from CCP4PluginScript import CPluginScript import CCP4Utils from lxml import etree class SubstituteLigand(CPluginScript): TASKNAME = 'SubstituteLigand' # Task name - should be same as class name TASKVERSION= 0.0 # Version of this plugin ASYNCHRONOUS = False TIMEOUT_PERIOD = 9999999.9 WHATNEXT = ['coot_rebuild'] MAINTAINER = 'martin.noble@newcastle.ac.uk' ERROR_CODES = { 201 : { 'description' : 'Failed in SubstituteLigand' },} def __init__(self, *args,**kws): super(SubstituteLigand, self).__init__(*args, **kws) self.xmlroot = etree.Element('SubstituteLigand') self.obsToUse = None self.freerToUse = None def process(self): invalidFiles = self.checkInputData() for invalidFile in invalidFiles: if self.container.controlParameters.OBSAS.__str__() == 'MERGED' and invalidFile.__str__() == 'UNMERGEDFILES': invalidFiles.remove(invalidFile) if len(invalidFiles)>0: self.reportStatus(CPluginScript.FAILED) self.checkOutputData() # Chop out the chunk of file we want to use import os selAtomsFilePath = os.path.normpath(os.path.join(self.getWorkDirectory(),'selected_atoms.pdb')) self.container.inputData.XYZIN.getSelectedAtomsPdbFile(selAtomsFilePath) from CCP4ModelData import CPdbDataFile self.selAtomsFile = CPdbDataFile(selAtomsFilePath) if self.container.controlParameters.LIGANDAS.__str__() == 'DICT': self.dictToUse = self.container.inputData.DICTIN self.dictDone() elif self.container.controlParameters.LIGANDAS.__str__() == 'NONE': self.dictDone() elif self.container.controlParameters.LIGANDAS.__str__() != 'NONE': self.lidiaAcedrgPlugin = self.makePluginObject('LidiaAcedrg') self.lidiaAcedrgPlugin.container.inputData.MOLSMILESORSKETCH = self.container.controlParameters.LIGANDAS if self.container.inputData.MOLIN.isSet(): self.lidiaAcedrgPlugin.container.inputData.MOLIN=self.container.inputData.MOLIN if self.container.inputData.SMILESIN.isSet(): self.lidiaAcedrgPlugin.container.inputData.SMILESIN=self.container.inputData.SMILESIN self.lidiaAcedrgPlugin.container.inputData.CONFORMERSFROM = 'RDKIT' self.lidiaAcedrgPlugin.container.inputData.TLC='DRG' self.connectSignal(self.lidiaAcedrgPlugin,'finished',self.lidiaAcedrg_finished) self.lidiaAcedrgPlugin.process() def lidiaAcedrg_finished(self, status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(CPluginScript.FAILED) pluginRoot = CCP4Utils.openFileToEtree(self.lidiaAcedrgPlugin.makeFileName('PROGRAMXML')) self.xmlroot.append(pluginRoot) self.flushXML() self.harvestFile(self.lidiaAcedrgPlugin.container.outputData.DICTOUT_LIST[0], self.container.outputData.DICTOUT) self.dictToUse = self.container.outputData.DICTOUT self.dictDone() def dictDone(self): if self.container.controlParameters.OBSAS.__str__() == 'UNMERGED': self.aimlessCycle = 0 self.aimlessPipe() else: self.obsToUse = self.container.inputData.F_SIGF_IN self.freerToUse = self.container.inputData.FREERFLAG_IN self.phaser_rnp_pipeline() def aimlessPipe(self): self.aimlessPlugin = self.makePluginObject('aimless_pipe') self.aimlessPlugin.container.controlParameters.MODE.set('MATCH') self.aimlessPlugin.container.controlParameters.RESOLUTION_RANGE = self.container.controlParameters.RESOLUTION_RANGE self.aimlessPlugin.container.controlParameters.SCALING_PROTOCOL.set('DEFAULT') self.aimlessPlugin.container.controlParameters.ONLYMERGE.set(False) self.aimlessPlugin.container.controlParameters.REFERENCE_DATASET.set('XYZ') self.aimlessPlugin.container.inputData.copyData(self.container.inputData,['UNMERGEDFILES']) self.aimlessPlugin.container.inputData.XYZIN_REF = self.container.inputData.XYZIN self.connectSignal(self.aimlessPlugin,'finished',self.aimlessPlugin_finished) self.aimlessPlugin.process() def aimlessPlugin_finished(self, status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(CPluginScript.FAILED) pluginRoot = CCP4Utils.openFileToEtree(self.aimlessPlugin.makeFileName('PROGRAMXML')) self.xmlroot.append(pluginRoot) #Here check on the resolution estimate, and cut dataset back accordingly if self.aimlessCycle == 0: datasetresultnodes = pluginRoot.xpath("//Result/Dataset") if len(datasetresultnodes) == 0: self.appendErrorReport(201,'No result nodes found') self.reportStatus(CPluginScript.FAILED) datasetresultnode = datasetresultnodes[0] dataresonodes = datasetresultnode.xpath("ResolutionHigh/Overall") reslimitnodes = datasetresultnode.xpath("ResolutionLimitEstimate") if len(dataresonodes)<1 or len(reslimitnodes)< 1: self.appendErrorReport(201,'Unable to identify resolution estimate limits') self.reportStatus(CPluginScript.FAILED) datareso = datasetresultnode.xpath("ResolutionHigh/Overall")[0].text reslimitnodes = datasetresultnode.xpath("ResolutionLimitEstimate") if reslimitnodes[0].get("type") == "CChalf": reslimit = reslimitnodes[0].xpath("MaximumResolution")[0].text else: self.appendErrorReport(201,'Reso detection failed (first estimate not on CCHalf)') self.reportStatus(CPluginScript.FAILED) if float(reslimit) == float(datareso): self.aimlessCyclesFinished() else: self.aimlessCycle = 1 self.container.controlParameters.RESOLUTION_RANGE.end = float(reslimit) self.aimlessPipe() else: self.aimlessCyclesFinished() def aimlessCyclesFinished(self): self.flushXML() self.harvestFile(self.aimlessPlugin.container.outputData.FREEROUT, self.container.outputData.FREERFLAG_OUT) self.harvestFile(self.aimlessPlugin.container.outputData.HKLOUT[0], self.container.outputData.F_SIGF_OUT) self.obsToUse = self.container.outputData.F_SIGF_OUT self.freerToUse = self.container.outputData.FREERFLAG_OUT self.phaser_rnp_pipeline() def phaser_rnp_pipeline(self): self.rnpPlugin = self.makePluginObject('phaser_rnp_pipeline') self.rnpPlugin.container.inputData.XYZIN_PARENT = self.selAtomsFile self.rnpPlugin.container.inputData.F_SIGF = self.obsToUse self.rnpPlugin.container.inputData.FREERFLAG = self.freerToUse self.rnpPlugin.container.inputData.SELECTIONS.append({'text':'/*/*/*/*','pdbFileKey':'XYZIN_PARENT'}) self.connectSignal(self.rnpPlugin,'finished',self.rnpPlugin_finished) self.rnpPlugin.process() def rnpPlugin_finished(self, status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) try: pluginRoot = CCP4Utils.openFileToEtree(self.rnpPlugin.makeFileName('PROGRAMXML')) self.xmlroot.append(pluginRoot) self.flushXML() self.harvestFile(self.rnpPlugin.container.outputData.MAPOUT_REFMAC, self.container.outputData.FPHIOUT) self.mapToUse = self.container.outputData.FPHIOUT self.harvestFile(self.rnpPlugin.container.outputData.DIFMAPOUT_REFMAC, self.container.outputData.DIFFPHIOUT) import os if os.path.isfile(str(self.rnpPlugin.container.outputData.FREERFLAG_OUT)): self.harvestFile(self.rnpPlugin.container.outputData.FREERFLAG_OUT, self.container.outputData.FREERFLAG_OUT) self.freerToUse = self.container.outputData.FREERFLAG_OUT if os.path.isfile(str(self.rnpPlugin.container.outputData.F_SIGF_OUT)): self.harvestFile(self.rnpPlugin.container.outputData.F_SIGF_OUT, self.container.outputData.F_SIGF_OUT) self.obsToUse = self.container.outputData.F_SIGF_OUT if self.container.controlParameters.LIGANDAS.__str__() == 'NONE': self.reportStatus(CPluginScript.SUCCEEDED) else: self.cootAddLigand() except: self.appendErrorReport(201,'Failed in rnpplugin finished') self.reportStatus(CPluginScript.FAILED) def cootAddLigand(self): self.cootPlugin = self.makePluginObject('coot_script_lines') xyzinList = self.cootPlugin.container.inputData.XYZIN xyzinList.append(xyzinList.makeItem()) xyzinList[-1].set(self.rnpPlugin.container.outputData.XYZOUT_REFMAC) fphiinList = self.cootPlugin.container.inputData.FPHIIN fphiinList.append(fphiinList.makeItem()) fphiinList[-1].set(self.mapToUse) self.cootPlugin.container.inputData.DICT = self.dictToUse #coot_stepped_refine,coot_fit_residues,coot_script_lines self.cootPlugin.container.controlParameters.SCRIPT = '''#Script to fit lignad into density monomerMolNo = get_monomer('DRG') add_ligand_clear_ligands() set_ligand_search_protein_molecule(MolHandle_1) set_ligand_search_map_molecule(MapHandle_1) add_ligand_search_wiggly_ligand_molecule(monomerMolNo) #Execute search nToCopy = 0 ligandsFound=execute_ligand_search() if ligandsFound is not False: nToCopy = len(ligandsFound) #Check on ncs equivs = ncs_chain_ids(0) if equivs is not False and len(equivs)>0: nToCopy = min(len(ligandsFound),len(equivs[0])) if nToCopy > 0: ligandsToCopy = ligandsFound[0:nToCopy] merge_molecules(ligandsToCopy,0) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb"))''' self.connectSignal(self.cootPlugin,'finished',self.cootPlugin_finished) self.cootPlugin.process() def cootPlugin_finished(self, status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) self.harvestFile(self.cootPlugin.container.outputData.XYZOUT[0], self.container.outputData.XYZOUT) #Substitute the composition section of REFMAC output to include new monomers #Perform analysis of output coordinate file composition import os if os.path.isfile(str(self.container.outputData.XYZOUT.fullPath)): from CCP4ModelData import CPdbData aCPdbData = CPdbData() aCPdbData.loadFile(self.container.outputData.XYZOUT.fullPath) #print 'aCPdbData',aCPdbData #print 'aCPdbData.chains',aCPdbData.composition.chains #print 'aCPdbData.monomers',aCPdbData.composition.monomers modelCompositionNode = self.xmlroot.xpath('//ModelComposition')[0] for monomer in aCPdbData.composition.monomers: monomerNode = etree.SubElement(modelCompositionNode,'Monomer',id=monomer) self.finishWithStatus(CPluginScript.SUCCEEDED) def harvestFile(self, pluginOutputItem, pipelineOutputItem): import shutil try: shutil.copyfile(str(pluginOutputItem.fullPath), str(pipelineOutputItem.fullPath)) pipelineOutputItem.annotation = pluginOutputItem.annotation pipelineOutputItem.contentFlag = pluginOutputItem.contentFlag #print '#harvestFile',pluginOutputItem.fullPath, pluginOutputItem.contentFlag pipelineOutputItem.subType = pluginOutputItem.subType except: self.appendErrorReport(202,str(pluginOutputItem.fullPath)+' '+str(pipelineOutputItem.fullPath)) self.finishWithStatus(CPluginScript.FAILED) def appendXML(self, changedFile, replacingElementOfType=None): newXML = CCP4Utils.openFileToEtree(changedFile) oldNodes = self.xmlroot.xpath(replacingElementOfType) if len(oldNodes) > 0: oldNodes[0].parent().remove(oldNodes[0]) self.xmlroot.append(newXML) with open(self.makeFileName('PROGRAMXML'),'w') as xmlfile: xmlfile.write(etree.tostring(self.xmlroot,pretty_print=True)) def checkFinishStatus( self, statusDict,failedErrCode,outputFile = None,noFileErrCode= None): import os if len(statusDict)>0 and statusDict['finishStatus'] == CPluginScript.FAILED: self.appendErrorReport(failedErrCode) self.reportStatus(statusDict['finishStatus']) try: assert outputFile.exists(),'Entity provided is not CDataFile or does not exist' except: self.appendErrorReport(noFileErrCode,'Expected file: '+str(outputFile)) self.finishWithStatus(CPluginScript.FAILED) def finishWithStatus(self, status=CPluginScript.SUCCEEDED): self.flushXML() self.reportStatus(status) def flushXML(self): with open(self.makeFileName('PROGRAMXML'),'w') as programXML: programXML.write(etree.tostring(self.xmlroot, pretty_print=True))