Package org.rcsb.cif.schema.mm

Class ReflnsShell

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.ReflnsShell
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ReflnsShell
extends DelegatingCategory
Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getDResHigh

      public FloatColumn getDResHigh()
      The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution.
      Returns:
      FloatColumn

    • getDResLow

      public FloatColumn getDResLow()
      The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution.
      Returns:
      FloatColumn

    • getMeanIOverSigIAll

      public FloatColumn getMeanIOverSigIAll()
      The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell.
      Returns:
      FloatColumn

    • getMeanIOverSigIObs

      public FloatColumn getMeanIOverSigIObs()
      The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell.
      Returns:
      FloatColumn

    • getNumberMeasuredAll

      public IntColumn getNumberMeasuredAll()
      The total number of reflections measured for this shell.
      Returns:
      IntColumn

    • getNumberMeasuredObs

      public IntColumn getNumberMeasuredObs()
      The number of reflections classified as 'observed' (see _reflns.observed_criterion) for this shell.
      Returns:
      IntColumn

    • getNumberPossible

      public IntColumn getNumberPossible()
      The number of unique reflections it is possible to measure in this shell.
      Returns:
      IntColumn

    • getNumberUniqueAll

      public IntColumn getNumberUniqueAll()
      The total number of measured reflections which are symmetry- unique after merging for this shell.
      Returns:
      IntColumn

    • getNumberUniqueObs

      public IntColumn getNumberUniqueObs()
      The total number of measured reflections classified as 'observed' (see _reflns.observed_criterion) which are symmetry-unique after merging for this shell.
      Returns:
      IntColumn

    • getPercentPossibleAll

      public FloatColumn getPercentPossibleAll()
      The percentage of geometrically possible reflections represented by all reflections measured for this shell.
      Returns:
      FloatColumn

    • getPercentPossibleObs

      public FloatColumn getPercentPossibleObs()
      The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns.observed_criterion) for this shell.
      Returns:
      FloatColumn

    • getRmergeFAll

      public FloatColumn getRmergeFAll()
      Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low. sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection
      Returns:
      FloatColumn

    • getRmergeFObs

      public FloatColumn getRmergeFObs()
      Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection
      Returns:
      FloatColumn

    • getRmergeIAll

      public FloatColumn getRmergeIAll()
      The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection
      Returns:
      FloatColumn

    • getRmergeIObs

      public FloatColumn getRmergeIObs()
      The value of Rmerge(I) for reflections classified as 'observed' (see _reflns.observed_criterion) in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection
      Returns:
      FloatColumn

    • getMeanIOverSigIGt

      public FloatColumn getMeanIOverSigIGt()
      The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell.
      Returns:
      FloatColumn

    • getMeanIOverUIAll

      public FloatColumn getMeanIOverUIAll()
      The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell.
      Returns:
      FloatColumn

    • getMeanIOverUIGt

      public FloatColumn getMeanIOverUIGt()
      The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell.
      Returns:
      FloatColumn

    • getNumberMeasuredGt

      public IntColumn getNumberMeasuredGt()
      The number of significantly intense reflections (see _reflns.threshold_expression) measured for this shell.
      Returns:
      IntColumn

    • getNumberUniqueGt

      public IntColumn getNumberUniqueGt()
      The total number of significantly intense reflections (see _reflns.threshold_expression) resulting from merging measured symmetry-equivalent reflections for this resolution shell.
      Returns:
      IntColumn

    • getPercentPossibleGt

      public FloatColumn getPercentPossibleGt()
      The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns.threshold_expression) measured for this shell.
      Returns:
      FloatColumn

    • getRmergeFGt

      public FloatColumn getRmergeFGt()
      The value of Rmerge(F) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | F~j~ - <F> | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ <F> ) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection.
      Returns:
      FloatColumn

    • getRmergeIGt

      public FloatColumn getRmergeIGt()
      The value of Rmerge(I) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | I~j~ - <I> | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ <I> ) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection.
      Returns:
      FloatColumn

    • getPdbxRedundancy

      public FloatColumn getPdbxRedundancy()
      Redundancy for the current shell.
      Returns:
      FloatColumn

    • getPdbxRsymValue

      public FloatColumn getPdbxRsymValue()
      R sym value in percent.
      Returns:
      FloatColumn

    • getPdbxChiSquared

      public FloatColumn getPdbxChiSquared()
      Chi-squared statistic for this resolution shell.
      Returns:
      FloatColumn

    • getPdbxNetIOverSigmaIAll

      public FloatColumn getPdbxNetIOverSigmaIAll()
      The mean of the ratio of the intensities to their standard uncertainties of all reflections in the resolution shell. _reflns_shell.pdbx_netI_over_sigmaI_all = <I/sigma(I)>
      Returns:
      FloatColumn

    • getPdbxNetIOverSigmaIObs

      public FloatColumn getPdbxNetIOverSigmaIObs()
      The mean of the ratio of the intensities to their standard uncertainties of observed reflections (see _reflns.observed_criterion) in the resolution shell. _reflns_shell.pdbx_netI_over_sigmaI_obs = <I/sigma(I)>
      Returns:
      FloatColumn

    • getPdbxRrimIAll

      public FloatColumn getPdbxRrimIAll()
      The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in a given shell. sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = -------------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
      Returns:
      FloatColumn

    • getPdbxRpimIAll

      public FloatColumn getPdbxRpimIAll()
      The precision-indicating merging R factor value Rpim, for merging all intensities in a given shell. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
      Returns:
      FloatColumn

    • getPdbxRejects

      public IntColumn getPdbxRejects()
      The number of rejected reflections in the resolution shell. Reflections may be rejected from scaling by setting the observation criterion, _reflns.observed_criterion.
      Returns:
      IntColumn

    • getPdbxOrdinal

      public IntColumn getPdbxOrdinal()
      An ordinal identifier for this resolution shell.
      Returns:
      IntColumn

    • getPdbxDiffrnId

      public StrColumn getPdbxDiffrnId()
      An identifier for the diffraction data set corresponding to this resolution shell. Multiple diffraction data sets specified as a comma separated list.
      Returns:
      StrColumn

    • getPdbxCCHalf

      public FloatColumn getPdbxCCHalf()
      The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets within the resolution shell. Ref: Karplus & Diederichs (2012), Science 336, 1030-33
      Returns:
      FloatColumn

    • getPdbxCCStar

      public FloatColumn getPdbxCCStar()
      Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets within the resolution shell. CC_star = sqrt(2*CC_half/(1+CC_half)) Ref: Karplus & Diederichs (2012), Science 336, 1030-33
      Returns:
      FloatColumn

    • getPdbxRSplit

      public FloatColumn getPdbxRSplit()
      R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the data within the resolution shell. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
      Returns:
      FloatColumn

    • getPdbxRedundancyReflnsObs

      public FloatColumn getPdbxRedundancyReflnsObs()
      For this shell, the redundancy in the observed reflections.
      Returns:
      FloatColumn

    • getPdbxNumberAnomalous

      public IntColumn getPdbxNumberAnomalous()
      This item is a duplicate of _reflns_shell.number_unique_all, but only for the observed Friedel pairs.
      Returns:
      IntColumn

    • getPdbxRrimIAllAnomalous

      public FloatColumn getPdbxRrimIAllAnomalous()
      This item is the duplicate of _reflns_shell.pdbx_Rrim_I_all, but is limited to observed Friedel pairs.
      Returns:
      FloatColumn

    • getPdbxRpimIAllAnomalous

      public FloatColumn getPdbxRpimIAllAnomalous()
      This item serves the same purpose as _reflns_shell.pdbx_Rpim_I_all, but applies to observed Friedel pairs only.
      Returns:
      FloatColumn

    • getPdbxRmergeIAllAnomalous

      public FloatColumn getPdbxRmergeIAllAnomalous()
      This item is the same as _reflns_shell.pdbx_Rmerge_I_all, but applies to observed Friedel pairs only.
      Returns:
      FloatColumn