Package org.rcsb.cif.schema.mm

Class ChemLinkChir

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.ChemLinkChir
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ChemLinkChir
extends DelegatingCategory
Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getAtomCompId

      public StrColumn getAtomCompId()
      This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link.
      Returns:
      StrColumn

    • getAtomId

      public StrColumn getAtomId()
      The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
      Returns:
      StrColumn

    • getAtomConfig

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

    • getId

      public StrColumn getId()
      The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list.
      Returns:
      StrColumn

    • getLinkId

      public StrColumn getLinkId()
      This data item is a pointer to _chem_link.id in the CHEM_LINK category.
      Returns:
      StrColumn

    • getNumberAtomsAll

      public IntColumn getNumberAtomsAll()
      The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id.
      Returns:
      IntColumn

    • getNumberAtomsNh

      public IntColumn getNumberAtomsNh()
      The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id.
      Returns:
      IntColumn

    • getVolumeFlag

      public StrColumn getVolumeFlag()
      A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.
      Returns:
      StrColumn

    • getVolumeThree

      public FloatColumn getVolumeThree()
      The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product
      Returns:
      FloatColumn

    • getVolumeThreeEsd

      public FloatColumn getVolumeThreeEsd()
      The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three.
      Returns:
      FloatColumn