def testUpdateDataFile(self): """Test case - update data file """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # Create a initial data file -- # myDataList=[] curContainer=DataContainer("myblock") aCat=DataCategory("pdbx_seqtool_mapping_ref") aCat.appendAttribute("ordinal") aCat.appendAttribute("entity_id") aCat.appendAttribute("auth_mon_id") aCat.appendAttribute("auth_mon_num") aCat.appendAttribute("pdb_chain_id") aCat.appendAttribute("ref_mon_id") aCat.appendAttribute("ref_mon_num") aCat.append([9,2,3,4,5,6,7]) aCat.append([10,2,3,4,5,6,7]) aCat.append([11,2,3,4,5,6,7]) aCat.append([12,2,3,4,5,6,7]) #self.lfh.write("Assigned data category state-----------------\n") #aCat.dumpIt(fh=self.lfh) tmpf = tempname(suffix='.cif') curContainer.append(aCat) myDataList.append(curContainer) ofh = open(tmpf, "w") pdbxW=PdbxWriter(ofh) pdbxW.write(myDataList) ofh.close() # # # Read and update the data - # myDataList=[] ifh = open(tmpf, "r") pRd=PdbxReader(ifh) pRd.read(myDataList) ifh.close() # myBlock=myDataList[0] myBlock.printIt() myCat=myBlock.getObj('pdbx_seqtool_mapping_ref') myCat.printIt() for iRow in range(0,myCat.getRowCount()): myCat.setValue('some value', 'ref_mon_id',iRow) myCat.setValue(100, 'ref_mon_num',iRow) ofh = open(tempname(suffix='.cif'), "w") pdbxW=PdbxWriter(ofh) pdbxW.write(myDataList) ofh.close() # except: traceback.print_exc(file=self.lfh) self.fail()
def testUpdateDataFile(self): """Test case - write data file """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # Create a initial data file -- # tmpf = tempname(suffix='.cif') myDataList=[] ofh = open(tmpf, "w") curContainer=DataContainer("myblock") aCat=DataCategory("pdbx_seqtool_mapping_ref") aCat.appendAttribute("ordinal") aCat.appendAttribute("entity_id") aCat.appendAttribute("auth_mon_id") aCat.appendAttribute("auth_mon_num") aCat.appendAttribute("pdb_chain_id") aCat.appendAttribute("ref_mon_id") aCat.appendAttribute("ref_mon_num") aCat.append((1,2,3,4,5,6,7)) aCat.append((1,2,3,4,5,6,7)) aCat.append((1,2,3,4,5,6,7)) aCat.append((1,2,3,4,5,6,7)) curContainer.append(aCat) myDataList.append(curContainer) pdbxW=PdbxWriter(ofh) pdbxW.write(myDataList) ofh.close() # # Read and update the data - # myDataList=[] ifh = open(tmpf, "r") pRd=PdbxReader(ifh) pRd.read(myDataList) ifh.close() # myBlock=myDataList[0] myBlock.printIt() myCat=myBlock.getObj('pdbx_seqtool_mapping_ref') myCat.printIt() for iRow in range(0,myCat.getRowCount()): myCat.setValue('some value', 'ref_mon_id',iRow) myCat.setValue(100, 'ref_mon_num',iRow) ofh = open(tempname(suffix='.cif'), "w") pdbxW=PdbxWriter(ofh) pdbxW.write(myDataList) ofh.close() except: traceback.print_exc(file=sys.stderr) self.fail()
def testReadSFDataFile(self): """Test case - read PDB structure factor data file and compute statistics on f/sig(f). """ self.lfh.write( "\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # myContainerList = [] ifh = open(self.pathSFDataFile, "r") pRd = PdbxReader(ifh) pRd.read(myContainerList) c0 = myContainerList[0] # catObj = c0.getObj("refln") if catObj is None: return False nRows = catObj.getRowCount() # # Get column name index. # itDict = {} itNameList = catObj.getItemNameList() for idxIt, itName in enumerate(itNameList): itDict[str(itName).lower()] = idxIt # idf = itDict['_refln.f_meas_au'] idsigf = itDict['_refln.f_meas_sigma_au'] minR = 100 maxR = -1 sumR = 0 icount = 0 for row in catObj.getRowList(): try: f = float(row[idf]) sigf = float(row[idsigf]) ratio = sigf / f #self.lfh.write(" %f %f %f\n" % (f,sigf,ratio)) maxR = max(maxR, ratio) minR = min(minR, ratio) sumR += ratio icount += 1 except: continue ifh.close() self.lfh.write("f/sig(f) min %f max %f avg %f count %d\n" % (minR, maxR, sumR / icount, icount)) except: traceback.print_exc(file=sys.stderr) self.fail()
def testReadSFDataFile(self): """Test case - read PDB structure factor data file and compute statistics on f/sig(f). """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # myContainerList=[] ifh = open(self.pathSFDataFile, "r") pRd=PdbxReader(ifh) pRd.read(myContainerList) c0=myContainerList[0] # catObj=c0.getObj("refln") if catObj is None: return False nRows=catObj.getRowCount() # # Get column name index. # itDict={} itNameList=catObj.getItemNameList() for idxIt,itName in enumerate(itNameList): itDict[str(itName).lower()]=idxIt # idf=itDict['_refln.f_meas_au'] idsigf=itDict['_refln.f_meas_sigma_au'] minR=100 maxR=-1 sumR=0 icount=0 for row in catObj.getRowList(): try: f=float(row[idf]) sigf=float(row[idsigf]) ratio=sigf/f #self.lfh.write(" %f %f %f\n" % (f,sigf,ratio)) maxR=max(maxR,ratio) minR=min(minR,ratio) sumR+=ratio icount+=1 except: continue ifh.close() self.lfh.write("f/sig(f) min %f max %f avg %f count %d\n" % (minR, maxR, sumR/icount,icount)) except: traceback.print_exc(file=sys.stderr) self.fail()
def testSimpleInitialization(self): """Test case - Simple initialization of a data category and data block """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # fn = tempname(suffix='.cif') attributeNameList=['aOne','aTwo','aThree','aFour','aFive','aSix','aSeven','aEight','aNine','aTen'] rowList=[[1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10], [1,2,3,4,5,6,7,8,9,10] ] nameCat='myCategory' # # curContainer=DataContainer("myblock") aCat=DataCategory(nameCat,attributeNameList,rowList) aCat.printIt() curContainer.append(aCat) curContainer.printIt() # myContainerList=[] myContainerList.append(curContainer) ofh = open(fn, "w") pdbxW=PdbxWriter(ofh) pdbxW.write(myContainerList) ofh.close() myContainerList=[] ifh = open(fn, "r") pRd=PdbxReader(ifh) pRd.read(myContainerList) ifh.close() for container in myContainerList: for objName in container.getObjNameList(): name,aList,rList=container.getObj(objName).get() self.lfh.write("Recovered data category %s\n" % name) self.lfh.write("Attribute list %r\n" % repr(aList)) self.lfh.write("Row list %r\n" % repr(rList)) except: traceback.print_exc(file=self.lfh) self.fail()
def testReadDataFile(self): """Test case - read data file """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: # myDataList=[] ifh = open(self.pathPdbxDataFile, "r") pRd=PdbxReader(ifh) pRd.read(myDataList) ifh.close() except: traceback.print_exc(file=sys.stderr) self.fail()
def testReadWriteDataFile(self): """Test case - data file read write test """ self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: myDataList=[] ifh = open(self.pathPdbxDataFile, "r") pRd=PdbxReader(ifh) pRd.read(myDataList) ifh.close() ofh = open(self.pathOutputFile, "w") pWr=PdbxWriter(ofh) pWr.write(myDataList) ofh.close() except: traceback.print_exc(file=self.lfh) self.fail()