Class PdbxDccDensity

  • All Implemented Interfaces:
    Category

    @Generated("org.rcsb.cif.generator.SchemaGenerator")
    public class PdbxDccDensity
    extends BaseCategory
    Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...).
    • Constructor Detail

      • PdbxDccDensity

        public PdbxDccDensity​(String name,
                              int rowCount,
                              Object[] encodedColumns)
      • PdbxDccDensity

        public PdbxDccDensity​(String name)
    • Method Detail

      • 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