def tes_execute_MosflmGeneratePredictionTask_2m_RNASE_1(self):
UtilsTest.loadTestImage('ref-2m_RNASE_1_0001.cbf')
UtilsTest.loadTestImage('ref-2m_RNASE_1_0002.cbf')
referenceDataPath = self.dataPath / 'mosflm_generatePrediction_2m_RNASE_1.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
mosflmIndexingTask = MosflmGeneratePredictionTask(inData=inData)
mosflmIndexingTask.execute()
self.assertTrue(mosflmIndexingTask.isSuccess())
def test_execute_MosflmGeneratePredictionTaskTRYP_X1_4(self):
UtilsTest.loadTestImage('ref-TRYP-X1_4_0001.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0002.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0003.cbf')
UtilsTest.loadTestImage('ref-TRYP-X1_4_0004.cbf')
referenceDataPath = self.dataPath / 'mosflm_generatePrediction_TRYP-X1_4.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
mosflmIndexingTask = MosflmGeneratePredictionTask(inData=inData)
mosflmIndexingTask.execute()
self.assertTrue(mosflmIndexingTask.isSuccess())
def test_generateMOSFLMCommands_generatePrediction(self):
tempdir = tempfile.mkdtemp(prefix='generateMOSFLMCommands_' +
'generatePrediction_test_')
tmpWorkingDir = pathlib.Path(tempdir)
referenceDataPath = self.dataPath / 'mosflm_generatePrediction_2m_RNASE_1.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
task = MosflmGeneratePredictionTask(inData)
listCommands = task.generateMOSFLMCommands(inData, tmpWorkingDir)
for command in ['WAVELENGTH 0.8729', 'DISTANCE 305.222',
'BEAM 113.5544 112.2936',
'TEMPLATE ref-2m_RNASE_1_####.cbf', 'SYMMETRY P1',
'EXIT']:
self.assertTrue(command in listCommands, command)
shutil.rmtree(tempdir)
def test_generateMOSFLMCommands_generatePrediction(self):
tempdir = tempfile.mkdtemp(prefix="generateMOSFLMCommands_" +
"generatePrediction_test_")
tmpWorkingDir = pathlib.Path(tempdir)
referenceDataPath = self.dataPath / "mosflm_generatePrediction_2m_RNASE_1.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
task = MosflmGeneratePredictionTask(inData)
listCommands = task.generateMOSFLMCommands(inData, tmpWorkingDir)
for command in [
"WAVELENGTH 0.8729",
"DISTANCE 305.222",
"BEAM 113.5544 112.2936",
"TEMPLATE ref-2m_RNASE_1_####.cbf",
"SYMMETRY P1",
"EXIT",
]:
self.assertTrue(command in listCommands, command)
shutil.rmtree(tempdir)
def run(self, inData):
outData = {}
xdsIndexingOutData = inData["indexingSolution"]
# Run MOSFLM prediction
mosflmUB = xdsIndexingOutData["xparm"]["mosflmUB"]
mosflmU = xdsIndexingOutData["xparm"]["mosflmU"]
matrix = {
"matrixA": mosflmUB,
"missettingsAngles": [0.0, 0.0, 0.0],
"matrixU": mosflmU,
"cell": {
"a": xdsIndexingOutData["idxref"]["a"],
"b": xdsIndexingOutData["idxref"]["b"],
"c": xdsIndexingOutData["idxref"]["c"],
"alpha": xdsIndexingOutData["idxref"]["alpha"],
"beta": xdsIndexingOutData["idxref"]["beta"],
"gamma": xdsIndexingOutData["idxref"]["gamma"]
},
}
mosflmInData = MosflmGeneratePredictionTask.generateMOSFLMInData(
inData={"subWedge": listSubWedge})
mosflmInData["matrix"] = matrix
mosflmInData.update({
"mosaicityEstimation":
xdsIndexingOutData["idxref"]["mosaicity"],
"deviationAngular":
1.0,
"refinedDistance":
xdsIndexingOutData["idxref"]["distance"],
"symmetry":
"P1"
})
mosflmGeneratePredictionTask = MosflmGeneratePredictionTask(
inData=mosflmInData)
mosflmGeneratePredictionTask.execute()
pass
return outData