from CCP4PluginScript import CInternalPlugin,CPluginScript from PyQt4 import QtCore import os,re,time,sys import CCP4XtalData from lxml import etree import math import CCP4Modules,CCP4Utils class ShelxCDEBase(CPluginScript): tagsAndKeys = {'N(data)':'NData','':'IOverSig','%Complete':'Completeness','':'AnomalousSignal'} MAINTAINER = 'matin.noble@newcastle.co.uk' ERROR_CODES = { 200 : { 'description' : 'ShelxCD exited with error status' }, 201 : { 'description' : 'ShelxCD failed in mtz2various' },202 : { 'description' : ' ShelxCD failed in processOutputFiles' },203 : { 'description' : 'ShelxCD failed in f2mtz - Map file' },204 : { 'description' : 'ShelxCD failed in f2mtz - PHS file' },205 : { 'description' : 'ShelxCD failed in sftools - MAP file' },206 : { 'description' : 'ShelxCD failed in sftools - PHS file' }, 207 : { 'description' : 'Failed scraping Shelxd logfile' }, 208 : { 'description' : 'Failed scraping Shelxe logfile' }, 209 : { 'description' : 'Failed converting .hat to pdb' }, 210 : { 'description' : 'ShelxE ended with non zero status' }, 211 : { 'description' : 'ShelxE ended with non zero code' }, 212 : { 'description' : 'ShelxE BETA EXPIRED' }} PeriodicTable = [{'Name':'Hydrogen','Symbol':'H','Number':1}, {'Name':'Helium','Symbol':'He','Number':2}, {'Name':'Lithium','Symbol':'Li','Number':3}, {'Name':'Beryllium','Symbol':'Be','Number':4}, {'Name':'Boron','Symbol':'B','Number':5}, {'Name':'Carbon','Symbol':'C','Number':6}, {'Name':'Nitrogen','Symbol':'N','Number':7}, {'Name':'Oxygen','Symbol':'O','Number':8}, {'Name':'Fluorine','Symbol':'F','Number':9}, {'Name':'Neon','Symbol':'Ne','Number':10}, {'Name':'Sodium','Symbol':'Na','Number':11}, {'Name':'Magnesium','Symbol':'Mg','Number':12}, {'Name':'Aluminium','Symbol':'Al','Number':13}, {'Name':'Silicon','Symbol':'Si','Number':14}, {'Name':'Phosphorus','Symbol':'P','Number':15}, {'Name':'Sulfur','Symbol':'S','Number':16}, {'Name':'Chlorine','Symbol':'Cl','Number':17}, {'Name':'Argon','Symbol':'Ar','Number':18}, {'Name':'Potassium','Symbol':'K','Number':19}, {'Name':'Calcium','Symbol':'Ca','Number':20}, {'Name':'Scandium','Symbol':'Sc','Number':21}, {'Name':'Titanium','Symbol':'Ti','Number':22}, {'Name':'Vanadium','Symbol':'V','Number':23}, {'Name':'Chromium','Symbol':'Cr','Number':24}, {'Name':'Manganese','Symbol':'Mn','Number':25}, {'Name':'Iron','Symbol':'Fe','Number':26}, {'Name':'Cobalt','Symbol':'Co','Number':27}, {'Name':'Nickel','Symbol':'Ni','Number':28}, {'Name':'Copper','Symbol':'Cu','Number':29}, {'Name':'Zinc','Symbol':'Zn','Number':30}, {'Name':'Gallium','Symbol':'Ga','Number':31}, {'Name':'Germanium','Symbol':'Ge','Number':32}, {'Name':'Arsenic','Symbol':'As','Number':33}, {'Name':'Selenium','Symbol':'Se','Number':34}, {'Name':'Bromine','Symbol':'Br','Number':35}, {'Name':'Krypton','Symbol':'Kr','Number':36}, {'Name':'Rubidium','Symbol':'Rb','Number':37}, {'Name':'Strontium','Symbol':'Sr','Number':38}, {'Name':'Yttrium','Symbol':'Y','Number':39}, {'Name':'Zirconium','Symbol':'Zr','Number':40}, {'Name':'Niobium','Symbol':'Nb','Number':41}, {'Name':'Molybdenum','Symbol':'Mo','Number':42}, {'Name':'Technetium','Symbol':'Tc','Number':43}, {'Name':'Ruthenium','Symbol':'Ru','Number':44}, {'Name':'Rhodium','Symbol':'Rh','Number':45}, {'Name':'Palladium','Symbol':'Pd','Number':46}, {'Name':'Silver','Symbol':'Ag','Number':47}, {'Name':'Cadmium','Symbol':'Cd','Number':48}, {'Name':'Indium','Symbol':'In','Number':49}, {'Name':'Tin','Symbol':'Sn','Number':50}, {'Name':'Antimony','Symbol':'Sb','Number':51}, {'Name':'Tellurium','Symbol':'Te','Number':52}, {'Name':'Iodine','Symbol':'I','Number':53}, {'Name':'Xenon','Symbol':'Xe','Number':54}, {'Name':'Caesium','Symbol':'Cs','Number':55}, {'Name':'Barium','Symbol':'Ba','Number':56}, {'Name':'Lanthanum','Symbol':'La','Number':57}, {'Name':'Cerium','Symbol':'Ce','Number':58}, {'Name':'Praseodymium','Symbol':'Pr','Number':59}, {'Name':'Neodymium','Symbol':'Nd','Number':60}, {'Name':'Promethium','Symbol':'Pm','Number':61}, {'Name':'Samarium','Symbol':'Sm','Number':62}, {'Name':'Europium','Symbol':'Eu','Number':63}, {'Name':'Gadolinium','Symbol':'Gd','Number':64}, {'Name':'Terbium','Symbol':'Tb','Number':65}, {'Name':'Dysprosium','Symbol':'Dy','Number':66}, {'Name':'Holmium','Symbol':'Ho','Number':67}, {'Name':'Erbium','Symbol':'Er','Number':68}, {'Name':'Thulium','Symbol':'Tm','Number':69}, {'Name':'Ytterbium','Symbol':'Yb','Number':70}, {'Name':'Lutetium','Symbol':'Lu','Number':71}, {'Name':'Hafnium','Symbol':'Hf','Number':72}, {'Name':'Tantalum','Symbol':'Ta','Number':73}, {'Name':'Tungsten','Symbol':'W','Number':74}, {'Name':'Rhenium','Symbol':'Re','Number':75}, {'Name':'Osmium','Symbol':'Os','Number':76}, {'Name':'Iridium','Symbol':'Ir','Number':77}, {'Name':'Platinum','Symbol':'Pt','Number':78}, {'Name':'Gold','Symbol':'Au','Number':79}, {'Name':'Mercury','Symbol':'Hg','Number':80}, {'Name':'Thallium','Symbol':'Tl','Number':81}, {'Name':'Lead','Symbol':'Pb','Number':82}, {'Name':'Bismuth','Symbol':'Bi','Number':83}, {'Name':'Polonium','Symbol':'Po','Number':84}, {'Name':'Astatine','Symbol':'At','Number':85}, {'Name':'Radon','Symbol':'Rn','Number':86}, {'Name':'Francium','Symbol':'Fr','Number':87}, {'Name':'Radium','Symbol':'Ra','Number':88}, {'Name':'Actinium','Symbol':'Ac','Number':89}, {'Name':'Thorium','Symbol':'Th','Number':90}, {'Name':'Protactinium','Symbol':'Pa','Number':91}, {'Name':'Uranium','Symbol':'U','Number':92}, {'Name':'Neptunium','Symbol':'Np','Number':93}, {'Name':'Plutonium','Symbol':'Pu','Number':94}, {'Name':'Americium','Symbol':'Am','Number':95}, {'Name':'Curium','Symbol':'Cm','Number':96}, {'Name':'Berkelium','Symbol':'Bk','Number':97}, {'Name':'Californium','Symbol':'Cf','Number':98}, {'Name':'Einsteinium','Symbol':'Es','Number':99}, {'Name':'Fermium','Symbol':'Fm','Number':100}, {'Name':'Mendelevium','Symbol':'Md','Number':101}, {'Name':'Nobelium','Symbol':'No','Number':102}, {'Name':'Lawrencium','Symbol':'Lr','Number':103}, {'Name':'Rutherfordium','Symbol':'Rf','Number':104}, {'Name':'Dubnium','Symbol':'Db','Number':105}, {'Name':'Seaborgium','Symbol':'Sg','Number':106}, {'Name':'Bohrium','Symbol':'Bh','Number':107}, {'Name':'Hassium','Symbol':'Hs','Number':108}, {'Name':'Meitnerium','Symbol':'Mt','Number':109}, {'Name':'Darmstadtium','Symbol':'Ds','Number':110}, {'Name':'Roentgenium','Symbol':'Rg','Number':111}, {'Name':'Copernicium','Symbol':'Cp','Number':112}, {'Name':'Ununtrium','Symbol':'Uut','Number':113}, {'Name':'Ununquadium','Symbol':'Uuq','Number':114}, {'Name':'Ununpentium','Symbol':'Uup','Number':115}, {'Name':'Ununhexium','Symbol':'Uuh','Number':116}, {'Name':'Ununseptium','Symbol':'Uus','Number':117}, {'Name':'Ununoctium','Symbol':'Uuo','Number':118}] def prepareShelxc(self): #Test for location of shelxc executable: bin = self.getCommand('shelxc') datasets = {} inp = self.container.inputData if self.container.controlParameters.MODE.__str__() == 'SAD': datasets = {'SAD':inp.SAD,'NAT':inp.NAT} elif self.container.controlParameters.MODE.__str__() == 'MAD': datasets = {'HREM':inp.HREM,'LREM':inp.LREM,'INFL':inp.INFL,'PEAK':inp.PEAK,'NAT':inp.NAT} elif self.container.controlParameters.MODE.__str__() == 'SIR': datasets = {'SIR':inp.SIR,'NAT':inp.NAT} elif self.container.controlParameters.MODE.__str__() == 'SIRAS': datasets = {'SIRA':inp.SIRA,'NAT':inp.NAT} elif self.container.controlParameters.MODE.__str__() == 'RIP': datasets = {'RIP':inp.RIP,'NAT':inp.NAT} elif self.container.controlParameters.MODE.__str__() == 'RIPAS': datasets = {'RIPA':inp.RIPA,'NAT':inp.NAT} for datasetName in datasets: from CCP4XtalData import CObsDataFile if datasets[datasetName].isSet(): self.makeHklin([datasetName]) mtzFilepath = os.path.join(self.getWorkDirectory(),'hklin.mtz') if datasets[datasetName].contentFlag == CObsDataFile.CONTENT_FLAG_IPAIR: hklFilepath = os.path.join(self.getWorkDirectory(),'result_'+datasetName+'.sca') result = self.makeScafile(infile=mtzFilepath, outfile=[hklFilepath,["Iplus","SIGIplus","Iminus","SIGIminus"]]) elif datasets[datasetName].contentFlag == CObsDataFile.CONTENT_FLAG_FPAIR: hklFilepath = os.path.join(self.getWorkDirectory(),'result_'+datasetName+'.sca') result = self.makeScafile(infile=mtzFilepath, outfile=[hklFilepath,["Fplus","SIGFplus","Fminus","SIGFminus"]]) elif datasets[datasetName].contentFlag == CObsDataFile.CONTENT_FLAG_IMEAN: hklFilepath = os.path.join(self.getWorkDirectory(),'result_'+datasetName+'.hkl') result = self.makeHklfile(infile=mtzFilepath, outfile=[hklFilepath,["I=I","SIGI=SIGI"]]) elif datasets[datasetName].contentFlag == CObsDataFile.CONTENT_FLAG_FMEAN: hklFilepath = os.path.join(self.getWorkDirectory(),'result_'+datasetName+'.hkl') result = self.makeHklfile(infile=mtzFilepath, outfile=[hklFilepath,["FP=SIGF","SIGFP=SIGF"]]) if result != CPluginScript.SUCCEEDED: return result return CPluginScript.SUCCEEDED def makeScafile( self, infile=None, outfile=[], parentPlugin=None ): bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'mtz2sca' )) name,colin = outfile logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'mtz2sca.log')) arglist = ['-p',colin[0],'-P',colin[1],'-m',colin[2],'-M',colin[3],infile,name] pid = CCP4Modules.PROCESSMANAGER().startProcess(bin,arglist,logFile=logFile) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status == 0 and os.path.exists(outfile[0]): return CPluginScript.SUCCEEDED else: self.appendErrorReport(201) return CPluginScript.FAILED def makeHklfile( self, infile=None, outfile=[], parentPlugin=None ): bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'mtz2various' )) name,colin = outfile logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'mtz2various.log')) arglist = ['hklin',infile,'hklout',name] inputText = 'output SHELX\n' inputText += ('LABIN ' + ' '.join(colin) + '\n') pid = CCP4Modules.PROCESSMANAGER().startProcess(bin,arglist,inputText=inputText, logFile=logFile) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status == 0 and os.path.exists(outfile[0]): return CPluginScript.SUCCEEDED else: self.appendErrorReport(201) return CPluginScript.FAILED def runShelxc( self ): # CpluginScript.getCommand checks preferences for shelxc directory bin = self.getCommand('shelxc') logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'shelxc.log')) arglist = ['result'] inputText = '' cell = self.container.inputData.SAD.fileContent.cell factor = 1.#180. / math.pi cellString, spaceGroupNumber, extantFile = self.cellString() inputText += cellString #From shelx docs # SPAG - the name of the space group. Only Sohncke space groups are permitted, but some common non-standard settings are allowed, # e.g. 'P22121'. Embedded spaces are ignored. SPAG is used to generate the LATT and SYMM instructions that are written to name_fa.ins. #If the space group is specified as 'R3' or 'R32' the program checks the cell dimensions to see whether the hexagonal or # primitive rhombohedral setting is required. inputText += 'SPAG %s\n'%extantFile.fileContent.spaceGroup.__str__().replace(' ','').replace(':H','').replace(':R','') try: inputText += 'SFAC %s\n'%self.container.controlParameters.SFAC except: print '#ShelxCDEBase runShelxc: SFAC unset or not relevant' #Simple float parameters for parameterName in ['RIPW','ASCA','DSCA']: if hasattr(self.container.controlParameters, parameterName): parameter = getattr(self.container.controlParameters, parameterName) if parameter.isSet(): inputText += (parameterName+' %8.2f\n'%(float(parameter))) #Float range parameters for parameterName in ['MIND','SHEL']: if hasattr(self.container.controlParameters, parameterName): parameter = getattr(self.container.controlParameters, parameterName) if parameter.isSet(): inputText += (parameterName+' %8.2f %8.2f\n'%(float(parameter.start), float(parameter.end ))) datasetNames = [] if self.container.controlParameters.MODE.__str__() == 'SAD': datasetNames = ['SAD', 'NAT'] elif self.container.controlParameters.MODE.__str__() == 'MAD': datasetNames = ['HREM','LREM','PEAK','INFL', 'NAT'] elif self.container.controlParameters.MODE.__str__() == 'SIR': datasetNames = ['SIR','NAT'] elif self.container.controlParameters.MODE.__str__() == 'SIRAS': datasetNames = ['SIRA','NAT'] elif self.container.controlParameters.MODE.__str__() == 'RIP': datasetNames = ['RIP','NAT'] elif self.container.controlParameters.MODE.__str__() == 'RIPAS': datasetNames = ['RIPA','NAT'] from CCP4XtalData import CObsDataFile inp = self.container.inputData for datasetName in datasetNames: dataset = getattr(inp,datasetName) if dataset.isSet(): if dataset.contentFlag == CObsDataFile.CONTENT_FLAG_IMEAN: inputText += (datasetName+' result_'+datasetName+'.hkl\n') elif dataset.contentFlag == CObsDataFile.CONTENT_FLAG_FMEAN: inputText += (datasetName+' result_'+datasetName+'.hkl\n') else: inputText += (datasetName+' result_'+datasetName+'.sca\n') try: inputText += 'FIND %d\n'%int(self.container.controlParameters.FIND) except: print '#ShelxCDEBase runShelxc: FIND unset or not relevant' try: if self.container.controlParameters.NTRY.isSet(): inputText += 'NTRY %d\n'%int(self.container.controlParameters.NTRY) except: print '#ShelxCDEBase runShelxc: NTRY unset or not relevant' pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status == 0 and os.path.exists(os.path.join(self.getWorkDirectory(),'result_fa.hkl')): return CPluginScript.SUCCEEDED else: self.appendErrorReport(201,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(logFile)) return CPluginScript.FAILED def scrapeShelxcLog(self, xmlroot, logFile): shelxcNode = etree.SubElement(xmlroot, 'Shelxc') analysisNode = None with open(logFile,'r') as insFile: insLines = [line.strip() for line in insFile.readlines()] datasetNode = None e2TableLine = -1 for line in insLines: tokens = line.split() if 'Reflections read from' in line: datasetNode = etree.SubElement(shelxcNode,'Dataset') self.subElementOfTypeWithText(datasetNode,'Name', tokens[4]) self.subElementOfTypeWithText(datasetNode,'ReflectionsRead', tokens[0]) elif 'Unique reflections, highest resolution' in line: self.subElementOfTypeWithText(datasetNode,'UniqueReflections', tokens[0]) self.subElementOfTypeWithText(datasetNode,'HighestResolution', tokens[5]) elif 'for input to SHELXD/E' in line: self.subElementOfTypeWithText(shelxcNode,'FAsWritten', tokens[0]) elif 'for input to SHELXE' in line: self.subElementOfTypeWithText(shelxcNode,'FsWritten', tokens[0]) elif len(tokens) == 6 and 'Unique reflections, highest resolution' in line and datasetNode is not None: self.subElementOfTypeWithText(datasetNode,'UniqueReflections', tokens[0]) self.subElementOfTypeWithText(datasetNode,'HighestResolutionRead', tokens[5]) elif len(tokens) == 8 and 'Friedel pairs used on average for local' in line and datasetNode is not None: self.subElementOfTypeWithText(datasetNode,'AverageFriedelsPerBin', tokens[0]) elif len(tokens) > 0 and tokens[0] == 'Resl.' and datasetNode is not None: analysisNode = etree.SubElement(datasetNode,'DataAnalysis') for iBin in range (1, len(tokens)-1): binNode = etree.SubElement(analysisNode,'Bin') self.subElementOfTypeWithText(binNode,'LowRes', tokens[iBin]) self.subElementOfTypeWithText(binNode,'HighRes', tokens[iBin+1]) elif len(tokens) > 0 and tokens[0] in ShelxCDEBase.tagsAndKeys and analysisNode is not None: for iBin in range (1, len(tokens)): binNode = analysisNode[iBin-1] self.subElementOfTypeWithText(binNode,ShelxCDEBase.tagsAndKeys[tokens[0]], tokens[iBin]) elif 'Correlation coefficients' in line: datasetNode = None elif e2TableLine >= 0: if len(tokens) == 0: e2TableLine = -1 else: datasetNodes = shelxcNode.xpath('//Dataset') if e2TableLine < len(datasetNodes): self.subElementOfTypeWithText(datasetNodes[e2TableLine],'eSquaredMinus1',tokens[1]) e2TableLine += 1 elif len(tokens) > 1 and tokens[0] == 'Dataset' and tokens[1] == '<|E^2-1|>': e2TableLine = 0 def handleShelxeLogChanged(self, logFilename): import datetime timeNow = datetime.datetime.now() if not hasattr(self,"lastScrapeTime"): self.lastScrapeTime = timeNow deltaTime = timeNow - self.lastScrapeTime if deltaTime.seconds > 0 or deltaTime.days > 0: self.scrapeShelxeLog(self.xmlroot) self.flushXML() self.lastScrapeTime = timeNow def handleShelxdLogChanged(self, logFilename): import datetime timeNow = datetime.datetime.now() if not hasattr(self,"lastScrapeTime"): self.lastScrapeTime = timeNow deltaTime = timeNow - self.lastScrapeTime if deltaTime.seconds > 0 or deltaTime.days > 0: self.scrapeShelxdLog(self.xmlroot) self.flushXML() self.lastScrapeTime = timeNow def subElementOfTypeWithText(self, parent, type, text): result = etree.SubElement(parent,type) result.text = str(text) return result def flushXML(self): tmpFileName = self.makeFileName('PROGRAMXML') + '_tmp' with open(tmpFileName,'w') as xmlFile: xmlFile.write(etree.tostring(self.xmlroot, pretty_print=True)) #This is attempt to fix error overwriting exisiting file on Windows PROGRAMXML = self.makeFileName('PROGRAMXML') #print 'flushXML',PROGRAMXML if os.path.exists(PROGRAMXML): os.remove(PROGRAMXML) self.renameFile(tmpFileName, PROGRAMXML) def pdbToRes( self, pdbDataFile, insFilePath): bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'coordconv' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'coordconv.log')) fracFilePath = os.path.normpath(os.path.join(self.getWorkDirectory(), 'ha.frac')) arglist = ['XYZIN',pdbDataFile.fullPath.__str__(),'XYZOUT',fracFilePath] inputText = '''INPUT pdb OUTPUT frac ''' pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(fracFilePath): self.appendErrorReport(201,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(fracFilePath)) return CPluginScript.FAILED linetypesToGrab = ['TITL','CELL','LATT','SYMM','SFAC','UNIT','HKLF','END'] grabbedLines = {} with open(insFilePath,'r') as insFile: insLines = insFile.readlines() for linetype in linetypesToGrab: grabbedLines[linetype] = [insLine for insLine in insLines if insLine.startswith(linetype)] coords = [] with open(fracFilePath,'r') as fracFile: fracLines = fracFile.readlines() for fracLine in fracLines: coord = {'NUMBER':fracLine[0:5].strip(), 'X':float(fracLine[5:15].strip()), 'Y':float(fracLine[15:25].strip()), 'Z':float(fracLine[25:35].strip()), 'BFAC':float(fracLine[35:45].strip()), 'OCC':float(fracLine[45:50].strip()), 'AtomicNr':int(fracLine[50:55].strip())} coords.append(coord) resFilePath = os.path.normpath(os.path.join(self.getWorkDirectory(),'result_fa.res')) # Get a list of atom cards to identify elements which should be on SFAC line atomLines = [] oldElements = [] if 'SFAC' in grabbedLines and len(grabbedLines['SFAC'][0].split()) > 1: oldElements = grabbedLines['SFAC'][0].split()[1:] elements = [element.upper() for element in oldElements] iAtom = 1 for coord in coords: #MN CHECKME FIXME The following line forces unknown elements to be Seleniums if coord['AtomicNr'] == 0: coord['AtomicNr'] = 34 element = [ element for element in ShelxCDEBase.PeriodicTable if element['Number'] == coord['AtomicNr']] elementSymbol = element[0]['Symbol'].upper() if elementSymbol not in elements: elements.append(elementSymbol) atomLine = '%s%d %d %10.6f%10.6f%10.6f%10.6f%10.6f\n'%(elementSymbol,iAtom,1,coord['X'],coord['Y'],coord['Z'],coord['OCC'],coord['BFAC']/100.) atomLines.append(atomLine) iAtom += 1 with open(resFilePath, 'w') as resFile: for linetype in ['TITL','CELL','LATT','SYMM','UNIT']: if linetype in grabbedLines: for grabbedLine in grabbedLines[linetype]: resFile.write(grabbedLine) resFile.write('SFAC '+' '.join(elements)+'\n') iAtom = 1 for atomLine in atomLines: resFile.write(atomLine) for linetype in ['HKLF','END']: if linetype in grabbedLines: for grabbedLine in grabbedLines[linetype]: resFile.write(grabbedLine) return CPluginScript.SUCCEEDED def cellString(self): fileTypes = ['NAT','SAD','HREM','LREM','INFL','PEAK','SIR','SIRA','RIP','RIPA'] extantFile = None for fileType in fileTypes: fileObj = getattr(self.container.inputData, fileType, None) if fileObj is not None and fileObj.isSet() and os.path.isfile(fileObj.fullPath.__str__()): extantFile = fileObj if extantFile is not None: break if extantFile is None: return CPluginScript.FAILED cell = extantFile.fileContent.cell factor = 1.#180. / math.pi cellString = 'CELL %.3f %.3f %.3f %.3f %.3f %.3f\n' %(cell.a, cell.b, cell.c, factor*float(cell.alpha), factor*float(cell.beta), factor*float(cell.gamma),) spaceGroupNumber = extantFile.fileContent.spaceGroup.number() return cellString, spaceGroupNumber, extantFile def harvestPhsFile(self, phsFilePath, mapFilePath, phsOutFilePath=None): bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'f2mtz' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'f2mtz_map.log')) tmpMtzFilePath = mapFilePath+'_tmp' arglist = ['HKLIN',phsFilePath,'HKLOUT',tmpMtzFilePath] inputText = "FORMAT '(F4.0,F4.0,F4.0,F9.2,F8.4,F8.1)'\n" inputText += "LABOUT H K L FOBS FOM PHI\n" inputText += "CTYPOUT H H H F W P\n" cellString, spaceGroupNumber, extantFile = self.cellString() inputText += cellString spgrName = extantFile.fileContent.spaceGroup.__str__().replace(' ','') cellTokens = cellString.split() if spgrName == 'H32' and cellTokens[1] == cellTokens[2] and cellTokens[1] == cellTokens[3] and cellTokens[4] == cellTokens[5] and cellTokens[4] == cellTokens[6]: spgrName = 'R32' elif spgrName == 'R32' and cellTokens[1] == cellTokens[2] and cellTokens[4] == '90.000' and cellTokens[6] == '120.000': spgrName = 'H32' inputText += 'SYMMETRY %s\n'%spgrName pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(tmpMtzFilePath): self.appendErrorReport(203,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(logFile)) return CPluginScript.FAILED #Separate out mFo,Phi map coefficents bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'sftools' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'sftools_map.log')) argList = [] inputText = "READ "+tmpMtzFilePath+"\n" inputText += "REDUCE\n" inputText += "SORT\n" inputText += "CALC COL F = COL 1 COL 2 *\n" inputText += "SET TYPE COL 4\n" inputText += "F\n" inputText += "WRITE "+mapFilePath+" COL 4 3\n" inputText += "STOP\n" pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(mapFilePath): self.appendErrorReport(205,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(logFile)) return CPluginScript.FAILED #Separate out PHI,FOM Phase probability distribution if phsOutFilePath is not None: bin = os.path.normpath(os.path.join( CCP4Utils.getCCP4Dir(), 'bin', 'sftools' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'sftools_phs.log')) argList = [] inputText = "READ "+tmpMtzFilePath+"\n" inputText += "REDUCE\n" inputText += "SORT\n" inputText += "WRITE "+phsOutFilePath+" COL 3 2\n" inputText += "STOP\n" pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(phsOutFilePath): self.appendErrorReport(206,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(logFile)) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def scrapeShelxdLog(self, xmlroot): if True: oldShelxdNodes = xmlroot.xpath('Shelxd') for oldShelxNode in oldShelxdNodes: xmlroot.remove(oldShelxNode) shelxdNode = etree.SubElement(xmlroot,'Shelxd') with open(self.makeFileName('LOG')) as logFile: longlines = logFile.readlines() lines = [line.strip() for line in longlines] for line in lines: #Good fun here: the number of the CPU was fixed format, so n> 10 bumped #into the word CPU :-) tokens = line.replace('CPU','CPU ').split() if len(tokens) > 0 and tokens[0] == 'Try': # Try 15, CPU 4, CC All/Weak 37.5 / 22.8, CFOM 60.3, best 60.7, PATFOM 45.67 tryNode = etree.SubElement(shelxdNode,'Try') self.subElementOfTypeWithText(tryNode,'Number',tokens[1][:-1]) self.subElementOfTypeWithText(tryNode,'CCAll',tokens[6]) self.subElementOfTypeWithText(tryNode,'CCWeak',tokens[8][:-1]) self.subElementOfTypeWithText(tryNode,'CFOM',tokens[10][:-1]) try: self.subElementOfTypeWithText(tryNode,'PATFOM',tokens[14]) except: print tokens lstPath = os.path.normpath(os.path.join(self.getWorkDirectory(),'result_fa.lst')) if not os.path.isfile(lstPath): lstPath = os.path.normpath(os.path.join(self.getWorkDirectory(),'result_fa.lst.txt')) if os.path.isfile(lstPath): with open(lstPath,'r') as lstFile: lstText = lstFile.read() lstNode = etree.SubElement(shelxdNode,'LstText') lstNode.text=etree.CDATA(lstText) return CPluginScript.SUCCEEDED else: self.appendErrorReport(207,self.getWorkDirectory()) return CPluginScript.FAILED def scrapeShelxeLog(self, xmlroot): try: oldShelxeNodes = xmlroot.xpath('Shelxe') for oldShelxNode in oldShelxeNodes: xmlroot.remove(oldShelxNode) shelxeNode = etree.SubElement(xmlroot,'Shelxe') globalTraceNode = etree.SubElement(shelxeNode,'GlobalAutotracingCycle') numberNode = self.subElementOfTypeWithText(globalTraceNode,'Number','1') with open(self.makeFileName('LOG')) as logFile: longlines = logFile.readlines() lines = [line.strip() for line in longlines] for line in lines: tokens = line.split() if len(tokens) > 0 and 'for dens.mod.' in line: # Try 15, CPU 4, CC All/Weak 37.5 / 22.8, CFOM 60.3, best 60.7, PATFOM 45.67 cycleNode = etree.SubElement(globalTraceNode,'Cycle') self.subElementOfTypeWithText(cycleNode,'Wt',tokens[2][:-1]) self.subElementOfTypeWithText(cycleNode,'Contrast',tokens[5][:-1]) self.subElementOfTypeWithText(cycleNode,'Connect',tokens[8]) self.subElementOfTypeWithText(cycleNode,'Number',tokens[12]) elif 'Global autotracing cycle' in line: globalTraceNode = etree.SubElement(shelxeNode,'GlobalAutotracingCycle') numberNode = self.subElementOfTypeWithText(globalTraceNode,'Number',tokens[3]) elif 'This beta-test version has expired - please update it' in line: betaExpiredNode = etree.SubElement(shelxeNode,'BETAEXPIRED') elif 'Estimated mean FOM =' in line: #Estimated mean FOM = 0.494 Pseudo-free CC = 52.89 % overallFOMsNode = etree.SubElement(globalTraceNode,'OverallFOMs') self.subElementOfTypeWithText(overallFOMsNode,'FOM',tokens[4]) self.subElementOfTypeWithText(overallFOMsNode,'PseudoFreeCC',tokens[8]) lstPath = os.path.normpath(os.path.join(self.getWorkDirectory(),'result.lst')) for lstRoot in ['result.lst','result_i.lst','result.lst.txt','result_i.lst.txt']: lstPath = os.path.normpath(os.path.join(self.getWorkDirectory(),lstRoot)) if os.path.isfile(lstPath): with open(lstPath,'r') as lstFile: lstText = lstFile.read() lstNode = etree.SubElement(shelxeNode,'LstText') lstNode.text=etree.CDATA(lstText) return CPluginScript.SUCCEEDED except: self.appendErrorReport(208,self.getWorkDirectory()) return CPluginScript.FAILED def invertCoordinates(self, inputPDBPath, outputPDBPath): inversion_operation = '-X,-Y,-Z' cellString, spaceGroupNumber, extantFile = self.cellString() if spaceGroupNumber==80: inversion_operation = '-X+1/2,-Y,-Z' elif spaceGroupNumber==98: inversion_operation = '-X+1/2,-Y,-Z+1/4' elif spaceGroupNumber==210: inversion_operation = '-X+1/4,-Y+1/4,-Z+1/4' bin = os.path.normpath(os.path.join( 'pdbcur' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'pdbcur.log')) arglist = ['XYZIN',inputPDBPath,'XYZOUT',outputPDBPath] inputText = 'SYMOP '+inversion_operation+'\n' inputText += 'symcommit\n' pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(outputPDBPath): self.appendErrorReport(201,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(inputPDBPath)) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def resToPDB(self, inputResPath, outputPDBPath): elements = [] coords = [] with open(inputResPath,'r') as inputRes: lines = [line.strip() for line in inputRes.readlines()] for line in lines: tokens = line.split() if len(tokens) > 0 and tokens[0] == 'SFAC': elements = [token.upper() for token in tokens[1:]] elif len(tokens) == 7: coordElement = elements[int(tokens[1])-1] coord = {'Element':coordElement,'X':float(tokens[2]),'Y':float(tokens[3]),'Z':float(tokens[4]),'OCC':float(tokens[5]),'B':float(tokens[6])} #coord = {'element':coordElement,'xFrac':float(tokens[2]),'yFrac':float(tokens[3]),'zFrac':float(tokens[4]),'occupancy':float(tokens[5]),'tempFactor':float(tokens[6])} coords.append(coord) """ # This code (with the alternate definition of coord above) is better way to create PDB file import CCP4ModelData pdb = CCP4ModelData.CPdbData() cellString, spaceGroupNumber, extantFile = self.cellString() pdb.makeOneResPdb(atomDefList=coords,cell=extantFile.fileContent.cell,spaceGroup=extantFile.fileContent.spaceGroup,fileName=outputPDBPath) """ outputFracPath = outputPDBPath+'.ha' with open(outputFracPath,'w') as outputHA: cellString, spaceGroupNumber, extantFile = self.cellString() outputHA.write(cellString) iCoord = 1 for coord in coords: element = [ element for element in ShelxCDEBase.PeriodicTable if element['Symbol'].upper() == coord['Element']][0] #I confess I don't understand negative occupancies here outputHA.write ('ATOM %s %10.5f %10.5f %10.5f %10.5f %10.5f\n'%(element['Symbol'], coord['X'], coord['Y'], coord['Z'], coord['OCC'], coord['B']*100.)) bin = os.path.normpath(os.path.join( 'coordconv' )) logFile = os.path.normpath(os.path.join(self.getWorkDirectory(), 'coordconv_2.log')) arglist = ['XYZIN',outputFracPath,'XYZOUT',outputPDBPath] inputText = '''INPUT HA OUTPUT pdb ''' inputText += self.cellString()[0] pid = CCP4Modules.PROCESSMANAGER().startProcess(bin, arglist, inputText=inputText, logFile=logFile,cwd=self.getWorkDirectory()) status = CCP4Modules.PROCESSMANAGER().getJobData(pid) exitCode = CCP4Modules.PROCESSMANAGER().getJobData(pid,'exitCode') if status != 0 or not os.path.exists(outputPDBPath): self.appendErrorReport(201,str(bin)+' '+str(arglist)+' '+str(inputText)+' '+str(outputFracPath)) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def txtOutputFiles(self): # Add '.txt' extension to files so will display correctly in i2 and desktop tools import glob,shutil # also : pha phs hat from shelxe for ext in [ '*.lst', '*.res', '*.ins', '*.frac' ]: fileList = glob.glob(os.path.join(self.getWorkDirectory(),ext)) for fName in fileList: try: shutil.move(fName,fName+'.txt') except: print 'Error moving',str(fName),'to',str(fName+'.txt')