Package org.rcsb.cif.model.generated
Class Refln
- java.lang.Object
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- org.rcsb.cif.model.BaseCategory
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- org.rcsb.cif.model.generated.Refln
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- 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.
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Field Summary
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Fields inherited from class org.rcsb.cif.model.BaseCategory
isText, textFields
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description FloatColumngetACalc()The calculated value of structure-factor component A in electrons.FloatColumngetACalcAu()The calculated value of structure-factor component A in arbitrary units.FloatColumngetAMeas()The measured value of structure-factor component A in electrons.FloatColumngetAMeasAu()The measured value of structure-factor component A in arbitrary units.FloatColumngetBCalc()The calculated value of structure-factor component B in electrons.FloatColumngetBCalcAu()The calculated value of structure-factor component B in arbitrary units.FloatColumngetBMeas()The measured value of structure-factor component B in electrons.FloatColumngetBMeasAu()The measured value of structure-factor component B in arbitrary units.StrColumngetClassCode()The code identifying the class to which this reflection has been assigned.StrColumngetCrystalId()This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.FloatColumngetDSpacing()The d spacing in angstroms for this reflection.FloatColumngetFCalc()The calculated value of the structure factor in electrons.FloatColumngetFCalcAu()The calculated value of the structure factor in arbitrary units.FloatColumngetFMeas()The measured value of the structure factor in electrons.FloatColumngetFMeasAu()The measured value of the structure factor in arbitrary units.FloatColumngetFMeasSigma()The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons.FloatColumngetFMeasSigmaAu()The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units.FloatColumngetFom()The figure of merit m for this reflection.FloatColumngetFSquaredCalc()The calculated value of the squared structure factor in electrons squared.FloatColumngetFSquaredMeas()The measured value of the squared structure factor in electrons squared.FloatColumngetFSquaredSigma()The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared.StrColumngetIncludeStatus()Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.IntColumngetIndexH()Miller index h of the reflection.IntColumngetIndexK()Miller index k of the reflection.IntColumngetIndexL()Miller index l of the reflection.FloatColumngetIntensityCalc()The calculated value of the intensity in the same units as _refln.intensity_meas.FloatColumngetIntensityMeas()The measured value of the intensity.FloatColumngetIntensitySigma()The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas.FloatColumngetMeanPathLengthTbar()Mean path length in millimetres through the crystal for this reflection.FloatColumngetPdbxAnomalousDiff()The measured anomalous difference.FloatColumngetPdbxAnomalousDiffSigma()The standard deviation in the anomalous difference.FloatColumngetPdbxAnomDifference()The amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).FloatColumngetPdbxAnomDifferenceSigma()The the standard deviation of the amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).FloatColumngetPdbxCosPhaseCalc()The cosine of the calculated phaseFloatColumngetPdbxDELFWT()The weighted structure factor amplitude for the mFo-DFc map.FloatColumngetPdbxDELPHWT()The weighted phase for the mFo-DFc map.StrColumngetPdbxDiffrnId()An optional identifier for the diffraction data set containing this reflection.FloatColumngetPdbxFCalcPartSolvent()The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model.FloatColumngetPdbxFCalcWithSolvent()The calculated value of the structure factor in arbitrary units including the contribution of the solvent model.FloatColumngetPdbxFiberCoordinate()The coordinate position in reciprocal space along the fiber layer line for this reflection.FloatColumngetPdbxFiberFMeasAu()The measured diffraction amplitude for this fiber reflection in arbitrary units.IntColumngetPdbxFiberLayer()The fiber layer line for this reflection.FloatColumngetPdbxFMinus()The structure factor F(-h,-k,-l) of the Friedel pair.FloatColumngetPdbxFMinusSigma()The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair.FloatColumngetPdbxFPlus()The structure factor F(h,k,l) of the Friedel pair.FloatColumngetPdbxFPlusSigma()The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair.FloatColumngetPdbxFWT()The weighted structure factor amplitude for the 2mFo-DFc map.FloatColumngetPdbxHLAIso()The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection.FloatColumngetPdbxHLBIso()The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection.FloatColumngetPdbxHLCIso()The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection.FloatColumngetPdbxHLDIso()The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection.FloatColumngetPdbxIMinus()The intensity of the I(-h,-k,-l) partner of the Friedel pair.FloatColumngetPdbxIMinusSigma()The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair.FloatColumngetPdbxIPlus()The intensity of the I(h,k,l) partner of the Friedel pair.FloatColumngetPdbxIPlusSigma()The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair.FloatColumngetPdbxPhaseCalcPartSolvent()The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model.FloatColumngetPdbxPhaseCalcWithSolvent()The calculated structure-factor phase in degrees including the contribution of the solvent model.FloatColumngetPdbxPhaseCycle()The phasing cycle.FloatColumngetPdbxPHWT()The weighted phase for the 2mFo-DFc map.IntColumngetPdbxRFreeFlag()The R-free flag originally assigned to the reflection.FloatColumngetPdbxSinPhaseCalc()The sine of the calculated phase.FloatColumngetPhaseCalc()The calculated structure-factor phase in degrees.FloatColumngetPhaseMeas()The measured structure-factor phase in degrees.StrColumngetRefinementStatus()Status of a reflection in the structure-refinement process.StrColumngetScaleGroupCode()This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category.FloatColumngetSintOverLambda()The (sin theta)/lambda value in reciprocal angstroms for this reflection.StrColumngetStatus()Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.IntColumngetSymmetryEpsilon()The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations.IntColumngetSymmetryMultiplicity()The number of symmetry-equivalent reflections.FloatColumngetWavelength()The mean wavelength in angstroms of radiation used to measure this reflection.StrColumngetWavelengthId()This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category.-
Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get
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Method Detail
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getACalc
public FloatColumn getACalc()
The calculated value of structure-factor component A in electrons. A = |F|cos(phase)- Returns:
- FloatColumn
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getACalcAu
public FloatColumn getACalcAu()
The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase)- Returns:
- FloatColumn
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getAMeas
public FloatColumn getAMeas()
The measured value of structure-factor component A in electrons. A = |F|cos(phase)- Returns:
- FloatColumn
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getAMeasAu
public FloatColumn getAMeasAu()
The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase)- Returns:
- FloatColumn
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getBCalc
public FloatColumn getBCalc()
The calculated value of structure-factor component B in electrons. B = |F|sin(phase)- Returns:
- FloatColumn
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getBCalcAu
public FloatColumn getBCalcAu()
The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase)- Returns:
- FloatColumn
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getBMeas
public FloatColumn getBMeas()
The measured value of structure-factor component B in electrons. B = |F|sin(phase)- Returns:
- FloatColumn
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getBMeasAu
public FloatColumn getBMeasAu()
The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase)- Returns:
- FloatColumn
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getCrystalId
public StrColumn getCrystalId()
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.- Returns:
- StrColumn
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getFCalc
public FloatColumn getFCalc()
The calculated value of the structure factor in electrons.- Returns:
- FloatColumn
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getFCalcAu
public FloatColumn getFCalcAu()
The calculated value of the structure factor in arbitrary units.- Returns:
- FloatColumn
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getFMeas
public FloatColumn getFMeas()
The measured value of the structure factor in electrons.- Returns:
- FloatColumn
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getFMeasAu
public FloatColumn getFMeasAu()
The measured value of the structure factor in arbitrary units.- Returns:
- FloatColumn
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getFMeasSigma
public FloatColumn getFMeasSigma()
The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons.- Returns:
- FloatColumn
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getFMeasSigmaAu
public FloatColumn getFMeasSigmaAu()
The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units.- Returns:
- FloatColumn
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getFSquaredCalc
public FloatColumn getFSquaredCalc()
The calculated value of the squared structure factor in electrons squared.- Returns:
- FloatColumn
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getFSquaredMeas
public FloatColumn getFSquaredMeas()
The measured value of the squared structure factor in electrons squared.- Returns:
- FloatColumn
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getFSquaredSigma
public FloatColumn getFSquaredSigma()
The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared.- Returns:
- FloatColumn
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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
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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
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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
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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
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getIntensityCalc
public FloatColumn getIntensityCalc()
The calculated value of the intensity in the same units as _refln.intensity_meas.- Returns:
- FloatColumn
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getIntensityMeas
public FloatColumn getIntensityMeas()
The measured value of the intensity.- Returns:
- FloatColumn
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getIntensitySigma
public FloatColumn getIntensitySigma()
The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas.- Returns:
- FloatColumn
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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
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getPhaseCalc
public FloatColumn getPhaseCalc()
The calculated structure-factor phase in degrees.- Returns:
- FloatColumn
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getPhaseMeas
public FloatColumn getPhaseMeas()
The measured structure-factor phase in degrees.- Returns:
- FloatColumn
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getRefinementStatus
public StrColumn getRefinementStatus()
Status of a reflection in the structure-refinement process.- Returns:
- StrColumn
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getScaleGroupCode
public StrColumn getScaleGroupCode()
This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category.- Returns:
- StrColumn
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getSintOverLambda
public FloatColumn getSintOverLambda()
The (sin theta)/lambda value in reciprocal angstroms for this reflection.- Returns:
- FloatColumn
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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
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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
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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
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getWavelengthId
public StrColumn getWavelengthId()
This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category.- Returns:
- StrColumn
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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
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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
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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
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getMeanPathLengthTbar
public FloatColumn getMeanPathLengthTbar()
Mean path length in millimetres through the crystal for this reflection.- Returns:
- FloatColumn
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getPdbxFCalcPartSolvent
public FloatColumn getPdbxFCalcPartSolvent()
The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model.- Returns:
- FloatColumn
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getPdbxPhaseCalcPartSolvent
public FloatColumn getPdbxPhaseCalcPartSolvent()
The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model.- Returns:
- FloatColumn
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getPdbxFCalcWithSolvent
public FloatColumn getPdbxFCalcWithSolvent()
The calculated value of the structure factor in arbitrary units including the contribution of the solvent model.- Returns:
- FloatColumn
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getPdbxPhaseCalcWithSolvent
public FloatColumn getPdbxPhaseCalcWithSolvent()
The calculated structure-factor phase in degrees including the contribution of the solvent model.- Returns:
- FloatColumn
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getPdbxAnomDifference
public FloatColumn getPdbxAnomDifference()
The amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).- Returns:
- FloatColumn
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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
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getPdbxIPlus
public FloatColumn getPdbxIPlus()
The intensity of the I(h,k,l) partner of the Friedel pair.- Returns:
- FloatColumn
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getPdbxIMinus
public FloatColumn getPdbxIMinus()
The intensity of the I(-h,-k,-l) partner of the Friedel pair.- Returns:
- FloatColumn
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getPdbxFPlus
public FloatColumn getPdbxFPlus()
The structure factor F(h,k,l) of the Friedel pair.- Returns:
- FloatColumn
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getPdbxFMinus
public FloatColumn getPdbxFMinus()
The structure factor F(-h,-k,-l) of the Friedel pair.- Returns:
- FloatColumn
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getPdbxIPlusSigma
public FloatColumn getPdbxIPlusSigma()
The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair.- Returns:
- FloatColumn
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getPdbxIMinusSigma
public FloatColumn getPdbxIMinusSigma()
The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair.- Returns:
- FloatColumn
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getPdbxFMinusSigma
public FloatColumn getPdbxFMinusSigma()
The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair.- Returns:
- FloatColumn
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getPdbxFPlusSigma
public FloatColumn getPdbxFPlusSigma()
The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair.- Returns:
- FloatColumn
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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
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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
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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
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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
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getPdbxFiberLayer
public IntColumn getPdbxFiberLayer()
The fiber layer line for this reflection.- Returns:
- IntColumn
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getPdbxFiberCoordinate
public FloatColumn getPdbxFiberCoordinate()
The coordinate position in reciprocal space along the fiber layer line for this reflection.- Returns:
- FloatColumn
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getPdbxFiberFMeasAu
public FloatColumn getPdbxFiberFMeasAu()
The measured diffraction amplitude for this fiber reflection in arbitrary units.- Returns:
- FloatColumn
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getPdbxFWT
public FloatColumn getPdbxFWT()
The weighted structure factor amplitude for the 2mFo-DFc map.- Returns:
- FloatColumn
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getPdbxPHWT
public FloatColumn getPdbxPHWT()
The weighted phase for the 2mFo-DFc map.- Returns:
- FloatColumn
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getPdbxDELFWT
public FloatColumn getPdbxDELFWT()
The weighted structure factor amplitude for the mFo-DFc map.- Returns:
- FloatColumn
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getPdbxDELPHWT
public FloatColumn getPdbxDELPHWT()
The weighted phase for the mFo-DFc map.- Returns:
- FloatColumn
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getPdbxDiffrnId
public StrColumn getPdbxDiffrnId()
An optional identifier for the diffraction data set containing this reflection.- Returns:
- StrColumn
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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
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getPdbxAnomalousDiff
public FloatColumn getPdbxAnomalousDiff()
The measured anomalous difference.- Returns:
- FloatColumn
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getPdbxAnomalousDiffSigma
public FloatColumn getPdbxAnomalousDiffSigma()
The standard deviation in the anomalous difference.- Returns:
- FloatColumn
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getPdbxPhaseCycle
public FloatColumn getPdbxPhaseCycle()
The phasing cycle.- Returns:
- FloatColumn
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getPdbxCosPhaseCalc
public FloatColumn getPdbxCosPhaseCalc()
The cosine of the calculated phase- Returns:
- FloatColumn
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getPdbxSinPhaseCalc
public FloatColumn getPdbxSinPhaseCalc()
The sine of the calculated phase.- Returns:
- FloatColumn
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