""" edstats.py: CCP4 GUI Project Copyright (C) 2014 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. """ """ Jon Agirre 2014 - Started development """ from CCP4PluginScript import CPluginScript from CCP4Modules import PROCESSMANAGER import CCP4ErrorHandling class edstats(CPluginScript): TASKMODULE = 'validation' # Where this plugin will appear on the gui TASKTITLE = 'Measure agreement between model and density' # A short title for gui menu TASKNAME = 'edstats' # Task name - should be same as class name TASKCOMMAND = 'edstats' # The command to execute, should be reachable DESCRIPTION = 'Calculates real-space metrics for evaluating the agreement between model and density (Edstats)' TASKVERSION = 0.1 # Version of this plugin WHATNEXT = ['coot_rebuild'] MAINTAINER = 'jon.agirre@york.ac.uk' def processInputFiles(self): import CCP4XtalData self.cfftPlugin1 = self.makeCfftPlugin1 ( ) error = self.cfftPlugin1.process ( ) if error == CPluginScript.FAILED: self.reportStatus ( error ) else : self.container.inputData.MAPIN1 = self.cfftPlugin1.container.outputData.MAPOUT self.cfftPlugin2 = self.makeCfftPlugin2 ( ) error = self.cfftPlugin2.process ( ) if error == CPluginScript.FAILED: self.reportStatus ( error ) else : self.container.inputData.MAPIN2 = self.cfftPlugin2.container.outputData.MAPOUT #print 'taskMakeHklin F_SIGF',self.container.inputData.F_SIGF,type(self.container.inputData.F_SIGF),self.container.inputData.F_SIGF.contentFlag #self.hklin,error = self.makeHklin ( [ ['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN ] ] ) #if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED return CPluginScript.SUCCEEDED def processOutputFiles(self): import os out = self.container.outputData self.path_wrk = str( self.getWorkDirectory() ) fileName3 = os.path.join ( self.path_wrk, 'coot_script.py' ) if os.path.isfile ( fileName3 ) : out.COOTSCRIPTOUT.set ( fileName3 ) out.COOTSCRIPTOUT.annotation.set ( 'guided tour on the reported issues' ) from lxml import etree xmlRoot = etree.Element('Edstats') segmentNode = None lines = open(self.makeFileName('LOG')).readlines() readingTable = False mcBadBits = [] scBadBits = [] zdm = float ( self.container.controlParameters.SIGMA_RZ_MINUS ) zdp = float ( self.container.controlParameters.SIGMA_RZ_PLUS ) zo = float ( self.container.controlParameters.SIGMA_RO ) for line in lines: if readingTable : if len( line.strip().split ( ) ) > 20: residueNode = etree.SubElement(xmlRoot,'Residue') resnameNode = etree.SubElement(residueNode,'Name') resnameNode.text = line.strip().split( )[0] resChainNode = etree.SubElement(residueNode,'Chain') resChainNode.text = line.strip().split( )[1] resNumberNode = etree.SubElement(residueNode,'Number') resNumberNode.text = line.strip().split( )[2] resZCCmNode = etree.SubElement(residueNode,'ZCCm') resZCCmNode.text = line.strip().split( )[10] resZOmNode = etree.SubElement(residueNode,'ZOm') resZOmNode.text = line.strip().split( )[11] resZDmmNode = etree.SubElement(residueNode,'ZDmm') resZDmmNode.text = line.strip().split( )[13] resZDpmNode = etree.SubElement(residueNode,'ZDpm') resZDpmNode.text = line.strip().split( )[14] resZCCsNode = etree.SubElement(residueNode,'ZCCs') resZCCsNode.text = line.strip().split( )[22] resZOsNode = etree.SubElement(residueNode,'ZOs') resZOsNode.text = line.strip().split( )[23] resZDmsNode = etree.SubElement(residueNode,'ZDms') resZDmsNode.text = line.strip().split( )[25] resZDpsNode = etree.SubElement(residueNode,'ZDps') resZDpsNode.text = line.strip().split( )[26] resZCCaNode = etree.SubElement(residueNode,'ZCCa') resZCCaNode.text = line.strip().split( )[34] resZOaNode = etree.SubElement(residueNode,'ZOa') resZOaNode.text = line.strip().split( )[35] resZDmaNode = etree.SubElement(residueNode,'ZDma') resZDmaNode.text = line.strip().split( )[37] resZDpaNode = etree.SubElement(residueNode,'ZDpa') resZDpaNode.text = line.strip().split( )[38] # Now we create a list with main chain outliers to be fixed within Coot if resZDmmNode.text != "n/a" and resZDpmNode.text != "n/a" and resZOmNode.text != "n/a" : if float ( resZDmmNode.text ) < zdm or float ( resZDpmNode.text ) > zdp or float ( resZOmNode.text ) < zo : badResidue = {"name":resnameNode.text, "id":resNumberNode.text, "chain":resChainNode.text, "minus":resZDmmNode.text, "plus":resZDpmNode.text} mcBadBits.append ( badResidue ) if resZDmsNode.text != "n/a" and resZDpsNode.text != "n/a" and resZOsNode.text != "n/a" : if float ( resZDmsNode.text ) < zdm or float ( resZDpsNode.text ) > zdp or float ( resZOsNode.text ) < zo : badResidue = {"name":resnameNode.text, "id":resNumberNode.text, "chain":resChainNode.text, "minus":resZDmmNode.text, "plus":resZDpmNode.text} scBadBits.append ( badResidue ) elif line.strip().startswith('RT CI'): readingTable = True with open(self.container.outputData.COOTSCRIPTOUT.fullPath.__str__(),"w") as cootscript: if len(mcBadBits) > 0: interestingMCBitsDef = 'interestingMCBits = [' for res in mcBadBits: interestingMCBitsDef += ('{"chain":"%s","firstResidue":"%s","lastResidue":"%s"}\n,'%(res['chain'],res['id'],res['id'])) interestingMCBitsDef += ']\n' cootscript.write(interestingMCBitsDef) cootscript.write('ccp4i2Interface.addInterestingBitsMenu(title="Edstats - main chain outliers", interestingBits=interestingMCBits)\n') if len(scBadBits) > 0: interestingSCBitsDef = 'interestingSCBits = [' for res in scBadBits: interestingSCBitsDef += ('{"chain":"%s","firstResidue":"%s","lastResidue":"%s"}\n,'%(res['chain'],res['id'],res['id'])) interestingSCBitsDef += ']\n' cootscript.write(interestingSCBitsDef) cootscript.write('ccp4i2Interface.addInterestingBitsMenu(title="Edstats - side chain outliers", interestingBits=interestingSCBits)\n') with open(self.makeFileName('PROGRAMXML'),'w') as xmlFile: xmlString = etree.tostring(xmlRoot, pretty_print=True) xmlFile.write(xmlString) return CPluginScript.SUCCEEDED def makeCommandAndScript(self): import os import CCP4XtalData self.path_wrk = str( self.getWorkDirectory() ) edstatsOut = os.path.join ( self.path_wrk, 'edstats.out' ) self.appendCommandLine([ 'XYZIN', self.container.inputData.XYZIN.fullPath ]) # INPUT DATA self.appendCommandLine([ 'MAPIN1', self.container.inputData.MAPIN1.fullPath ]) if self.container.inputData.MAPIN2.isSet(): self.appendCommandLine([ 'MAPIN2', self.container.inputData.MAPIN2.fullPath ]) self.appendCommandLine ( [ ' OUT edstats.out ' ] ) self.appendCommandLine ( [ ' XYZOUT XYZOUT.pdb ' ] ) self.appendCommandScript( "reslo=%s"%( str ( self.container.inputData.RES_LOW ) )) self.appendCommandScript( "reshi=%s"%( str ( self.container.inputData.RES_HIGH ) )) if self.container.controlParameters.MAIN_AVERAGING.isSet() : self.appendCommandScript("main=%s"%(str(self.container.controlParameters.MAIN_AVERAGING))) if self.container.controlParameters.SIDE_AVERAGING.isSet() : self.appendCommandScript("side=%s"%(str(self.container.controlParameters.SIDE_AVERAGING))) if self.container.controlParameters.SCALING : self.appendCommandScript("resc=%s"%(str(self.container.controlParameters.SCALING_TYPE))) else : self.appendCommandScript("resc=none") return CPluginScript.SUCCEEDED def makeCfftPlugin1 ( self ): cfftPlugin1 = self.makePluginObject( 'fft' ) cfftPlugin1.container.inputData.FPHIIN = self.container.inputData.FPHIIN1 cfftPlugin1.container.inputData.RESOLUTION = self.container.inputData.RES_HIGH * 3.0 / 4.1 return cfftPlugin1 # I'd like to keep separate plugins because I plan to do divergent stuff in the future. 3/4.1 seemed to work. def makeCfftPlugin2 ( self ): cfftPlugin2 = self.makePluginObject( 'fft' ) cfftPlugin2.container.inputData.FPHIIN = self.container.inputData.FPHIIN2 cfftPlugin2.container.inputData.RESOLUTION = self.container.inputData.RES_HIGH * 3.0 / 4.1 return cfftPlugin2 #============================================================================================= import unittest class testEdstats(unittest.TestCase): def test1(self): # Test creation of log file using ../test_data/test1.params.xml input from CCP4Utils import getCCP4I2Dir import CCP4Utils, os workDirectory = CCP4Utils.getTestTmpDir() logFile = os.path.join(workDirectory,'edstats_test1.log') # Delete any existing log file if os.path.exists(logFile): os.remove(logFile) self.wrapper = edstats(name='edstats_test1',workDirectory=workDirectory) self.wrapper.container.loadDataFromXml(os.path.join(getCCP4I2Dir(),'wrappers','edstats','test_data','test1.params.xml')) self.wrapper.setWaitForFinished(1000000) pid = self.wrapper.process() self.wrapper.setWaitForFinished(-1) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() #self.assertTrue(os.path.exists(logFile),'No log file found') def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(testEdstats) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)