Package org.rcsb.cif.schema.mm

Class AtomSites

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.AtomSites
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomSites
extends DelegatingCategory
Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getEntryId

      public StrColumn getEntryId()
      This data item is a pointer to _entry.id in the ENTRY category.
      Returns:
      StrColumn

    • getCartnTransfMatrix11

      public FloatColumn getCartnTransfMatrix11()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix12

      public FloatColumn getCartnTransfMatrix12()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix13

      public FloatColumn getCartnTransfMatrix13()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix21

      public FloatColumn getCartnTransfMatrix21()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix22

      public FloatColumn getCartnTransfMatrix22()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix23

      public FloatColumn getCartnTransfMatrix23()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix31

      public FloatColumn getCartnTransfMatrix31()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix32

      public FloatColumn getCartnTransfMatrix32()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfMatrix33

      public FloatColumn getCartnTransfMatrix33()
      The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfVector1

      public FloatColumn getCartnTransfVector1()
      The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfVector2

      public FloatColumn getCartnTransfVector2()
      The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransfVector3

      public FloatColumn getCartnTransfVector3()
      The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getCartnTransformAxes

      public StrColumn getCartnTransformAxes()
      A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][].
      Returns:
      StrColumn

    • getFractTransfMatrix11

      public FloatColumn getFractTransfMatrix11()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix12

      public FloatColumn getFractTransfMatrix12()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix13

      public FloatColumn getFractTransfMatrix13()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix21

      public FloatColumn getFractTransfMatrix21()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix22

      public FloatColumn getFractTransfMatrix22()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix23

      public FloatColumn getFractTransfMatrix23()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix31

      public FloatColumn getFractTransfMatrix31()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix32

      public FloatColumn getFractTransfMatrix32()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfMatrix33

      public FloatColumn getFractTransfMatrix33()
      The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfVector1

      public FloatColumn getFractTransfVector1()
      The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfVector2

      public FloatColumn getFractTransfVector2()
      The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getFractTransfVector3

      public FloatColumn getFractTransfVector3()
      The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
      Returns:
      FloatColumn

    • getSolutionPrimary

      public StrColumn getSolutionPrimary()
      This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. ***
      Returns:
      StrColumn

    • getSolutionSecondary

      public StrColumn getSolutionSecondary()
      This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary. *** This data item would not in general be used in a macromolecular data block. ***
      Returns:
      StrColumn

    • getSolutionHydrogens

      public StrColumn getSolutionHydrogens()
      This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. ***
      Returns:
      StrColumn

    • getSpecialDetails

      public StrColumn getSpecialDetails()
      Additional information about the atomic coordinates not coded elsewhere in the CIF.
      Returns:
      StrColumn