Package org.rcsb.cif.schema.mm

Class ChemCompAtom

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.ChemCompAtom
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ChemCompAtom
extends DelegatingCategory
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 Details

  • Method Details

    • createDelegate

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

    • 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

    • getPdbxStndAtomId

      public StrColumn getPdbxStndAtomId()
      A standard identifier for the atom. This data item is used when IUPAC/IUBMB nomenclature exists for labeling atoms.
      Returns:
      StrColumn