""" ShelxCD_gui.py Copyright (C) 2014 Newcastle University Author: Martin Noble """ from PyQt4 import QtGui,QtCore from CCP4TaskWidget import CTaskWidget def whatNext(jobId=None,childTaskName=None,childJobNumber=None,projectName=None): import os from lxml import etree import CCP4Modules, CCP4Utils, CCP4File, CCP4Container, CCP4Data try: jobDirectory = CCP4Modules.PROJECTSMANAGER().db().jobDirectory(jobId=jobId) returnList = [] for taskName in ['ShelxCE','ShelxCECompareHands']: cont = CCP4Modules.PROJECTSMANAGER().getJobParams(jobId) fileRoot = 'Subsequent'+taskName+'.params.xml' paramsPath = os.path.normpath(os.path.join(jobDirectory,fileRoot)) if not os.path.isfile(paramsPath): cont_new = CCP4Container.CContainer(name=taskName) cont_new.__dict__['header']=CCP4File.CI2XmlHeader() cont_new.__dict__['header'].pluginName = taskName for ic in ('inputData','controlParameters'): cont_new.addObject( getattr(cont,ic), reparent=True ) cont_new.inputData.addObject( cont.outputData.XYZOUT, reparent=True ) cont_new.inputData.renameObject('XYZOUT','HAIN') cont_new.addObject(CCP4Container.CContainer(parent=cont_new,name='keywords'),name='keywords') cont_new.keywords.addContent( name='z', cls=CCP4Data.CBoolean, value=True ) cont_new.saveDataToXml(fileName=paramsPath) returnList.append([taskName, paramsPath]) if cont.controlParameters.MODE.__str__() == 'SAD': cont = CCP4Modules.PROJECTSMANAGER().getJobParams(jobId) taskName='phaser_EP_AUTO' fileRoot = 'Subsequent'+taskName+'.params.xml' paramsPath = os.path.normpath(os.path.join(jobDirectory,fileRoot)) if not os.path.isfile(paramsPath): cont_new = CCP4Container.CContainer(name=taskName) cont_new.__dict__['header']=CCP4File.CI2XmlHeader() cont_new.__dict__['header'].pluginName = taskName cont_new.addParamsSubContainers() cont_new.inputData.addObject( cont.outputData.XYZOUT, reparent=True ) cont_new.inputData.renameObject('XYZOUT','XYZIN_HA') cont_new.inputData.addObject( cont.inputData.SAD, reparent=True ) cont_new.inputData.renameObject('SAD','F_SIGF') cont_new.inputData.addContent( name='LLGC_CYCLES', cls=CCP4Data.CInt, value=10 ) cont_new.inputData.addContent( name='ELEMENTS', cls=CCP4Data.CList, subItem={'class':CCP4Data.CString} ) cont_new.inputData.ELEMENTS.addItem(value=cont.controlParameters.SFAC.__str__()) cont_new.addObject(CCP4Container.CContainer(parent=cont_new,name='keywords'),name='keywords') cont_new.keywords.addContent( name='HAND', cls=CCP4Data.CString, value='Off' ) cont_new.saveDataToXml(fileName=paramsPath) returnList.append([taskName, paramsPath]) return returnList except: print 'Exception in ShelxCD_gui.whatNext' return ['ShelxCECompareHands','ShelxCE','phaser_EP_AUTO'] #------------------------------------------------------------------- class ShelxCD_gui(CTaskWidget): #------------------------------------------------------------------- # Subclass CTaskWidget to give specific task window TASKMODULE = 'test' # Where this plugin will appear on the gui TASKTITLE = 'Find HA sites - SHELXC/D' # A short title for gui menu SHORTTASKTITLE = 'ShelxCD' # No - this one really is a short title for gui menu TASKVERSION = 0.1 DESCRIPTION = 'Find sites from SAD/MAD/SIR/SIRAS/RIP/RIPAS data' TASKNAME = 'ShelxCD' # Task name - should be same as class name MGDISPLAYFILES = ['XYZOUT'] def __init__(self,*args,**kw): super(ShelxCD_gui,self).__init__(*args, **kw) def drawContents(self): self.openFolder(folderFunction='inputData') import CCP4Utils,CCP4Modules if (not hasattr(CCP4Modules.PREFERENCES(),'SHELXDIR')) and CCP4Utils.which('shelxc') is None: if (not CCP4Modules.PREFERENCES().SHELXDIR.exists()) and CCP4Utils.which('shelxc') is None: self.createLine ( [ 'warning','The Shelx programs have not been found. They are not part of CCP4 but you can get them from\nhttp://shelx.uni-ac.gwdg.de/SHELX/download.php\nIf you already have them make sure they are on the search path\nOR specify where they are in the Preferences window - under Other Software.' ]) self.createLine ( [ 'label','Experiment type','stretch','tip','What sort of data are available for finding heavy atoms','widget','MODE' ] ) self.openSubFrame( frame=[True]) self.createLine(['label','Atom type to seek','stretch','widget','SFAC']) self.createLine(['label','Number to find','stretch','widget','FIND']) self.createLine(['label','Number of trys','stretch','widget','NTRY']) self.closeSubFrame() self.openSubFrame( frame=True) self.createLine(['advice','Anomalous (SAD) dataset'],toggle=['MODE','open', ['SAD']]) self.createLine(['widget','SAD'],toggle=['MODE','open', ['SAD']]) self.openSubFrame( toggle=['MODE','open',['MAD']]) self.createLine(['advice','High energy remote dataset']) self.createLine(['widget','HREM']) self.createLine(['advice','Low energy remote dataset']) self.createLine(['widget','LREM']) self.createLine(['advice','Inflection point dataset']) self.createLine(['widget','INFL']) self.createLine(['advice','Peak dataset']) self.createLine(['widget','PEAK']) self.closeSubFrame() self.createLine(['advice','Derivative dataset'],toggle=['MODE','open',['SIR']]) self.createLine(['widget','SIR'],toggle=['MODE','open',['SIR']]) self.createLine(['advice','Anomalous derivative dataset'], toggle=['MODE','open',['SIRAS']]) self.createLine(['widget','SIRA'], toggle=['MODE','open',['SIRAS']]) self.createLine(['advice','Native dataset']) self.createLine(['widget','NAT']) self.createLine(['advice','Radiation damaged dataset'], toggle=['MODE','open',['RIP']]) self.createLine(['widget','RIP'], toggle=['MODE','open',['RIP']]) self.createLine(['advice','Radiation damaged anomalous dataset'], toggle=['MODE','open',['RIPAS']]) self.createLine(['widget','RIPA'], toggle=['MODE','open',['RIPAS']]) self.closeSubFrame() self.dShelxCDKeywords() def whichShelx(self): # Test and report is shelx executable available import CCP4Utils if CCP4Utils.which('shelxc') is None: QtGui.QMessageBox.warning( self, 'Shelx', 'The ShelxC program has not been found.\nIt is not part of CCP4 but you can get if from\nhttp://shelx.uni-ac.gwdg.de/SHELX/download.php\nIf you already have it then make sure it is on the search path or specify where it is in the Preferences window - under Other Software.' ) def dShelxCDKeywords(self): #From here on, GUI is autogenerated from the keywords container self.openFolder(folderFunction='controlParameters', title='Keywords') self.openSubFrame() self.autoGenerate(container=self.container.controlParameters,selection={'excludeParameters' : ['MODE','FIND','NTRY','SFAC']}) self.closeSubFrame() def isValid(self): inp = self.container.inputData requires = { 'SAD':[inp.SAD], 'MAD':[inp.HREM,inp.LREM,inp.INFL,inp.PEAK], 'SIR':[inp.SIR,inp.NAT], 'SIRAS':[inp.SIRA,inp.NAT], 'RIP':[inp.RIP,inp.NAT], 'RIPAS':[inp.RIPA,inp.NAT],} modeStr = self.container.controlParameters.MODE.__str__() # Need to unset the unused inputs before calling the CTaskWidget.isValid() or invalid data # will be flagged to user for fObj in [inp.SAD,inp.HREM,inp.LREM,inp.INFL,inp.PEAK,inp.SIR,inp.SIRA,inp.RIP,inp.RIPA]: if fObj not in requires[modeStr]: fObj.unSet() # Generic validity test invalidElements = super(ShelxCD_gui,self).isValid() if modeStr == 'MAD': nset = len([setDataset for setDataset in requires['MAD'] if setDataset.isSet()]) if nset < 2: for require in requires[modeStr]: # Check whether all of the datasets required by this mode are set if not require.isSet() and not require in invalidElements: invalidElements.append(require) else: for require in requires[modeStr]: # Check whether all of the datasets required by this mode are set if not require.isSet() and not require in invalidElements: invalidElements.append(require) return invalidElements