Class Refln

  • All Implemented Interfaces:
    Category

    @Generated("org.rcsb.cif.generator.SchemaGenerator")
    public class Refln
    extends BaseCategory
    Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
    • Method Detail

      • getACalc

        public FloatColumn getACalc()
        The calculated value of structure-factor component A in electrons. A = |F|cos(phase)
        Returns:
        FloatColumn
      • getACalcAu

        public FloatColumn getACalcAu()
        The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase)
        Returns:
        FloatColumn
      • getAMeas

        public FloatColumn getAMeas()
        The measured value of structure-factor component A in electrons. A = |F|cos(phase)
        Returns:
        FloatColumn
      • getAMeasAu

        public FloatColumn getAMeasAu()
        The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase)
        Returns:
        FloatColumn
      • getBCalc

        public FloatColumn getBCalc()
        The calculated value of structure-factor component B in electrons. B = |F|sin(phase)
        Returns:
        FloatColumn
      • getBCalcAu

        public FloatColumn getBCalcAu()
        The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase)
        Returns:
        FloatColumn
      • getBMeas

        public FloatColumn getBMeas()
        The measured value of structure-factor component B in electrons. B = |F|sin(phase)
        Returns:
        FloatColumn
      • getBMeasAu

        public FloatColumn getBMeasAu()
        The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase)
        Returns:
        FloatColumn
      • getCrystalId

        public StrColumn getCrystalId()
        This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
        Returns:
        StrColumn
      • getFCalc

        public FloatColumn getFCalc()
        The calculated value of the structure factor in electrons.
        Returns:
        FloatColumn
      • getFCalcAu

        public FloatColumn getFCalcAu()
        The calculated value of the structure factor in arbitrary units.
        Returns:
        FloatColumn
      • getFMeas

        public FloatColumn getFMeas()
        The measured value of the structure factor in electrons.
        Returns:
        FloatColumn
      • getFMeasAu

        public FloatColumn getFMeasAu()
        The measured value of the structure factor in arbitrary units.
        Returns:
        FloatColumn
      • getFMeasSigma

        public FloatColumn getFMeasSigma()
        The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons.
        Returns:
        FloatColumn
      • getFMeasSigmaAu

        public FloatColumn getFMeasSigmaAu()
        The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units.
        Returns:
        FloatColumn
      • getFSquaredCalc

        public FloatColumn getFSquaredCalc()
        The calculated value of the squared structure factor in electrons squared.
        Returns:
        FloatColumn
      • getFSquaredMeas

        public FloatColumn getFSquaredMeas()
        The measured value of the squared structure factor in electrons squared.
        Returns:
        FloatColumn
      • getFSquaredSigma

        public FloatColumn getFSquaredSigma()
        The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared.
        Returns:
        FloatColumn
      • getFom

        public FloatColumn getFom()
        The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi.
        Returns:
        FloatColumn
      • getIndexH

        public IntColumn getIndexH()
        Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
        Returns:
        IntColumn
      • getIndexK

        public IntColumn getIndexK()
        Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
        Returns:
        IntColumn
      • getIndexL

        public IntColumn getIndexL()
        Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
        Returns:
        IntColumn
      • getIntensityCalc

        public FloatColumn getIntensityCalc()
        The calculated value of the intensity in the same units as _refln.intensity_meas.
        Returns:
        FloatColumn
      • getIntensityMeas

        public FloatColumn getIntensityMeas()
        The measured value of the intensity.
        Returns:
        FloatColumn
      • getIntensitySigma

        public FloatColumn getIntensitySigma()
        The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas.
        Returns:
        FloatColumn
      • getStatus

        public StrColumn getStatus()
        Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.
        Returns:
        StrColumn
      • getPhaseCalc

        public FloatColumn getPhaseCalc()
        The calculated structure-factor phase in degrees.
        Returns:
        FloatColumn
      • getPhaseMeas

        public FloatColumn getPhaseMeas()
        The measured structure-factor phase in degrees.
        Returns:
        FloatColumn
      • getRefinementStatus

        public StrColumn getRefinementStatus()
        Status of a reflection in the structure-refinement process.
        Returns:
        StrColumn
      • getScaleGroupCode

        public StrColumn getScaleGroupCode()
        This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category.
        Returns:
        StrColumn
      • getSintOverLambda

        public FloatColumn getSintOverLambda()
        The (sin theta)/lambda value in reciprocal angstroms for this reflection.
        Returns:
        FloatColumn
      • getSymmetryEpsilon

        public IntColumn getSymmetryEpsilon()
        The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations.
        Returns:
        IntColumn
      • getSymmetryMultiplicity

        public IntColumn getSymmetryMultiplicity()
        The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship.
        Returns:
        IntColumn
      • getWavelength

        public FloatColumn getWavelength()
        The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method.
        Returns:
        FloatColumn
      • getWavelengthId

        public StrColumn getWavelengthId()
        This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category.
        Returns:
        StrColumn
      • getClassCode

        public StrColumn getClassCode()
        The code identifying the class to which this reflection has been assigned. This code must match a value of _reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice.
        Returns:
        StrColumn
      • getDSpacing

        public FloatColumn getDSpacing()
        The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression _refln.d_spacing = 2/(_refln.sint/lambda).
        Returns:
        FloatColumn
      • getIncludeStatus

        public StrColumn getIncludeStatus()
        Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.
        Returns:
        StrColumn
      • getMeanPathLengthTbar

        public FloatColumn getMeanPathLengthTbar()
        Mean path length in millimetres through the crystal for this reflection.
        Returns:
        FloatColumn
      • getPdbxFCalcPartSolvent

        public FloatColumn getPdbxFCalcPartSolvent()
        The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model.
        Returns:
        FloatColumn
      • getPdbxPhaseCalcPartSolvent

        public FloatColumn getPdbxPhaseCalcPartSolvent()
        The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model.
        Returns:
        FloatColumn
      • getPdbxFCalcWithSolvent

        public FloatColumn getPdbxFCalcWithSolvent()
        The calculated value of the structure factor in arbitrary units including the contribution of the solvent model.
        Returns:
        FloatColumn
      • getPdbxPhaseCalcWithSolvent

        public FloatColumn getPdbxPhaseCalcWithSolvent()
        The calculated structure-factor phase in degrees including the contribution of the solvent model.
        Returns:
        FloatColumn
      • getPdbxAnomDifference

        public FloatColumn getPdbxAnomDifference()
        The amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).
        Returns:
        FloatColumn
      • getPdbxAnomDifferenceSigma

        public FloatColumn getPdbxAnomDifferenceSigma()
        The the standard deviation of the amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).
        Returns:
        FloatColumn
      • getPdbxIPlus

        public FloatColumn getPdbxIPlus()
        The intensity of the I(h,k,l) partner of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxIMinus

        public FloatColumn getPdbxIMinus()
        The intensity of the I(-h,-k,-l) partner of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxFPlus

        public FloatColumn getPdbxFPlus()
        The structure factor F(h,k,l) of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxFMinus

        public FloatColumn getPdbxFMinus()
        The structure factor F(-h,-k,-l) of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxIPlusSigma

        public FloatColumn getPdbxIPlusSigma()
        The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxIMinusSigma

        public FloatColumn getPdbxIMinusSigma()
        The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxFMinusSigma

        public FloatColumn getPdbxFMinusSigma()
        The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxFPlusSigma

        public FloatColumn getPdbxFPlusSigma()
        The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair.
        Returns:
        FloatColumn
      • getPdbxHLAIso

        public FloatColumn getPdbxHLAIso()
        The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
        Returns:
        FloatColumn
      • getPdbxHLBIso

        public FloatColumn getPdbxHLBIso()
        The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
        Returns:
        FloatColumn
      • getPdbxHLCIso

        public FloatColumn getPdbxHLCIso()
        The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
        Returns:
        FloatColumn
      • getPdbxHLDIso

        public FloatColumn getPdbxHLDIso()
        The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
        Returns:
        FloatColumn
      • getPdbxFiberLayer

        public IntColumn getPdbxFiberLayer()
        The fiber layer line for this reflection.
        Returns:
        IntColumn
      • getPdbxFiberCoordinate

        public FloatColumn getPdbxFiberCoordinate()
        The coordinate position in reciprocal space along the fiber layer line for this reflection.
        Returns:
        FloatColumn
      • getPdbxFiberFMeasAu

        public FloatColumn getPdbxFiberFMeasAu()
        The measured diffraction amplitude for this fiber reflection in arbitrary units.
        Returns:
        FloatColumn
      • getPdbxFWT

        public FloatColumn getPdbxFWT()
        The weighted structure factor amplitude for the 2mFo-DFc map.
        Returns:
        FloatColumn
      • getPdbxPHWT

        public FloatColumn getPdbxPHWT()
        The weighted phase for the 2mFo-DFc map.
        Returns:
        FloatColumn
      • getPdbxDELFWT

        public FloatColumn getPdbxDELFWT()
        The weighted structure factor amplitude for the mFo-DFc map.
        Returns:
        FloatColumn
      • getPdbxDELPHWT

        public FloatColumn getPdbxDELPHWT()
        The weighted phase for the mFo-DFc map.
        Returns:
        FloatColumn
      • getPdbxDiffrnId

        public StrColumn getPdbxDiffrnId()
        An optional identifier for the diffraction data set containing this reflection.
        Returns:
        StrColumn
      • getPdbxRFreeFlag

        public IntColumn getPdbxRFreeFlag()
        The R-free flag originally assigned to the reflection. The convention used for labeling the work and test sets differs depending on choice of data processing software and refinement program.
        Returns:
        IntColumn
      • getPdbxAnomalousDiff

        public FloatColumn getPdbxAnomalousDiff()
        The measured anomalous difference.
        Returns:
        FloatColumn
      • getPdbxAnomalousDiffSigma

        public FloatColumn getPdbxAnomalousDiffSigma()
        The standard deviation in the anomalous difference.
        Returns:
        FloatColumn
      • getPdbxPhaseCycle

        public FloatColumn getPdbxPhaseCycle()
        The phasing cycle.
        Returns:
        FloatColumn
      • getPdbxCosPhaseCalc

        public FloatColumn getPdbxCosPhaseCalc()
        The cosine of the calculated phase
        Returns:
        FloatColumn
      • getPdbxSinPhaseCalc

        public FloatColumn getPdbxSinPhaseCalc()
        The sine of the calculated phase.
        Returns:
        FloatColumn