        The partial charge assigned to this atom.
        Returns:
        FloatColumn

      • getSubstructCode

        public StrColumn getSubstructCode()
        This data item assigns the atom to a substructure of the component, if appropriate.
        Returns:
        StrColumn

      • getTypeSymbol

        public StrColumn getTypeSymbol()
        The code used to identify the atom species representing this atom type. Normally this code is the element symbol.
        Returns:
        StrColumn

      • getPdbxAlign

        public IntColumn getPdbxAlign()
        Atom name alignment offset in PDB atom field.
        Returns:
        IntColumn

      • getPdbxOrdinal

        public IntColumn getPdbxOrdinal()
        Ordinal index for the component atom list.
        Returns:
        IntColumn

      • getPdbxComponentAtomId

        public StrColumn getPdbxComponentAtomId()
        The atom identifier in the subcomponent where a larger component has been divided subcomponents.
        Returns:
        StrColumn

      • getPdbxComponentCompId

        public StrColumn getPdbxComponentCompId()
        The component identifier for the subcomponent where a larger component has been divided subcomponents.
        Returns:
        StrColumn

      • getPdbxAltAtomId

        public StrColumn getPdbxAltAtomId()
        An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
        Returns:
        StrColumn

      • getPdbxAltCompId

        public StrColumn getPdbxAltCompId()
        An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
        Returns:
        StrColumn

      • getPdbxModelCartnXIdeal

        public FloatColumn getPdbxModelCartnXIdeal()
        An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms.
        Returns:
        FloatColumn

      • getPdbxModelCartnYIdeal

        public FloatColumn getPdbxModelCartnYIdeal()
        An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms.
        Returns:
        FloatColumn

      • getPdbxModelCartnZIdeal

        public FloatColumn getPdbxModelCartnZIdeal()
        An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms.
        Returns:
        FloatColumn

      • getPdbxStereoConfig

        public StrColumn getPdbxStereoConfig()
        The chiral configuration of the atom that is a chiral center.
        Returns:
        StrColumn

      • getPdbxAromaticFlag

        public StrColumn getPdbxAromaticFlag()
        A flag indicating an aromatic atom.
        Returns:
        StrColumn

      • getPdbxLeavingAtomFlag

        public StrColumn getPdbxLeavingAtomFlag()
        A flag indicating a leaving atom.
        Returns:
        StrColumn

      • getPdbxResidueNumbering

        public IntColumn getPdbxResidueNumbering()
        Preferred residue numbering in the BIRD definition.
        Returns:
        IntColumn

      • getPdbxPolymerType

        public StrColumn getPdbxPolymerType()
        Is the atom in a polymer or non-polymer subcomponent in the BIRD definition.
        Returns:
        StrColumn

      • getPdbxRefId

        public StrColumn getPdbxRefId()
        A reference to _pdbx_reference_entity_list.ref_entity_id
        Returns:
        StrColumn

      • getPdbxComponentId

        public IntColumn getPdbxComponentId()
        A reference to _pdbx_reference_entity_list.component_id
        Returns:
        IntColumn

      • getPdbxComponentEntityId

        public IntColumn getPdbxComponentEntityId()
        A reference to entity identifier in data category pdbx_chem_comp_subcomponent_entity_list.
        Returns:
        IntColumn