""" lorestr_i2.py: CCP4 GUI Project 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 os from CCP4PluginScript import CPluginScript from lxml import etree import CCP4Utils import CCP4ErrorHandling from CCP4ErrorHandling import * import CCP4Modules from lxml import etree from xml.etree import ElementTree as ET class lorestr_i2(CPluginScript): TASKNAME = 'lorestr_i2' # Task name - should be same as class name and match pluginTitle in the .def.xml file TASKVERSION= 0.1 # Version of this plugin MAINTAINER = 'kovoleg' ERROR_CODES = { 201 : {'description' : 'Failed to analyse output files' }, 202 : {'description' : 'Failed applying selection ot PDB file' } } PURGESEARCHLIST = [ [ 'hklin.mtz' , 0 ], ['log_mtzjoin.txt', 0] ] TASKCOMMAND="lorestr" #_dummy PERFORMANCECLASS = 'CRefinementPerformance' def __init__(self, *args, **kws): super(lorestr_i2, self).__init__(*args, **kws) self._readyReadStandardOutputHandler = self.handleReadyReadStandardOutput self.xmlroot = etree.Element('lorestr_i2') # from refmacLogScraper import logScraper # self.logScraper = logScraper(xmlroot=self.xmlroot, flushXML=self.flushXML) self.xmlLength = 0 def processInputFiles(self): #Preprocess reflections to generate an "HKLIN" file ''' #makeHklin0 takes as arguments a list of sublists #Each sublist comprises 1) A reflection data object identifier (one of those specified in the inputData container # the task in the corresponding .def.xml # 2) The requested data representation type to be placed into the file that is generated # #makeHklin0 returns a tuple comprising: # 1) the file path of the file that has been created # 2) a list of strings, each of which contains a comma-separated list of column labels output from # the input data objects # 3) A CCP4 Error object import CCP4XtalData self.hklin, self.columns, error = self.makeHklin0([ ['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN] ]) self.columnsAsArray = self.columns.split(",") import CCP4ErrorHandling if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED ''' #Preprocess coordinates to extract a subset ''' # The method "getSelectedAtomsPdbFile" applied to a coordinate data object # selects those atoms declared in the objects "selectionString" property and writes them into # a pruned down file, the name of which is provided in the argument self.selectedCoordinatesPath = os.path.join(self.getWorkDirectory(), "selected_xyzin.pdb") self.container.inputData.XYZIN.getSelectedAtomsPdbFile(self.selectedCoordinatesPath) ''' import CCP4XtalData error = None self.hklin = None dataObjects = [] #print '\n\n\n***contentFlag',self.container.inputData.F_SIGF.contentFlag #Append Observation with representation dependent on whether we are detwining on Is or not obsTypeRoot = 'CONTENT_FLAG_F' obsPairOrMean = 'MEAN' obsType = getattr(CCP4XtalData.CObsDataFile, obsTypeRoot+obsPairOrMean) dataObjects += [['F_SIGF',obsType]] # ,obsType #Apply coordinate selection if set import os self.inputCoordPath = os.path.normpath(self.container.inputData.XYZIN.fullPath.__str__()) if self.container.inputData.XYZIN.isSelectionSet(): self.inputCoordPath = os.path.normpath(os.path.join(self.getWorkDirectory(),'selected.pdb')) self.container.inputData.XYZIN.getSelectedAtomsPdbFile(self.inputCoordPath) #Include FreeRflag if called for if self.container.inputData.FREERFLAG.isSet(): dataObjects += ['FREERFLAG'] self.hklin,error = self.makeHklin(dataObjects) import CCP4ErrorHandling if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED else: return CPluginScript.SUCCEEDED def handleReadyReadStandardOutput(self): print 'Runtime call handleReadyReadStandardOutput\n\n' if not hasattr(self,'logFileHandle'): self.logFileHandle = open(self.makeFileName('LOG'),'w') if not hasattr(self,'logFileBuffer'): self.logFileBuffer = '' pid = self.getProcessId() qprocess = CCP4Modules.PROCESSMANAGER().getJobData(pid,attribute='qprocess') availableStdout = qprocess.readAllStandardOutput() self.logFileHandle.write(availableStdout) self.logFileHandle.flush() self.xmlroot = etree.Element("lorestr_i2") logText = etree.SubElement(self.xmlroot,"LogText") logText.text = etree.CDATA(availableStdout) self.flushXML() # self.logScraper.processLogChunk(str(availableStdout)) def flushXML(self): newXml = etree.tostring(self.xmlroot,pretty_print=True) if len(newXml)>self.xmlLength: self.xmlLength = len(newXml) with open (self.makeFileName('PROGRAMXML')+'_tmp','w') as programXmlFile: programXmlFile.write(newXml) import shutil shutil.move(self.makeFileName('PROGRAMXML')+'_tmp', self.makeFileName('PROGRAMXML')) def makeCommandAndScript(self, **kw): import os self.hklout = os.path.join(self.workDirectory,"hklout.mtz") # ccp4-python -m lorestr.main # -f 1.mtz # -p1 1.pdb # -xyzout 1_lorestr1.pdb # -hklout 1_lorestr1.mtz # -o ./8_lorestr # -nc 3 # -minres 3.5 # -nh 5 # -auto # -save_space # Input self.appendCommandLine(['-p1', self.inputCoordPath]) self.appendCommandLine(['-f', self.hklin]) if self.container.inputData.TLSIN.isSet(): self.appendCommandLine(['-tls', self.container.inputData.TLSIN.fullPath]) # if self.container.inputData.REFERENCE_MODEL.isSet(): # self.appendCommandLine(['-p2', self.container.inputData.REFERENCE_MODEL.fullPath]) p2 = ['-p2'] for iCoordSet, xyzRef in enumerate(self.container.inputData.REFERENCE_LIST): p2.append(str(xyzRef.fullPath)) if len(p2) > 1: self.appendCommandLine(p2) # Output self.appendCommandLine(['-xyzout', self.container.outputData.XYZOUT.fullPath]) self.appendCommandLine(['-hklout', self.hklout]) self.appendCommandLine(['-o', self.workDirectory + '/lorestrOutput']) # self.appendCommandLine(['LIBOUT',self.container.outputData.LIBOUT.fullPath]) # self.appendCommandLine(['XMLOUT',os.path.normpath(os.path.join(self.getWorkDirectory(),'XMLOUT.xml'))]) # Parameters self.appendCommandLine(['-xml', str(self.makeFileName('PROGRAMXML'))]) # ccp4i2 compatibility if self.container.controlParameters.AUTO: self.appendCommandLine(['-auto']) if self.container.controlParameters.MR: self.appendCommandLine(['-mr']) if self.container.controlParameters.SS: self.appendCommandLine(['-save_space']) if self.container.controlParameters.DNA: self.appendCommandLine(['-dna']) if self.container.controlParameters.CPU: self.appendCommandLine(['-cpu', str(self.container.controlParameters.CPU)]) if self.container.controlParameters.MINRES: self.appendCommandLine(['-minres', str(self.container.controlParameters.MINRES)]) if self.container.controlParameters.NC: self.appendCommandLine(['-nc', str(self.container.controlParameters.NC)]) if self.container.controlParameters.NH: self.appendCommandLine(['-nh', str(self.container.controlParameters.NH)]) return CPluginScript.SUCCEEDED def processOutputFiles(self): #Associate the tasks output coordinate file with the output coordinate object XYZOUT: self.container.outputData.XYZOUT.setFullPath(os.path.join(self.getWorkDirectory(),"XYZOUT.pdb")) # Split an MTZ file into minimtz data objects # outputFilesToMake = ['FPHIOUT','DIFFPHIOUT'] # columnsToTake = ['FWT,PHWT','DELFWT,PHDELWT'] # infile = self.hklout # error = self.splitHklout(outputFilesToMake, columnsToTake, infile=infile) self.container.outputData.XYZOUT.annotation = 'Refined model' self.container.outputData.FPHIOUT.annotation = 'Weighted map after refinement' self.container.outputData.DIFFPHIOUT.annotation = 'Weighted difference map after refinement' self.container.outputData.FPHIOUT.subType = 1 self.container.outputData.DIFFPHIOUT.subType = 2 outputFiles = ['FPHIOUT','DIFFPHIOUT'] outputColumns = ['FWT,PHWT','DELFWT,PHDELWT'] error = self.splitHklout(outputFiles,outputColumns) xmlRoot = ET.parse(self.makeFileName('PROGRAMXML')).getroot() bestProtocolNumber = int(xmlRoot.find("Protocols").findtext("BestProtocol")) rFact = xmlRoot.find("Protocols").find("P%d" % bestProtocolNumber).findtext("Rfact") rFree = xmlRoot.find("Protocols").find("P%d" % bestProtocolNumber).findtext("Rfree") self.container.outputData.PERFORMANCE.RFactor = float(rFact) self.container.outputData.PERFORMANCE.RFree = float(rFree) import CCP4ErrorHandling if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED return CPluginScript.SUCCEEDED