from CCP4PluginScript import CPluginScript import sys, os import CCP4ErrorHandling import CCP4Modules import phaser_MR from lxml import etree class EPAUTOCallbackObject(phaser_MR.CallbackObject): def __init__(self, xmlroot=None, xmlResponders = [],workDirectory=None): super(EPAUTOCallbackObject, self).__init__(xmlroot, xmlResponders) #self.summaryFile = open(os.path.join(workDirectory,'summary.txt'),'w') self._summary_buffer = "" def call_back(self, label, text): if label == 'current best solution': try: for oldNode in self.xmlroot.xpath('//PhaserCurrentBestSolution'): oldNode.getparent().remove(oldNode) bestSolNode =etree.SubElement(self.xmlroot,'PhaserCurrentBestSolution') phaser_MR.xmlFromSol(text, bestSolNode) self.notifyResponders() except: print '\n\n Exception in analysing current best solution' elif label == 'summary': print '***Summary callback:[', text.replace('\n','\n***********'),'\n******]\n' if text.startswith("**********") and not self._summary_buffer.strip().endswith("***"): self.flushSummary() self._summary_buffer += text else: print '***',label,' callback:', text def flushSummary(self): summaryNode = etree.SubElement(self.xmlroot,'Summary') summaryNode.text = self._summary_buffer self.notifyResponders() self._summary_buffer = "" class phaser_EP_AUTO(phaser_MR.phaser_MR): TASKNAME = 'phaser_EP_AUTO' # Task name - should be same as class name TASKCOMMAND = '' # The command to run the executable TASKVERSION= 0.0 # Version of this plugin COMTEMPLATE = None # The program com file template COMTEMPLATEFILE = None # Name of file containing com file template ASYNCHRONOUS = False RUNEXTERNALPROCESS=False ERROR_CODES = { 201 : { 'description' : 'Failed to find file' }, 202 : { 'description' : 'Failed to interpret searches from Ensemble list' },} ''' def __init__(self,parent=None,name=None,workDirectory=''): phaser_MR.phaser_MR. __init__(self,parent=parent,name=name,workDirectory=workDirectory) ''' def __init__(self, *args, **kw): super(phaser_EP_AUTO, self).__init__(*args, **kw) #Create a callback Object that will respond to callbacks from Phaser, principally by putting information #intp the outputXML of this plugin self.xmlroot = etree.Element('PhaserEpResults') self.callbackObject = EPAUTOCallbackObject(self.xmlroot, [self.flushXML]) def startProcess(self, command, **kw): import phaser outputObject = phaser.Output() outputObject.setPhenixCallback(self.callbackObject) xtalid = 'Scatterers' #Note, in phaser distributed with ccp4-7, waveid is nolonger "space" toleratnt waveid = 'Wave1' inputObject = phaser.InputEP_DAT() inputObject.setHKLI(str(self.hklin)) inputObject.addCRYS_ANOM_LABI(xtalid,waveid,"Fplus","SIGFplus","Fminus","SIGFminus") inp = self.container.inputData if inp.RESOLUTION_LOW.isSet(): if inp.RESOLUTION_HIGH.isSet(): inputObject.setRESO(float(inp.RESOLUTION_LOW), float(inp.RESOLUTION_HIGH)) else: inputObject.setHIRES(float(inp.RESOLUTION_LOW)) elif inp.RESOLUTION_HIGH.isSet(): inputObject.setHIRES(float(inp.RESOLUTION_HIGH)) inputObject.setMUTE(False) resultObject = phaser.runEP_DAT(inputObject, outputObject) self.inputHall = resultObject.getSpaceGroupHall() if not resultObject.Success(): self.appendErrorReport(105, resultObject.ErrorName() + '-' + resultObject.ErrorMessage()) return CPluginScript.FAILED with open (self.makeFileName('LOG'),'w') as logfile: logfile.write(resultObject.logfile()) hkl = resultObject.getMiller() Fpos = resultObject.getFpos(xtalid,waveid) Spos = resultObject.getSIGFpos(xtalid,waveid) Ppos = resultObject.getPpos(xtalid,waveid) Fneg = resultObject.getFneg(xtalid,waveid) Sneg = resultObject.getSIGFneg(xtalid,waveid) Pneg = resultObject.getPneg(xtalid,waveid) i = phaser.InputEP_AUTO() i.setSPAC_HALL(resultObject.getSpaceGroupHall()) cell = resultObject.getUnitCell() i.setCELL(cell[0],cell[1],cell[2],cell[3],cell[4],cell[5]) i.setCRYS_MILLER(hkl) i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg) if self.setKeywords(i) == CPluginScript.FAILED: return CPluginScript.FAILED if self.container.inputData.PARTIALMODELORMAP.__str__() == 'MODEL': if self.container.inputData.XYZIN_PARTIAL.isSet() and os.path.isfile(self.container.inputData.XYZIN_PARTIAL.fullPath.__str__()): i.setPART_PDB(self.container.inputData.XYZIN_PARTIAL.fullPath.__str__()) elif self.container.inputData.PARTIALMODELORMAP.__str__() == 'MAP': if self.container.inputData.MAPCOEFF_PARTIAL.isSet() and os.path.isfile(self.container.inputData.MAPCOEFF_PARTIAL.fullPath.__str__()): i.setPART_HKLI(self.container.inputData.MAPCOEFF_PARTIAL.fullPath.__str__()) i.setPART_LABI_FC('F') i.setPART_LABI_PHIC('PHI') elif self.container.inputData.PARTIALMODELORMAP.__str__() == 'NONE' and self.container.inputData.XYZIN_HA.isSet() and os.path.isfile(self.container.inputData.XYZIN_HA.fullPath.__str__()): i.setATOM_PDB(xtalid, self.container.inputData.XYZIN_HA.fullPath.__str__()) i.setLLGC_COMP(True) i.setLLGC_NCYC(int(self.container.inputData.LLGC_CYCLES)) # Search for "Generic" anomalous scatterer if self.container.inputData.PURE_ANOMALOUS.isSet() and self.container.inputData.PURE_ANOMALOUS: i.addLLGC_ANOM(True) else: i.addLLGC_ANOM(False) for element in self.container.inputData.ELEMENTS: i.addLLGC_ELEM(str(element)) i.setWAVE(float(self.container.inputData.WAVELENGTH)) if self.parseContent(i) == CPluginScript.FAILED: return CPluginScript.FAILED i.setMUTE(False) i.setVERB(True) i.setOUTP_LEVE('SUMMARY') self.resultObject = phaser.runEP_AUTO(i, outputObject) if not self.resultObject.Success(): self.appendErrorReport(105, self.resultObject.ErrorName() + '-' + self.resultObject.ErrorMessage()) return CPluginScript.FAILED with open (self.makeFileName('LOG'),'a') as logfile: logfile.write(self.resultObject.logfile()) return CPluginScript.SUCCEEDED def processInputFiles(self): import CCP4XtalData self.hklin,error = self.makeHklin([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR]]) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: for report in error._reports: if report['code'] == 32: report['details'] = 'F+ and F- cannot be derived from data. Check file import.' return CPluginScript.FAILED return CPluginScript.SUCCEEDED def subElementWithNameAndText(self, parentNode, name, text): newNode = etree.SubElement(parentNode, name) newNode.text = text return newNode def flushXML(self, xml): from lxml import etree import os tmpFilename = self.makeFileName('PROGRAMXML')+'_tmp' with open(tmpFilename,'w') as tmpFile: tmpFile.write(etree.tostring(xml, pretty_print=True)) self.renameFile(tmpFilename, self.makeFileName('PROGRAMXML')) def processOutputFiles(self): import os,shutil resultObject = self.resultObject import CCP4XtalData for hand in ['','.hand']: possibleCoords = os.path.join(self.getWorkDirectory(),'PHASER.1'+hand+'.pdb') if os.path.isfile(possibleCoords): self.container.outputData.XYZOUT.append(self.container.outputData.XYZOUT.makeItem()) self.container.outputData.XYZOUT[-1].setFullPath(possibleCoords) self.container.outputData.XYZOUT[-1].annotation = 'Sites' if len(self.container.outputData.XYZOUT)>0: self.container.outputData.XYZOUT[0].annotation += ' - original hand' self.container.outputData.XYZOUT[0].subType = 4 if len(self.container.outputData.XYZOUT)>1: self.container.outputData.XYZOUT[1].annotation += ' - reversed hand' self.container.outputData.XYZOUT[1].subType = 4 for hand in ['','.hand']: possibleHKLOUT = os.path.join(self.getWorkDirectory(),'PHASER.1'+hand+'.mtz') if os.path.isfile(possibleHKLOUT): self.container.outputData.HKLOUT.append(self.container.outputData.HKLOUT.makeItem()) self.container.outputData.HKLOUT[-1].setFullPath(possibleHKLOUT) if len(self.container.outputData.HKLOUT) > 0: self.splitHkloutList(miniMtzsOut=['ABCDOUT','MAPOUT'],programColumnNames=['HLA,HLB,HLC,HLD','FWT,PHWT'],outputBaseName=['ABCDOUT','MAPOUT'],outputContentFlags=[CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL,1],infileList=self.container.outputData.HKLOUT) for hlCoeffs in self.container.outputData.ABCDOUT: hlCoeffs.annotation = 'Phase estimates' if len(self.container.outputData.ABCDOUT)>0:self.container.outputData.ABCDOUT[0].annotation += ' - original hand' if len(self.container.outputData.ABCDOUT)>1:self.container.outputData.ABCDOUT[1].annotation += ' - reversed hand' for map in self.container.outputData.MAPOUT: map.annotation = 'Phased map' map.subType = 1 if len(self.container.outputData.MAPOUT)>0:self.container.outputData.MAPOUT[0].annotation += ' - original hand' if len(self.container.outputData.MAPOUT)>1:self.container.outputData.MAPOUT[1].annotation += ' - reversed hand' while len(self.container.outputData.HKLOUT) > 0: self.container.outputData.HKLOUT.remove(self.container.outputData.HKLOUT[-1]) for hand in ['','.hand']: possibleHKLOUT = os.path.join(self.getWorkDirectory(),'PHASER.1'+hand+'.llgmaps.mtz') if os.path.isfile(possibleHKLOUT): self.container.outputData.HKLOUT.append(self.container.outputData.HKLOUT.makeItem()) self.container.outputData.HKLOUT[-1].setFullPath(possibleHKLOUT) if len(self.container.outputData.HKLOUT) > 0: self.splitHkloutList(miniMtzsOut=['LLGMAPOUT'],programColumnNames=['FLLG_AX,PHLLG_AX'],outputBaseName=['LLGMAPOUT'],infileList=self.container.outputData.HKLOUT) for llgMap in self.container.outputData.LLGMAPOUT: llgMap.annotation = 'Anomalous LLG map' llgMap.contentFlag = 1 llgMap.subType = 2 if len(self.container.outputData.LLGMAPOUT)>0:self.container.outputData.LLGMAPOUT[0].annotation += ' - original hand' if len(self.container.outputData.LLGMAPOUT)>1:self.container.outputData.LLGMAPOUT[1].annotation += ' - reversed hand' return CPluginScript.SUCCEEDED