""" cmapcoeff.py: CCP4 GUI 2 Project Copyright (C) 2014 The University of York This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ from CCP4PluginScript import CPluginScript class cmapcoeff(CPluginScript): TASKMODULE = 'wrappers' TASKTITLE = 'Prepare map coefficients' TASKNAME = 'cmapcoeff' TASKCOMMAND = 'cmapcoeff' TASKVERSION= 0.0 WHATNEXT = [ 'coot_rebuild' ] MAINTAINER = 'jon.agirre@york.ac.uk' def processInputFiles ( self ): list_of_stuff = [ ] import CCP4XtalData inp = self.container.inputData con = self.container.controlParameters if con.ANOMALOUS : list_of_stuff.append ( [ 'F_SIGF1', CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR ] ) if inp.ABCD1.isSet ( ) : list_of_stuff.append ( [ 'ABCD1', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL ] ) else : list_of_stuff.append ( [ 'F_SIGF1', CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN ] ) if inp.ABCD1.isSet ( ) : list_of_stuff.append ( [ 'ABCD1', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL ] ) if inp.F_SIGF2.isSet ( ) : list_of_stuff.append ( [ 'F_SIGF2', CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN ] ) if inp.ABCD2.isSet ( ) : list_of_stuff.append ( [ 'ABCD2', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL ] ) self.hklin, columns, error = self.makeHklin0 ( list_of_stuff ) def makeCommandAndScript(self): inp = self.container.inputData out = self.container.outputData con = self.container.controlParameters import os self.hklout = os.path.join(self.workDirectory,"hklout.mtz") self.appendCommandLine([ '-stdin' ]) self.appendCommandScript( '-mtzin ' + self.hklin ) self.appendCommandScript( '-mtzout ' + self.hklout ) self.appendCommandScript( '-colout i2' ) import CCP4XtalData if con.ANOMALOUS : self.appendCommandScript ([ '-colin-fano F_SIGF1_Fplus,F_SIGF1_SIGFplus,F_SIGF1_Fminus,F_SIGF1_SIGFminus' ]) self.appendCommandScript ([ '-colin-hl-1 ABCD1_HLA,ABCD1_HLB,ABCD1_HLC,ABCD1_HLD' ]) else : self.appendCommandScript ([ '-colin-fo-1 F_SIGF1_F,F_SIGF1_SIGF' ]) self.appendCommandScript ([ '-colin-hl-1 ABCD1_HLA,ABCD1_HLB,ABCD1_HLC,ABCD1_HLD' ]) if inp.F_SIGF2.isSet ( ) : self.appendCommandScript ([ '-colin-fo-2 F_SIGF2_F,F_SIGF2_SIGF' ]) if inp.ABCD2.isSet ( ) : self.appendCommandScript ([ '-colin-hl-2 ABCD2_HLA,ABCD2_HLB,ABCD2_HLC,ABCD2_HLD' ]) if inp.RESOLUTION.isSet(): self.appendCommandScript ([ '-resolution %s'%(str(inp.RESOLUTION)) ]) if con.B_VALUE.isSet(): self.appendCommandScript ([ '-b-value %s'%(str(con.B_VALUE)) ]) if con.U_VALUE.isSet(): self.appendCommandScript ([ '-u-value %s'%(str(con.U_VALUE)) ]) if con.SCALE : if con.F1_TO_F2 : self.appendCommandScript ([ '-scale-fo-1 ' ]) else : self.appendCommandScript ([ '-scale-fo-2 ' ]) return CPluginScript.SUCCEEDED def processOutputFiles(self): import CCP4ErrorHandling error = self.splitHklout ( [ 'FPHIOUT' ],[ 'i2.F_phi.F,i2.F_phi.phi' ] ) if error.maxSeverity ( ) > CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED self.container.outputData.FPHIOUT.subType = 2 if self.container.controlParameters.ANOMALOUS : self.container.outputData.FPHIOUT.annotation = 'Anomalous difference map coefficients' elif self.container.inputData.F_SIGF2.isSet (): if self.container.inputData.ABCD2.isSet (): self.container.outputData.FPHIOUT.annotation = 'Fobs - Fobs double difference map coefficients' else : self.container.outputData.FPHIOUT.annotation = 'Fobs - Fobs difference map coefficients' else : self.container.outputData.FPHIOUT.annotation = 'Fobs weighted map coefficients' self.container.outputData.FPHIOUT.subType = 1 if self.container.controlParameters.MAP_OUTPUT : # get ready for producing a map file self.cfftPlugin = self.makeCfftPlugin ( ) error = self.cfftPlugin.process ( ) if error == CPluginScript.FAILED: self.reportStatus ( error ) else : self.container.outputData.MAPOUT = self.cfftPlugin.container.outputData.MAPOUT self.container.outputData.MAPOUT.annotation.set ( 'Computed using ' + str ( self.container.outputData.FPHIOUT.annotation ) ) from lxml import etree with open ( self.makeFileName('PROGRAMXML'),'w' ) as xmlFile: xmlRoot = etree.Element('cmapcoeff') xmlString = etree.tostring ( xmlRoot, pretty_print=True ) xmlFile.write(xmlString) return CPluginScript.SUCCEEDED def makeCfftPlugin ( self ): cfftPlugin = self.makePluginObject( 'fft' ) cfftPlugin.container.inputData.FPHIIN = self.container.outputData.FPHIOUT cfftPlugin.container.inputData.RESOLUTION = self.container.inputData.RESOLUTION cfftPlugin.container.inputData.INDEX_U = self.container.inputData.INDEX_U cfftPlugin.container.inputData.INDEX_V = self.container.inputData.INDEX_V cfftPlugin.container.inputData.INDEX_W = self.container.inputData.INDEX_W return cfftPlugin #===================================================================================================== #=================================test suite========================================================= #===================================================================================================== import unittest from CCP4Utils import getCCP4I2Dir,getTMP # unit testing asynchronous processes potential tricky but QProcess has option to wait for finished class testCmapcoeff(unittest.TestCase): def setUp(self): # make all background jobs wait for completion PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): PROCESSMANAGER().setWaitForFinished(-1) def testCmapcoeff(self): import os inputData = CScriptDataContainer(name='cmapcoeff_test',containerType='inputData',initialise=cmapcoeff.INPUTDATA) outputData = CScriptDataContainer(name='cmapcoeff_test',containerType='outputData',initialise=cmapcoeff.OUTPUTDATA) try: inputData.importXML(os.path.join(getCCP4I2Dir(),'wrappers','cmapcoeff','test_data','cmapcoeff_test_1.def.xml')) except CException as e: self.fail(e.errorType) try: outputData.importXML(os.path.join(getCCP4I2Dir(),'wrappers','cmapcoeff','test_data','cmapcoeff_test_1.def.xml')) except CException as e: self.fail(e.errorType) wrapper = cmapcoeff() pid = wrapper.process() def testSuite(): suite = unittest.TestLoader().loadTestsFromTestCase(testCmapcoeff) return suite def runAllTests(): suite = testSuite() unittest.TextTestRunner(verbosity=2).run(suite)