def doSuccess_RefmacRigidBody(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlDIMPLERefmacRigidBodyPhaserv10.doSuccess_RefmacRigidBody"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlDIMPLERefmacRigidBodyPhaserv10.doSuccess_RefmacRigidBody"
)
dimple_FinalRFree = self._refmacrigidbody_plugin.getDataOutput(
).getFinalRFree().getValue()
if dimple_FinalRFree > 0.45:
phaser_input = CCP4DataInputPhaser(HKLIN=HKL(self._hklin),
XYZIN=XYZ(self._xyzin),
HKLOUT=HKL(self._hklout),
XYZOUT=XYZ(self._xyzout),
ColLabels=self._ColLabels)
self._phaser_plugin.setDataInput(phaser_input)
self._phaser_plugin.connectSUCCESS(self.doSuccess_Phaser)
self._phaser_plugin.connectFAILURE(self.doFailure_Phaser)
self._phaser_plugin.executeSynchronous()
return
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 _success_pdbdump(self, _edPlugin=None):
EDVerbose.DEBUG('*** CopySpaceGroupPDBtoMTZv10._success_pdbdump')
self.retrieveSuccessMessages(
_edPlugin, 'CopySpaceGroupPDBtoMTZv10._success_pdbdump')
# self._reindex_plugin.set_space_group_name(
# self._pdbdump_plugin.get_space_group_name())
reindex_input = CCP4DataInputREINDEX(
HKLIN=HKL(self._hklin),
HKLOUT=HKL(self._hklout),
spaceGroup=self._pdbdump_plugin.getDataOutput().getSpaceGroup(),
reindexingOperation=CCP4ReindexingOperation('h,k,l'))
self._reindex_plugin.setDataInput(reindex_input)
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('*** 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 process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG(
"EDPluginControlDIMPLERefmacRigidBodyPhaserv10.process")
self._refmacrigidbody_plugin.setDataInput(
CCP4DataInputREFMACRigidBody(XYZIN=XYZ(self._xyzin),
HKLIN=HKL(self._hklin),
XYZOUT=XYZ(self._xyzout),
ColLabels=self._ColLabels))
self._refmacrigidbody_plugin.connectSUCCESS(
self.doSuccess_RefmacRigidBody)
self._refmacrigidbody_plugin.connectFAILURE(
self.doFailure_RefmacRigidBody)
self._refmacrigidbody_plugin.executeSynchronous()
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
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG('*** PrepareMTZFileForRefinementv10.process')
# ok, first query xyzin to get the space group for input to unique
self._pdbdump_plugin.setDataInput(
CCP4DataInputPDBDUMP(XYZIN=XYZ(self._xyzin)))
self._pdbdump_plugin.connectSUCCESS(self._generic_success)
self._pdbdump_plugin.connectFAILURE(self._generic_failure)
self._pdbdump_plugin.executeSynchronous()
dimple_spacegroup = self._pdbdump_plugin.getDataOutput().getSpaceGroup(
)
dimple_sequence = self._pdbdump_plugin.getDataOutput().getSequence()
# then query the mtz object for the cell constants &c.
self._mtzdump_plugin.setDataInput(
CCP4DataInputMTZDUMP(HKLIN=HKL(self._hklin)))
self._mtzdump_plugin.connectSUCCESS(self._generic_success)
self._mtzdump_plugin.connectFAILURE(self._generic_failure)
self._mtzdump_plugin.executeSynchronous()
mtzdump_results = self._mtzdump_plugin.getDataOutput()
dimple_unitcell = mtzdump_results.getUnitCell()
dimple_dmin = mtzdump_results.getUpperResolutionLimit()
# then run unique with this
hklout = os.path.join(self.getWorkingDirectory(), 'unique.mtz')
self._unique_plugin.setDataInput(
CCP4DataInputUNIQUE(HKLOUT=HKL(hklout),
spaceGroup=dimple_spacegroup,
unitCell=dimple_unitcell,
resolutionLimit=dimple_dmin))
self._unique_plugin.connectSUCCESS(self._generic_success)
self._unique_plugin.connectFAILURE(self._generic_failure)
self._unique_plugin.executeSynchronous()
# and then freerflag on this one
hklin = hklout
hklout = os.path.join(self.getWorkingDirectory(), 'free.mtz')
self._freerflag_plugin.setDataInput(
CCP4DataInputFREERFLAG(HKLIN=HKL(hklin), HKLOUT=HKL(hklout)))
self._freerflag_plugin.connectSUCCESS(self._generic_success)
self._freerflag_plugin.connectFAILURE(self._generic_failure)
self._freerflag_plugin.executeSynchronous()
# then start processing the input reflection file - first copy
# the spacegroup across, then run truncate, then cad together the
# twain
hklout = os.path.join(self.getWorkingDirectory(), 'spacegroup.mtz')
self._copy_spacegroup_plugin.setDataInput(
CCP4DataInputControlCopySpaceGroupPDBtoMTZ(HKLIN=HKL(self._hklin),
XYZIN=HKL(self._xyzin),
HKLOUT=HKL(hklout)))
self._copy_spacegroup_plugin.connectSUCCESS(self._generic_success)
self._copy_spacegroup_plugin.connectFAILURE(self._generic_failure)
self._copy_spacegroup_plugin.executeSynchronous()
# only run truncate if structure factors where not given in the input
hklin = hklout
hklout = os.path.join(self.getWorkingDirectory(), 'truncate.mtz')
self._truncate_plugin.setDataInput(
CCP4DataInputTRUNCATE(HKLIN=HKL(hklin),
HKLOUT=HKL(hklout),
sequence=dimple_sequence,
ColLabels=self._ColLabels))
self._truncate_plugin.connectSUCCESS(self._generic_success)
self._truncate_plugin.connectFAILURE(self._generic_failure)
self._truncate_plugin.executeSynchronous()
# cad together free.mtz and truncate.mtz
hklin1 = os.path.join(self.getWorkingDirectory(), 'truncate.mtz')
hklin2 = os.path.join(self.getWorkingDirectory(), 'free.mtz')
self._cad_plugin.setDataInput(
CCP4DataInputCAD(
HKLIN=[HKL(hklin1), HKL(hklin2)],
columnLabels=[XSDataListOfStrings(),
XSDataListOfStrings()],
HKLOUT=HKL(self._hklout)))
self._cad_plugin.connectSUCCESS(self._generic_success)
self._cad_plugin.connectFAILURE(self._generic_failure)
self._cad_plugin.executeSynchronous()
# we should be all good by here - clean up perhaps?
return
def process(self, _edObject = None):
EDPluginControl.process(self)
EDVerbose.DEBUG('*** PipelineCalcDiffMapv10.process')
#----------------------------------------------------------------------------
# Verify that the input file self._hklin is actually an mtz file
self._check_for_Validity_of_HKL.setDataInput(CCP4DataInputCheckValidHKL(HKLIN=HKL(self._hklin)))
self._check_for_Validity_of_HKL.connectSUCCESS(self._generic_success)
self._check_for_Validity_of_HKL.connectFAILURE(self._generic_failure)
self._check_for_Validity_of_HKL.executeSynchronous()
returnStatusHKL = self._check_for_Validity_of_HKL.getDataOutput()
if returnStatusHKL.getReturnStatus().getCode().getValue() == 0:
raise RuntimeError, returnStatusHKL.getReturnStatus().getMessage().getValue()
return
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
# Verify that the input file self._xyzin is actually a pdb file
self._check_for_Validity_of_XYZ.setDataInput(CCP4DataInputCheckValidXYZ(XYZIN=XYZ(self._xyzin)))
self._check_for_Validity_of_XYZ.connectSUCCESS(self._generic_success)
self._check_for_Validity_of_XYZ.connectFAILURE(self._generic_failure)
self._check_for_Validity_of_XYZ.executeSynchronous()
returnStatusXYZ = self._check_for_Validity_of_XYZ.getDataOutput()
if returnStatusXYZ.getReturnStatus().getCode().getValue() == 0:
raise RuntimeError, returnStatusXYZ.getReturnStatus().getMessage().getValue()
return
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
# Pointless Origin Check
hklout = os.path.join(self.getWorkingDirectory(),
'pointlessOriginCheck.mtz')
self._pointless_origin_check.setDataInput(
CCP4DataInputPointlessOrigin(
HKLIN=HKL(self._hklin),
XYZIN=XYZ(self._xyzin),
HKLOUT=HKL(hklout)))
self._pointless_origin_check.connectSUCCESS(self._generic_success)
self._pointless_origin_check.connectFAILURE(self._generic_failure)
self._pointless_origin_check.executeSynchronous()
#----------------------------------------------------------------------------
# first prepare the input reflection file
hklin = hklout
hklout = os.path.join(self.getWorkingDirectory(),
'prepared.mtz')
self._prepare_mtz_plugin.setDataInput(
CCP4DataInputControlPrepareMTZFileForRefinement(
XYZIN = XYZ(self._xyzin),
HKLIN = HKL(hklin),
HKLOUT = HKL(hklout),
ColLabels = self._ColLabels))
self._prepare_mtz_plugin.connectSUCCESS(self._generic_success)
self._prepare_mtz_plugin.connectFAILURE(self._generic_failure)
self._prepare_mtz_plugin.executeSynchronous()
# then prepare the input pdb file
xyzout = os.path.join(self.getWorkingDirectory(),
'prepared.pdb')
self._prepare_pdb_plugin.setDataInput(
CCP4DataInputControlCopyUnitCellMTZtoPDB(
XYZIN = XYZ(self._xyzin),
HKLIN = HKL(self._hklin),
XYZOUT = XYZ(xyzout)))
self._prepare_pdb_plugin.connectSUCCESS(self._generic_success)
self._prepare_pdb_plugin.connectFAILURE(self._generic_failure)
self._prepare_pdb_plugin.executeSynchronous()
# then run the rigid body refinement
xyzin = xyzout
hklin = hklout
xyzout = os.path.join(self.getWorkingDirectory(),
'rigidbody.pdb')
self._rigigbody_phaser_plugin.setDataInput(
CCP4DataInputControlRefmacRigidBodyPhaser(
XYZIN = XYZ(xyzin),
HKLIN = HKL(hklin),
XYZOUT = XYZ(xyzout),
ColLabels = self._prepare_mtz_plugin.getDataInput().getColLabels()))
self._rigigbody_phaser_plugin.connectSUCCESS(self._generic_success)
self._rigigbody_phaser_plugin.connectFAILURE(self._generic_failure)
self._rigigbody_phaser_plugin.executeSynchronous()
# and finally run the restrained refinement
xyzin = xyzout
self._restrained_plugin.setDataInput(
CCP4DataInputREFMACRestrainedRefinement(
XYZIN = XYZ(xyzin),
HKLIN = HKL(hklin),
XYZOUT = XYZ(self._xyzout),
HKLOUT = HKL(self._hklout),
ColLabels = self._prepare_mtz_plugin.getDataInput().getColLabels()))
self._restrained_plugin.connectSUCCESS(self._generic_success)
self._restrained_plugin.connectFAILURE(self._generic_failure)
self._restrained_plugin.executeSynchronous()
return