complex type XSDataInputControlXDSGenerateBackgroundImage extends XSDataInput {
dataCollection : XSDataCollection
}
complex type XSDataInputInducedRadiationProcess extends XSDataInput {
characterisationResult : XSDataResultCharacterisation
}
complex type XSDataInputReadImageHeader extends XSDataInput {
"These two definitions are used by the read image header plugin."
image : XSDataFile
}
complex type XSDataInputSubWedgeAssemble extends XSDataInput {
"These two definitions are used by the sub wedge assemble plugin."
file : XSDataFile []
}
complex type XSDataInputSubWedgeMerge extends XSDataInput {
"These two definitions are used by the sub wedge merge plugins."
subWedge : XSDataSubWedge []
}
complex type XSDataResultReadImageHeader extends XSDataResult {
"These two definitions are used by the read image header plugin."
subWedge : XSDataSubWedge
}
complex type XSDataResultSubWedgeAssemble extends XSDataResult {
"These two definitions are used by the sub wedge assemble plugin."
subWedge : XSDataSubWedge []
}
complex type XSDataResultSubWedgeMerge extends XSDataResult {
"These two definitions are used by the sub wedge merge plugins."
subWedge : XSDataSubWedge []
}
complex type XSDataSpaceGroup extends XSData {
"Crystallographic properties"
ITNumber : XSDataInteger optional
name : XSDataString
}
}
package MXv1DataCollection {
complex type XSDataBeam extends XSData {
"This object contains all the properties related to the beam:\r\n- the exposure time (sec)\r\n- the flux (photons/sec)\r\n- The minimum exposure time permitted by hardware (sec)\r\n- The size of the beam (mm x mm)\r\n- The wavelength (a)\r\n- Transmission in %"
exposureTime : XSDataTime optional
flux : XSDataFlux optional
minExposureTimePerImage : XSDataTime optional
size : XSDataSize optional
transmission : XSDataDouble optional
wavelength : XSDataWavelength optional
}
complex type XSDataCollection extends XSData {
"The data collection carried out or to be carried out with a particular sample with specific user inputs defined by the diffraction plan."
diffractionPlan : XSDataDiffractionPlan optional
sample : XSDataSampleCrystalMM optional
subWedge : XSDataSubWedge []
}
complex type XSDataDetector extends XSData {
"The properties of a detector. "
beamPositionX : XSDataLength
beamPositionY : XSDataLength
bin : XSDataString
byteOrder : XSDataString
dataType : XSDataString
distance : XSDataLength
gain : XSDataFloat optional
imageSaturation : XSDataInteger
name : XSDataString
numberBytesInHeader : XSDataInteger
numberPixelX : XSDataInteger
numberPixelY : XSDataInteger
pixelSizeX : XSDataLength
pixelSizeY : XSDataLength
serialNumber : XSDataString
twoTheta : XSDataAngle
^type : XSDataString
}
complex type XSDataExperimentalCondition extends XSData {
"This object encapsulates all the physical properties of an experiment instrumentation. i.e: Beam, detector, Goniostat."
beam : XSDataBeam optional
detector : XSDataDetector optional
goniostat : XSDataGoniostat optional
}
complex type XSDataGoniostat extends XSData {
"The properties of a goniostat:\r\n- the maximal rotation speed permitted\r\n- the minimal width for an oscillation width of subwedge\r\n- the name of the rotation axis (typically phi)\r\n- the rotation start angle\r\n- the rotation end angle"
maxOscillationSpeed : XSDataAngularSpeed optional
minOscillationWidth : XSDataAngle optional
oscillationWidth : XSDataAngle
overlap : XSDataAngle optional
rotationAxis : XSDataString
rotationAxisEnd : XSDataAngle
rotationAxisStart : XSDataAngle
samplePosition : XSDataVectorDouble [] optional
}
complex type XSDataSubWedge extends 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.\r\nThe subWedgeNumber is an optional number for relating different subwedges, especially for planning data collections."
action : XSDataString optional
experimentalCondition : XSDataExperimentalCondition
image : XSDataImage []
optional
subWedgeNumber : XSDataInteger optional
}
}
package MXv1DiffractionPlan {
complex type XSDataDiffractionPlan extends XSData {
"This object contains the main properties a user can parameterize for a crystal characterisation:\r\n\r\n- the aimed* parameters are the parameters that a user would like to reach for a BEST run.\r\n- the required* are not yet used (the idea is to warn the user if these parameters cannot be reached)\r\n- complexity: BEST complexity input, can be either \"none\" (always single wedge strategy). \"min\" (few subwedges) or \"full\" (many subwedges).\r\n- maxExposureTimePerDataCollection is the max total exposure time (shutter open, not including readout time) the crystal can be exposed to the X-ray beam.\r\n- forcedSpaceGroup: option to force the space group of the indexing solution\r\n- strategyOption: extra option for BEST for more advanced strategies like estimating the sensitivity to radiation damage\r\n- anomalousData: Depreccated! Boolean value for enabling anomalous strategy. In the future the strategyOption should be used instead of anomalousData.\r\n- 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.\r\n- 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.\n- minTransmission: optional input for BEST\r\n- kappaStrategyOption: optional input for kappa strategies\r\n- numberOfPositions: optional input for BEST"
aimedCompleteness : XSDataDouble optional
aimedIOverSigmaAtHighestResolution : XSDataDouble optional
aimedMultiplicity : XSDataDouble optional
aimedResolution : XSDataDouble optional
anomalousData : XSDataBoolean optional
complexity : XSDataString optional
detectorDistanceMax : XSDataLength
optional
detectorDistanceMin : XSDataLength optional
estimateRadiationDamage : XSDataBoolean optional
forcedSpaceGroup : XSDataString optional
goniostatMaxOscillationSpeed : XSDataAngularSpeed optional
goniostatMinOscillationWidth : XSDataAngle optional
kappaStrategyOption : XSDataString [] optional
maxExposureTimePerDataCollection : XSDataTime optional
minExposureTimePerImage : XSDataTime optional
minTransmission : XSDataDouble optional
numberOfPositions : XSDataInteger optional
requiredCompleteness : XSDataDouble optional
requiredMultiplicity : XSDataDouble optional
requiredResolution : XSDataDouble optional
strategyOption : XSDataString optional
userDefinedRotationRange : XSDataAngle optional
userDefinedRotationStart : XSDataAngle optional
}
complex type XSDataGeneratePredictionInput extends XSDataInput {
"This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49)."
dataCollection : XSDataCollection
selectedIndexingSolution : XSDataIndexingSolutionSelected
}
complex type XSDataIntegrationInput extends XSDataGeneratePredictionInput {
"This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49)."
crystalRefined : XSDataCrystal optional
experimentalConditionRefined : XSDataExperimentalCondition optional
}
complex type XSDataAtom extends 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"
concentration : XSDataDouble optional
numberOf : XSDataDouble optional
symbol : XSDataString
}
complex type XSDataAtomicComposition extends XSData {
atom : XSDataAtom [] optional
}
complex type XSDataChain extends 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."
heavyAtoms : XSDataAtomicComposition
numberOfCopies : XSDataDouble
"number of identical chain within the structure"
numberOfMonomers : XSDataDouble
"should be the number of amino-acid, ribonuclotides or desoxyribonucleotides depending on the type"
^type : XSDataString "should be either: \'protein\', \'dna\'or \'rna\'"
}
complex type XSDataChemicalCompositionMM extends XSData {
"This is the composition of a crystal sample of a Macro Molecule (MM stand for Macro Molecule)"
solvent : XSDataSolvent
structure : XSDataStructure
}
complex type XSDataLigand extends 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."
heavyAtoms : XSDataAtomicComposition
numberOfCopies : XSDataDouble
"should be the number of chemically identical ligands in the structure"
numberOfLightAtoms : XSDataDouble
"Should be the total of the number of atoms of C, O, N\r\nH is negligible"
}
complex type XSDataSample extends XSData {
"This defines the main properties of a sample:\r\n- absorbed dose rate in Gray/sec\r\n- 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).\r\n- sample size\r\n- the susceptibility of the sample to radiation damage."
absorbedDoseRate : XSDataAbsorbedDoseRate optional
radiationDamageModelBeta : XSDataDouble optional
radiationDamageModelGamma : XSDataDouble optional
shape : XSDataDouble optional
size : XSDataSize optional
susceptibility : XSDataDouble optional
}
complex type XSDataSampleCrystal extends XSDataSample {
"A crystal sample. Inherites of all the XSDataSample attributes (inheritance relationship). In addition has the crystallographic properties (cell, mosaicity, space, group)"
crystal : XSDataCrystal
}
complex type XSDataSampleCrystalMM extends XSDataSampleCrystal {
"A particular crystal sample that contains a macro molecule defined by its chemical composition."
chemicalComposition : XSDataChemicalCompositionMM
}
complex type XSDataSolvent extends 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."
atoms : XSDataAtomicComposition
}
complex type XSDataStructure extends XSData {
"This is the polymer structure composed by a list of chains and a list of ligands.\r\nThis structure is also defined by its number in the asymmetric unit."
chain : XSDataChain [] optional
ligand : XSDataLigand [] optional
numberOfCopiesInAsymmetricUnit : XSDataDouble
}
}
package MXv1Strategy {
complex type XSDataCollectionPlan extends XSData {
"The comment can be used for describing exotic data collections, for example without collecting any images."
collectionPlanNumber : XSDataInteger
collectionStrategy : XSDataCollection
comment : XSDataString optional
statistics : XSDataStatisticsStrategy
strategySummary : XSDataStrategySummary
}
