mxcubecore.HardwareObjects.XSDataMXv1#

Functions

`showIndent`(outfile, level)
`warnEmptyAttribute`(_strName, _strTypeName)

Classes

`MixedContainer`(category, content_type, name, ...)
`XSDataAtom`([symbol, numberOf, concentration])	This object describes a single atom content (of type 'symbol' i.e 'S') that could be either expressed in concentration if dilute in a solvent (mM) or in number in a structure
`XSDataAtomicComposition`([atom])
`XSDataBeam`([apertureSize, wavelength, ...])	This object contains all the properties related to the beam: - the exposure time (sec) - the flux (photons/sec) - The minimum exposure time permitted by hardware (sec) - The size of the beam (mm x mm) - The wavelength (a) - Transmission in %
`XSDataCell`([length_c, length_b, length_a, ...])	Crystallographic properties
`XSDataChain`([type, numberOfMonomers, ...])	A polymer chain of type 'protein', 'dna' or 'rna' that contains monomers (which number is defined by numberOfMonomers) and a list of heavy atoms.
`XSDataChemicalCompositionMM`([structure, solvent])	This is the composition of a crystal sample of a Macro Molecule (MM stand for Macro Molecule)
`XSDataCollection`([subWedge, sample, ...])	The data collection carried out or to be carried out with a particular sample with specific user inputs defined by the diffraction plan.
`XSDataCollectionPlan`([strategySummary, ...])	The comment can be used for describing exotic data collections, for example without collecting any images.
`XSDataCrystal`([spaceGroup, mosaicity, cell])	Crystallographic properties
`XSDataDetector`([type, twoTheta, ...])	The properties of a detector.
`XSDataDiffractionPlan`([...])	This object contains the main properties a user can parameterize for a crystal characterisation:
`XSDataDozorInput`([configuration, ...])
`XSDataExperimentalCondition`([goniostat, ...])	This object encapsulates all the physical properties of an experiment instrumentation.
`XSDataGeneratePredictionInput`([...])	This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49).
`XSDataGeneratePredictionResult`([status, ...])
`XSDataGoniostat`([phi, kappa, ...])	The properties of a goniostat: - the maximal rotation speed permitted - the minimal width for an oscillation width of subwedge - the name of the rotation axis (typically phi) - the rotation start angle - the rotation end angle
`XSDataImageQualityIndicators`([...])
`XSDataIndexingInput`([configuration, ...])
`XSDataIndexingResult`([status, solution, ...])
`XSDataIndexingSolution`([penalty, number, ...])
`XSDataIndexingSolutionSelected`([penalty, ...])
`XSDataInputCharacterisation`([configuration, ...])
`XSDataInputControlISPyB`([configuration, ...])
`XSDataInputControlImageQualityIndicators`([...])
`XSDataInputControlKappa`([selectedSolution, ...])
`XSDataInputControlXDSGenerateBackgroundImage`([...])
`XSDataInputInducedRadiationProcess`([...])
`XSDataInputReadImageHeader`([configuration, ...])	These two definitions are used by the read image header plugin.
`XSDataInputStrategy`([configuration, ...])
`XSDataInputSubWedgeAssemble`([configuration, ...])	These two definitions are used by the sub wedge assemble plugin.
`XSDataInputSubWedgeMerge`([configuration, ...])	These two definitions are used by the sub wedge merge plugins.
`XSDataIntegrationInput`([configuration, ...])	This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49).
`XSDataIntegrationResult`([status, ...])
`XSDataIntegrationSubWedgeResult`([...])
`XSDataKappaSolution`([settings, phi, kappa])
`XSDataLigand`([numberOfLightAtoms, ...])	A polymer ligand that contains a set of heavy atoms, the number of all the light atoms (weight <= Oxygen) and the number of copies of this particular ligand in the polymer.
`XSDataOrientation`([matrixU, matrixA])
`XSDataResolutionBin`([redundancy, rFriedel, ...])
`XSDataResultCharacterisation`([status, ...])
`XSDataResultControlISPyB`([status, ...])
`XSDataResultControlImageQualityIndicators`([...])
`XSDataResultControlKappa`([status, solution, ...])
`XSDataResultControlXDSGenerateBackgroundImage`([...])
`XSDataResultInducedRadiationProcess`([...])
`XSDataResultReadImageHeader`([status, subWedge])	These two definitions are used by the read image header plugin.
`XSDataResultStrategy`([status, ...])	Several collection plans could be present in case of multi-sweep strategy
`XSDataResultSubWedgeAssemble`([status, subWedge])	These two definitions are used by the sub wedge assemble plugin.
`XSDataResultSubWedgeMerge`([status, subWedge])	These two definitions are used by the sub wedge merge plugins.
`XSDataSample`([susceptibility, omegaMin, ...])	This defines the main properties of a sample: - absorbed dose rate in Gray/sec - shape: the factor that is related to the sample and the beam size (1 if crystal smaller than beam size or = to the ratio of crystal size to the beam size if the beam is smaller then crystal).
`XSDataSampleCrystal`([susceptibility, ...])	A crystal sample.
`XSDataSampleCrystalMM`([susceptibility, ...])	A particular crystal sample that contains a macro molecule defined by its chemical composition.
`XSDataSolvent`([atoms])	Defines the content of the solvent by defining the concentration of elements in millimoles/litre.
`XSDataSpaceGroup`([name, ITNumber])	Crystallographic properties
`XSDataStatisticsIndexing`([spotsUsed, ...])
`XSDataStatisticsIntegration`([...])
`XSDataStatisticsIntegrationAverageAndNumberOfReflections`([...])
`XSDataStatisticsIntegrationPerReflectionType`([...])
`XSDataStatisticsIntegrationPerResolutionBin`([...])
`XSDataStatisticsStrategy`([resolutionBin])
`XSDataStrategySummary`([totalExposureTime, ...])	The attribute "attenuation" in XSDataStrategySummary is deprecated, see bug #379.
`XSDataStructure`([...])	This is the polymer structure composed by a list of chains and a list of ligands.
`XSDataSubWedge`([subWedgeNumber, image, ...])	A subwedge is defined as a list of images that been collected or is to be collected with some particular experimental condition.

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataAtom(symbol=None, numberOf=None, concentration=None)[source]#

Bases: XSData

This object describes a single atom content (of type ‘symbol’ i.e ‘S’) that could be either expressed in concentration if dilute in a solvent (mM) or in number in a structure

property concentration#: Property for concentration

property numberOf#: Property for numberOf

property symbol#: Property for symbol

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataBeam(apertureSize=None, wavelength=None, transmission=None, size=None, minExposureTimePerImage=None, flux=None, exposureTime=None)[source]#

Bases: XSData

This object contains all the properties related to the beam: - the exposure time (sec) - the flux (photons/sec) - The minimum exposure time permitted by hardware (sec) - The size of the beam (mm x mm) - The wavelength (a) - Transmission in %

property apertureSize#: Property for apertureSize

property exposureTime#: Property for exposureTime

property flux#: Property for flux

property minExposureTimePerImage#: Property for minExposureTimePerImage

property size#: Property for size

property transmission#: Property for transmission

property wavelength#: Property for wavelength

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataCell(length_c=None, length_b=None, length_a=None, angle_gamma=None, angle_beta=None, angle_alpha=None)[source]#

Bases: XSData

Crystallographic properties

property angle_alpha#: Property for angle_alpha

property angle_beta#: Property for angle_beta

property angle_gamma#: Property for angle_gamma

property length_a#: Property for length_a

property length_b#: Property for length_b

property length_c#: Property for length_c

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataChain(type=None, numberOfMonomers=None, numberOfCopies=None, heavyAtoms=None)[source]#

Bases: XSData

A polymer chain of type ‘protein’, ‘dna’ or ‘rna’ that contains monomers (which number is defined by numberOfMonomers) and a list of heavy atoms. The number of this is particular chain in the whole polymer is defined by numberOfCopies.

property heavyAtoms#: Property for heavyAtoms

property numberOfCopies#: Property for numberOfCopies

property numberOfMonomers#: Property for numberOfMonomers

property type#: Property for type

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataChemicalCompositionMM(structure=None, solvent=None)[source]#

Bases: XSData

This is the composition of a crystal sample of a Macro Molecule (MM stand for Macro Molecule)

property solvent#: Property for solvent

property structure#: Property for structure

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataCollection(subWedge=None, sample=None, diffractionPlan=None)[source]#

Bases: XSData

The data collection carried out or to be carried out with a particular sample with specific user inputs defined by the diffraction plan.

property diffractionPlan#: Property for diffractionPlan

property sample#: Property for sample

property subWedge#: Property for subWedge

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataCollectionPlan(strategySummary=None, statistics=None, comment=None, collectionStrategy=None, collectionPlanNumber=None)[source]#

Bases: XSData

The comment can be used for describing exotic data collections, for example without collecting any images.

property collectionPlanNumber#: Property for collectionPlanNumber

property collectionStrategy#: Property for collectionStrategy

property comment#: Property for comment

property statistics#: Property for statistics

property strategySummary#: Property for strategySummary

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataCrystal(spaceGroup=None, mosaicity=None, cell=None)[source]#

Bases: XSData

Crystallographic properties

property cell#: Property for cell

property mosaicity#: Property for mosaicity

property spaceGroup#: Property for spaceGroup

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataDetector(type=None, twoTheta=None, serialNumber=None, pixelSizeY=None, pixelSizeX=None, numberPixelY=None, numberPixelX=None, numberBytesInHeader=None, name=None, imageSaturation=None, gain=None, distance=None, dataType=None, byteOrder=None, bin=None, beamPositionY=None, beamPositionX=None)[source]#

Bases: XSData

The properties of a detector.

property beamPositionX#: Property for beamPositionX

property beamPositionY#: Property for beamPositionY

property bin#: Property for bin

property byteOrder#: Property for byteOrder

property dataType#: Property for dataType

property distance#: Property for distance

property gain#: Property for gain

property imageSaturation#: Property for imageSaturation

property name#: Property for name

property numberBytesInHeader#: Property for numberBytesInHeader

property numberPixelX#: Property for numberPixelX

property numberPixelY#: Property for numberPixelY

property pixelSizeX#: Property for pixelSizeX

property pixelSizeY#: Property for pixelSizeY

property serialNumber#: Property for serialNumber

property twoTheta#: Property for twoTheta

property type#: Property for type

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataDiffractionPlan(userDefinedRotationStart=None, userDefinedRotationRange=None, strategyType=None, strategyOption=None, rFriedel=None, requiredResolution=None, requiredMultiplicity=None, requiredCompleteness=None, numberOfPositions=None, minTransmission=None, minExposureTimePerImage=None, maxExposureTimePerDataCollection=None, kappaStrategyOption=None, goniostatMinOscillationWidth=None, goniostatMaxOscillationSpeed=None, forcedSpaceGroup=None, estimateRadiationDamage=None, doseLimit=None, detectorDistanceMin=None, detectorDistanceMax=None, complexity=None, anomalousData=None, aimedResolution=None, aimedMultiplicity=None, aimedIOverSigmaAtHighestResolution=None, aimedCompleteness=None)[source]#

Bases: XSData

This object contains the main properties a user can parameterize for a crystal characterisation:

the aimed* parameters are the parameters that a user would like to reach for a BEST run.
the required* are not yet used (the idea is to warn the user if these parameters cannot be reached)
complexity: BEST complexity input, can be either “none” (always single wedge strategy). “min” (few subwedges) or “full” (many subwedges).
maxExposureTimePerDataCollection is the max total exposure time (shutter open, not including readout time) the crystal can be exposed to the X-ray beam.
forcedSpaceGroup: option to force the space group of the indexing solution
strategyOption: extra option for BEST for more advanced strategies like estimating the sensitivity to radiation damage
anomalousData: Depreccated! Boolean value for enabling anomalous strategy. In the future the strategyOption should be used instead of anomalousData.
estimateRadiationDamage: Boolean value for enabling or disabling the use of Raddose for estimation of radiation damage. If estimateRadiationDamage is enabled also the flux and beamsize must be provided.
detectorDistanceMin and detectorDistanceMax: optimal input to BEST for limiting the calculated strategy resolution to be in the range of the detector displacements with respect to the sample.
minTransmission: optional input for BEST
kappaStrategyOption: optional input for kappa strategies
numberOfPositions: optional input for BEST

property aimedCompleteness#: Property for aimedCompleteness

property aimedIOverSigmaAtHighestResolution#: Property for aimedIOverSigmaAtHighestResolution

property aimedMultiplicity#: Property for aimedMultiplicity

property aimedResolution#: Property for aimedResolution

property anomalousData#: Property for anomalousData

property complexity#: Property for complexity

property detectorDistanceMax#: Property for detectorDistanceMax

property detectorDistanceMin#: Property for detectorDistanceMin

property doseLimit#: Property for doseLimit

property estimateRadiationDamage#: Property for estimateRadiationDamage

property forcedSpaceGroup#: Property for forcedSpaceGroup

property goniostatMaxOscillationSpeed#: Property for goniostatMaxOscillationSpeed

property goniostatMinOscillationWidth#: Property for goniostatMinOscillationWidth

property kappaStrategyOption#: Property for kappaStrategyOption

property maxExposureTimePerDataCollection#: Property for maxExposureTimePerDataCollection

property minExposureTimePerImage#: Property for minExposureTimePerImage

property minTransmission#: Property for minTransmission

property numberOfPositions#: Property for numberOfPositions

property rFriedel#: Property for rFriedel

property requiredCompleteness#: Property for requiredCompleteness

property requiredMultiplicity#: Property for requiredMultiplicity

property requiredResolution#: Property for requiredResolution

property strategyOption#: Property for strategyOption

property strategyType#: Property for strategyType

property userDefinedRotationRange#: Property for userDefinedRotationRange

property userDefinedRotationStart#: Property for userDefinedRotationStart

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataDozorInput(configuration=None, nameTemplateImage=None, numberImages=None, firstImageNumber=None, startingAngle=None, imageStep=None, oscillationRange=None, orgy=None, orgx=None, fractionPolarization=None, wavelength=None, detectorDistance=None, spotSize=None, exposureTime=None, detectorType=None)[source]#

Bases: XSDataInput

property detectorDistance#: Property for detectorDistance

property detectorType#: Property for detectorType

property exposureTime#: Property for exposureTime

property firstImageNumber#: Property for firstImageNumber

property fractionPolarization#: Property for fractionPolarization

property imageStep#: Property for imageStep

property nameTemplateImage#: Property for nameTemplateImage

property numberImages#: Property for numberImages

property orgx#: Property for orgx

property orgy#: Property for orgy

property oscillationRange#: Property for oscillationRange

property spotSize#: Property for spotSize

property startingAngle#: Property for startingAngle

property wavelength#: Property for wavelength

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataExperimentalCondition(goniostat=None, detector=None, beam=None)[source]#

Bases: XSData

This object encapsulates all the physical properties of an experiment instrumentation. i.e: Beam, detector, Goniostat.

property beam#: Property for beam

property detector#: Property for detector

property goniostat#: Property for goniostat

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataGeneratePredictionInput(configuration=None, selectedIndexingSolution=None, dataCollection=None)[source]#

Bases: XSDataInput

This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49).

property dataCollection#: Property for dataCollection

property selectedIndexingSolution#: Property for selectedIndexingSolution

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataGeneratePredictionResult(status=None, predictionImage=None)[source]#

Bases: XSDataResult

property predictionImage#: Property for predictionImage

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataGoniostat(phi=None, kappa=None, samplePosition=None, rotationAxisStart=None, rotationAxisEnd=None, rotationAxis=None, overlap=None, oscillationWidth=None, minOscillationWidth=None, maxOscillationSpeed=None)[source]#

Bases: XSData

The properties of a goniostat: - the maximal rotation speed permitted - the minimal width for an oscillation width of subwedge - the name of the rotation axis (typically phi) - the rotation start angle - the rotation end angle

property kappa#: Property for kappa

property maxOscillationSpeed#: Property for maxOscillationSpeed

property minOscillationWidth#: Property for minOscillationWidth

property oscillationWidth#: Property for oscillationWidth

property overlap#: Property for overlap

property phi#: Property for phi

property rotationAxis#: Property for rotationAxis

property rotationAxisEnd#: Property for rotationAxisEnd

property rotationAxisStart#: Property for rotationAxisStart

property samplePosition#: Property for samplePosition

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataIndexingInput(configuration=None, experimentalCondition=None, dataCollection=None, crystal=None)[source]#

Bases: XSDataInput

property crystal#: Property for crystal

property dataCollection#: Property for dataCollection

property experimentalCondition#: Property for experimentalCondition

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataIndexingResult(status=None, solution=None, selectedSolution=None, predictionResult=None, labelitIndexing=None, indexingLogFile=None, image=None)[source]#

Bases: XSDataResult

property image#: Property for image

property indexingLogFile#: Property for indexingLogFile

property labelitIndexing#: Property for labelitIndexing

property predictionResult#: Property for predictionResult

property selectedSolution#: Property for selectedSolution

property solution#: Property for solution

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputCharacterisation(configuration=None, currentResolution=None, token=None, dataCollection=None)[source]#

Bases: XSDataInput

property currentResolution#: Property for currentResolution

property dataCollection#: Property for dataCollection

property token#: Property for token

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputControlISPyB(configuration=None, phi=None, kappa=None, dataCollectionGroupId=None, characterisationResult=None)[source]#

Bases: XSDataInput

property characterisationResult#: Property for characterisationResult

property dataCollectionGroupId#: Property for dataCollectionGroupId

property kappa#: Property for kappa

property phi#: Property for phi

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputControlImageQualityIndicators(configuration=None, endNo=None, startNo=None, template=None, directory=None, wedgeNumber=None, fastMesh=None, batchSize=None, image=None, doUploadToIspyb=None, doIndexing=None, doDistlSignalStrength=None)[source]#

Bases: XSDataInput

property batchSize#: Property for batchSize

property directory#: Property for directory

property doDistlSignalStrength#: Property for doDistlSignalStrength

property doIndexing#: Property for doIndexing

property doUploadToIspyb#: Property for doUploadToIspyb

property endNo#: Property for endNo

property fastMesh#: Property for fastMesh

property image#: Property for image

property startNo#: Property for startNo

property template#: Property for template

property wedgeNumber#: Property for wedgeNumber

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputControlXDSGenerateBackgroundImage(configuration=None, dataCollection=None)[source]#

Bases: XSDataInput

property dataCollection#: Property for dataCollection

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputInducedRadiationProcess(configuration=None, characterisationResult=None)[source]#

Bases: XSDataInput

property characterisationResult#: Property for characterisationResult

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputReadImageHeader(configuration=None, image=None)[source]#

Bases: XSDataInput

These two definitions are used by the read image header plugin.

property image#: Property for image

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputStrategy(configuration=None, xdsBackgroundImage=None, sample=None, experimentalCondition=None, diffractionPlan=None, dataCollection=None, crystalRefined=None, bestFileContentPar=None, bestFileContentHKL=None, bestFileContentDat=None)[source]#

Bases: XSDataInput

property bestFileContentDat#: Property for bestFileContentDat

property bestFileContentHKL#: Property for bestFileContentHKL

property bestFileContentPar#: Property for bestFileContentPar

property crystalRefined#: Property for crystalRefined

property dataCollection#: Property for dataCollection

property diffractionPlan#: Property for diffractionPlan

property experimentalCondition#: Property for experimentalCondition

property sample#: Property for sample

property xdsBackgroundImage#: Property for xdsBackgroundImage

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputSubWedgeAssemble(configuration=None, file=None)[source]#

Bases: XSDataInput

These two definitions are used by the sub wedge assemble plugin.

property file#: Property for file

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataInputSubWedgeMerge(configuration=None, subWedge=None)[source]#

Bases: XSDataInput

These two definitions are used by the sub wedge merge plugins.

property subWedge#: Property for subWedge

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataIntegrationInput(configuration=None, selectedIndexingSolution=None, dataCollection=None, experimentalConditionRefined=None, crystalRefined=None)[source]#

Bases: XSDataGeneratePredictionInput

This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49).

property crystalRefined#: Property for crystalRefined

property experimentalConditionRefined#: Property for experimentalConditionRefined

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataIntegrationResult(status=None, integrationSubWedgeResult=None)[source]#

Bases: XSDataResult

property integrationSubWedgeResult#: Property for integrationSubWedgeResult

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataLigand(numberOfLightAtoms=None, numberOfCopies=None, heavyAtoms=None)[source]#

Bases: XSData

A polymer ligand that contains a set of heavy atoms, the number of all the light atoms (weight <= Oxygen) and the number of copies of this particular ligand in the polymer.

property heavyAtoms#: Property for heavyAtoms

property numberOfCopies#: Property for numberOfCopies

property numberOfLightAtoms#: Property for numberOfLightAtoms

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultCharacterisation(status=None, kappaReorientation=None, xdsBackgroundImage=None, strategyResult=None, statusMessage=None, shortSummary=None, integrationResult=None, indexingResult=None, imageQualityIndicators=None, executiveSummary=None, thumbnailImage=None, jpegImage=None, dataCollection=None)[source]#

Bases: XSDataResult

property dataCollection#: Property for dataCollection

property executiveSummary#: Property for executiveSummary

property imageQualityIndicators#: Property for imageQualityIndicators

property indexingResult#: Property for indexingResult

property integrationResult#: Property for integrationResult

property jpegImage#: Property for jpegImage

property kappaReorientation#: Property for kappaReorientation

property shortSummary#: Property for shortSummary

property statusMessage#: Property for statusMessage

property strategyResult#: Property for strategyResult

property thumbnailImage#: Property for thumbnailImage

property xdsBackgroundImage#: Property for xdsBackgroundImage

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultControlISPyB(status=None, dataCollectionId=None, screeningId=None)[source]#

Bases: XSDataResult

property dataCollectionId#: Property for dataCollectionId

property screeningId#: Property for screeningId

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultControlImageQualityIndicators(status=None, inputDozor=None, imageQualityIndicators=None)[source]#

Bases: XSDataResult

property imageQualityIndicators#: Property for imageQualityIndicators

property inputDozor#: Property for inputDozor

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultControlKappa(status=None, solution=None, logFile=None)[source]#

Bases: XSDataResult

property logFile#: Property for logFile

property solution#: Property for solution

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultControlXDSGenerateBackgroundImage(status=None, xdsBackgroundImage=None)[source]#

Bases: XSDataResult

property xdsBackgroundImage#: Property for xdsBackgroundImage

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultInducedRadiationProcess(status=None, scale=None, crystal=None, bFactor=None)[source]#

Bases: XSDataResult

property bFactor#: Property for bFactor

property crystal#: Property for crystal

property scale#: Property for scale

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultReadImageHeader(status=None, subWedge=None)[source]#

Bases: XSDataResult

These two definitions are used by the read image header plugin.

property subWedge#: Property for subWedge

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultStrategy(status=None, timeToReachHendersonLimit=None, sample=None, raddoseLogFile=None, collectionPlan=None, bestLogFile=None, bestGraphFile=None)[source]#

Bases: XSDataResult

Several collection plans could be present in case of multi-sweep strategy

property bestGraphFile#: Property for bestGraphFile

property bestLogFile#: Property for bestLogFile

property collectionPlan#: Property for collectionPlan

property raddoseLogFile#: Property for raddoseLogFile

property sample#: Property for sample

property timeToReachHendersonLimit#: Property for timeToReachHendersonLimit

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultSubWedgeAssemble(status=None, subWedge=None)[source]#

Bases: XSDataResult

These two definitions are used by the sub wedge assemble plugin.

property subWedge#: Property for subWedge

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataResultSubWedgeMerge(status=None, subWedge=None)[source]#

Bases: XSDataResult

These two definitions are used by the sub wedge merge plugins.

property subWedge#: Property for subWedge

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSample(susceptibility=None, omegaMin=None, size=None, shape=None, radiationDamageModelGamma=None, radiationDamageModelBeta=None, absorbedDoseRate=None)[source]#

Bases: XSData

This defines the main properties of a sample: - absorbed dose rate in Gray/sec - shape: the factor that is related to the sample and the beam size (1 if crystal smaller than beam size or = to the ratio of crystal size to the beam size if the beam is smaller then crystal). - sample size - the susceptibility of the sample to radiation damage.

property absorbedDoseRate#: Property for absorbedDoseRate

property omegaMin#: Property for omegaMin

property radiationDamageModelBeta#: Property for radiationDamageModelBeta

property radiationDamageModelGamma#: Property for radiationDamageModelGamma

property shape#: Property for shape

property size#: Property for size

property susceptibility#: Property for susceptibility

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSampleCrystal(susceptibility=None, omegaMin=None, size=None, shape=None, radiationDamageModelGamma=None, radiationDamageModelBeta=None, absorbedDoseRate=None, crystal=None)[source]#

Bases: XSDataSample

A crystal sample. Inherites of all the XSDataSample attributes (inheritance relationship). In addition has the crystallographic properties (cell, mosaicity, space, group)

property crystal#: Property for crystal

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSampleCrystalMM(susceptibility=None, omegaMin=None, size=None, shape=None, radiationDamageModelGamma=None, radiationDamageModelBeta=None, absorbedDoseRate=None, crystal=None, chemicalComposition=None)[source]#

Bases: XSDataSampleCrystal

A particular crystal sample that contains a macro molecule defined by its chemical composition.

property chemicalComposition#: Property for chemicalComposition

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSolvent(atoms=None)[source]#

Bases: XSData

Defines the content of the solvent by defining the concentration of elements in millimoles/litre. Note that this atom composition should not include oxygen and lighter atoms.

property atoms#: Property for atoms

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSpaceGroup(name=None, ITNumber=None)[source]#

Bases: XSData

Crystallographic properties

property ITNumber#: Property for ITNumber

property name#: Property for name

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataStrategySummary(totalExposureTime=None, totalDataCollectionTime=None, resolutionReasoning=None, resolution=None, redundancy=None, rankingResolution=None, iSigma=None, completeness=None, attenuation=None)[source]#

Bases: XSData

The attribute “attenuation” in XSDataStrategySummary is deprecated, see bug #379. Please use instead “transmission” in XSDataBeam.

property attenuation#: Property for attenuation

property completeness#: Property for completeness

property iSigma#: Property for iSigma

property rankingResolution#: Property for rankingResolution

property redundancy#: Property for redundancy

property resolution#: Property for resolution

property resolutionReasoning#: Property for resolutionReasoning

property totalDataCollectionTime#: Property for totalDataCollectionTime

property totalExposureTime#: Property for totalExposureTime

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataStructure(numberOfCopiesInAsymmetricUnit=None, ligand=None, chain=None)[source]#

Bases: XSData

This is the polymer structure composed by a list of chains and a list of ligands. This structure is also defined by its number in the asymmetric unit.

property chain#: Property for chain

property ligand#: Property for ligand

property numberOfCopiesInAsymmetricUnit#: Property for numberOfCopiesInAsymmetricUnit

class mxcubecore.HardwareObjects.XSDataMXv1.XSDataSubWedge(subWedgeNumber=None, image=None, experimentalCondition=None, action=None)[source]#

Bases: XSData

A subwedge is defined as a list of images that been collected or is to be collected with some particular experimental condition. If the images are to be collected, the image list is empty. The subWedgeNumber is an optional number for relating different subwedges, especially for planning data collections.

property action#: Property for action

property experimentalCondition#: Property for experimentalCondition

property image#: Property for image

property subWedgeNumber#: Property for subWedgeNumber