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b/dataproc/api/models/autoPROC_model.py index f2427940e2824b116b6e886d939fe4864c067cd8..9169e5d1d0422110d376ce640ac9f2ab8f48e2e0 100644 --- a/dataproc/api/models/autoPROC_model.py +++ b/dataproc/api/models/autoPROC_model.py @@ -10,18 +10,10 @@ class autoPROC(StructuredNode): Defines node properties and relationships Provides data serializer """ - + # Properties uuid=StringProperty(unique_index=True, default=uuid4) - refinedCell_beta=StringProperty() - refinedCell_b=StringProperty() - wavelength=StringProperty() - refinedCell_a=StringProperty() - refinedCell_alpha=StringProperty() - spaceGroup=StringProperty() - refinedCell_c=StringProperty() - refinedCell_gamma=StringProperty() - + @property def serialize(self): @@ -32,13 +24,5 @@ class autoPROC(StructuredNode): return { 'autoPROC_node_properties': { 'uuid': self.uuid, - 'refinedCell_beta': self.refinedCell_beta, - 'refinedCell_b': self.refinedCell_b, - 'wavelength': self.wavelength, - 'refinedCell_a': self.refinedCell_a, - 'refinedCell_alpha': self.refinedCell_alpha, - 'spaceGroup': self.spaceGroup, - 'refinedCell_c': self.refinedCell_c, - 'refinedCell_gamma': self.refinedCell_gamma, }, } \ No newline at end of file diff --git a/dataproc/api/models/draft.py b/dataproc/api/models/draft.py new file mode 100644 index 0000000000000000000000000000000000000000..489673a220d1e33b72a9a74fb2299cd9f3477464 --- /dev/null +++ b/dataproc/api/models/draft.py @@ -0,0 +1,85 @@ + +'recordTimeStamp': self.recordTimeStamp, +'resolutionEllipsoidAxis13': self.resolutionEllipsoidAxis13, +'resolutionEllipsoidAxis33': self.resolutionEllipsoidAxis33, +'resolutionEllipsoidAxis23': self.resolutionEllipsoidAxis23, +'resolutionEllipsoidValue2': self.resolutionEllipsoidValue2, +'resolutionEllipsoidAxis21': self.resolutionEllipsoidAxis21, +'resolutionEllipsoidAxis31': self.resolutionEllipsoidAxis31, +'resolutionEllipsoidAxis22': self.resolutionEllipsoidAxis22, +'resolutionEllipsoidAxis32': self.resolutionEllipsoidAxis32, +'resolutionEllipsoidValue3': self.resolutionEllipsoidValue3, +'resolutionEllipsoidAxis12': self.resolutionEllipsoidAxis12, +'resolutionEllipsoidValue1': self.resolutionEllipsoidValue1, +'resolutionEllipsoidAxis11': self.resolutionEllipsoidAxis11, +'multiplicity': self.multiplicity, +'resolutionLimitLow': self.resolutionLimitLow, +'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus, +'DanoOverSigDano': self.DanoOverSigDano, +'completenessSpherical': self.completenessSpherical, +'nTotalUniqueObservations': self.nTotalUniqueObservations, +'rMerge': self.rMerge, +'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus, +'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal, +'nTotalObservations': self.nTotalObservations, +'completenessEllipsoidal': self.completenessEllipsoidal, +'anomalousCompleteness': self.anomalousCompleteness, +'anomalousMultiplicity': self.anomalousMultiplicity, +'resolutionLimitHigh': self.resolutionLimitHigh, +'completeness': self.completeness, +'ccHalf': self.ccHalf, +'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus, +'meanIOverSigI': self.meanIOverSigI, +'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical, +'ccAnomalous': self.ccAnomalous, +'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus, +'nTotalObservations': self.nTotalObservations, +'completenessEllipsoidal': self.completenessEllipsoidal, +'anomalousMultiplicity': self.anomalousMultiplicity, +'anomalousCompleteness': self.anomalousCompleteness, +'resolutionLimitHigh': self.resolutionLimitHigh, +'completeness': self.completeness, +'ccHalf': self.ccHalf, +'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus, +'meanIOverSigI': self.meanIOverSigI, +'ccAnomalous': self.ccAnomalous, +'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical, +'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus, +'resolutionLimitLow': self.resolutionLimitLow, +'multiplicity': self.multiplicity, +'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus, +'DanoOverSigDano': self.DanoOverSigDano, +'completenessSpherical': self.completenessSpherical, +'nTotalUniqueObservations': self.nTotalUniqueObservations, +'rMerge': self.rMerge, +'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus, +'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal, +'DanoOverSigDano': self.DanoOverSigDano, +'completenessSpherical': self.completenessSpherical, +'rMerge': self.rMerge, +'nTotalUniqueObservations': self.nTotalUniqueObservations, +'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus, +'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal, +'multiplicity': self.multiplicity, +'resolutionLimitLow': self.resolutionLimitLow, +'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus, +'ccHalf': self.ccHalf, +'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus, +'meanIOverSigI': self.meanIOverSigI, +'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical, +'ccAnomalous': self.ccAnomalous, +'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus, +'nTotalObservations': self.nTotalObservations, +'completenessEllipsoidal': self.completenessEllipsoidal, +'anomalousCompleteness': self.anomalousCompleteness, +'anomalousMultiplicity': self.anomalousMultiplicity, +'resolutionLimitHigh': self.resolutionLimitHigh, +'completeness': self.completeness, +'refinedCell_beta': self.refinedCell_beta, +'refinedCell_b': self.refinedCell_b, +'wavelength': self.wavelength, +'refinedCell_a': self.refinedCell_a, +'refinedCell_alpha': self.refinedCell_alpha, +'spaceGroup': self.spaceGroup, +'refinedCell_c': self.refinedCell_c, +'refinedCell_gamma': self.refinedCell_gamma, \ No newline at end of file diff --git a/dataproc/api/models/ligand_model.py b/dataproc/api/models/ligand_model.py index 1986193fa94713f9ef4f707cfd104b18aef95f3d..5ee43461e0b8163b787ac23ce81d4223c7758ac3 100644 --- a/dataproc/api/models/ligand_model.py +++ b/dataproc/api/models/ligand_model.py @@ -16,33 +16,6 @@ class Ligand(StructuredNode): # Properties uuid=StringProperty(unique_index=True, default=uuid4) - id=StringProperty() - ligandomin=StringProperty() - mogulzbond=StringProperty() - ligandbmin=StringProperty() - mogulring=StringProperty() - moguldihe=StringProperty() - ligandbavg=StringProperty() - mogulangl=StringProperty() - mogulbond=StringProperty() - ligandbmax=StringProperty() - ligandid=StringProperty() - ligandomax=StringProperty() - ligandcc=StringProperty() - mogulzangl=StringProperty() - molprobitypercentile=StringProperty() - ramaoutlierpercent=StringProperty() - cbetadeviations=StringProperty() - ramafavoredpercent=IntegerProperty() - poorrotamers=IntegerProperty() - rmsbonds=IntegerProperty() - rmsangles=IntegerProperty() - clashpercentile=StringProperty() - poorrotamerspercent=IntegerProperty() - clashscore=IntegerProperty() - ramafavored=StringProperty() - molprobityscore=IntegerProperty() - ramaoutlier=StringProperty() # Relationships associated=RelationshipTo(Dataset, 'ASSOCIATED') @@ -58,32 +31,5 @@ class Ligand(StructuredNode): 'ligand_node_properties': { 'uuid': self.uuid, - 'id': self.id, - 'ligandomin': self.ligandomin, - 'mogulzbond': self.mogulzbond, - 'ligandbmin': self.ligandbmin, - 'mogulring': self.mogulring, - 'moguldihe': self.moguldihe, - 'ligandbavg': self.ligandbavg, - 'mogulangl': self.mogulangl, - 'mogulbond': self.mogulangl, - 'ligandbmax': self.ligandbmax, - 'ligandid': self.ligandid, - 'ligandomax': self.ligandomax, - 'ligandcc': self.ligandcc, - 'mogulzangl': self.mogulzangl, - 'molprobitypercentile': self.molprobitypercentile, - 'ramaoutlierpercent': self.ramaoutlierpercent, - 'cbetadeviations': self.cbetadeviations, - 'ramafavoredpercent': self.ramafavoredpercent, - 'poorrotamers': self.poorrotamers, - 'rmsbonds': self.rmsbonds, - 'rmsangles': self.rmsangles, - 'clashpercentile': self.clashpercentile, - 'poorrotamerspercent': self.poorrotamerspercent, - 'clashscore': self.clashscore, - 'ramafavored': self.ramafavored, - 'molprobityscore': self.molprobityscore, - 'ramaoutlier': self.ramaoutlier, } }, diff --git a/dataproc/api/models/pipedream_model.py b/dataproc/api/models/pipedream_model.py index fe49269b9c3d870b229ad91febd801a3d62f0d17..edf4510c208c1c3843ed9bdc6da02e795758d891 100644 --- a/dataproc/api/models/pipedream_model.py +++ b/dataproc/api/models/pipedream_model.py @@ -12,13 +12,13 @@ class GPhLPipedream(StructuredNode): """ # Properties - command=StringProperty() - jsonversion=StringProperty() - runby=StringProperty() - runfrom=StringProperty() + command=StringProperty(max_length=500) + jsonversion=StringProperty(max_length=500) + runby=StringProperty(max_length=500) + runfrom=StringProperty(max_length=500) jobid=StringProperty(unique_index=True, default=uuid4) - output=StringProperty() - version=StringProperty() + output=StringProperty(max_length=500) + version=StringProperty(max_length=500) @property def serialize(self): @@ -33,7 +33,7 @@ class GPhLPipedream(StructuredNode): 'jsonversion': self.jsonversion, 'runby': self.runby, 'runfrom': self.runfrom, - 'jobid': self.uuid, + 'jobid': self.jobid, 'output': self.output, 'version': self.version, }, diff --git a/dataproc/api/models/refinement_model.py b/dataproc/api/models/refinement_model.py index 6d0715c62c6702009f5c077025ddacb00b1f7bc5..b9a38fe2a4c83c4fcad99fb925e6f8d1296c5876 100644 --- a/dataproc/api/models/refinement_model.py +++ b/dataproc/api/models/refinement_model.py @@ -13,17 +13,6 @@ class Refinement(StructuredNode): # Properties uuid=StringProperty(unique_index=True, default=uuid4) - WilsonB=StringProperty() - Rfree=IntegerProperty() - MeanB=StringProperty() - type=StringProperty() - step=StringProperty() - RMSbonds=IntegerProperty() - RMSangles=IntegerProperty() - R=IntegerProperty() - WatersPresent=StringProperty() - selectedmodel=StringProperty() - refinementprotocol=StringProperty() @property def serialize(self): @@ -34,17 +23,6 @@ class Refinement(StructuredNode): return { 'postrefinement_node_properties': { 'uuid': self.uuid, - 'WilsonB': self.WilsonB, - 'Rfree': self.Rfree, - 'MeanB': self.MeanB, - 'type': self.type, - 'step': self.step, - 'RMSbonds': self.RMSbonds, - 'RMSangles': self.RMSangles, - 'R': self.R, - 'WatersPresent': self.WatersPresent, - 'selectedmodel': self.selectedmodel, - 'refinementprotocol': self.refinementprotocol, }, } diff --git a/dataproc/api/models/report_model.py b/dataproc/api/models/report_model.py index 2c9b1e1424dd2c190d9f4037746cb4c4f99c699d..b530f3e29bd33314176295aaebe198fc6e86a9ba 100644 --- a/dataproc/api/models/report_model.py +++ b/dataproc/api/models/report_model.py @@ -11,15 +11,115 @@ from api.models.summaryhtml_model import SummaryHtml class Report(StructuredNode): - """ + ''' Defines node properties and relationships Provides data serializer - """ + ''' # Properties - report_path=StringProperty() - report_source=StringProperty() - report_size=StringProperty() + uuid=StringProperty(unique_index=True, default=uuid4) + + # GPhL_pipedream report properties + command=StringProperty(max_length=700) + jsonversion=StringProperty(max_length=700) + runby=StringProperty(max_length=700) + runfrom=StringProperty(max_length=700) + jobid=StringProperty(unique_index=True, default=uuid4) + gphlpipedream_output=StringProperty(max_length=700) + version=StringProperty(max_length=700) + + # Ligands fitting (Rhofit) report properties + ligandomin=StringProperty() + mogulzbond=StringProperty() + ligandbmin=StringProperty() + mogulring=StringProperty() + moguldihe=StringProperty() + ligandbavg=StringProperty() + mogulangl=StringProperty() + mogulbond=StringProperty() + ligandbmax=StringProperty() + ligandid=StringProperty() + ligandomax=StringProperty() + ligandcc=StringProperty() + mogulzangl=StringProperty() + molprobitypercentile=StringProperty() + ramaoutlierpercent=StringProperty() + cbetadeviations=StringProperty() + ramafavoredpercent=StringProperty() + poorrotamers=IntegerProperty() + rmsbonds=IntegerProperty() + rmsangles=IntegerProperty() + clashpercentile=StringProperty() + poorrotamerspercent=IntegerProperty() + clashscore=IntegerProperty() + ramafavored=StringProperty() + molprobityscore=IntegerProperty() + ramaoutliers=StringProperty() + closecontacts=StringProperty() + chain=StringProperty() + contactscore=StringProperty() + ligandstrain=StringProperty() + poorfit=StringProperty() + output=StringProperty() + correlationcoefficient=StringProperty() + rhofitscore=StringProperty() + + # Refinement/Post-refinement report properties + WilsonB=StringProperty() + Rfree=IntegerProperty() + MeanB=StringProperty() + type=StringProperty() + step=StringProperty() + RMSbonds=IntegerProperty() + RMSangles=IntegerProperty() + R=IntegerProperty() + WatersPresent=StringProperty() + selectedmodel=StringProperty() + refinementprotocol=StringProperty() + + # AutoPROC report properties (includes AutoProcscaling, AutoProcScalingStatistics and AutoProc (cf pipdream_summary.json)) + recordTimeStamp=StringProperty() + resolutionEllipsoidAxis13=StringProperty() + resolutionEllipsoidAxis33=StringProperty() + resolutionEllipsoidAxis23=StringProperty() + resolutionEllipsoidValue2=StringProperty() + resolutionEllipsoidAxis21=StringProperty() + resolutionEllipsoidAxis31=StringProperty() + resolutionEllipsoidAxis22=StringProperty() + resolutionEllipsoidAxis32=StringProperty() + resolutionEllipsoidValue3=StringProperty() + resolutionEllipsoidAxis12=StringProperty() + resolutionEllipsoidValue1=StringProperty() + resolutionEllipsoidAxis11=StringProperty() + multiplicity=StringProperty() + resolutionLimitLow=StringProperty() + rMeasWithinIPlusIMinus=StringProperty() + DanoOverSigDano=StringProperty() + completenessSpherical=StringProperty() + nTotalUniqueObservations=StringProperty() + rMerge=StringProperty() + rPimWithinIPlusIMinus=StringProperty() + anomalousCompletenessEllipsoidal=StringProperty() + nTotalObservations=StringProperty() + completenessEllipsoidal=StringProperty() + anomalousCompleteness=StringProperty() + anomalousMultiplicity=StringProperty() + resolutionLimitHigh=StringProperty() + completeness=StringProperty() + ccHalf=StringProperty() + rPimAllIPlusIMinus=StringProperty() + meanIOverSigI=StringProperty() + anomalousCompletenessSpherical=StringProperty() + ccAnomalous=StringProperty() + rMeasAllIPlusIMinus=StringProperty() + refinedCell_beta=StringProperty() + refinedCell_b=StringProperty() + wavelength=StringProperty() + refinedCell_a=StringProperty() + refinedCell_alpha=StringProperty() + spaceGroup=StringProperty() + refinedCell_c=StringProperty() + refinedCell_gamma=StringProperty() # Relationships is_statisticalreport=RelationshipTo(StatisticalReport, 'IS') @@ -29,14 +129,113 @@ class Report(StructuredNode): @property def serialize(self): - """ + ''' Serializer for node properties - """ + ''' return { 'node_properties': { - 'report_path': self.report_path, - 'report_source': self.report_source, - 'report_size': self.report_size, + + # GPhL_pipedream report properties + 'command': self.command, + 'jsonversion': self.jsonversion, + 'runby': self.runby, + 'runfrom': self.runfrom, + 'jobid': self.jobid, + 'gphlpipedream_output': self.gphlpipedream_output, + 'version': self.version, + + # Ligands fitting (Rhofit) report properties + 'ligandomin': self.ligandomin, + 'mogulzbond': self. mogulzbond, + 'ligandbmin': self.ligandbmin, + 'mogulring': self.mogulring, + 'moguldihe': self.moguldihe, + 'ligandbavg': self.ligandbavg, + 'mogulangl': self.mogulangl, + 'mogulbond': self.mogulbond, + 'ligandbmax': self.ligandbmax, + 'ligandid': self.ligandid, + 'ligandomax': self.ligandomax, + 'ligandcc': self.ligandcc, + 'mogulzangl': self.mogulzangl, + 'molprobitypercentile': self.molprobitypercentile, + 'ramaoutlierpercent': self.ramaoutlierpercent, + 'cbetadeviations': self.cbetadeviations, + 'ramafavoredpercent': self.ramafavoredpercent, + 'poorrotamers': self.poorrotamers, + 'rmsbonds': self.rmsbonds, + 'rmsangles': self.rmsangles, + 'clashpercentile': self.clashpercentile, + 'poorrotamerspercent': self.poorrotamerspercent, + 'clashscore': self.clashscore, + 'ramafavored': self.ramafavored, + 'molprobityscore': self.molprobityscore, + 'ramaoutliers': self.ramaoutlers, + 'closecontacts': self.closecontacts, + 'chain': self.chain, + 'contactscore': self.contactscore, + 'ligandstrain': self.ligandstrain, + 'poorfit': self.poorfit, + 'output': self.output, + 'correlationcoefficient': self.correlationcoefficient, + 'rhofitscore': self.rhofitscore, + + # Refinement/Post-refinement report properties + 'WilsonB': self.WilsonB, + 'Rfree': self.Rfree, + 'MeanB': self.MeanB, + 'type': self.type, + 'step': self.step, + 'RMSbonds': self.RMSbonds, + 'RMSangles': self.RMSangles, + 'R': self.R, + 'WatersPresent': self.WatersPresent, + 'selectedmodel': self.selectedmodel, + 'refinementprotocol': self.refinementprotocol, + + # AutoPROC report properties (includes AutoProcscaling, AutoProcScalingStatistics and AutoProc (cf pipdream_summary.json)) + 'recordTimeStamp': self.recordTimeStamp, + 'resolutionEllipsoidAxis13': self.resolutionEllipsoidAxis13, + 'resolutionEllipsoidAxis33': self.resolutionEllipsoidAxis33, + 'resolutionEllipsoidAxis23': self.resolutionEllipsoidAxis23, + 'resolutionEllipsoidValue2': self.resolutionEllipsoidValue2, + 'resolutionEllipsoidAxis21': self.resolutionEllipsoidAxis21, + 'resolutionEllipsoidAxis31': self.resolutionEllipsoidAxis31, + 'resolutionEllipsoidAxis22': self.resolutionEllipsoidAxis22, + 'resolutionEllipsoidAxis32': self.resolutionEllipsoidAxis32, + 'resolutionEllipsoidValue3': self.resolutionEllipsoidValue3, + 'resolutionEllipsoidAxis12': self.resolutionEllipsoidAxis12, + 'resolutionEllipsoidValue1': self.resolutionEllipsoidValue1, + 'resolutionEllipsoidAxis11': self.resolutionEllipsoidAxis11, + 'multiplicity': self.multiplicity, + 'resolutionLimitLow': self.resolutionLimitLow, + 'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus, + 'DanoOverSigDano': self.DanoOverSigDano, + 'completenessSpherical': self.completenessSpherical, + 'nTotalUniqueObservations': self.nTotalUniqueObservations, + 'rMerge': self.rMerge, + 'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus, + 'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal, + 'nTotalObservations': self.nTotalObservations, + 'completenessEllipsoidal': self.completenessEllipsoidal, + 'anomalousCompleteness': self.anomalousCompleteness, + 'anomalousMultiplicity': self.anomalousMultiplicity, + 'resolutionLimitHigh': self.resolutionLimitHigh, + 'completeness': self.completeness, + 'ccHalf': self.ccHalf, + 'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus, + 'meanIOverSigI': self.meanIOverSigI, + 'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical, + 'ccAnomalous': self.ccAnomalous, + 'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus, + 'refinedCell_beta': self.refinedCell_beta, + 'refinedCell_b': self.refinedCell_b, + 'wavelength': self.wavelength, + 'refinedCell_a': self.refinedCell_a, + 'refinedCell_alpha': self.refinedCell_alpha, + 'spaceGroup': self.spaceGroup, + 'refinedCell_c': self.refinedCell_c, + 'refinedCell_gamma': self.refinedCell_gamma, }, - } \ No newline at end of file + }