def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDIMPLEPHASERv10.postProcess")
self.programTermination()
# Create some output data
xsDataResult = CCP4DataResultPhaser(HKLOUT=HKL(self._hklout),
XYZOUT=XYZ(self._xyzout),
returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
xyzout = None
for record in self.readProcessLogFile().split('\n'):
if 'Solution' in record and 'written to PDB file:' in record and ".pdb" in record:
xyzout = record.split()[-1]
assert (xyzout)
shutil.copyfile(os.path.join(self.getWorkingDirectory(), xyzout),
self._xyzout)
if not os.path.isfile(self._xyzout):
raise RuntimeError, 'File %s does not exist' % self._xyzout
return
def postProcess(self, _edObject = None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG(
'*** EDPluginExecDIMPLEREFMACRestrainedRefinementv10.postProcess')
init_r, init_r_free, final_r, final_r_free = self.parse_refmac_log()
xsDataResult = CCP4DataResultREFMACRestrainedRefinement(
HKLOUT = HKL(self._hklout),
XYZOUT = XYZ(self._xyzout),
initialR = XSDataFloat(init_r),
initialRFree = XSDataFloat(init_r_free),
finalR = XSDataFloat(final_r),
finalRFree = XSDataFloat(final_r_free),
returnStatus = CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
if not os.path.isfile(self.getDataOutput().getHKLOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput().getHKLOUT().getPath().getValue()
if not os.path.isfile(self.getDataOutput().getXYZOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput().getXYZOUT().getPath().getValue()
return
def postProcess(self, _edObject = None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG('*** PipelineCalcDiffMapv10.postProcess')
results = self._restrained_plugin.getDataOutput()
xsDataResult = CCP4DataResultControlPipelineCalcDiffMap(
HKLOUT = HKL(self._hklout),
XYZOUT = XYZ(self._xyzout),
initialR = results.getInitialR(),
initialRFree = results.getInitialRFree(),
finalR = results.getFinalR(),
finalRFree = results.getFinalRFree(),
returnStatus = CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
# and also produce a summary file? - first pull out the residuals
refmac_out = self._restrained_plugin.readProcessLogFile().split('\n')
residuals = { }
collect_residuals = False
for record in refmac_out:
if '$TABLE: Rfactor analysis, stats vs cycle' in record:
collect_residuals = True
continue
if not collect_residuals:
continue
if record.strip()[0] in '0123456789':
tokens = record.split()
cycle = int(tokens[0])
r_rfree_fom = map(float, tokens[1:4])
residuals[cycle] = r_rfree_fom
if 'Final results' in record:
collect_residuals = False
# now need to write this someplace...
summary = open(os.path.join(self.getWorkingDirectory(),
'summary.log'), 'w')
for c in sorted(residuals):
summary.write('%2d %.4f %.4f %.3f\n' % (c, residuals[c][0],
residuals[c][1],
residuals[c][2]))
summary.close()
# Create a Coot script launcher
self.createCootLauncher()
return
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG('*** CopySpaceGroupPDBtoMTZv10.postProcess')
xsDataResult = CCP4DataResultControlCopySpaceGroupPDBtoMTZ(
HKLOUT=HKL(self._hklout), returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
return
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG(
"EDPluginControlDIMPLERefmacRigidBodyPhaserv10.postProcess")
# Create some output data
xsDataResult = CCP4DataResultControlRefmacRigidBodyPhaser(
XYZOUT=XYZ(self._xyzout), returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDIMPLERefmacMonomerCheckv10.postProcess")
xsDataResult = CCP4DataResultRefmacMonomerCheck(
returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
return
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG('*** PrepareMTZFileForRefinementv10.postProcess')
postProcessColLabels = self._truncate_plugin.getDataOutput(
).getColLabels()
xsDataResult = CCP4DataResultControlPrepareMTZFileForRefinement(
HKLOUT=HKL(self._hklout),
ColLabels=postProcessColLabels,
returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDIMPLEPointlessOriginv10.postProcess")
xsDataResult = CCP4DataResultPointlessOrigin(
HKLOUT=HKL(self._hklout), returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
if not os.path.isfile(
self.getDataOutput().getHKLOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput(
).getHKLOUT().getPath().getValue()
return
def postProcess(self, _edObject = None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG('*** EDPluginExecDIMPLECADv10.postProcess')
self.programTermination()
xsDataResult = CCP4DataResultCAD(
HKLOUT = HKL(self._hklout),
returnStatus = CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
if not os.path.isfile(self.getDataOutput().getHKLOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput().getHKLOUT().getPath().getValue()
return
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("*** EDPluginExecDIMPLEUNIQUEv10.postProcess")
self.programTermination()
# call something to parse out the results
xsDataResult = CCP4DataResultUNIQUE(HKLOUT=HKL(self._hklout),
returnStatus=CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
if not os.path.isfile(
self.getDataOutput().getHKLOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput(
).getHKLOUT().getPath().getValue()
return