Package org.rcsb.cif.schema.mm

Class PdbxDccDensity

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxDccDensity
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxDccDensity
extends DelegatingCategory
Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...).

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getDCCVersion

      public StrColumn getDCCVersion()
      The version of the DCC program.
      Returns:
      StrColumn

    • getPdbid

      public StrColumn getPdbid()
      The PDB id code.
      Returns:
      StrColumn

    • getPdbtype

      public StrColumn getPdbtype()
      The keywords of the structure (taken from _struct_keywords.pdbx_keywords).
      Returns:
      StrColumn

    • getUnitCell

      public StrColumn getUnitCell()
      The unit cell parameters (a b c alpha beta gamma) separated by a space.
      Returns:
      StrColumn

    • getSpaceGroupNameH_M

      public StrColumn getSpaceGroupNameH_M()
      Hermann-Mauguin space-group symbol reported in the model file.
      Returns:
      StrColumn

    • getSpaceGroupPointless

      public StrColumn getSpaceGroupPointless()
      Hermann-Mauguin space-group symbol calculated by the POINTLESS program using the structure factor file.
      Returns:
      StrColumn

    • getLsDResHigh

      public FloatColumn getLsDResHigh()
      The highest resolution limit reported in the model file.
      Returns:
      FloatColumn

    • getLsDResHighSf

      public FloatColumn getLsDResHighSf()
      The highest resolution limit calculated from the structure factor file.
      Returns:
      FloatColumn

    • getLsDResLowSf

      public FloatColumn getLsDResLowSf()
      The lowest resolution limit calculated from the structure factor file.
      Returns:
      FloatColumn

    • getRValueRWork

      public FloatColumn getRValueRWork()
      The Rwork reported in the model file.
      Returns:
      FloatColumn

    • getRValueRFree

      public FloatColumn getRValueRFree()
      The Rfree reported in the model file.
      Returns:
      FloatColumn

    • getWorkingSetCount

      public IntColumn getWorkingSetCount()
      The number of unique reflections for refinement (working set) reported in the model file.
      Returns:
      IntColumn

    • getFreeSetCount

      public IntColumn getFreeSetCount()
      The number of unique reflections for calculating Rfree (testing set) reported in the model file.
      Returns:
      IntColumn

    • getOccupancyMin

      public FloatColumn getOccupancyMin()
      The minimum occupancy reported in the model file.
      Returns:
      FloatColumn

    • getOccupancyMax

      public FloatColumn getOccupancyMax()
      The maximum occupancy reported in the model file.
      Returns:
      FloatColumn

    • getOccupancyMean

      public FloatColumn getOccupancyMean()
      The averaged occupancy reported in the model file.
      Returns:
      FloatColumn

    • getBisoMin

      public FloatColumn getBisoMin()
      The minimum isotropic B factor reported in the model file.
      Returns:
      FloatColumn

    • getBisoMax

      public FloatColumn getBisoMax()
      The maximum isotropic B factor reported in the model file.
      Returns:
      FloatColumn

    • getBisoMean

      public FloatColumn getBisoMean()
      The occupancy weighted mean isotropic B factor reported in the model file.
      Returns:
      FloatColumn

    • getBWilson

      public FloatColumn getBWilson()
      The estimated B factor from the structure factor file by the Wilson plot (from Xtriage).
      Returns:
      FloatColumn

    • getBWilsonScale

      public FloatColumn getBWilsonScale()
      The scale factor for calculating the B factor by the Wilson plot (from Xtriage).
      Returns:
      FloatColumn

    • getMeanI2OverMeanISquare

      public FloatColumn getMeanI2OverMeanISquare()
      Value of <I^2>/<I>^2 calculated by Xtriage using acentric reflections.(untwinned: 2.000; perfect twin 1.500).
      Returns:
      FloatColumn

    • getMeanFSquareOverMeanF2

      public FloatColumn getMeanFSquareOverMeanF2()
      Value of <F>^2/<F^2> calculated by Xtriage using acentric reflections.(untwinned: 0.785; perfect twin 0.885).
      Returns:
      FloatColumn

    • getMeanE21Abs

      public FloatColumn getMeanE21Abs()
      Value of <|E^2 - 1|> calculated by Xtriage using acentric reflections.(untwinned: 0.736; perfect twin 0.541).
      Returns:
      FloatColumn

    • getPadilla_YeatesLMean

      public FloatColumn getPadilla_YeatesLMean()
      Value of <|L|> calculated by Xtriage using acentric reflections. (untwinned: 0.500; perfect twin: 0.375).
      Returns:
      FloatColumn

    • getPadilla_YeatesL2Mean

      public FloatColumn getPadilla_YeatesL2Mean()
      Value of <L^2> calculated by Xtriage using acentric reflections. (untwinned: 0.333; perfect twin: 0.200).
      Returns:
      FloatColumn

    • getPadilla_YeatesL2MeanPointless

      public FloatColumn getPadilla_YeatesL2MeanPointless()
      Value of <L^2> calculated by Pointless using acentric reflections. (untwinned: 0.333; perfect twin: 0.200).
      Returns:
      FloatColumn

    • getZScoreLTest

      public FloatColumn getZScoreLTest()
      Multivariate Z score for the L-test calculated by Xtriage using acentric reflections. It is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5.
      Returns:
      FloatColumn

    • getTwinType

      public StrColumn getTwinType()
      Type of twin (merohedral,Pseudo-merohedral or non-merohedral) determined by Xtriage.
      Returns:
      StrColumn

    • getTwinOperatorXtriage

      public StrColumn getTwinOperatorXtriage()
      A list of the twin operators determined by Xtriage.
      Returns:
      StrColumn

    • getTwinFractionXtriage

      public FloatColumn getTwinFractionXtriage()
      The twin fraction determined by Xtriage.
      Returns:
      FloatColumn

    • getTwinRfactor

      public FloatColumn getTwinRfactor()
      The Rfactor calculated by Xtriage using the twin operator related data. (Smaller values indicate twins).
      Returns:
      FloatColumn

    • getIOverSigIResh

      public FloatColumn getIOverSigIResh()
      The <I/SigmaI> at the highest resolution bin calculated by Xtriage.
      Returns:
      FloatColumn

    • getIOverSigIDiff

      public FloatColumn getIOverSigIDiff()
      The difference of the <I/SigmaI> in the last two points of the plot of <I/SigmaI> vs resolution (expected to be negative).
      Returns:
      FloatColumn

    • getIOverSigIMean

      public FloatColumn getIOverSigIMean()
      The overall mean value of <I/SigmaI> for the reflections.
      Returns:
      FloatColumn

    • getIceRing

      public StrColumn getIceRing()
      Boolean whether ice ring exists (Y) or not (N) as determined by Xtriage.
      Returns:
      StrColumn

    • getAnisotropy

      public FloatColumn getAnisotropy()
      The anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) calculated by Xtriage.
      Returns:
      FloatColumn

    • getZ_score

      public FloatColumn getZ_score()
      Z-scores are computed (by Xtriage) on the basis of a Bernoulli model assuming independence of weak reflections with respect to anisotropy.
      Returns:
      FloatColumn

    • getProbPeakValue

      public FloatColumn getProbPeakValue()
      The probability to tell the existence of translational pseudo symmetry. p_values smaller than 0.05 (1e-3) might indicate weak (strong) translational pseudo symmetry (by Xtriage).
      Returns:
      FloatColumn

    • getTranslationalPseudoSymmetry

      public StrColumn getTranslationalPseudoSymmetry()
      Boolean whether translational pseudo symmetry exist (Y) or not (N) as determined by Xtriage.
      Returns:
      StrColumn

    • getWavelength

      public FloatColumn getWavelength()
      The wavelength reported from the model file.
      Returns:
      FloatColumn

    • getBSolvent

      public FloatColumn getBSolvent()
      One of the scale factors used in the bulk solvent correction (from REFMAC).
      Returns:
      FloatColumn

    • getKSolvent

      public FloatColumn getKSolvent()
      One of the scale factors used in the bulk solvent correction (from REFMAC).
      Returns:
      FloatColumn

    • getTLSRefinementReported

      public StrColumn getTLSRefinementReported()
      Whether TLS was used in refinement. Y for yes, and N for no.
      Returns:
      StrColumn

    • getPartialBValueCorrectionAttempted

      public StrColumn getPartialBValueCorrectionAttempted()
      Whether attempt to convert the partial to full B factors before validation.
      Returns:
      StrColumn

    • getPartialBValueCorrectionSuccess

      public StrColumn getPartialBValueCorrectionSuccess()
      Whether the the conversion of partial B to full B factor is successful (Y) or not (N).
      Returns:
      StrColumn

    • getReflectionStatusArchived

      public StrColumn getReflectionStatusArchived()
      Whether the status is of reflection is archived (Y) or not (N).
      Returns:
      StrColumn

    • getReflectionStatusUsed

      public StrColumn getReflectionStatusUsed()
      Whether the status of the reflection is used (Y) or not (N).
      Returns:
      StrColumn

    • getIsoBValueType

      public StrColumn getIsoBValueType()
      The type of B factors (partial or full) for the residue.
      Returns:
      StrColumn

    • getReflnsTwin

      public StrColumn getReflnsTwin()
      Boolean (Y/N) whether the twin is reported.
      Returns:
      StrColumn

    • getTwinByXtriage

      public StrColumn getTwinByXtriage()
      Boolean (Y/N) whether twin is detected by Xtriage.
      Returns:
      StrColumn

    • getTwinOperator

      public StrColumn getTwinOperator()
      Twin operators determined by REFMAC.
      Returns:
      StrColumn

    • getTwinFraction

      public StrColumn getTwinFraction()
      Twin fractions determined by REFMAC.
      Returns:
      StrColumn

    • getTlsGroupNumber

      public IntColumn getTlsGroupNumber()
      Number of TLS groups used in refinement.
      Returns:
      IntColumn

    • getNcsGroupNumber

      public IntColumn getNcsGroupNumber()
      Number of NCS groups used in refinement.
      Returns:
      IntColumn

    • getMtrixNumber

      public IntColumn getMtrixNumber()
      Number of matrix for the NCS groups used in refinement.
      Returns:
      IntColumn

    • getMatthewCoeff

      public FloatColumn getMatthewCoeff()
      The Matthew coefficient.
      Returns:
      FloatColumn

    • getSolventContent

      public FloatColumn getSolventContent()
      The solvent content.
      Returns:
      FloatColumn

    • getCruickshankDpiXyz

      public FloatColumn getCruickshankDpiXyz()
      The DPI on the model determined by REFMAC.
      Returns:
      FloatColumn

    • getDpiFreeR

      public FloatColumn getDpiFreeR()
      The DPI calculated based on the free set, determined by REFMAC.
      Returns:
      FloatColumn

    • getFom

      public FloatColumn getFom()
      The mean figure of merit after refinement.
      Returns:
      FloatColumn

    • getCorrelationOverall

      public FloatColumn getCorrelationOverall()
      The overall electron density correlation coefficient.
      Returns:
      FloatColumn

    • getRealSpaceROverall

      public FloatColumn getRealSpaceROverall()
      The overall real space R factor.
      Returns:
      FloatColumn

    • getMFo_DFc_3sigmaPositive

      public IntColumn getMFo_DFc_3sigmaPositive()
      The number of electron density positive peaks larger than 3 sigma.
      Returns:
      IntColumn

    • getMFo_DFc_6sigmaPositive

      public IntColumn getMFo_DFc_6sigmaPositive()
      The number of electron density positive peaks larger than 6 sigma.
      Returns:
      IntColumn

    • getMFo_DFc_3sigmaNegative

      public IntColumn getMFo_DFc_3sigmaNegative()
      The number of electron density negative peaks less than 3 sigma.
      Returns:
      IntColumn

    • getMFo_DFc_6sigmaNegative

      public IntColumn getMFo_DFc_6sigmaNegative()
      The number of electron density negative peaks less than 6 sigma.
      Returns:
      IntColumn

    • getBmean_Bwilson

      public FloatColumn getBmean_Bwilson()
      The difference between the isotropic B factor and the Bfators from Wilson plot.
      Returns:
      FloatColumn

    • getRfree_Rwork

      public FloatColumn getRfree_Rwork()
      The difference between reported Rfree and reported Rwork.
      Returns:
      FloatColumn

    • getError

      public StrColumn getError()
      Details of any error or warning messages.
      Returns:
      StrColumn