from CCP4PluginScript import CPluginScript from PyQt4 import QtCore import os,re,time,sys from lxml import etree import CCP4Utils class ccp4mg_general(CPluginScript): TASKMODULE = 'model_building' # Where this plugin will appear on the gui TASKTITLE = 'Molecular graphics visualization and figure creation - CCP4MG' # A short title for gui menu TASKNAME = 'ccp4mg_general' # Task name - should be same as class name TASKCOMMAND = 'ccp4mg' # The command to run the executable TASKVERSION= 0.1 # Version of this plugin ASYNCHRONOUS = True TIMEOUT_PERIOD = 9999999.9 MAINTAINER = 'stuart.mcnicholas@york.ac.uk' ERROR_CODES = { 200 : { 'description' : 'CCP4MG exited with error status' }, 201 : { 'description' : 'Failed in harvest operation' },202 : { 'description' : 'Failed in processOutputFiles' }} def makeCommandAndScript(self): import CCP4Utils self.dropDir = os.path.join(self.workDirectory,'CCP4MG_FILE_DROP') if not os.path.exists(self.dropDir): try: os.mkdir(self.dropDir) except: self.dropDir = self.workDirectory print 'Could not make dropDir reset to',self.dropDir # Make a script file with additional menu options to save to i2 self.mgStatusPath = os.path.normpath(os.path.join(self.workDirectory,'script.mgpic.xml')) if sys.platform == 'win32': self.mgStatusPath = re.sub(r'\\\\',r'\\',self.mgStatusPath) # Declare script text then re.sub in the variables if sys.platform == "win32": i2dir = CCP4Utils.getCCP4I2Dir().replace('\\','/') else: i2dir = CCP4Utils.getCCP4I2Dir() status_xml = "" NSMAP = {'xsi':"http://www.w3.org/2001/XMLSchema-instance"} NS = NSMAP['xsi'] location_attribute = '{%s}noNamespaceSchemaLocation' % NS tree = etree.Element("CCP4MG_Status",nsmap = NSMAP,attrib={location_attribute: 'http://www.ysbl.york.ac.uk/~mcnicholas/schema/CCP4MGApplicationOutput.xsd'}) if self.container.inputData.XYZIN_LIST.isSet(): if len(self.container.inputData.XYZIN_LIST)>0: try: View = etree.Element('View') scale_auto = etree.Element('scale_auto') scale_auto.text = "true" View.append(scale_auto) centre_molData = etree.Element('centre_MolData') XYZIN = self.container.inputData.XYZIN_LIST[0] centre_molData.text = os.path.splitext(os.path.basename(XYZIN.__str__()))[0] View.append(centre_molData) orientation_auto = etree.Element('orientation_auto') molData = etree.Element('molData') molData.text = os.path.splitext(os.path.basename(XYZIN.__str__()))[0] orientation_auto.append(molData) selection = etree.Element('selection') selection.text = "all" orientation_auto.append(selection) View.append(orientation_auto) tree.append(View) except: #an issue with the existence of files pass try: iFile = 1 for XYZIN in self.container.inputData.XYZIN_LIST: if os.path.isfile(XYZIN.__str__()): molData = etree.Element('MolData') name = etree.Element('name') name.text = os.path.splitext(os.path.basename(XYZIN.__str__()))[0] molData.append(name) filename = etree.Element('filename') filetype = etree.Element('filetype') filetype.text = "FULLPATH" filename.append(filetype) shortPath = etree.Element('shortPath') shortPath.text = os.path.basename(XYZIN.__str__()) filename.append(shortPath) fullPath = etree.Element('fullPath') fullPath.text = XYZIN.__str__() filename.append(fullPath) molData.append(filename) molDisp = etree.Element("MolDisp") style = etree.Element("style") style.text = "BONDS" molDisp.append(style) molData.append(molDisp) tree.append(molData) else: print 'ccp4mg_general.makeCommandAndScript XYZIN does not exist:',XYZIN.__str__() iFile += 1 except: #an issue with the existence of files pass if self.container.inputData.FPHIIN_LIST.isSet(): try: iFile = 1 for FPHIIN in self.container.inputData.FPHIIN_LIST: print ' reading file number ' + str ( iFile ) if os.path.isfile(FPHIIN.__str__()): mapData = etree.Element('MapData') name = etree.Element('name') name.text = os.path.splitext(os.path.basename(FPHIIN.__str__()))[0] mapData.append(name) filename = etree.Element('filename') filetype = etree.Element('filetype') filetype.text = "FULLPATH" filename.append(filetype) shortPath = etree.Element('shortPath') shortPath.text = os.path.basename(FPHIIN.__str__()) filename.append(shortPath) fullPath = etree.Element('fullPath') fullPath.text = FPHIIN.__str__() filename.append(fullPath) mapData.append(filename) f = etree.Element('f') f.text = "F" mapData.append(f) phi = etree.Element('phi') phi.text = "PHI" mapData.append(phi) mapDisp = etree.Element("MapDisp") style = etree.Element("style") style.text = "surface_style_chickenwire" mapDisp.append(style) surface_style = etree.Element("surface_style") surface_style.text = "surface_style_chickenwire" mapDisp.append(surface_style) colour = etree.Element("colour") colour.text = "blue" mapDisp.append(colour) radius = etree.Element("radius") radius.text = "10.0" mapDisp.append(radius) contour_level = etree.Element("contour_level") contour_level.text = "1.5" mapDisp.append(contour_level) mapData.append(mapDisp) tree.append(mapData) else: print 'ccp4mg_general.makeCommandAndScript FPHIIN does not exist:',FPHIIN.__str__() iFile += 1 except: print ' Exception ' #an issue with the existence of files pass if self.container.inputData.DELFPHIIN_LIST.isSet(): try: iFile = 1 for DELFPHIIN in self.container.inputData.DELFPHIIN_LIST: print ' reading diff file number ' + str ( iFile ) if os.path.isfile(DELFPHIIN.__str__()): mapData = etree.Element('MapData') name = etree.Element('name') name.text = os.path.splitext(os.path.basename(DELFPHIIN.__str__()))[0] mapData.append(name) filename = etree.Element('filename') filetype = etree.Element('filetype') filetype.text = "FULLPATH" filename.append(filetype) shortPath = etree.Element('shortPath') shortPath.text = os.path.basename(DELFPHIIN.__str__()) filename.append(shortPath) fullPath = etree.Element('fullPath') fullPath.text = DELFPHIIN.__str__() filename.append(fullPath) mapData.append(filename) f = etree.Element('f') f.text = "F" mapData.append(f) phi = etree.Element('phi') phi.text = "PHI" mapData.append(phi) difference = etree.Element('difference') difference.text = "1" mapData.append(difference) mapDisp = etree.Element("MapDisp") style = etree.Element("style") style.text = "surface_style_chickenwire" mapDisp.append(style) surface_style = etree.Element("surface_style") surface_style.text = "surface_style_chickenwire" mapDisp.append(surface_style) colour = etree.Element("colour") colour.text = "green" mapDisp.append(colour) radius = etree.Element("radius") radius.text = "10.0" mapDisp.append(radius) contour_level = etree.Element("contour_level") contour_level.text = "3.0" mapDisp.append(contour_level) mapData.append(mapDisp) mapDisp = etree.Element("MapDisp") style = etree.Element("style") style.text = "surface_style_chickenwire" mapDisp.append(style) surface_style = etree.Element("surface_style") surface_style.text = "surface_style_chickenwire" mapDisp.append(surface_style) colour = etree.Element("colour") colour.text = "red" mapDisp.append(colour) radius = etree.Element("radius") radius.text = "10.0" mapDisp.append(radius) contour_level = etree.Element("contour_level") contour_level.text = "-3.0" mapDisp.append(contour_level) mapData.append(mapDisp) tree.append(mapData) else: print 'ccp4mg_general.makeCommandAndScript DELFPHIIN does not exist:',DELFPHIIN.__str__() iFile += 1 except: print ' Exception ' #an issue with the existence of files pass status_xml += etree.tostring(tree,encoding='utf-8', pretty_print=True) print "Writing",self.mgStatusPath print status_xml CCP4Utils.saveFile(self.mgStatusPath,status_xml) clArgs = [ '-norestore',self.mgStatusPath ] origInterface_fname = os.path.join(CCP4Utils.getCCP4I2Dir(),"wrappers","ccp4mg_general","script","ccp4i2CCP4MGInterface.py") origInterface = open(origInterface_fname) origInterface_s = origInterface.read() origInterface.close() interface_s = origInterface_s.replace('XXXXX_WORK_DIR_XXXXX',self.workDirectory) interface_fname = os.path.join(self.workDirectory,"ccp4i2CCP4MGInterface.py") interface = open(interface_fname,"w+") interface.write(interface_s) interface.close() clArgs.extend(['-scr',interface_fname]) if self.container.inputData.SEQUENCE_LIST.isSet(): for sequenceFile in self.container.inputData.SEQUENCE_LIST: clArgs.append(sequenceFile) self.appendCommandLine(clArgs) # Use Qt class to watch the drop directory self.fileSystemWatcher = QtCore.QFileSystemWatcher(parent=self) self.fileSystemWatcher.addPath(self.dropDir) self.connect(self.fileSystemWatcher,QtCore.SIGNAL('directoryChanged(const QString &)'),self.handleFileDrop) return CPluginScript.SUCCEEDED def numberOfOutputFiles(self): import glob outList = glob.glob(os.path.normpath(os.path.join(self.dropDir,'output*.pdb'))) #print 'numberOfOutputFiles outList',os.path.join(self.dropDir,'output*.pdb'),outList #print 'numberOfOutputFiles xmlList',glob.glob(os.path.normpath(os.path.join(self.workDirectory,'*.xml'))) maxIndx = 0 for f in outList: fpath,fname = os.path.split(f) #print 'numberOfOutputFiles fpath,fname', fpath,fname maxIndx = max(maxIndx,int(fname[6:-4])) return maxIndx def handleFileDrop(self,directory): import time,glob print 'ccp4mg_general',time.time() print 'ccp4mg_general',glob.glob(os.path.join(self.workDirectory,'*.*')) #print 'handleFileDrop',directory #Note that I don't copy the file to the appropriate xyzout filename here, since the file may not yet #be closed and/or flushed def processOutputFiles(self): try: # First up import PDB files that have been output import os, glob, shutil globPath = os.path.normpath(os.path.join(self.dropDir,'output*.pdb')) outList = glob.glob(globPath) xyzoutList = self.container.outputData.XYZOUT for outputPDB in outList: fpath,fname = os.path.split(outputPDB) iFile = int(fname[6:-4]) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'XYZOUT_'+str(iFile)+'-coordinates.pdb')) shutil.copyfile(outputPDB, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation = "CCP4MG coordinate output file number"+str(iFile) xyzoutList[-1].subType = 1 """ # Comment out this for now, may be used in future ... # I believe that these will need processing into mini mtz files somehow.... So this is likely to be very different globPath = os.path.normpath(os.path.join(self.dropDir,'mtzout*.mtz')) outList = glob.glob(globPath) xyzoutList = self.container.outputData.FPHIOUT for outputMTZ in outList: fpath,fname = os.path.split(outputMTZ) iFile = int(fname[6:-4]) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'MTZOUT_'+str(iFile)+'-density.mtz')) shutil.copyfile(outputMTZ, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation = "CCP4MG density output file number"+str(iFile) xyzoutList[-1].subType = 1 globPath = os.path.normpath(os.path.join(self.dropDir,'delmtz*.mtz')) outList = glob.glob(globPath) xyzoutList = self.container.outputData.DELFPHIOUT for outputMTZ in outList: fpath,fname = os.path.split(outputMTZ) iFile = int(fname[6:-4]) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'DELMTZ_'+str(iFile)+'-density.mtz')) shutil.copyfile(outputMTZ, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation = "CCP4MG difference density output file number"+str(iFile) xyzoutList[-1].subType = 1 """ # Create a trivial xml output file from lxml import etree self.xmlroot = etree.Element('ccp4mg_general') e = etree.Element('number_output_files') e.text = str(self.numberOfOutputFiles()) self.xmlroot.append(e) #Separate out here activity to attempt merge into project dictionary....this seems flakey, #but is needed for ongoing work, so I am making it give an report a warning in case of failure, rather than #offer the sad face of doom except: exc_type, exc_value,exc_tb = sys.exc_info()[:3] sys.stderr.write(str(exc_type)+'\n') sys.stderr.write(str(exc_value)+'\n') self.appendErrorReport(202,'Data harvesting failed') CCP4Utils.saveEtreeToFile(self.xmlroot,self.makeFileName('PROGRAMXML')) if ( len(outList) ) > 0: return CPluginScript.SUCCEEDED else: return CPluginScript.MARK_TO_DELETE def addReportWarning(self, text): from lxml import etree warningsNode = None warningsNodes = self.xmlroot.xpath('//Warnings') if len(warningsNodes) == 0: warningsNode = etree.SubElement(self.xmlroot, 'Warnings') else: warningsNode = warningsNodes[0] warningNode = etree.SubElement(warningsNode,'Warning') warningNode.text = text