import CCP4RvapiParser class arp_warp_classic_report(CCP4RvapiParser.RvapiReport): TASKNAME="arp_warp_classic" """ from CCP4ReportParser import * class arp_warp_classic_report(Report): # Specify which gui task and/or pluginscript this applies to TASKNAME = 'arp_warp_classic' # Flag that a 'Running' mode is supported RUNNING = True # Indicate css version that this code was written against CSS_VERSION = '0.1.0' def __init__(self,xmlnode=None,jobInfo={},jobStatus=None,taskVersion=None,**kw): Report. __init__(self,xmlnode=xmlnode,jobInfo=jobInfo,cssVersion=self.CSS_VERSION,**kw) if self.errorReport().maxSeverity()>SEVERITY_WARNING: print 'FAILED instantiating buccaneer_build_refine_mr report generator' self.errorReport().report() return # 'nooutput' mode would be used by another report class that wanted # to use some method(s) from this class for its own report if jobStatus is not None and jobStatus.lower() == 'nooutput': return elif jobStatus.count('Running'): #summaryFold = self.addFold(label='Summary by cycle', initiallyOpen=True) self.runningText(self) self.summaryTable(self) self.completenessGraph(self) clearingDiv = self.addDiv(style="clear:both;") else: results = self.addResults() #summaryFold = results.addFold(label='Summary by cycle', initiallyOpen=True) self.finishedText() self.table1(self) self.completenessGraph(self) clearingDiv = self.addDiv(style="clear:both;") self.details(self) self.picture(self) def summaryTable(self, parent=None): if parent is None: parent=self if self.xmlnode.haspath("//BuccaneerBuildRefineResult"): xmlPath = '//BuccaneerBuildRefineResult/BuildRefineCycle' xmlNodes = self.xmlnode.xpath(xmlPath) if len(xmlNodes)>0: selectString = "//BuccaneerBuildRefineResult/BuildRefineCycle[1] " if len(xmlNodes)>2: selectString += " | //BuccaneerBuildRefineResult/BuildRefineCycle[%d]" % (len(xmlNodes)-1) if len(xmlNodes)>1: selectString += " | //BuccaneerBuildRefineResult/BuildRefineCycle[%d]" % len(xmlNodes) tableDiv = parent.addDiv(style="height:250px;width:30em;float:left;border:0px solid black;") progressTable = tableDiv.addTable(select=selectString) progressTable.addData(title="Cycle", select="Number") progressTable.addData(title="Completeness by residue", select="BuccaneerResult/Final/CompletenessByResiduesBuilt") progressTable.addData(title="Completeness by chains", select="BuccaneerResult/Final/CompletenessByChainsBuilt") progressTable.addData(title="RWork", select="RefmacResult/r_factor") progressTable.addData(title="RFree", select="RefmacResult/r_free", expr="x if float(x)>=0.0 else '-'") def completenessGraph(self,parent=None): graph = parent.addFlotGraph( title="Progress by build-refine iteration", select="//BuccaneerBuildRefineResult/BuildRefineCycle",style="height:300px; width:450px; float:right; border:0px;") graph.addData (title="Cycle", select="Number" ) graph.addData (title="Complres", select="BuccaneerResult/Final/CompletenessByResiduesBuilt") # graph.addData (title="by_chains", select="BuccaneerResult/Final/CompletenessByChainsBuilt") graph.addData (title="RWork", select="RefmacResult/r_factor") graph.addData (title="RFree", select="RefmacResult/r_free" ) graph.addData (title="RMSBonds", select="RefmacResult/rmsBONDx100", expr="x/100.0" ) graph.addData (title="RMSAngles", select="RefmacResult/rmsANGLE" ) p = graph.addPlotObject() p.append('title','Progress by iteration') textLabel = p.append("text",xpos=3,ypos=0.5) textLabel.text = "foobar"; p.append('plottype','xy') p.append('xintegral','true') p.append('xlabel','Cycle') p.append('ylabel','Completeness') l = p.append('plotline',xcol=1,ycol=2) l.append('label','By residue') l.append('colour','blue') # l = p.append('plotline',xcol=1,ycol=3) # l.append('label','By chain') # l.append('colour','red') #p.append('yrange', rightaxis='true', min='auto',max='auto') p.append('yrange', rightaxis='false', min='0.0',max='1.0') l = p.append('plotline',xcol=1,ycol=4,rightaxis='true') l.append('colour','gold') l = p.append('plotline',xcol=1,ycol=3,rightaxis='true') l.append('colour','lightblue') if len(p.validate())>0: print p.validate() p = graph.addPlotObject() p.append('title','R-factors after each iteration') p.append('plottype','xy') p.append('xintegral','true') p.append('xlabel','Cycle') l = p.append('plotline',xcol=1,ycol=4) l.append('label','RFree') l.append('colour','gold') l = p.append('plotline',xcol=1,ycol=3) l.append('label','RWork') l.append('colour','lightblue') if len(p.validate())>0: print p.validate() p = graph.addPlotObject() p.append('title','Geometry after each iteration') #p.append('yrange', rightaxis='true', min='auto',max='auto') p.append('plottype','xy') p.append('xintegral','true') p.append('xlabel','Cycle') l = p.append('plotline',xcol=1,ycol=5, rightaxis='true') l.append('label','RMSBonds') l.append('colour','firebrick') l = p.append('plotline',xcol=1,ycol=6) l.append('label','RMSAngles') l.append('colour','green') if len(p.validate())>0: print p.validate() def details(self,parent=None): if parent is None: parent = self fold = parent.addFold(label="Detailed progress by iteration") table = fold.addTable(select="//BuccaneerBuildRefineResult/BuildRefineCycle", transpose=True, downloadable=True,id='details') table.addData ( title='Iteration', select='Number', expr='int(x)' ) for title,select in [ [ "Completeness by residue" ,"BuccaneerResult/Final/CompletenessByResiduesBuilt" ], [ "Completeness by chains" , "BuccaneerResult/Final/CompletenessByChainsBuilt" ]]: table.addData(title=title,select=select,expr='round(x,2)') for title,select in [[ "Number of chains" , "BuccaneerResult/Final/ChainsBuilt"], [ "Residues built" , "BuccaneerResult/Final/ResiduesBuilt" ], [ "Residues sequenced" , "BuccaneerResult/Final/ResiduesSequenced"], [ "Longest fragment" , "BuccaneerResult/Final/ResiduesLongestFragment" ], [ "Number of fragments" , "BuccaneerResult/Final/FragmentsBuilt" ] ]: table.addData(title=title,select=select) for title,select,expr in [[ "RWork" , "RefmacResult/r_factor", "x"], [ "RFree" , "RefmacResult/r_free","x if float(x)>0.0 else '-' " ], [ "RMSBonds" , "RefmacResult/rmsBONDx100", "round(x/100,3)"], [ "RMSAngles", "RefmacResult/rmsANGLE","x" ] ]: table.addData(title=title,select=select,expr=expr) def table1(self,parent=None): if parent is None: parent = self tableDiv = parent.addDiv(style="height:30em;width:20em;float:left;border:0px;") table = tableDiv.addTable(select="//BuccaneerBuildRefineResult", transpose=True, id='table_1') for title,select in [[ "Completeness by residue" ,"BuildRefineCycle[last()]/BuccaneerResult/Final/CompletenessByResiduesBuilt" ], [ "Completeness by chains" , "BuildRefineCycle[last()]/BuccaneerResult/Final/CompletenessByChainsBuilt" ]]: table.addData(title=title,select=select,expr='round(x,2)') for title,select in [[ "Number of chains" , "BuildRefineCycle[last()]/BuccaneerResult/Final/ChainsBuilt"], [ "Residues built" , "BuildRefineCycle[last()]/BuccaneerResult/Final/ResiduesBuilt" ], [ "Residues sequenced" , "BuildRefineCycle[last()]/BuccaneerResult/Final/ResiduesSequenced"], [ "Longest fragment" , "BuildRefineCycle[last()]/BuccaneerResult/Final/ResiduesLongestFragment" ], [ "Number of fragments" , "BuildRefineCycle[last()]/BuccaneerResult/Final/FragmentsBuilt" ] ]: table.addData(title=title,select=select) for title,select,expr in [[ "RWork" , "BuildRefineCycle[last()]/RefmacResult/r_factor", "x"], [ "RFree" , "BuildRefineCycle[last()]/RefmacResult/r_free","x if float(x)>0.0 else '-' " ], [ "RMSBonds" , "BuildRefineCycle[last()]/RefmacResult/rmsBONDx100", "round(x/100,3)"], [ "RMSAngles", "BuildRefineCycle[last()]/RefmacResult/rmsANGLE","x" ] ]: table.addData(title=title,select=select,expr=expr) def picture(self,parent=None) : # sceneFile = '$CCP4I2/pipelines/bucref_mr/script/buccaneer_1.scene.xml' sceneFile = '$CCP4I2/wrappers/arp_warp_classic/script/arp_warp_classic_1.scene.xml' pic = parent.addPicture(label="Autobuilt structure",sceneFile=sceneFile,id='autobuild_1') def runningText(self,parent=None) : if parent is None: parent = self parent.append ( "

The job is currently running. Updates will be shown here for each iteration of model building and refinement.

" ) self.finishedText() def finishedText(self,parent=None) : if parent is None: parent = self try: cres = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/CompletenessByResiduesBuilt')[-1].text) cchn = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/CompletenessByChainsBuilt')[-1].text) frgb = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/FragmentsBuilt')[-1].text) chnb = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/ChainsBuilt')[-1].text) resb = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/ResiduesBuilt')[-1].text) ress = float(self.xmlnode.xpath('BuildRefineCycle/BuccaneerResult/Final/ResiduesSequenced')[-1].text) parent.append( "

%d residues were built in %d fragments. Of these, %d residues were assigned to the sequence.

The number of chains is estimated to be %d. Of these chains, %5.1f%% of the residues have been built.
Of the residues that were built, %5.1f%% were assigned to a chain.

"%(resb,frgb,ress,chnb,100*cchn,100*cres) ) except Exception,e: parent.append( "

Model building results are not yet available.

" ) print >> sys.stderr, "ERROR buccaneer_build_refine_mr_report ",e try: rwrk = float(self.xmlnode.xpath('BuildRefineCycle/RefmacResult/r_factor')[-1].text) rfre = float(self.xmlnode.xpath('BuildRefineCycle/RefmacResult/r_free')[-1].text) rbnd = float(self.xmlnode.xpath('BuildRefineCycle/RefmacResult/rmsBONDx100')[-1].text)*0.01 rang = float(self.xmlnode.xpath('BuildRefineCycle/RefmacResult/rmsANGLE')[-1].text) if rwrk > 0.5: s = "the model is very incomplete or wrong" elif rwrk > 0.4: s = "the model is substantially incomplete and may contain incorrect regions" elif rwrk > 0.35: s = "the model is likely to contain correct regions but requires further work" else: s = "the model is approaching completion" parent.append( "

The refinement R-factor is %5.2f, and the free-R factor is %5.2f. The RMS bond angle deviation is %5.3f A.
On the basis of the refinement statistics, %s.

"%(rwrk,rfre,rbnd,s) ) except Exception,e: parent.append( "

Refinement results are not yet available.

" ) def test(xmlFile=None,jobId=None,reportFile=None): import sys,os if reportFile is None: if xmlFile is not None: reportFile = os.path.join(os.path.split(xmlFile)[0],'report.html') else: reportFile = os.path.join(os.getcwd(),'report.html') r = bucref_report(xmlFile=xmlFile,jobId=jobId) r.as_html_file(reportFile) if len(r.errorReport())>0: print 'ERRORS:',r.errorReport() # Temporary hard-wire to save typing.. #r = bucref_report(xmlFile='/Users/lizp/Desktop/test_projects/t10/CCP4_JOBS/job_2/program.xml',jobId='1b86b099978d11e2822c3c0754185dfb') #r.as_html_file('/Users/lizp/Desktop/test_projects/t10/CCP4_JOBS/job_2/report.html') """