""" buccaneer_build_refine_mr.py: CCP4 GUI Project Copyright (C) 2010 University of York This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ import sys, time import os,shutil from lxml import etree from copy import deepcopy from CCP4PluginScript import CPluginScript import CCP4Utils r_work_essentially_complete_model = 0.25 class buccaneer_build_refine_mr(CPluginScript): TASKMODULE = 'model_building' TASKTITLE = 'Autobuild protein (Buccaneer pipeline)' TASKNAME = 'buccaneer_build_refine_mr' TASKVERSION= 0.0 INTERRUPTABLE = True GUINAME = 'buccaneer_build_refine_mr' RESTARTABLE = True ASYNCHRONOUS = True PERFORMANCECLASS = 'CModelBuildPerformance' MAINTAINER = 'jon.agirre@york.ac.uk' WHATNEXT = ['coot_rebuild','prosmart_refmac','buccaneer_build_refine_mr'] PURGESEARCHLIST = [ [ 'buccaneer_mr%*/XYZOUT.*' , 5 , 'XYZOUT' ], [ 'refmac%*/ABCDOUT.mtz', 5, 'ABCDOUT' ], [ 'refmac%*/FPHIOUT.mtz', 5, 'FPHIOUT' ], [ 'refmac%*/DIFFPHIOUT.mtz', 5, 'DIFFPHIOUT' ], [ 'refmac%*/XYZOUT.pdb', 5, 'XYZOUT' ], [ 'refmac%*/COOTSCRIPTOUT.scm', 5, 'COOTSCRIPTOUT' ], [ 'prosmart_refmac%*/ABCDOUT.mtz', 5, 'ABCDOUT' ], [ 'prosmart_refmac%*/FPHIOUT.mtz', 5, 'FPHIOUT' ], [ 'prosmart_refmac%*/DIFFPHIOUT.mtz', 5, 'DIFFPHIOUT' ], [ 'prosmart_refmac%*/XYZOUT.pdb', 5, 'XYZOUT' ], [ 'prosmart_refmac%*/COOTSCRIPTOUT.scm', 5, 'COOTSCRIPTOUT' ], [ 'prosmart_refmac%*/refmac%*/ABCDOUT.mtz', 5, 'ABCDOUT' ], [ 'prosmart_refmac%*/refmac%*/FPHIOUT.mtz', 5, 'FPHIOUT' ], [ 'prosmart_refmac%*/refmac%*/DIFFPHIOUT.mtz', 5, 'DIFFPHIOUT' ], [ 'prosmart_refmac%*/refmac%*/XYZOUT.pdb', 5, 'XYZOUT' ], [ 'prosmart_refmac%*/refmac%*/COOTSCRIPTOUT.scm', 5, 'COOTSCRIPTOUT' ] ] ERROR_CODES = { 200 : { 'description' : 'Buccaneer task failed' }, 201 : { 'description' : 'Refmac task failed' }, 202 : { 'description' : 'Buccaneer output coordinate file not found' }, 203 : { 'description' : 'Refmac output coordinate file not found' }, 204 : { 'description' : 'Coot realspace operation output coordinate file not found' }, 205 : { 'description' : 'Coot realspace operation output coordinate file not found' }, 206 : { 'description' : 'Accessory refmac job failed' }, 207 : { 'description' : 'Accessory refmac job output reflection file not found' } } # For a pipeline it is only necessary to reimplement CPluginScript.process() - it must create and control the # running of sub-jobs. There are two different ways for process() to work: # --- blocking mode: after starting a sub-job process it waits for the job to finish # --- asynchronous mode: there is no waiting for a sub-job to finish and a signals-slots mechanism # must be used to specify a 'handler' method for when a subjob finishes # The blocking mode approach is more straightforward. The asynchronous approach is described more fully in # the documentation ccp4i2/docs/developers/pipelines.html#running processes # This demonstration pipeline is implemented in both approaches - the process() method calls either processInBlockingMode() # or startAsynchronousProcess() dependent on the class parameter ASYNCHRONOUS # def process(self): if self.ASYNCHRONOUS: self.startAsynchronousProcess() else: self.processInBlockingMode() def setProgramVersion(self): print 'autobuild.getProgramVersion' return CPluginScript.setProgramVersion(self,'Autobuild protein') # ==== Run in straight-forward 'blocking' mode ( this is simplified script that does not use prosmart or coot )================================ # This version alternates running buccaneer and refmac wrappers and does not use the prosmart-refmac pipeline or have # an option to run Coot. def processInBlockingMode(self): # set up first cycle and number of cycles - beware we could be restarting restarted = self.container.interruptStatus.LASTCYCLE.isSet() if restarted: self.cycle = int(self.container.interruptStatus.LASTCYCLE) + 1 else: self.cycle = 0 self.ncycles = int( self.container.controlParameters.ITERATIONS ) # Keep track of the current best coordinate file in self.currentCoordinates # For this simple case of running buccaneer and refmac tracking the currentCoordinates # is not absolutely necessary but it clarifies coding when there is an optional coot plugin # If restarting job then look for the coordinate file in the last sub-job if self.cycle > 0 and os.path.exists(os.path.join(self.getSubDirectories()[-1],'XYZOUT.pdb')): # Look for the coordinate file in the last sub-job # this sets currentCoordinates to a string but that is OK self.currentCoordinates = os.path.join(self.getSubDirectories()[-1],'XYZOUT.pdb') print 'Restarting with coordinates in file:',self.currentCoordinates else: self.currentCoordinates = self.container.inputData.XYZIN # Initialise the XML output file self.initialiseXML(restarted=restarted) # Do ncycles repetitions of buccaneer-refmac while self.cycle < self.ncycles: self.xmlcyc = etree.SubElement(self.xmlroot,"BuildRefineCycle") etree.SubElement(self.xmlcyc,"Number").text = str(self.cycle+1) # Create, run and check the buccaneer process self.buccaneerPlugin = self.makeBuccaneerPlugin(restarted=restarted) finishStatus = self.buccaneerPlugin.process() self.checkFinishStatus(statusDict={'finishStatus':finishStatus},failedErrCode=200, outputFile = self.buccaneerPlugin.container.outputData.XYZOUT,noFileErrCode=202) self.currentCoordinates = self.buccaneerPlugin.container.outputData.XYZOUT # Copy some buccaneer data to the xml file self.copyBuccaneerXML() xmlFile = self.buccaneerPlugin.makeFileName('PROGRAMXML') if os.path.exists(xmlFile): bxml = CCP4Utils.openFileToEtree(xmlFile) self.xmlcyc.append(bxml) # Create, run and check the refmac process self.refmacPlugin = self.makeRefmacPlugin() finishStatus = self.refmacPlugin.process() self.checkFinishStatus(statusDict={'finishStatus':finishStatus},failedErrCode=201, outputFile=self.refmacPlugin.container.outputData.XYZOUT ,noFileErrCode=203) #self.currentCoordinates = self.refmacPlugin.container.outputData.XYZOUT # process XML from refmac and append to the pipeline XMLOUT self.copyRefmacXML() # Save the pipeline xml on every cycle open( self.pipelinexmlfile,'w').write( etree.tostring(self.xmlroot,pretty_print=True) ) # Test for interrupt if self.testForInterrupt() and self.cycle 0 and os.path.exists(os.path.join(self.getSubDirectories()[-1],'XYZOUT.pdb')): # Look for the coordinate file in the last sub-job # this sets currentCoordinates to a string but that is OK self.container.controlParameters.XYZIN_MODE.set( 'partial' ) self.currentCoordinates = os.path.join(self.getSubDirectories()[-1],'XYZOUT.pdb') print 'Restarting with coordinates in file:',self.currentCoordinates else: # self.container.controlParameters.XYZIN_MODE = 'partial' self.currentCoordinates = self.container.inputData.XYZIN if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "mr" and not self.container.inputData.ABCD.isSet() : self.mrmodel = self.container.inputData.BUCCANEER_MR_MODE_XYZIN self.refmacABCD = self.makeRefmacABCD(self.mrmodel, False) error = self.refmacABCD.process() running = True while running: if self.refmacABCD.container.outputData.ABCDOUT.isSet() : running = False time.sleep(0.5) if error == CPluginScript.FAILED: self.reportStatus ( error ) self.container.inputData.ABCD = self.refmacABCD.container.outputData.ABCDOUT self.container.inputData.ABCD.annotation.set ( 'Initial MR phases' ) self.container.inputData.BUCCANEER_MR_MODE_XYZIN = self.refmacABCD.container.outputData.XYZOUT self.container.inputData.BUCCANEER_MR_MODE_XYZIN.annotation.set ( 'Refined molecular replacement solution' ) if self.container.controlParameters.XYZIN_MODE and self.cycle == 0 : self.refmacABCD2 = self.makeRefmacABCD(self.currentCoordinates, False) error = self.refmacABCD2.process() running = True while running: if self.refmacABCD2.container.outputData.ABCDOUT.isSet() : running = False time.sleep(0.5) if error == CPluginScript.FAILED: self.reportStatus ( error ) self.container.inputData.XYZIN = self.refmacABCD2.container.outputData.XYZOUT self.container.inputData.XYZIN.annotation.set ( 'Refined initial model' ) # Start first buccaneer self.buccaneerPlugin = self.makeBuccaneerPlugin(restarted=restarted) self.connectSignal(self.buccaneerPlugin,'finished',self.buccaneerFinished) rv = self.buccaneerPlugin.process() return rv def buccaneerFinished(self, statusDict={}): # Check buccaneer finished and start either refmacPlugin0 (which is preparation for running coot) or go directly to refmacPlugin self.checkFinishStatus(statusDict=statusDict,failedErrCode=200,outputFile = self.buccaneerPlugin.container.outputData.XYZOUT,noFileErrCode=202) try: # Copy some data to the xml file xmlFile = self.buccaneerPlugin.makeFileName('PROGRAMXML') if os.path.exists(xmlFile): bxml = CCP4Utils.openFileToEtree(xmlFile) self.xmlcyc.append(bxml) open( self.pipelinexmlfile,'w').write( etree.tostring(self.xmlroot,pretty_print=True) ) self.n_fragments = int(bxml.xpath('//BuccaneerResult/Final/FragmentsBuilt')[-1].text) print '\nNumber of fragments built is ', self.n_fragments if self.n_fragments == 0: self.reportStatus(CPluginScript.UNSATISFACTORY) self.currentCoordinates = self.buccaneerPlugin.container.outputData.XYZOUT #Depending on whether there is/is not a cootPlugin defined, jump into refmacPlugin0 or prosmartRefmacPlugin if self.container.controlParameters.COOT_REALSPACE_OPERATION.__str__() != "none" and self.rwork < self.container.controlParameters.BUCCANEER_RSR_RWORK_LIMIT : self.refmacPlugin0 = self.makeRefmac0Plugin() self.refmacPlugin0.connectSignal(self.refmacPlugin0,'finished',self.refmac0Finished) rv = self.refmacPlugin0.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) else: self.refmacPlugin = self.makeProsmartRefmacPlugin() self.refmacPlugin.connectSignal(self.refmacPlugin,'finished',self.refmacFinished) rv = self.refmacPlugin.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) except Exception as e: print e self.appendErrorReport(CPluginScript,39,str(e)) def refmac0Finished(self, statusDict={}): # Check refmac status and then start coot self.checkFinishStatus(statusDict=statusDict,failedErrCode=206,outputFile = self.refmacPlugin0.container.outputData.ABCDOUT,noFileErrCode=207) try: print "Trying to access XML" self.accessRefmac0XML ( ) print "XML accessed" self.currentCoordinates = self.refmacPlugin0.container.outputData.XYZOUT print "Current XYZOUT: ", self.currentCoordinates if self.rwork < self.container.controlParameters.BUCCANEER_RSR_RWORK_LIMIT : self.cootPlugin = self.makeCootPlugin() self.cootPlugin.connectSignal(self.cootPlugin,'finished',self.cootFinished) rv = self.cootPlugin.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) else : self.refmacPlugin = self.makeProsmartRefmacPlugin() self.refmacPlugin.connectSignal(self.refmacPlugin,'finished',self.refmacFinished) rv = self.refmacPlugin.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) except Exception as e: print e self.appendErrorReport(CPluginScript,39,str(e)) def cootFinished(self, statusDict={}): # Check coot status and start refmac if len(self.cootPlugin.container.outputData.XYZOUT) == 0: self.appendErrorReport(205,'Coot failed to produce an output file') self.reportStatus(CPluginScript.FAILED) self.checkFinishStatus(statusDict=statusDict,failedErrCode=204, outputFile= self.cootPlugin.container.outputData.XYZOUT[0],noFileErrCode=205) try: self.cootPlugin.container.outputData.XYZOUT[0].subType = 1 self.currentCoordinates = self.cootPlugin.container.outputData.XYZOUT[0] self.refmacPlugin = self.makeProsmartRefmacPlugin() self.refmacPlugin.connectSignal(self.refmacPlugin,'finished',self.refmacFinished) rv = self.refmacPlugin.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) except Exception as e: print e self.appendErrorReport(CPluginScript,39,str(e)) def refmacFinished(self, statusDict={}): # Check refmac status and either start on next cycle with a run of buccaneer # or, if we have done required number of cycles, copy data from last jobs # to be output for the pipeline self.checkFinishStatus(statusDict=statusDict,failedErrCode=201, outputFile=self.refmacPlugin.container.outputData.XYZOUT ,noFileErrCode=203) try: # process XML from refmac and append to the pipeline XMLOUT # Copy xml from refmac to pipeline and write out self.copyRefmacXML() open( self.pipelinexmlfile,'w').write( etree.tostring(self.xmlroot,pretty_print=True) ) # Test for interrupt or that we have done last cycle if self.testForInterrupt() and self.cycle 0: buccaneerPlugin.container.controlParameters.CYCLES = self.container.controlParameters.BUCCANEER_CYCLES_NEXT else: buccaneerPlugin.container.controlParameters.CYCLES = self.container.controlParameters.BUCCANEER_CYCLES # the other input data is the same pipleine input for all cycles if self.cycle > 0 and self.rwork < 0.30 : self.container.controlParameters.BUCCANEER_MR_MODE = 'nothing' if self.container.controlParameters.BUCCANEER_USE_FREER : buccaneerPlugin.container.inputData.copyData(otherContainer=self.container.inputData, dataList= ( 'F_SIGF','FREERFLAG','SEQIN','XYZIN_SEQ', 'XYZIN_MODE', ( 'BUCCANEER_MR_MODE_XYZIN', 'MR_MODE_XYZIN' ) , 'XYZIN' ) ) else : buccaneerPlugin.container.inputData.copyData(otherContainer=self.container.inputData, dataList= ( 'F_SIGF', 'SEQIN', 'XYZIN_SEQ', 'XYZIN_MODE', ( 'BUCCANEER_MR_MODE_XYZIN', 'MR_MODE_XYZIN' ) , 'XYZIN' ) ) buccaneerPlugin.container.controlParameters.copyData(otherContainer=self.container.controlParameters, dataList= ( ( 'BUCCANEER_ANISOTROPY_CORRECTION', 'ANISOTROPY_CORRECTION' ), ( 'BUCCANEER_BUILD_SEMET','BUILD_SEMET' ), ( 'BUCCANEER_FAST','FAST' ), ( 'BUCCANEER_FIX_POSITION', 'FIX_POSITION' ), ( 'BUCCANEER_RESOLUTION', 'RESOLUTION' ), ( 'BUCCANEER_SEQUENCE_RELIABILITY', 'SEQUENCE_RELIABILITY' ), ( 'BUCCANEER_NEW_RESIDUE_NAME', 'NEW_RESIDUE_NAME' ), ( 'BUCCANEER_MODEL_SIGMA', 'MODEL_SIGMA' ), ( 'BUCCANEER_JOBS', 'JOBS' ), ( 'BUCCANEER_VERBOSE', 'VERBOSE' ), ( 'BUCCANEER_PHSIN_TYPE', 'PHSIN_TYPE' ), ( 'BUCCANEER_MR_MODE', 'MR_MODE' ), ( 'BUCCANEER_MR_MODE_SIGMA', 'MR_MODE_SIGMA' ), 'F_SIGF_REF','ABCD_REF', 'XYZIN_REF','KNOWN_STRUCTURE' ) ) if self.cycle > 0: print 'This is cycle number ',self.cycle # get the partially built model from the previous cycle and extend it buccaneerPlugin.container.inputData.XYZIN_MODE.set( True ) buccaneerPlugin.container.inputData.XYZIN.set( self.currentCoordinates ) elif self.container.inputData.XYZIN.isSet(): buccaneerPlugin.container.inputData.XYZIN_MODE.set( True ) buccaneerPlugin.container.inputData.XYZIN.set( self.container.inputData.XYZIN ) return buccaneerPlugin def makeRefmacABCD(self, coordinates=None, jelly=False): # generate phases and figures of merit from MR model and reflection data refmacPlugin = self.makePluginObject('refmac') refmacPlugin.container.inputData.XYZIN.set( coordinates ) refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','FREERFLAG','DICT')) print 'makeRefmacABCD self',self.container.controlParameters.EXTRAREFMACKEYWORDS refmacPlugin.container.controlParameters.copyData(otherContainer=self.container.controlParameters,dataList=('EXTRAREFMACKEYWORDS',)) print 'makeRefmacABCD refmacPlugin',refmacPlugin.container.controlParameters.EXTRAREFMACKEYWORDS refmacPlugin.container.controlParameters.HYDROGENS = 'NO' refmacPlugin.container.controlParameters.PHOUT = True refmacPlugin.container.controlParameters.USE_LOCAL_SYMMETRY = False if jelly : refmacPlugin.container.controlParameters.JELLY_SIGMA = 0.05 refmacPlugin.container.controlParameters.USE_JELLY = True refmacPlugin.container.controlParameters.NCYCLES = 50 else : refmacPlugin.container.controlParameters.NCYCLES = 10 return refmacPlugin def makeRefmac0Plugin(self): # refmac wrapper run to generate 2mFo-DFc map coefficients and more accurate B-factors for coot refmacPlugin0 = self.makePluginObject('refmac') refmacPlugin0.container.inputData.XYZIN.set( self.currentCoordinates ) if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "mr" and self.container.controlParameters.REFMAC_MR_USEPHI: refmacPlugin0.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','DICT')) elif self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "experimental" and self.container.controlParameters.REFMAC_EXP_USEPHI: refmacPlugin0.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','DICT')) else: refmacPlugin0.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','FREERFLAG','DICT')) refmacPlugin0.container.controlParameters.copyData(otherContainer=self.container.controlParameters,dataList=('EXTRAREFMACKEYWORDS',)) refmacPlugin0.container.controlParameters.HYDROGENS = 'NO' refmacPlugin0.container.controlParameters.NCYCLES = 20 refmacPlugin0.container.controlParameters.PHOUT = True if self.container.controlParameters.REFMAC_LOCAL_NCS and self.n_fragments < 14 : refmacPlugin0.container.controlParameters.USE_LOCAL_SYMMETRY = True else: refmacPlugin0.container.controlParameters.USE_LOCAL_SYMMETRY = False return refmacPlugin0 def makeRefmacPlugin(self): refmacPlugin = self.makePluginObject('refmac') refmacPlugin.container.inputData.XYZIN.set( self.currentCoordinates ) if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "mr" and self.container.controlParameters.REFMAC_MR_USEPHI: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','DICT')) elif self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "experimental" and self.container.controlParameters.REFMAC_EXP_USEPHI: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','DICT')) else: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','FREERFLAG','DICT')) refmacPlugin.container.inputData.FREERFLAG = self.container.inputData.FREERFLAG refmacPlugin.container.controlParameters.copyData(otherContainer=self.container.controlParameters,dataList=('EXTRAREFMACKEYWORDS',)) refmacPlugin.container.controlParameters.HYDROGENS = 'NO' refmacPlugin.container.controlParameters.NCYCLES = self.container.controlParameters.REFMAC_CYCLES refmacPlugin.container.controlParameters.PHOUT = True if self.rwork > r_work_essentially_complete_model : refmacPlugin.container.controlParameters.EXTRAREFMACKEYWORDS += '''\nsolvent NO scal type BULK LSSC ANIS EXPE FIXBulk BBULk 200.0 ''' else : refmacPlugin.container.controlParameters.EXTRAREFMACKEYWORDS += '''\nsolvent yes VDWProb 1.4 IONProb 0.8 RSHRink 0.8 scal type SIMPLE LSSC ANIS EXPE ''' if self.container.controlParameters.REFMAC_LOCAL_NCS and self.n_fragments < 14 : refmacPlugin.container.controlParameters.USE_LOCAL_SYMMETRY = True else: refmacPlugin.container.controlParameters.USE_LOCAL_SYMMETRY = False return refmacPlugin def makeProsmartRefmacPlugin(self): # Create an instance of the prosmart-refmac pipeline refmacPlugin = self.makePluginObject('prosmart_refmac') # coordinates are those saved from preceeding coot run or buccaneer run refmacPlugin.container.inputData.XYZIN.set( self.currentCoordinates ) # all other data from the input to the pipeline if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "mr" and self.container.controlParameters.REFMAC_MR_USEPHI: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','TARGET','DICT')) elif self.rwork > self.container.controlParameters.BUCCANEER_MLHL_RWORK_LIMIT and self.container.controlParameters.BUCCANEER_PHSIN_TYPE == "experimental" and self.container.controlParameters.REFMAC_EXP_USEPHI: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','ABCD','FREERFLAG','TARGET','DICT')) else: refmacPlugin.container.inputData.copyData(otherContainer=self.container.inputData,dataList=('F_SIGF','FREERFLAG','TARGET','DICT')) refmacPlugin.container.inputData.FREERFLAG = self.container.inputData.FREERFLAG if self.container.inputData.TARGET.isSet(): refmacPlugin.container.inputData.TARGET = self.container.inputData.TARGET refmacPlugin.container.controlParameters.copyData(otherContainer=self.container.controlParameters,dataList=('EXTRAREFMACKEYWORDS',)) refmacPlugin.container.controlParameters.HYDROGENS = 'NO' refmacPlugin.container.controlParameters.MAKE_NEW_LIGAND_EXIT.set(False) refmacPlugin.container.controlParameters.NCYCLES = self.container.controlParameters.REFMAC_CYCLES refmacPlugin.container.controlParameters.PHOUT = True if self.rwork > r_work_essentially_complete_model : refmacPlugin.container.controlParameters.EXTRAREFMACKEYWORDS += '''\nsolvent NO scal type BULK LSSC ANIS EXPE FIXBulk BBULk 200.0 ''' else : refmacPlugin.container.controlParameters.EXTRAREFMACKEYWORDS += '''\nsolvent yes VDWProb 1.4 IONProb 0.8 RSHRink 0.8 scal type SIMPLE LSSC ANIS EXPE ''' if self.container.controlParameters.REFMAC_LOCAL_NCS and self.n_fragments < 14 : refmacPlugin.container.controlParameters.USE_LOCAL_SYMMETRY = True else: refmacPlugin.container.controlParameters.USE_LOCAL_SYMMETRY = False return refmacPlugin def makeCootPlugin(self): cootPlugin = self.makePluginObject('coot_script_lines') xyzinList = cootPlugin.container.inputData.XYZIN xyzinList.append(xyzinList.makeItem()) xyzinList[-1].set(self.currentCoordinates) fphiinList = cootPlugin.container.inputData.FPHIIN fphiinList.append(fphiinList.makeItem()) fphiinList[-1].set(self.refmacPlugin0.container.outputData.FPHIOUT) #coot_stepped_refine,coot_fit_residues,coot_script_lines rso = self.container.controlParameters.COOT_REALSPACE_OPERATION.__str__() if rso == "coot_script_lines": cootPlugin.container.controlParameters.SCRIPT = self.container.controlParameters.SCRIPT elif rso == "coot_fit_residues": cootPlugin.container.controlParameters.SCRIPT = '''fill_partial_residues(MolHandle_1) fit_protein(MolHandle_1) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' elif rso == "coot_stepped_refine": if self.container.controlParameters.USERAMA.isSet() and self.container.controlParameters.USERAMA: cootPlugin.container.controlParameters.SCRIPT = '''fill_partial_residues(MolHandle_1) stepped_refine_protein_for_rama(MolHandle_1) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' else: cootPlugin.container.controlParameters.SCRIPT = '''fill_partial_residues(MolHandle_1) stepped_refine_protein(MolHandle_1) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' elif rso == "coot_add_waters": cootPlugin.container.controlParameters.SCRIPT = '''set_ligand_water_to_protein_distance_limits(2.2, 3.3) execute_find_waters_real(MapHandle_1,MolHandle_1,0,1.3) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' elif rso == "none": cootPlugin.container.controlParameters.SCRIPT = '''write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' return cootPlugin # ===== Utility methods ======================================================================================== def initialiseXML(self,restarted=False): # Set up the xml output self.pipelinexmlfile = self.makeFileName(format='PROGRAMXML') if restarted and os.path.exists(self.pipelinexmlfile): try: f = open(self.pipelinexmlfile) self.xmlroot = etree.fromstring(f.read()) f.close() except: self.xmlroot = etree.Element("BuccaneerBuildRefineResult") else: self.xmlroot = etree.Element("BuccaneerBuildRefineResult") self.xmlcyc = etree.SubElement(self.xmlroot,"BuildRefineCycle") etree.SubElement(self.xmlcyc,"Number").text = str(self.cycle+1) def copyRefmacXML(self): rxml = CCP4Utils.openFileToEtree(self.refmacPlugin.makeFileName('PROGRAMXML')) rstats = rxml.xpath("//REFMAC/Overall_stats/stats_vs_cycle") #print 'refmac xml rstats',len(rstats) if len(rstats)>0: refele = etree.Element('RefmacResult') for node in rstats[0].xpath("new_cycle[last()]/r_factor | new_cycle[last()]/r_free | new_cycle[last()]/rmsBOND | new_cycle[last()]/rmsANGLE"): node.text = str(node.text).strip() if node.tag == 'rmsBOND': node.text = str(100*float(node.text)) node.tag='rmsBONDx100' #print 'refmac xml',etree.tostring(node,pretty_print=True) refele.append( deepcopy( node ) ) self.xmlcyc.append(refele) self.xmlroot.append(self.xmlcyc) def accessRefmac0XML(self) : r0xml = CCP4Utils.openFileToEtree ( self.refmacPlugin0.makeFileName ( 'PROGRAMXML' ) ) statistics = r0xml.xpath ( "//REFMAC/Overall_stats/stats_vs_cycle " ) rwork_tmp = 1.0 rfree_tmp = 1.0 if len ( statistics ) > 0 : print "We have stats" rwork_tmp = float ( statistics[0].xpath ( "new_cycle[last()]/r_factor" )[0].text ) print "assignment does not crash" rfree_tmp = float ( statistics[0].xpath ( "new_cycle[last()]/r_free" )[0].text ) #print "Rwork: ", self.rwork, "Rfree: ", self.rfree if rwork_tmp > 0 and rwork_tmp < 0.7 : self.rwork = rwork_tmp print "New Rwork: ", self.rwork if rfree_tmp > 0 and rfree_tmp < 0.7 : self.rfree = rfree_tmp print "New Rfree: ", self.rfree def copyBuccaneerXML(self): xmlFile = str(self.buccaneerPlugin.makeFileName('PROGRAMXML')) if os.path.exists(xmlFile): bxml = CCP4Utils.openFileToEtree(xmlFile) self.xmlcyc.append(bxml) def checkFinishStatus( self,statusDict,failedErrCode,outputFile = None,noFileErrCode= None): if len(statusDict)>0 and statusDict['finishStatus'] == CPluginScript.FAILED: self.appendErrorReport(failedErrCode) self.reportStatus(statusDict['finishStatus']) if outputFile is not None and not outputFile.exists(): self.appendErrorReport(noFileErrCode,'Expected file: '+str(outputFile)) self.reportStatus(CPluginScript.FAILED) return def copyPipelineOutputFiles(self): # CCP4i2 has strict conventions for the path and filename of output files. The pipeline output file names # (i.e. self.container.outputData.XXXXOUT) have been set automatically. We need to physically copy refmac # output files to the right place for them to be recognised as the pipeline output. shutil.copyfile( str(self.refmacPlugin.container.outputData.XYZOUT), str(self.container.outputData.XYZOUT.fullPath) ) shutil.copyfile( str(self.refmacPlugin.container.outputData.FPHIOUT), str(self.container.outputData.FPHIOUT.fullPath) ) shutil.copyfile( str(self.refmacPlugin.container.outputData.DIFFPHIOUT), str(self.container.outputData.DIFFPHIOUT.fullPath) ) shutil.copyfile( str(self.refmacPlugin.container.outputData.ABCDOUT), str(self.container.outputData.ABCDOUT.fullPath) ) # Tag the output data objects with the subType and annotation that we know self.container.outputData.XYZOUT.annotation.set('Model built by Autobuild protein') self.container.outputData.XYZOUT.subType=1 self.container.outputData.FPHIOUT.subType=1 self.container.outputData.FPHIOUT.annotation.set('2mFo-DFc map coefficients') self.container.outputData.DIFFPHIOUT.annotation.set('mFo-DFc map coefficients') self.container.outputData.DIFFPHIOUT.subType=2 return def setPerformanceData(self): # Set the outputData.PERFORMANCE data by extracting from self.xmlcyc (the XML output for the latest cycle) #print 'setPerformanceData',etree.tostring(self.xmlcyc, pretty_print=True) self.rwork = self.container.outputData.PERFORMANCE.RFactor = float(self.xmlcyc.xpath('//BuildRefineCycle/RefmacResult/r_factor')[-1].text) self.rfree = float(self.xmlcyc.xpath('//BuildRefineCycle/RefmacResult/r_free')[-1].text) print 'Rwork=',self.rwork, " Rfree=",self.rfree self.container.outputData.PERFORMANCE.completeness = float(self.xmlcyc.xpath('//BuildRefineCycle/BuccaneerResult/Final/CompletenessByResiduesBuilt')[-1].text) return #======================================================================================================= import unittest class test_buccaneer_build_refine_mr(unittest.TestCase): def setUp(self): # make all background jobs wait for completion from CCP4Modules import QTAPPLICATION,PROCESSMANAGER self.app = QTAPPLICATION() PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): from CCP4Modules import PROCESSMANAGER PROCESSMANAGER().setWaitForFinished(-1) def test_1(self): from CCP4Modules import QTAPPLICATION import os from CCP4Utils import getCCP4I2Dir # Run the pipeline wrapper = buccaneer_build_refine_mr(parent=QTAPPLICATION(),name='buccaneer_build_refine_mr') wrapper.container.loadDataFromXml(os.path.join(getCCP4I2Dir(),'pipelines','buccaneer_build_refine_mr','test_data','test_1.params.xml')) # Ensure no output file exists already xyzout = wrapper.container.outputData.XYZOUT.fullPath.get() if xyzout is not None and os.path.exists(xyzout): os.remove(xyzout) xmlout = wrapper.makeFileName('PROGRAMXML') if xmlout is not None and os.path.exists(xmlout): os.remove(xmlout) pid = wrapper.process() #test if output file created self.assertEqual(os.path.exists( xyzout),1,'Failed to create copied pdb file '+xyzout) def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(test_buccaneer_build_refine_mr) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)