""" lorestr_i2_report.py: CCP4 GUI Project 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 CCP4ReportParser import Report import sys from lxml import etree class lorestr_i2_report(Report): # Specify which gui task and/or pluginscript this applies to TASKNAME = 'lorestr_i2' RUNNING = True def __init__(self,xmlnode=None,jobInfo={},jobStatus=None,**kw): Report. __init__(self,xmlnode=xmlnode,jobInfo=jobInfo,jobStatus=jobStatus,**kw) self.outputXml = jobStatus is not None and jobStatus.lower().count('running') if jobStatus is not None and jobStatus.lower() == 'nooutput': return self.molProbity = False self.addDiv(style='clear:both;') if jobStatus.lower().count('running'): self.addRunningProgress(self) else: #Finished job self.addDefaultReport(self) def addRunningProgress(self, parent=None): if parent is None: parent=self self.addDefaultReport(self) def addDefaultReport(self, parent=None): if parent is None: parent=self # Decided not to display parameters # if len(self.xmlnode.xpath("Parameters")) > 0: # parametersFold = parent.addFold(label="LORESTR Parameters", initiallyOpen=True) # # parametersFold.addPre(text = 'Received parameters:' ) # # table = parametersFold.addTable(select="Parameters[last()]", transpose = True ) # ,style="width:250px;") # # nh = self.xmlnode.xpath('Parameters/nh') # if len(nh) > 0: # table.addData(title="Maximal number of homologues", data=[nh[0].text]) # nc = self.xmlnode.xpath('Parameters/nc') # if len(nc) > 0: # table.addData(title="Maximal number of chains", data=[nc[0].text]) # dna = self.xmlnode.xpath('Parameters/dna') # if len(dna) > 0: # table.addData(title="Use DNA/RNA restraints", data=[dna[0].text]) # mr = self.xmlnode.xpath('Parameters/mr') # if len(mr) > 0: # table.addData(title="Run 100-200 cycles of jelly body after MR", data=[mr[0].text]) # molprob = self.xmlnode.xpath('Parameters/molprobity') # if len(molprob) > 0: # table.addData(title="Use Molprobity to evaluate geometrical quality", data=[molprob[0].text]) # if molprob[0].text == 'True': # self.molProbity = True # auto = self.xmlnode.xpath('Parameters/auto') # if len(auto) > 0: # table.addData(title="Automatically download homologues from the PDB", data=[auto[0].text]) # minres = self.xmlnode.xpath('Parameters/minRes') # if len(minres) > 0: # table.addData(title="Lowest resolution for auto download of homologues (A)", data=[minres[0].text]) # else: # table.addData(title="Automatically download homologues fromt the PDB", data=['False']) # cpu = self.xmlnode.xpath('Parameters/nCPU') # if len(cpu) > 0: # table.addData(title="Number of CPUs to use", data=[cpu[0].text]) # # newFold.addPre(text = 'Auto: ' + self.xmlnode.xpath("Parameters/auto")[0].text) # # newFold.addPre(text = 'Molprobity: ' + self.xmlnode.xpath("Parameters/molprobity")[0].text) # End of Parameters section # Global parameter - availability of Molprobity - determines additional columns in the tables molprob = self.xmlnode.xpath('Parameters/molprobity') if len(molprob) > 0: if molprob[0].text == 'True': self.molProbity = True # Displaying current status if len(self.xmlnode.xpath("Protocols/BestProtocol")) < 1: # not finished yet parametersFold = parent.addFold(label="LORESTR Status", initiallyOpen=True) table = parametersFold.addTable(transpose = True ) # ,style="width:250px;") currentStatus = 'Starting...' if len(self.xmlnode.xpath("AutoDownload")) > 0: currentStatus = 'Downloading homologues for restraint generation...' if len(self.xmlnode.xpath("StartingStructure")) > 0: currentStatus = 'Analysing input data...' if len(self.xmlnode.xpath("Protocols")) > 0: currentStatus = 'Running refinement protocols...' table.addData(title="Current status:", data=[currentStatus]) # End of Status # Auto Download if len(self.xmlnode.xpath("AutoDownload")) > 0: if len(self.xmlnode.xpath("StartingStructure")) > 0: autoDownloadFold = parent.addFold(label="Automatically downloaded homologues for restraint generation", initiallyOpen=False) else: autoDownloadFold = parent.addFold(label="Automatically downloaded homologues for restraint generation", initiallyOpen=True) # self.printXML('AutoDownload', 'failed', 'True') if len(self.xmlnode.xpath("AutoDownload/failed")) < 1: # Not failed table = autoDownloadFold.addTable(select="AutoDownload[last()]" ) # ,style="width:250px;") table.addData(title="PDB code", select="pdb") table.addData(title="Target chain", select="targetChain") table.addData(title="% of residues aligned", select="alignmentLength") table.addData(title="Sequence Identity (%)", select="identity") else: # Failed BLAST (most likely internet connection problems) table = autoDownloadFold.addTable(transpose=True) # ,style="width:250px;") table.addData(title="BLAST search failed", data=['Unexpected BLAST output for this chain; trying to continue. Could be internet connection problem - please check your internet connection']) # End of Auto Download # Analysing starting structure if len(self.xmlnode.xpath("StartingStructure")) > 0: if len(self.xmlnode.xpath("Protocols")) > 0: startingStructureFold = parent.addFold(label="Starting Parameters Of The Structure", initiallyOpen=False) else: startingStructureFold = parent.addFold(label="Starting Parameters Of The Structure", initiallyOpen=True) table = startingStructureFold.addTable(select="StartingStructure[last()]", transpose = True ) # ,style="width:250px;") for title, select in [[ "Twinning" ,"StartingStructure/twin" ], [ "Scaling method" , "StartingStructure/scaling" ], [ "Solvent parameters
(VDW, ION, RSHR)" , "StartingStructure/solvent" ], ["Starting R-factor","StartingStructure/Rfact"], ["Starting R-free","StartingStructure/Rfree"]]: node = self.xmlnode.xpath(select) if len(node) > 0: table.addData(title=title, data=[node[0].text]) else: table.addData(title=title, data=['Calculating...']) if self.molProbity: for title, select in [[ "Ramachandran outliers (%)" ,"StartingStructure/ramaOut" ], [ "Ramachandran favourite (%)" , "StartingStructure/ramaFav" ], [ "ClashScore percentile" , "StartingStructure/clashPercentile" ], ["MolProbity score percentile","StartingStructure/molprobPercentile"]]: node = self.xmlnode.xpath(select) if len(node) > 0: table.addData(title=title, data=[node[0].text]) else: table.addData(title=title, data=['Calculating...']) dna = self.xmlnode.xpath('StartingStructure/dna') if len(dna) > 0: table.addData(title="DNA/RNA restraints", select="dna") # End Starting Structure # Protocols description if len(self.xmlnode.xpath("Protocols")) > 0: protocolsDescriptionFold = parent.addFold(label="Description of Refinement Protocols", initiallyOpen=False) protocols = self.xmlnode.xpath('Protocols/*') if len(protocols)> 0: name = [] desc = [] for protocolNode in protocols: try: name.append(protocolNode.xpath('Name')[0].text) except: name.append('') try: desc.append(protocolNode.xpath('Description')[0].text) except: desc.append('') table = protocolsDescriptionFold.addTable(select="Protocols[last()]/*" ) # ,style="width:250px;") table.addData(title="Protocol", data=name) table.addData(title="Description", data=desc) # End protocol description # Protocols execution if len(self.xmlnode.xpath("Protocols/BestProtocol")) > 0: protocolsFold = parent.addFold(label="Execution of Refinement Protocols", initiallyOpen=False) else: protocolsFold = parent.addFold(label="Execution of Refinement Protocols", initiallyOpen=True) table = protocolsFold.addTable(select="Protocols[last()]/*" ) # ,style="width:250px;") table.addData(title="Protocol", select="Name") table.addData(title="Status", select="Status") table.addData(title="R-factor", select="Rfact", expr="x if float(x)>0.0 else '-'") table.addData(title="R-free", select="Rfree", expr="x if float(x)>0.0 else '-'") if self.molProbity: table.addData(title="Ramachandran outliers (%)", select="ramaOut", expr="x if float(x)>0.0 else '-'") table.addData(title="Ramachandran favourite (%)", select="ramaFav", expr="x if float(x)>0.0 else '-'") table.addData(title="ClashScore percentile", select="clashPercentile", expr="x if float(x)>0.0 else '-'") table.addData(title="Molprobity score percentile", select="molprobPercentile", expr="x if float(x)>0.0 else '-'") table.addData(title="Q-factor", select="qfact", expr="x if float(x)>0.0 else '-'") # End Protocols execution if len(self.xmlnode.xpath("Protocols/BestProtocol")) > 0: protocolBestFold = parent.addFold(label="Best Refinement Protocol", initiallyOpen=True) # Q-score graph if self.molProbity: COLOUR = ( ('ice blue', '#9cb0fe', '156,176,254,255'), ('gold', '#b3b13d', '179,177,61,255'), ('coral', '#ff7f50', '255,127,80,255'), ('grey', '#808080', '128,128,128,255'), ('pink', '#ff92ff', '255,146,255,255'), ('sea green', '#7fbbb5', '127,187,181,255'), ('pale brown', '#a97d5e', '169,125,94,255'), ('lilac', '#ae87b9', '174,135,185,255'), ('lemon', '#ffff80', '255,255,128,255'), ('lawn green', '#459c4f', '69,156,79,255'), ('pale crimson', '#d23c3e', '210,60,62,255'), ('light blue', '#419ae1', '65,154,225,255'), ('tan', '#780000', '120,0,0,255'), ('light green', '#9aff9a', '154,255,154,255'), ('yellow', '#ffff00', '255,255,0,255'), ('white', '#ffffff', '255,255,255,255'), ('blue', '#0000ff', '0,0,255,255'), ('red', '#ff0000', '255,0,0,255'), ('green', '#00ff00', '0,255,0,255'), ('magenta', '#ff00ff', '255,0,255,255'), ('cyan', '#00ffe1', '0,255,225,255'), ('purple', '#9400ff', '148,0,255,255'), ('dark purple', '#922057', '146,32,87,255'), ('dark cyan', '#1095a6', '16,149,166,255'), ('black', '#000000', '0,0,0,255'), ) graph = protocolBestFold.addFlotGraph( title="Statistics for Protocols", select="//Protocols",style="height:300px; width:450px; float:left; border:0px;") p = graph.addPlotObject() p.append('title','Rfree vs. MolProbity score') p.append('plottype','xy') p.append('xlabel','Rfree') p.append('ylabel','MolProbity Score') protocols = self.xmlnode.xpath('Protocols/*') rFrees = [] for protocolNode in protocols: try: rFrees.append(float(protocolNode.xpath('Rfree')[0].text)) except: pass maxRfree = max(rFrees) minRfree = min(rFrees) maxX = maxRfree + ((maxRfree-minRfree) * 0.3) counter = 1 while len(self.xmlnode.xpath('//Protocols/P%d' % counter)) > 0: graph.addData (title="Rfree", select="P%d/Rfree" %counter) graph.addData (title="Molprob", select="P%d/molprobPercentile" %counter) l = p.append('plotline',xcol=2* counter - 1,ycol=2* counter) l.append('label','%d' % counter) l.append('colour', COLOUR[counter][1]) p.append('xrange', rightaxis='false', max='%0.2f' % maxX ) # min= counter += 1 # End graph bestProtocolNumber = int(self.xmlnode.xpath("Protocols/BestProtocol")[0].text) table = protocolBestFold.addTable(select="Protocols[last()]/*") # ,style="width:250px;") for title, select1 in [["Name", "Protocols/P%d/Name" % bestProtocolNumber], ["Description", "Protocols/P%d/Description" % bestProtocolNumber]]: node1 = self.xmlnode.xpath(select1) table.addData(title=title, data=[node1[0].text]) table = protocolBestFold.addTable(select="Protocols[last()]/*" ) # ,style="width:250px;") table.addData(title='Structure', data=['Before Refinement', 'After Refinement']) for title, select1, select2 in [["R-factor","StartingStructure/Rfact", "Protocols/P%d/Rfact" % bestProtocolNumber], ["R-free","StartingStructure/Rfree", "Protocols/P%d/Rfree" % bestProtocolNumber]]: node1 = self.xmlnode.xpath(select1) node2 = self.xmlnode.xpath(select2) table.addData(title=title, data=[node1[0].text, node2[0].text]) if self.molProbity: for title, select1, select2 in [[ "Ramachandran outliers (%)" ,"StartingStructure/ramaOut", "Protocols/P%d/ramaOut" % bestProtocolNumber ], [ "Ramachandran favourite (%)" , "StartingStructure/ramaFav", "Protocols/P%d/ramaFav" % bestProtocolNumber ], [ "ClashScore percentile" , "StartingStructure/clashPercentile", "Protocols/P%d/clashPercentile" % bestProtocolNumber ], ["MolProbity score percentile","StartingStructure/molprobPercentile", "Protocols/P%d/molprobPercentile" % bestProtocolNumber]]: node1 = self.xmlnode.xpath(select1) node2 = self.xmlnode.xpath(select2) table.addData(title=title, data=[node1[0].text, node2[0].text]) # End Best Protocol