from CCP4PluginScript import CPluginScript from PyQt4 import QtCore class coot_script_lines(CPluginScript): TASKMODULE = 'model_building' # Where this plugin will appear on the gui TASKTITLE = 'Execute arbitrary script code within Coot' # A short title for gui menu TASKNAME = 'coot_script_lines' # Task name - should be same as class name TASKCOMMAND = 'coot' # The command to run the executable TASKVERSION= 0.0 # Version of this plugin WHATNEXT = ['prosmart_refmac'] ASYNCHRONOUS = True TIMEOUT_PERIOD = 9999999.9 ''' def __init__(self,parent=None,name=None,workDirectory=''): CPluginScript. __init__(self,parent=parent,name=name) ''' def makeCommandAndScript(self): import os self.dropDir = os.path.join(self.workDirectory,'COOT_FILE_DROP') if not os.path.exists(self.dropDir): try: os.mkdir(self.dropDir) except: self.dropDir = self.workDirectory cootScriptPath = os.path.join(self.workDirectory,'script.py') if self.container.inputData.DICT.isSet(): self.appendCommandLine(['--dictionary',self.container.inputData.DICT.fullPath.__str__()]) self.appendCommandLine(['--no-state-script','--no-graphics','--python','--script',cootScriptPath]) cootScript = open(cootScriptPath,"w") i = 1 for XYZIN in self.container.inputData.XYZIN: if XYZIN.exists(): cootScript.write ("MolHandle_"+str(i)+"=read_pdb('"+str(XYZIN.fullPath)+"')\n\n") i += 1 else: pass #print '\n\n ** Non-file :[' + str(i)+ ']'+str(XYZIN.fullPath) i = 1 for FPHIIN in self.container.inputData.FPHIIN: if FPHIIN.exists(): cootScript.write ("MapHandle_"+str(i)+"=make_and_draw_map('" + str(FPHIIN.fullPath)+"', 'F', 'PHI', 'PHI', 0, 0)\n\n") i += 1 else: pass #print '\n\n ** Non-file :[' +str(i)+ ']'+ str(FPHIIN.fullPath) i = 1 for DELFPHIIN in self.container.inputData.DELFPHIIN: if DELFPHIIN.exists(): cootScript.write ("DifmapHandle_"+str(i)+"=make_and_draw_map('" + str(DELFPHIIN.fullPath)+"', 'F', 'PHI', 'PHI', 0, 1)\n\n") i += 1 else: pass #print '\n\n ** Non-file :[' +str(i)+ ']'+str(DELFPHIIN.fullPath) cootScript.write ('dropDir="'+self.dropDir+'"\n\n') if self.container.controlParameters.SCRIPT.isSet(): #Here try to except and exit if script is faulty scriptLines = self.container.controlParameters.SCRIPT.__str__().split('\n') cootScript.write ('try:\n') for scriptLine in scriptLines: cootScript.write(' '+scriptLine+'\n') cootScript.write('except:\n coot_real_exit(0)\n') cootScript.write ('\n') cootScript.write("coot_real_exit(0)\n") cootScript.close() return CPluginScript.SUCCEEDED def processOutputFiles(self): print '#coot_script_lines.processOutputFiles' #First up check for exit status of the program from CCP4Modules import PROCESSMANAGER exitStatus = 0 try: exitStatus = PROCESSMANAGER().getJobData(pid=self.getProcessId(), attribute='exitStatus') if exitStatus != CPluginScript.SUCCEEDED: return exitStatus except: print 'Unable to recover exitStatus' return CPluginScript.FAILED iPDBOut = 0 try: import os, glob, shutil outList = glob.glob(os.path.join(self.dropDir,'*.pdb')) xyzoutList = self.container.outputData.XYZOUT print outList for outputPDB in outList: fpath,fname = os.path.split(outputPDB) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.join(self.workDirectory,'XYZOUT_'+str(iPDBOut)+'-coordinates.pdb') shutil.copyfile(outputPDB, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation=fname iPDBOut += 1 except: return CPluginScript.FAILED iCIFOut = 0 try: outList = glob.glob(os.path.join(self.dropDir,'coot-ccp4', 'prodrg-out*.cif')) dictoutList = self.container.outputData.DICTOUT for outputCIF in outList: fpath,fname = os.path.split(outputCIF) dictoutList.append(dictoutList.makeItem()) outputFilePath = os.path.join(self.workDirectory,'COOT_'+str(iCIFOut)+'-prodrg.cif') shutil.copyfile(outputCIF, outputFilePath) dictoutList[-1].setFullPath(outputFilePath) dictoutList[-1].annotation=fname iCIFOut += 1 except: return CPluginScript.FAILED # Create a trivial xml output file import CCP4File from lxml import etree self.xmlroot = etree.Element('coot_script_lines') e = etree.Element('number_output_pdbs') e.text = str(iPDBOut) self.xmlroot.append(e) e = etree.Element('number_output_cifs') e.text = str(iCIFOut) self.xmlroot.append(e) tableElement = self.logToXML() if tableElement is not None: self.xmlroot.append(tableElement) try: aFile=open( self.makeFileName('PROGRAMXML'),'w') aFile.write( etree.tostring(self.xmlroot,pretty_print=True) ) aFile.close() except: print 'Oops' return CPluginScript.FAILED return CPluginScript.SUCCEEDED def logToXML(self): from lxml import etree tableelement = etree.Element('Table', title='Per residue statistics') pairs = [('Col_0','N'),('Col_1','StartBonds'),('Col_2','FinalBonds')] for pair in pairs: headerElement = etree.SubElement(tableelement,'Header',label=pair[1],identifier=pair[0]) cootlines = open(self.makeFileName('LOG')).readlines() iRow = 1 currentChangeList = [] for line in cootlines: if line.startswith('bonds:'): #Possibilities are that this is the first or second bonds reported, i.e. this is an initial or final value if len(currentChangeList) == 0: currentChangeList.append(line.split()[1]) else: currentChangeList.append(line.split()[1]) rowElement = etree.SubElement(tableelement,"row") rowNoElement = etree.SubElement(rowElement,'Col_0') rowNoElement.text = str(iRow) startBondsElement = etree.SubElement(rowElement,'Col_1') startBondsElement.text = str(currentChangeList[0]) finalBondsElement = etree.SubElement(rowElement,'Col_2') finalBondsElement.text = str(currentChangeList[1]) currentChangeList = [] iRow += 1 if iRow == 1: return None graphElement = etree.SubElement(tableelement,"Graph", title = "By residue bonds") graphColumnElement = etree.SubElement(graphElement,"Column", label='N', positionInList=str(0)) graphColumnElement = etree.SubElement(graphElement,"Column", label='StartBonds', positionInList=str(1)) graphColumnElement = etree.SubElement(graphElement,"Column", label='FinalBonds', positionInList=str(2)) return tableelement #==================================================================================================== # PLUGIN TESTS # See Python documentation on unittest module import unittest class testcoot_script_lines(unittest.TestCase): def setUp(self): # make all background jobs wait for completion # this is essential for unittest to work from CCP4Modules import QTAPPLICATION,PROCESSMANAGER self.app = QTAPPLICATION() PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): from CCP4Modules import PROCESSMANAGER PROCESSMANAGER().setWaitForFinished(-1) def test_1(self): from CCP4Modules import QTAPPLICATION wrapper = coot_script_lines(parent=QTAPPLICATION(),name='coot_script_lines_test1') wrapper.container.loadDataFromXml() def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(testcoot_script_lines) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)