from CCP4ReportParser import * class privateer_report(Report): # Specify which gui task and/or pluginscript this applies to TASKNAME = 'privateer' CSS_VERSION = '0.1.0' def __init__(self,xmlnode=None,jobInfo={},**kw): Report. __init__(self,xmlnode=xmlnode,jobInfo=jobInfo,cssVersion=self.CSS_VERSION,**kw) import CCP4Utils,os imageFile = os.path.join(CCP4Utils.getCCP4I2Dir(), 'wrappers/privateer/script/pyranose_pseudorotational.svg' ) background_pyranoses = os.path.join(CCP4Utils.getCCP4I2Dir(), 'wrappers/privateer/script/mercator_pyranoses.png' ) results = self.addResults() results.append('The Cremer-Pople analysis (Cremer and Pople, 1975, JACS 97:1354-58) is used to determine sugar ring conformation. Below is a 2D plot of the conformational'+\ ' parameters (Q, Phi, Theta for pyranoses; Q and Theta for furanoses) along with a depiction of the conformational sphere for pyranoses:') # chartFold = self.addFold(label='graphical representations', initiallyOpen=True) graph = results.addFlotGraph(title="graphical representations", select="//ValidationData", style="height:300px; width:385px; border:0px; float:right;" ) graph.addData ( title="PhiPyranoses", select="Pyranose/SugarPhi" ) graph.addData ( title="ThetaPyranoses", select="Pyranose/SugarTheta" ) graph.addData ( title="PhiFuranoses", select="Furanose/SugarPhi" ) graph.addData ( title="QFuranoses", select="Furanose/SugarQ" ) graph.addData ( title="Pyranose", select="Pyranose/SugarRSCC" ) graph.addData ( title="Furanose", select="Furanose/SugarRSCC" ) graph.addData ( title="BfacPyranoses", select="Pyranose/SugarBFactor" ) graph.addData ( title="BfacFuranoses", select="Furanose/SugarBFactor" ) ########## Pyranose conformation ########### p = graph.addPlotObject() p.append( 'description', 'This graph is a 2D projection of the Cremer-Pople sphere, with chairs at the poles, boats '+\ 'and skew-boats at the equator, and envelopes and half-chairs elsewhere.') p.append( 'title', 'Conformational landscape for pyranoses' ) p.append( 'plottype', 'xy' ) p.append( 'showlegend', 'false' ) p.append ( 'background' ).text = background_pyranoses p.append( 'xintegral', 'true' ) p.append( 'yintegral', 'true' ) p.append( 'xlabel', 'Phi' ) p.append( 'ylabel', 'Theta' ) p.append( 'xrange', min = '0.0', max = '360.0' ) p.append( 'yrange', rightaxis='false', max = '0', min = '180.0' ) l = p.append( 'plotline', xcol = 1, ycol = 2 ) l.append( 'colour', 'red' ) l.append( 'linestyle', '.' ) # l.append( 'symbolsize', '7' ) # l.append( 'symbol', 'x' ) pyranoses = self.xmlnode.select("//ValidationData/Pyranose") furanoses = self.xmlnode.select("//ValidationData/Furanose") ########## Furanose conformation VS Q ########### if furanoses != "" : p = graph.addPlotObject() p.append( 'title', 'Furanose conformation VS puckering amplitude' ) p.append( 'description', 'A plot of conformation (Theta) VS puckering amplitude (Q). Q measures how much atoms separate from the mean ring plane.') p.append( 'plottype', 'xy' ) p.append( 'showlegend', 'false' ) p.append( 'xintegral', 'true' ) p.append( 'yintegral', 'true' ) p.append( 'xrange', min = '0.0', max = '360.0' ) p.append( 'yrange', rightaxis='false', min = '0.0', max = '1.0' ) l = p.append( 'plotline', xcol = 3, ycol = 4 ) l.append( 'colour', 'blue' ) l.append( 'linestyle', '.' ) ########## Conformation VS RSCC ########### p = graph.addPlotObject() p.append( 'title', 'Conformation VS Real Space Correlation Coefficient' ) p.append( 'plottype', 'xy' ) p.append( 'description', 'Here you can see how sugars in the different conformations match the electron density.') if furanoses != "" : p.append( 'showlegend', 'true' ) else : p.append( 'showlegend', 'false' ) p.append( 'xintegral', 'true' ) p.append( 'yintegral', 'true' ) p.append( 'xrange', min = '0.0', max = '360.0' ) p.append( 'yrange', rightaxis='false', min = '0.0', max = '1.0' ) if furanoses != "" : p.append( 'yrange', rightaxis='true', min = '0.0', max = '1.0' ) l = p.append( 'plotline', xcol = 2, ycol = 5 ) l.append( 'colour','red' ) l.append( 'linestyle', '.' ) if furanoses != "" : l = p.append( 'plotline', xcol = 3, ycol = 6, rightaxis='true') l.append('colour','blue') l.append( 'linestyle', '.' ) ########## B-factor VS RSCC ########### p = graph.addPlotObject() p.append( 'title', ' VS Real Space Correlation Coefficient' ) p.append( 'plottype', 'xy' ) if furanoses != "" : p.append( 'showlegend', 'true' ) else : p.append( 'showlegend', 'false' ) p.append( 'xintegral', 'true' ) p.append( 'yintegral', 'true' ) p.append( 'yrange', rightaxis='false', min = '0.0', max = '1.0' ) if furanoses != "" : p.append( 'yrange', rightaxis='true' , min = '0.0', max = '1.0' ) l = p.append( 'plotline', xcol = 7, ycol = 5 ) l.append('colour','red') l.append( 'linestyle', '.' ) if furanoses != "" : l = p.append( 'plotline', xcol = 8, ycol = 6 ) l.append( 'colour', 'blue' ) l.append( 'linestyle', '.' ) htmlCode = 'Diagram' results.append(htmlCode) results.append('
') clearingDiv = results.addDiv(style="clear:both;") ########## Glycan structures ######## trees = self.xmlnode.select ( "//ValidationData/Glycan" ) if trees != "" : treesFold = results.addFold ( label="N- and O-glycan structure 2D descriptions", initiallyOpen=False ) index = 0 chain = 'empty' treesFold.append ( 'Below are graphical plots of the detected glycan trees. Placing your mouse pointer' +\ ' over any of the sugars will display a tooltip containing its residue name and number from the PDB file.' ) directory = jobInfo['fileroot'] for glycan in self.xmlnode.xpath ( "//ValidationData/Glycan/GlycanSVG" ) : if chain != self.xmlnode.xpath ( "//ValidationData/Glycan/GlycanChain" )[index].text : chain = self.xmlnode.xpath ( "//ValidationData/Glycan/GlycanChain" )[index].text treesFold.append ( '

Chain ' + chain + '

' ) chaindiv = treesFold.addDiv(style="border-width: 1px; padding-top: 10px; padding-bottom:10px; border-color:black; border-style:solid; border-radius:15px;") # treesFold.append ( '

Chain ' + chain + '

' ) index = index + 1 svg_filename = os.path.join ( directory, glycan.text ) svg_file = open(svg_filename, 'r') svg_string = svg_file.read() svg_file.close() #chaindiv.append ('
'#width="415" height="183" />' # treesFold.append ( treeshtmlCode ) chaindiv.append ( '
' ) treesFold.append ( '
' ) ######### Detailed validation data ###### tableFold = results.addFold(label='Detailed monosaccharide validation data', initiallyOpen=True) if pyranoses != "" : tableFold.append( 'Validation results for pyranose sugars:
' ) table1 = tableFold.addTable(select="//ValidationData/Pyranose") for title,select in [ [ "Name" ,"SugarName" ], [ "Chain" , "SugarChain" ], [ "Q1" , "SugarQ"], [ "Phi" , "SugarPhi" ], [ "Theta" , "SugarTheta" ], [ "Anomer" , "SugarAnomer" ], [ "D/L2", "SugarHand" ], [ "Conformation" ,"SugarConformation" ], [ "RSCC3" , "SugarRSCC" ], [ "<Bfactor>", "SugarBFactor" ], [ "Diagnostic" , "SugarDiagnostic" ] ] : table1.addData(title=title,select=select) if furanoses != "" : tableFold.append( 'Validation results for furanose sugars:
' ) table2 = tableFold.addTable(select="//ValidationData/Furanose") for title,select in [ [ "Name" ,"SugarName" ], [ "Chain" , "SugarChain" ], [ "Q" , "SugarQ"], [ "Phi" , "SugarPhi" ], [ "Anomer" , "SugarAnomer" ], [ "D/L", "SugarHand" ], [ "Conformation" ,"SugarConformation" ], [ "RSCC" , "SugarRSCC" ], [ "<Bfactor>", "SugarBFactor" ], [ "Diagnostic" , "SugarDiagnostic" ] ] : table2.addData(title=title,select=select) tableFold.append('1Q is the total puckering amplitude, measured in Angstroems.
'+\ '2Whenever N is displayed in the D/L column, it means that Privateer has been unable to determine the handedness based solely on the structure.
'+\ '3RSCC, short for Real Space Correlation Coefficient, measures the agreement between model and positive omit density. A RSCC below 0.8 is tipically considered poor.') ############ Summary ############## summaryFold = self.addFold ( label='Summary and information for Table 1', initiallyOpen=True ) ngeom = nconf = nanom = ndl = nq = 0 for diagnostics in self.xmlnode.xpath("//ValidationData/Pyranose/SugarDiagnostic") : ngeom += diagnostics.text.count ( "geometry" ) nconf += diagnostics.text.count ( "mistaken" ) nanom += diagnostics.text.count ( "anomer" ) ndl += diagnostics.text.count ( "configuration" ) nq += diagnostics.text.count ( "Q=" ) for diagnostics in self.xmlnode.xpath("//ValidationData/Furanose/SugarDiagnostic") : ngeom += diagnostics.text.count ( "geometry" ) nconf += diagnostics.text.count ( "mistaken" ) nanom += diagnostics.text.count ( "anomer" ) ndl += diagnostics.text.count ( "configuration" ) nq += diagnostics.text.count ( "Q=" ) tableSummary = summaryFold.addTable ( transpose=True ) #tableSummary.addData ( title = "Check ring geometry", data = [ ngeom ] ) tableSummary.addData ( title = "Stereochemical problems", data = [ nanom + ndl ] ) tableSummary.addData ( title = "Unphysical puckering amplitude", data = [ nq ] ) tableSummary.addData ( title = "In unlikely ring conformation", data = [ nconf ] ) # svgFile = '' # results.append(svgFile) totalIssues = ngeom + nconf + nanom + ndl + nq if totalIssues > 0 : summaryFold.append ( "There are " + str(totalIssues) + " issues with your model, and they may need correcting.
" ) summaryFold.append ( "Please select 'Manual model rebuilding' at the bottom of this window, so Coot can guide you through all the problems raised.
" ) else : summaryFold.append ( "No issues were found while analysing the data." ) self.addTaskReferences() # def unescape(s): # s = s.replace("<", "<") # s = s.replace(">", ">") # s = s.replace("&", "&") # return s if __name__ == "__main__": import sys privateer_report(xmlFile=sys.argv[1],jobId=sys.argv[2])