Package org.rcsb.cif.schema.mm

Class Refln

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.Refln
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Refln
extends DelegatingCategory
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.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • 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