from CCP4PluginScript import CInternalPlugin, CPluginScript from PyQt4 import QtCore import os,glob,re,time,sys,shutil import CCP4XtalData from lxml import etree import math import CCP4Modules,CCP4Utils import CCP4ErrorHandling class PrepareDeposit(CPluginScript): TASKNAME = 'PrepareDeposit' TASKVERSION= 0.0 ASYNCHRONOUS = False TIMEOUT_PERIOD = 240 MAXNJOBS = 4 SUBTASKS=['refmac'] MAINTAINER = 'martin.noble@newcastle.ac.uk' ERROR_CODES = { 200 : { 'description' : 'Alignments yielded nBestPairs != 1' }, 201 : { 'description' : 'Failed to copy files to destination directory...do you have write access ?' },} def process(self): self.xmlroot = etree.Element('PrepareDeposit') invalidFiles = self.checkInputData() if len(invalidFiles)>0: self.reportStatus(CPluginScript.FAILED) self.checkOutputData() #Do sequence alignemtns if needed chainsOfSequence = [] if self.container.inputData.PROVIDESEQUENCES: iSequence = 0 for sequenceFile in self.container.inputData.SEQUENCE_LIST: tmpFilename = os.path.normpath(os.path.join(self.getWorkDirectory(),'ProvidedSequence_'+str(iSequence)+'.fasta')) import shutil shutil.copyfile(sequenceFile.fullPath.__str__(), tmpFilename) #sequenceData = sequenceFile.fileContent.saveFile(tmpFilename) chainsOfSequence.append([]) iSequence += 1 sequences = self.sequencesFromPDB(self.container.inputData.XYZIN.__str__()) for chainId in sequences: tmpFilename = os.path.normpath(os.path.join(self.getWorkDirectory(),'catenated.fasta')) providedFiles = [] with open(tmpFilename,'w') as tmpFile: tmpFile.write('>CHAIN_'+chainId+'\n') tmpFile.write(sequences[chainId]) from glob import glob providedFiles = glob(os.path.normpath(os.path.join(self.getWorkDirectory(),'ProvidedSequence_*.fasta'))) for fname in providedFiles: with open(fname,'r') as infile: tmpFile.write(infile.read()) tmpFile.write ('\n') #Align all of these sequences using clustalw clustalPlugin = self.makePluginObject('clustalw') clustalPlugin.container.inputData.SEQUENCELISTORALIGNMENT.set('ALIGNMENT') clustalPlugin.container.inputData.ALIGNMENTIN.setFullPath(tmpFilename) clustalPlugin.container.outputData.ALIGNMENTOUT.setFullPath(tmpFilename+'_out') rv = clustalPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) #Identify best pair from the above, and rerun using only these sequences programXML = CCP4Utils.openFileToEtree(clustalPlugin.makeFileName('PROGRAMXML')) bestPairNodes = programXML.xpath('BestPair') if len(bestPairNodes) != 1: self.appendErrorReport(200,str(len(bestPairNodes))) self.reportStatus(CPluginScript.FAILED) partnerNodes = bestPairNodes[0].xpath('Partner') otherPartner = [int(partnerNode.text) for partnerNode in partnerNodes if partnerNode.text != '1'][0] chainsOfSequence[otherPartner-2].append(chainId) #Rerun using only the best partner with open(tmpFilename,'w') as tmpFile: tmpFile.write('>CHAIN_'+chainId+'\n') tmpFile.write(sequences[chainId]) from glob import glob providedFiles = glob(os.path.normpath(os.path.join(self.getWorkDirectory(),'ProvidedSequence_*.fasta'))) fname = providedFiles[otherPartner-2] with open(fname,'r') as infile: tmpFile.write(infile.read()) tmpFile.write ('\n') #Align all of these sequences using clustalw clustalPlugin = self.makePluginObject('clustalw') clustalPlugin.container.inputData.SEQUENCELISTORALIGNMENT.set('ALIGNMENT') clustalPlugin.container.inputData.ALIGNMENTIN.setFullPath(tmpFilename) clustalPlugin.container.outputData.ALIGNMENTOUT.setFullPath(tmpFilename+'_out') rv = clustalPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) alignChainNode = etree.SubElement(self.xmlroot,'AlignChain') chainIdNode = etree.SubElement(alignChainNode,'ChainId') chainIdNode.text = chainId clustalwNode = CCP4Utils.openFileToEtree(clustalPlugin.makeFileName('PROGRAMXML')) alignChainNode.append(clustalwNode) self.flushXML() refmacPlugin = self.makePluginObject('refmac') for propertyName in ['F_SIGF','FREERFLAG','XYZIN','TLSIN','DICT']: if hasattr(self.container.inputData,propertyName) and getattr(self.container.inputData,propertyName).isSet(): setattr(refmacPlugin.container.inputData, propertyName, getattr(self.container.inputData,propertyName)) #Here spoof forcing anomalous. Really refmac should have this as explicit settable stuff if self.container.inputData.USINGIORF.__str__() == 'I': refmacPlugin.container.controlParameters.USE_TWIN.set(True) refmacPlugin.container.controlParameters.TWIN_TYPE.set('I') refmacPlugin.container.controlParameters.NCYCLES.set(0) #Fold TLS into the B-factors ofthe output PDB if refmacPlugin.container.inputData.TLSIN.isSet() or refmacPlugin.container.inputData.get('AUTOTLS', False): refmacPlugin.container.controlParameters.TLSOUT_ADDU.set(True) refmacPlugin.container.controlParameters.NTLSCYCLES.set(0) refmacPlugin.container.controlParameters.NTLSCYCLES_AUTO.set(0) refmacPlugin.container.controlParameters.TLSBFACSETUSE.set(False) #Don't dip out just because DICT not available refmacPlugin.container.controlParameters.MAKE_NEW_LIGAND_EXIT.set(False) rv = refmacPlugin.process() if rv is not CPluginScript.SUCCEEDED: self.reportStatus(rv) refmacRootNode = CCP4Utils.openFileToEtree(refmacPlugin.makeFileName('PROGRAMXML')) self.xmlroot.append(refmacRootNode) self.flushXML() #Now convert refmac input to mmcif self.hklin2cifPlugin = self.makePluginObject('hklin2cif') hklinPath = os.path.normpath(os.path.join(refmacPlugin.getWorkDirectory(),'hklin.mtz')) self.hklin2cifPlugin.container.inputData.HKLIN.setFullPath(hklinPath) rv = self.hklin2cifPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) #First pass of pdb_extract pdbExtract1Plugin = self.makePluginObject('pdb_extract_wrapper') pdbExtract1Plugin.container.inputData.XYZIN = refmacPlugin.container.outputData.XYZOUT pdbExtract1Plugin.container.outputData.ENTRYDATA.setFullPath(os.path.normpath(os.path.join(pdbExtract1Plugin.getWorkDirectory(),'data_template.text'))) rv = pdbExtract1Plugin.process() if rv is not CPluginScript.SUCCEEDED: self.reportStatus(rv) modifiedTemplatePath = os.path.normpath(os.path.join(self.getWorkDirectory(),'modifiedTemplate.text')) templatePath = pdbExtract1Plugin.container.outputData.ENTRYDATA.__str__() print 'templatePath, modifiedTemplatePath',templatePath, modifiedTemplatePath with open(templatePath,'r') as blankTemplate: lines = blankTemplate.readlines() with open(modifiedTemplatePath,'w') as modifiedTemplate: inMolecules = False for line in lines: if "molecule_entity_id" in line: inMolecules = True elif "CATEGORY 3:" in line: inMolecules = False iEntity = 1 for sequence in self.container.inputData.get('SEQUENCE_LIST', []): modifiedTemplate.write('\n'%(iEntity)) modifiedTemplate.write('\n') modifiedTemplate.write('\n'%(sequence.fileContent.sequence.__str__())) if len(chainsOfSequence) > iEntity-1: modifiedTemplate.write('\n'%(','.join(chainsOfSequence[iEntity-1]))) modifiedTemplate.write('< target_DB_id=" " > (if known) \n\n\n') iEntity += 1 if not inMolecules: modifiedTemplate.write(line) #Second pass of pdb_extract pdbExtract2Plugin = self.makePluginObject('pdb_extract_wrapper') pdbExtract2Plugin.container.inputData.XYZIN = refmacPlugin.container.outputData.XYZOUT pdbExtract2Plugin.container.inputData.ENTRYDATAIN.set(modifiedTemplatePath) rv = pdbExtract2Plugin.process() if rv is not CPluginScript.SUCCEEDED: self.reportStatus(rv) import shutil structureCifPath = os.path.normpath(os.path.join(self.container.inputData.OUTPUT_DIRECTORY.__str__(),'Coordinates.cif')) reflectionCifPath = os.path.normpath(os.path.join(self.container.inputData.OUTPUT_DIRECTORY.__str__(),'Reflections.cif')) try: shutil.copyfile(pdbExtract2Plugin.container.outputData.CIFFILE.__str__(), structureCifPath) shutil.copyfile(self.hklin2cifPlugin.container.outputData.CIFFILE.__str__(), reflectionCifPath) except: self.appendErrorReport(201) self.reportStatus(CPluginScript.FAILED) self.reportStatus(CPluginScript.SUCCEEDED) def flushXML(self, xml=None): if xml is None: if hasattr(self,'xmlroot'): xml=self.xmlroot 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 sequencesFromPDB(self, filePath): tlcOlcMap = {'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F','GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L','MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R','SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y'} sequences = {} import mmut if os.path.isfile(filePath): from CCP4ModelData import CPdbData aCPdbData = CPdbData() aCPdbData.loadFile(filePath) mmdbManager = aCPdbData.mmdbManager for peptideChainId in aCPdbData.composition.peptides: sequences[peptideChainId] = '' peptideChain = mmdbManager.GetChain(1,peptideChainId) for i in range(peptideChain.GetNumberOfResidues()): residueName = peptideChain.GetResidue(i).GetResName() if residueName in tlcOlcMap: sequences[peptideChainId]+= tlcOlcMap[residueName] else: sequences[peptideChainId]+= '-' if (i+1)%60 == 0: sequences[peptideChainId]+= '\n' if sequences[peptideChainId][-1] is not '\n': sequences[peptideChainId] += '\n' return sequences