from CCP4PluginScript import CPluginScript import sys, os import CCP4ErrorHandling import CCP4Modules import CCP4Data from lxml import etree class CallbackObject(object): def __init__(self, xmlroot=None, xmlResponders = []): super(CallbackObject,self).__init__() self.xmlroot = xmlroot self.xmlResponders = xmlResponders def currentActivityNode(self): try: aNode = self.xmlroot.xpath('CurrentActivity')[0] except: aNode = etree.SubElement(self.xmlroot,'CurrentActivity') self.currentActivityLabel = etree.SubElement(aNode,'label') self.currentActivityMax = etree.SubElement(aNode,'max') self.currentActivityValue = etree.SubElement(aNode,'value') return aNode def startProgressBar(self, arg1, arg2): aNode = self.currentActivityNode() self.currentActivityLabel.text = str(arg1) self.currentActivityMax.text = str(arg2) self.currentActivityValue.text = '0' self.notifyResponders() def incrementProgressBar(self): #print '**Increment progress bar called\n' aNode = self.currentActivityNode() self.currentActivityValue.text = str(int(self.currentActivityValue.text) + 1) self.notifyResponders() def endProgressBar(self): #print '**End progress bar called\n' pass def warn(self, warning): try: warningsElement = self.xmlroot.xpath('PhaserWarnings')[0] except: warningsElement = etree.SubElement(self.xmlroot,'PhaserWarnings') warningElement = etree.SubElement(warningsElement,'Warning') warningElement.text = warning self.notifyResponders() def loggraph(self, arg1, arg2): #print '\n**loggraph called',arg1 try: import MGQTmatplotlib tableelement = MGQTmatplotlib.CCP4LogToEtree(arg2) self.xmlroot.append(tableelement) except: print '\n\n\ failed reading MGQTMatPlotLib' self.notifyResponders() def call_back(self, arg1, arg2): #print '\n**call_back called: *Arg1:', arg1, '*Arg2:', arg2 self.notifyResponders() def notifyResponders(self): try: for boundMethod in self.xmlResponders: boundMethod(self.xmlroot) except: print 'Exception raised in notifyResponders' def addResponder(self, responder): self.xmlResponders.append(responder) class phaser_MR(CPluginScript): TASKNAME = 'phaser_MR' # 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 ERROR_CODES = { 101 : { 'description' : 'Failed to run MR_DAT' }, 102 : { 'description' : 'Failed to set keywords' }, 103 : { 'description' : 'Failed to parse Ensembles' }, 104 : { 'description' : 'Failed to parse Asymmetric unit contents' }, 105 : { 'description' : 'Phaser error' }, 106 : { 'description' : 'Failed to parse Solutions' }, 107 : { 'description' : 'Failed to parse Solutions' }, 108 : { 'description' : 'Failed to add Fixed solutions' }, } ''' def __init__(self,parent=None,name=None,workDirectory=''): CPluginScript. __init__(self,parent=parent,name=name) ''' def setKeywords(self, inputObject): #methodsOfInputObject = [getattr(inputObject, maybeMethod) for maybeMethod in dir(inputObject) if callable(getattr(inputObject, maybeMethod))] try: for parameterName in self.container.keywords.dataOrder(): parameterObject = getattr(self.container.keywords, parameterName, None) if parameterObject.isSet(): setterName = 'set'+parameterName if hasattr(inputObject, setterName) and callable(getattr(inputObject,setterName)): if type(parameterObject) == CCP4Data.CString: setterEval = 'inputObject.'+setterName+'("'+str(parameterObject)+'")' else: setterEval = 'inputObject.'+setterName+'('+str(parameterObject)+')' eval(setterEval,{"__builtins__":None},{"inputObject":inputObject,"True":True,"False":False}) rootPath = os.path.join(self.getWorkDirectory(), "PHASER") inputObject.setROOT(rootPath) except: self.appendErrorReport(102) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def parseContent(self, inputObject): inputData = self.container.inputData try: #ASymmetric unit contents if inputData.COMP_BY == 'DEFAULT': #Default is 50% solvent ? inputObject.setCOMP_BY("AVERAGE") elif inputData.COMP_BY == 'MW': if inputData.ASU_PROTEIN_MW.isSet(): inputObject.addCOMP_PROT_MW_NUM(float(inputData.ASU_PROTEIN_MW), 1.0) if inputData.ASU_NUCLEICACID_MW.isSet(): inputObject.addCOMP_NUCL_MW_NUM(float(inputData.ASU_NUCLEICACID_MW), 1.0) elif inputData.COMP_BY == 'ASU': inputObject.setCOMP_BY("ASU") for i in range(len(inputData.ASU_COMPONENTS)): #Convert to simple seq seqLines = [] #print 'seqFile',inputData.ASU_COMPONENTS[i].seqFile.__str__() with open(inputData.ASU_COMPONENTS[i].seqFile.__str__(),'r') as inputFile: seqLines = inputFile.readlines() #print 'seqLines',seqLines catenatedSeq = ''.join([seqLine.strip().replace('-','') for seqLine in seqLines if (len(seqLine.strip())>0 and not seqLine.strip().startswith('>'))]) seqFilename = os.path.join(self.workDirectory,'seqFile_'+str(i)+'.seq') #print 'catenatedSeq',catenatedSeq, seqFilename with open(seqFilename,'w') as seqFile: seqFile.write(catenatedSeq) inputObject.addCOMP_PROT_SEQ_NUM(seqFilename,int(inputData.ASU_COMPONENTS[i].numberOfCopies)) except: self.appendErrorReport(104) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def parseEnsembles(self, inputObject): inputData = self.container.inputData if True: for i, ensemble in enumerate(inputData.ENSEMBLES): for j, pdbItem in enumerate(ensemble.pdbItemList): #Get selected subset of atoms if appropriate atomsFile = str(pdbItem.structure) if pdbItem.structure.isSelectionSet(): try: atomsFile = os.path.join(self.workDirectory,'selectedAtomModel_'+str(i)+'_'+str(j)+'.pdb') pdbItem.structure.getSelectedAtomsPdbFile(atomsFile) except: self.appendErrorReport(107,'Issue with getSelected') return CPluginScript.FAILED # CARD ON is selected by unSet pdbItem.identity_to_target and pdbItem.rms_to_target if not pdbItem.identity_to_target.isSet() and not pdbItem.rms_to_target.isSet(): # Check for special remark cardFound = False with open (atomsFile,'r') as pdbFile: for line in pdbFile: if "REMARK PHASER ENSEMBLE MODEL" in line: cardFound = True break elif line[0:4] == "ATOM": break if cardFound: self.appendErrorReport(107,'So far...') inputObject.addENSE_PDB_CARD(str(ensemble.label), atomsFile, True) self.appendErrorReport(107,[a for a in dir(inputObject) if 'addENSE' in a].__str__()) else: elf.appendErrorReport(107,'Failed to addENSE_PDB_CARD') else: if pdbItem.identity_to_target.isSet() and pdbItem.identity_to_target is not None: try: inputObject.addENSE_PDB_ID(str(ensemble.label), atomsFile, float(pdbItem.identity_to_target)) except: self.appendErrorReport(107,'Failed to addENSE_PDB_ID') return CPluginScript.FAILED elif pdbItem.rms_to_target.isSet() and pdbItem.rms_to_target is not None: try: inputObject.addENSE_PDB_RMS(str(ensemble.label), atomsFile, float(pdbItem.rms_to_target)) except: self.appendErrorReport(107,'Failed to addENSE_PDB_RMS') return CPluginScript.FAILED else: self.appendErrorReport(103,'Failed to parse ensembles') return CPluginScript.FAILED return CPluginScript.SUCCEEDED def parseSolutions(self, inputObject): inp = self.container.inputData try: #Solutions for elements of the Ensemblelist provided by the user if inp.SOLIN.isSet() and len(inp.USINGSOLELEMENTS) > 0: with open(str(self.container.inputData.SOLIN.fullPath),'r') as file: import pickle solutionsObject = pickle.load(file) import phaser_ext filteredSolutionsObject = phaser_ext.mr_solution() for solutionString in inp.USINGSOLELEMENTS: iSol = int(solutionString.split(":")[0].strip()) filteredSolutionsObject.append(solutionsObject.__getitem__(iSol)) inputObject.setSOLU(filteredSolutionsObject) except: self.appendErrorReport(106) return CPluginScript.FAILED try: if self.container.inputData.FIXENSEMBLES.isSet(): for ensembleName in self.container.inputData.FIXENSEMBLES: inputObject.addSOLU_ORIG_ENSE(ensembleName.__str__()) except: self.appendErrorReport(108) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def subElementWithText(parent, type, value): from lxml import etree result = etree.SubElement(parent,type) result.text = str(value) return result def xmlFromSol(solText, parentNode): #print 'Soltext is ',solText solutionElement = None for line in solText.split('\n'): if line.strip().startswith( 'SOLU SET' ): solutionElement = etree.SubElement(parentNode,'Solution') splitLine = line.strip().split() if len(splitLine) > 2: annotationElement = etree.SubElement(solutionElement,'Annotation') annotationElement.text = ' '.join(splitLine[2:]) elif line.strip().startswith( 'SOLU SPAC' ): spaceGroupElement = etree.SubElement(solutionElement,'spaceGroup') spaceGroupElement.text = line.strip()[10:] elif line.strip().startswith('SOLU 6DIM'): componentElement=etree.SubElement(solutionElement,'Component') nameElement = etree.SubElement(componentElement,'Name') nameElement.text = line.strip().split()[3] elif not line.strip().startswith('SOLU') and not line.strip().startswith('#') and solutionElement is not None: #Here if the annotation is spread over multiple lines: annotationElements = solutionElement.xpath('Annotation') if len(annotationElements) > 0: annotationElements[0].text += (' ' + line.strip()) solutionSets = parentNode.xpath('Solution') for solutionSet in solutionSets: expandSolutionAnnotation(solutionSet) def parseAnnotation(annotation): noNewLines = " ".join(annotation.split('\n')) words = [word.strip() for word in noNewLines.split()] solutions = [] inAmalgamation = False for word in words: if word.startswith('RFZ='): solutions.append({'RFZ':word.split('=')[1],'TFZ':'-','PAK':'-','LLG':'-','refTFZ':'-','overallLLG':'-'}) elif word.startswith('RF++'): solutions.append({'RFZ':'=','TFZ':'-','PAK':'-','LLG':'-','refTFZ':'-','overallLLG':'-'}) elif word.startswith('RF*0'): solutions.append({'RFZ':'Zero Rot.','TFZ':'-','PAK':'-','LLG':'-','refTFZ':'-','overallLLG':'-'}) elif word.startswith('(&'): inAmalgamation = True elif word.startswith('TFZ'): if inAmalgamation: solutions.append({'RFZ':'Amalg.','TFZ':'-','PAK':'-','LLG':'-','refTFZ':'-','overallLLG':'-'}) if word.startswith('TFZ*0'): solutions[-1]['TFZ'] = 'Zero trans.' elif word.startswith('TFZ=*'): solutions[-1]['TFZ'] = 'P1 - Arbitrary' elif word.startswith('TFZ=='): solutions[-1]['refTFZ'] = word.split('==')[1] elif word.startswith('TFZ='): solutions[-1]['TFZ'] = word.split('=')[1] if solutions[-1]['TFZ'].endswith(')'): solutions[-1]['TFZ'] = solutions[-1]['TFZ'][:-1] inAmalgamation = False elif word.startswith('PAK='): try: if len(solutions) == 0: solutions.append({'RFZ':'-','TFZ':'-','PAK':word.split('=')[1],'LLG':'-','refTFZ':'-','overallLLG':'-'}) else: solutions[-1]['PAK'] = word.split('=')[1] if solutions[-1]['PAK'].endswith(')'): solutions[-1]['PAK'] = solutions[-1]['PAK'][:-1] inAmalgamation = False except Exception as inst: print inst elif word.startswith('LLG='): #For phaser_rnp, we might get here with no solution...check and make one if necessary if len(solutions)<1: solutions.append({'RFZ':'Amalg.','TFZ':'-','PAK':'-','LLG':'-','refTFZ':'-','overallLLG':'-'}) if 'LLG' in solutions[-1] and solutions[-1]['LLG'] != '-': solutions[-1]['overallLLG'] = word.split('=')[1] else: solutions[-1]['LLG'] = word.split('=')[1] if solutions[-1]['LLG'].endswith(')'): solutions[-1]['LLG'] = solutions[-1]['LLG'][:-1] inAmalgamation = False return solutions def expandSolutionAnnotation(solutionSet): componentNodes = solutionSet.xpath('Component') annotationNodes = solutionSet.xpath('Annotation') if len(annotationNodes)>0: annotation = annotationNodes[0].text solnArray = parseAnnotation(annotation) for iComponent, solution in enumerate(solnArray): try: for property in solution: result = subElementWithText(componentNodes[iComponent],property,solution[property]) except: pass