Package org.rcsb.cif.model.generated
Class PdbxDccDensity
- java.lang.Object
-
- org.rcsb.cif.model.BaseCategory
-
- org.rcsb.cif.model.generated.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 ...).
-
-
Field Summary
-
Fields inherited from class org.rcsb.cif.model.BaseCategory
isText, textFields
-
-
Constructor Summary
Constructors Constructor Description PdbxDccDensity(String name)PdbxDccDensity(String name, int rowCount, Object[] encodedColumns)PdbxDccDensity(String name, Map<String,Column> columns)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description FloatColumngetAnisotropy()The anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) calculated by Xtriage.FloatColumngetBisoMax()The maximum isotropic B factor reported in the model file.FloatColumngetBisoMean()The occupancy weighted mean isotropic B factor reported in the model file.FloatColumngetBisoMin()The minimum isotropic B factor reported in the model file.FloatColumngetBmean_Bwilson()The difference between the isotropic B factor and the Bfators from Wilson plot.FloatColumngetBSolvent()One of the scale factors used in the bulk solvent correction (from REFMAC).FloatColumngetBWilson()The estimated B factor from the structure factor file by the Wilson plot (from Xtriage).FloatColumngetBWilsonScale()The scale factor for calculating the B factor by the Wilson plot (from Xtriage).FloatColumngetCorrelationOverall()The overall electron density correlation coefficient.FloatColumngetCruickshankDpiXyz()The DPI on the model determined by REFMAC.StrColumngetDCCVersion()The version of the DCC program.FloatColumngetDpiFreeR()The DPI calculated based on the free set, determined by REFMAC.StrColumngetError()Details of any error or warning messages.FloatColumngetFom()The mean figure of merit after refinement.IntColumngetFreeSetCount()The number of unique reflections for calculating Rfree (testing set) reported in the model file.StrColumngetIceRing()Boolean whether ice ring exists (Y) or not (N) as determined by Xtriage.FloatColumngetIOverSigIDiff()The difference of the <I/SigmaI> in the last two points of the plot of <I/SigmaI> vs resolution (expected to be negative).FloatColumngetIOverSigIMean()The overall mean value of <I/SigmaI> for the reflections.FloatColumngetIOverSigIResh()The <I/SigmaI> at the highest resolution bin calculated by Xtriage.StrColumngetIsoBValueType()The type of B factors (partial or full) for the residue.FloatColumngetKSolvent()One of the scale factors used in the bulk solvent correction (from REFMAC).FloatColumngetLsDResHigh()The highest resolution limit reported in the model file.FloatColumngetLsDResHighSf()The highest resolution limit calculated from the structure factor file.FloatColumngetLsDResLowSf()The lowest resolution limit calculated from the structure factor file.FloatColumngetMatthewCoeff()The Matthew coefficient.FloatColumngetMeanE21Abs()Value of <|E^2 - 1|> calculated by Xtriage using acentric reflections.(untwinned: 0.736; perfect twin 0.541).FloatColumngetMeanFSquareOverMeanF2()Value of <F>^2/<F^2> calculated by Xtriage using acentric reflections.(untwinned: 0.785; perfect twin 0.885).FloatColumngetMeanI2OverMeanISquare()Value of <I^2>/<I>^2 calculated by Xtriage using acentric reflections.(untwinned: 2.000; perfect twin 1.500).IntColumngetMFo_DFc_3sigmaNegative()The number of electron density negative peaks less than 3 sigma.IntColumngetMFo_DFc_3sigmaPositive()The number of electron density positive peaks larger than 3 sigma.IntColumngetMFo_DFc_6sigmaNegative()The number of electron density negative peaks less than 6 sigma.IntColumngetMFo_DFc_6sigmaPositive()The number of electron density positive peaks larger than 6 sigma.IntColumngetMtrixNumber()Number of matrix for the NCS groups used in refinement.IntColumngetNcsGroupNumber()Number of NCS groups used in refinement.FloatColumngetOccupancyMax()The maximum occupancy reported in the model file.FloatColumngetOccupancyMean()The averaged occupancy reported in the model file.FloatColumngetOccupancyMin()The minimum occupancy reported in the model file.FloatColumngetPadilla_YeatesL2Mean()Value of <L^2> calculated by Xtriage using acentric reflections.FloatColumngetPadilla_YeatesL2MeanPointless()Value of <L^2> calculated by Pointless using acentric reflections.FloatColumngetPadilla_YeatesLMean()Value of <|L|> calculated by Xtriage using acentric reflections.StrColumngetPartialBValueCorrectionAttempted()Whether attempt to convert the partial to full B factors before validation.StrColumngetPartialBValueCorrectionSuccess()Whether the the conversion of partial B to full B factor is successful (Y) or not (N).StrColumngetPdbid()The PDB id code.StrColumngetPdbtype()The keywords of the structure (taken from _struct_keywords.pdbx_keywords).FloatColumngetProbPeakValue()The probability to tell the existence of translational pseudo symmetry.FloatColumngetRealSpaceROverall()The overall real space R factor.StrColumngetReflectionStatusArchived()Whether the status is of reflection is archived (Y) or not (N).StrColumngetReflectionStatusUsed()Whether the status of the reflection is used (Y) or not (N).StrColumngetReflnsTwin()Boolean (Y/N) whether the twin is reported.FloatColumngetRfree_Rwork()The difference between reported Rfree and reported Rwork.FloatColumngetRValueRFree()The Rfree reported in the model file.FloatColumngetRValueRWork()The Rwork reported in the model file.FloatColumngetSolventContent()The solvent content.StrColumngetSpaceGroupNameH_M()Hermann-Mauguin space-group symbol reported in the model file.StrColumngetSpaceGroupPointless()Hermann-Mauguin space-group symbol calculated by the POINTLESS program using the structure factor file.IntColumngetTlsGroupNumber()Number of TLS groups used in refinement.StrColumngetTLSRefinementReported()Whether TLS was used in refinement.StrColumngetTranslationalPseudoSymmetry()Boolean whether translational pseudo symmetry exist (Y) or not (N) as determined by Xtriage.StrColumngetTwinByXtriage()Boolean (Y/N) whether twin is detected by Xtriage.StrColumngetTwinFraction()Twin fractions determined by REFMAC.FloatColumngetTwinFractionXtriage()The twin fraction determined by Xtriage.StrColumngetTwinOperator()Twin operators determined by REFMAC.StrColumngetTwinOperatorXtriage()A list of the twin operators determined by Xtriage.FloatColumngetTwinRfactor()The Rfactor calculated by Xtriage using the twin operator related data.StrColumngetTwinType()Type of twin (merohedral,Pseudo-merohedral or non-merohedral) determined by Xtriage.StrColumngetUnitCell()The unit cell parameters (a b c alpha beta gamma) separated by a space.FloatColumngetWavelength()The wavelength reported from the model file.IntColumngetWorkingSetCount()The number of unique reflections for refinement (working set) reported in the model file.FloatColumngetZ_score()Z-scores are computed (by Xtriage) on the basis of a Bernoulli model assuming independence of weak reflections with respect to anisotropy.FloatColumngetZScoreLTest()Multivariate Z score for the L-test calculated by Xtriage using acentric reflections.-
Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined
-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get
-
-
-
-
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
-
-