Package org.rcsb.cif.schema.core

Class Reflns

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.Reflns
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Reflns
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items used to specify parameters for the complete set of reflections used in the structure refinement process. Note that these parameters are often similar measures to those defined in the DIFFRN categories, but differ in that the parameters refer to the reduced/transformed reflections which have been used to refine the atom site data in the ATOM_SITE category. The DIFFRN definitions refer to the diffraction measurements and the raw reflection data.

  • Constructor Details

  • Method Details

    • getApplyDispersionToFcalc

      public StrColumn getApplyDispersionToFcalc()
      Yes or No flag on whether the anomalous dispersion scattering components will be applied in the F complex calculation. See _refln.F_complex
      Returns:
      StrColumn

    • getDResolutionHigh

      public FloatColumn getDResolutionHigh()
      Highest resolution for the final REFLN data set. This corresponds to the smallest interpanar d value.
      Returns:
      FloatColumn

    • getDResolutionLow

      public FloatColumn getDResolutionLow()
      Lowest resolution for the final REFLN data set. This corresponds to the largest interpanar d value.
      Returns:
      FloatColumn

    • getFriedelCoverage

      public FloatColumn getFriedelCoverage()
      The proportion of Friedel related reflections present in the number of the 'independent reflections' specified by the item _reflns.number_total. This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. (a) For centrosymmetric structures its value is necessarily equal to 0.0 as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, _reflns.Friedel_coverage is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, the value will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are non-zero, they are when l=0. (d) For a crystal in the group Pmm2 measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for _reflns.Friedel_coverage.
      Returns:
      FloatColumn

    • getFriedelFractionFull

      public FloatColumn getFriedelFractionFull()
      The ratio of Friedel pairs measured to _diffrn_reflns.theta_full to the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns.Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be given as not-applicable '.'
      Returns:
      FloatColumn

    • getFriedelFractionMax

      public FloatColumn getFriedelFractionMax()
      The ratio of Friedel pairs measured to _diffrn_reflns.theta_max to the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns.Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be given as not-applicable '.'
      Returns:
      FloatColumn

    • getLimitHMax

      public IntColumn getLimitHMax()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitHMin

      public IntColumn getLimitHMin()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitKMax

      public IntColumn getLimitKMax()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitKMin

      public IntColumn getLimitKMin()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitLMax

      public IntColumn getLimitLMax()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitLMin

      public IntColumn getLimitLMin()
      The index of a reciprocal space vector.
      Returns:
      IntColumn

    • getLimitMax

      public FloatColumn getLimitMax()
      Maximum Miller indices of refined diffraction reflections.
      Returns:
      FloatColumn

    • getNumberObs

      public IntColumn getNumberObs()
      Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which are significantly intense (see _reflns.threshold_expression). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending to the nature of the structure and the procedures used.
      Returns:
      IntColumn

    • getNumberGt

      public IntColumn getNumberGt()
      Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which are significantly intense (see _reflns.threshold_expression). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending to the nature of the structure and the procedures used.
      Returns:
      IntColumn

    • getNumberAll

      public IntColumn getNumberAll()
      Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending to the nature of the structure and the procedures used.
      Returns:
      IntColumn

    • getNumberTotal

      public IntColumn getNumberTotal()
      Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending to the nature of the structure and the procedures used.
      Returns:
      IntColumn

    • getDetails

      public StrColumn getDetails()
      Description of the properties of the REFLN reflection list that is not given in other data items. Should include details about the averaging of symmetry-equivalent reflections including Friedel pairs.
      Returns:
      StrColumn

    • getSpecialDetails

      public StrColumn getSpecialDetails()
      Description of the properties of the REFLN reflection list that is not given in other data items. Should include details about the averaging of symmetry-equivalent reflections including Friedel pairs.
      Returns:
      StrColumn

    • getObservedCriterion

      public StrColumn getObservedCriterion()
      Description of the criterion used to classify a reflection as having a "significant intensity". This criterion is usually expressed in terms of a u(I) or u(F) threshold. "u" is the standard uncertainty.
      Returns:
      StrColumn

    • getThresholdExpression

      public StrColumn getThresholdExpression()
      Description of the criterion used to classify a reflection as having a "significant intensity". This criterion is usually expressed in terms of a u(I) or u(F) threshold. "u" is the standard uncertainty.
      Returns:
      StrColumn