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)

            curContainer.append(aCat)
            myDataList.append(curContainer)
            ofh = open("test-output-1.cif", "w")
            pdbxW = PdbxWriter(ofh)
            pdbxW.write(myDataList)
            ofh.close()
            #
            #
            # Read and update the data -
            #
            myDataList = []
            ifh = open("test-output-1.cif", "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 xrange(0, myCat.getRowCount()):
                myCat.setValue('some value', 'ref_mon_id', iRow)
                myCat.setValue(100, 'ref_mon_num', iRow)
            ofh = open("test-output-2.cif", "w")
            pdbxW = PdbxWriter(ofh)
            pdbxW.write(myDataList)
            ofh.close()
            #

        except:
            traceback.print_exc(file=self.lfh)
            self.fail()
示例#2
0
    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)

            curContainer.append(aCat)
            myDataList.append(curContainer)
            ofh = open("test-output-1.cif", "w")            
            pdbxW=PdbxWriter(ofh)
            pdbxW.write(myDataList)
            ofh.close()
            #
            #
            # Read and update the data -
            # 
            myDataList=[]
            ifh = open("test-output-1.cif", "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 xrange(0,myCat.getRowCount()):
                myCat.setValue('some value', 'ref_mon_id',iRow)
                myCat.setValue(100, 'ref_mon_num',iRow)
            ofh = open("test-output-2.cif", "w")            
            pdbxW=PdbxWriter(ofh)
            pdbxW.write(myDataList)
            ofh.close()
            #
            
        except:
            traceback.print_exc(file=self.lfh)
            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 = "test-simple.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()
示例#4
0
    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()
示例#5
0
 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()
示例#6
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    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="test-simple.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()
示例#7
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 def testReadBigDataFile(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.pathBigPdbxDataFile, "r")
         pRd=PdbxReader(ifh)
         pRd.read(myDataList)
         ifh.close()            
     except:
         traceback.print_exc(file=sys.stderr)
         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()
示例#9
0
 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()
    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()
示例#11
0
    def __init__(self, file):
        """Load a PDBx/mmCIF file.

        The atom positions and Topology can be retrieved by calling
        getPositions() and getTopology().

        Parameters
        ----------
        file : string
            the name of the file to load.  Alternatively you can pass an open
            file object.
        """
        top = Topology()
        ## The Topology read from the PDBx/mmCIF file
        self.topology = top
        self._positions = []

        # Load the file.

        inputFile = file
        if isinstance(file, str):
            inputFile = open(file)
        reader = PdbxReader(inputFile)
        data = []
        reader.read(data)
        block = data[0]

        # Build the topology.

        atomData = block.getObj('atom_site')
        atomNameCol = atomData.getAttributeIndex('auth_atom_id')
        atomIdCol = atomData.getAttributeIndex('id')
        resNameCol = atomData.getAttributeIndex('auth_comp_id')
        resNumCol = atomData.getAttributeIndex('auth_seq_id')
        resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
        chainIdCol = atomData.getAttributeIndex('auth_asym_id')
        elementCol = atomData.getAttributeIndex('type_symbol')
        altIdCol = atomData.getAttributeIndex('label_alt_id')
        modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
        xCol = atomData.getAttributeIndex('Cartn_x')
        yCol = atomData.getAttributeIndex('Cartn_y')
        zCol = atomData.getAttributeIndex('Cartn_z')
        lastChainId = None
        lastResId = None
        atomTable = {}
        atomsInResidue = set()
        models = []
        for row in atomData.getRowList():
            atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol]))
            model = ('1' if modelCol == -1 else row[modelCol])
            if model not in models:
                models.append(model)
                self._positions.append([])
            modelIndex = models.index(model)
            if row[altIdCol] != '.' and atomKey in atomTable and len(self._positions[modelIndex]) > atomTable[atomKey].index:
                # This row is an alternate position for an existing atom, so ignore it.

                continue
            if modelIndex == 0:
                # This row defines a new atom.

                if lastChainId != row[chainIdCol]:
                    # The start of a new chain.
                    chain = top.addChain(row[chainIdCol])
                    lastChainId = row[chainIdCol]
                    lastResId = None
                if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
                    # The start of a new residue.
                    resId = (None if resNumCol == -1 else row[resNumCol])
                    resIC = ('' if resInsertionCol == -1 else row[resInsertionCol])
                    res = top.addResidue(row[resNameCol], chain, resId, resIC)
                    lastResId = row[resNumCol]
                    atomsInResidue.clear()
                element = None
                try:
                    element = elem.get_by_symbol(row[elementCol])
                except KeyError:
                    pass
                atom = top.addAtom(row[atomNameCol], element, res, row[atomIdCol])
                atomTable[atomKey] = atom
                atomsInResidue.add(row[atomNameCol])
            else:
                # This row defines coordinates for an existing atom in one of the later models.

                try:
                    atom = atomTable[atomKey]
                except KeyError:
                    raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resNumCol], model))
                if atom.index != len(self._positions[modelIndex]):
                    raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0]))
            self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
        for i in range(len(self._positions)):
            self._positions[i] = self._positions[i]*nanometers
        ## The atom positions read from the PDBx/mmCIF file.  If the file contains multiple frames, these are the positions in the first frame.
        self.positions = self._positions[0]
        self.topology.createStandardBonds()
        self._numpyPositions = None

        # Record unit cell information, if present.

        cell = block.getObj('cell')
        if cell is not None and cell.getRowCount() > 0:
            row = cell.getRow(0)
            (a, b, c) = [float(row[cell.getAttributeIndex(attribute)])*0.1 for attribute in ('length_a', 'length_b', 'length_c')]
            (alpha, beta, gamma) = [float(row[cell.getAttributeIndex(attribute)])*math.pi/180.0 for attribute in ('angle_alpha', 'angle_beta', 'angle_gamma')]
            self.topology.setPeriodicBoxVectors(computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))

        # Add bonds based on struct_conn records.

        connectData = block.getObj('struct_conn')
        if connectData is not None:
            res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
            res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
            atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
            atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
            asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
            asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
            typeCol = connectData.getAttributeIndex('conn_type_id')
            connectBonds = []
            for row in connectData.getRowList():
                type = row[typeCol][:6]
                if type in ('covale', 'disulf', 'modres'):
                    key1 = (row[res1Col], row[asym1Col], row[atom1Col])
                    key2 = (row[res2Col], row[asym2Col], row[atom2Col])
                    if key1 in atomTable and key2 in atomTable:
                        connectBonds.append((atomTable[key1], atomTable[key2]))
            if len(connectBonds) > 0:
                # Only add bonds that don't already exist.
                existingBonds = set(top.bonds())
                for bond in connectBonds:
                    if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
                        top.addBond(bond[0], bond[1])
                        existingBonds.add(bond)
示例#12
0
文件: pdbxfile.py 项目: mrG7/openmm
    def __init__(self, file):
        """Load a PDBx/mmCIF file.

        The atom positions and Topology can be retrieved by calling getPositions() and getTopology().

        Parameters:
         - file (string) the name of the file to load.  Alternatively you can pass an open file object.
        """
        top = Topology()
        ## The Topology read from the PDBx/mmCIF file
        self.topology = top
        self._positions = []

        # Load the file.

        inputFile = file
        if isinstance(file, str):
            inputFile = open(file)
        reader = PdbxReader(inputFile)
        data = []
        reader.read(data)
        block = data[0]

        # Build the topology.

        atomData = block.getObj('atom_site')
        atomNameCol = atomData.getAttributeIndex('label_atom_id')
        atomIdCol = atomData.getAttributeIndex('id')
        resNameCol = atomData.getAttributeIndex('label_comp_id')
        resIdCol = atomData.getAttributeIndex('label_seq_id')
        resNumCol = atomData.getAttributeIndex('auth_seq_id')
        asymIdCol = atomData.getAttributeIndex('label_asym_id')
        chainIdCol = atomData.getAttributeIndex('label_entity_id')
        elementCol = atomData.getAttributeIndex('type_symbol')
        altIdCol = atomData.getAttributeIndex('label_alt_id')
        modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
        xCol = atomData.getAttributeIndex('Cartn_x')
        yCol = atomData.getAttributeIndex('Cartn_y')
        zCol = atomData.getAttributeIndex('Cartn_z')
        lastChainId = None
        lastResId = None
        lastAsymId = None
        atomTable = {}
        atomsInResidue = set()
        models = []
        for row in atomData.getRowList():
            atomKey = ((row[resIdCol], row[asymIdCol], row[atomNameCol]))
            model = ('1' if modelCol == -1 else row[modelCol])
            if model not in models:
                models.append(model)
                self._positions.append([])
            modelIndex = models.index(model)
            if row[altIdCol] != '.' and atomKey in atomTable and len(
                    self._positions[modelIndex]) > atomTable[atomKey].index:
                # This row is an alternate position for an existing atom, so ignore it.

                continue
            if modelIndex == 0:
                # This row defines a new atom.

                if lastChainId != row[chainIdCol]:
                    # The start of a new chain.
                    chain = top.addChain(row[asymIdCol])
                    lastChainId = row[chainIdCol]
                    lastResId = None
                    lastAsymId = None
                if lastResId != row[resIdCol] or lastAsymId != row[
                        asymIdCol] or (lastResId == '.'
                                       and row[atomNameCol] in atomsInResidue):
                    # The start of a new residue.
                    res = top.addResidue(
                        row[resNameCol], chain,
                        None if resNumCol == -1 else row[resNumCol])
                    lastResId = row[resIdCol]
                    lastAsymId = row[asymIdCol]
                    atomsInResidue.clear()
                element = None
                try:
                    element = elem.get_by_symbol(row[elementCol])
                except KeyError:
                    pass
                atom = top.addAtom(row[atomNameCol], element, res,
                                   row[atomIdCol])
                atomTable[atomKey] = atom
                atomsInResidue.add(row[atomNameCol])
            else:
                # This row defines coordinates for an existing atom in one of the later models.

                try:
                    atom = atomTable[atomKey]
                except KeyError:
                    raise ValueError(
                        'Unknown atom %s in residue %s %s for model %s' %
                        (row[atomNameCol], row[resNameCol], row[resIdCol],
                         model))
                if atom.index != len(self._positions[modelIndex]):
                    raise ValueError(
                        'Atom %s for model %s does not match the order of atoms for model %s'
                        % (row[atomIdCol], model, models[0]))
            self._positions[modelIndex].append(
                Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol])) *
                0.1)
        for i in range(len(self._positions)):
            self._positions[i] = self._positions[i] * nanometers
        ## The atom positions read from the PDBx/mmCIF file.  If the file contains multiple frames, these are the positions in the first frame.
        self.positions = self._positions[0]
        self.topology.createStandardBonds()
        self._numpyPositions = None

        # Record unit cell information, if present.

        cell = block.getObj('cell')
        if cell is not None and cell.getRowCount() > 0:
            row = cell.getRow(0)
            (a, b, c) = [
                float(row[cell.getAttributeIndex(attribute)]) * 0.1
                for attribute in ('length_a', 'length_b', 'length_c')
            ]
            (alpha, beta, gamma) = [
                float(row[cell.getAttributeIndex(attribute)]) * math.pi / 180.0
                for attribute in ('angle_alpha', 'angle_beta', 'angle_gamma')
            ]
            self.topology.setPeriodicBoxVectors(
                computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))

        # Add bonds based on struct_conn records.

        connectData = block.getObj('struct_conn')
        if connectData is not None:
            res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
            res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
            atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
            atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
            asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
            asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
            typeCol = connectData.getAttributeIndex('conn_type_id')
            connectBonds = []
            for row in connectData.getRowList():
                type = row[typeCol][:6]
                if type in ('covale', 'disulf', 'modres'):
                    key1 = (row[res1Col], row[asym1Col], row[atom1Col])
                    key2 = (row[res2Col], row[asym2Col], row[atom2Col])
                    if key1 in atomTable and key2 in atomTable:
                        connectBonds.append((atomTable[key1], atomTable[key2]))
            if len(connectBonds) > 0:
                # Only add bonds that don't already exist.
                existingBonds = set(top.bonds())
                for bond in connectBonds:
                    if bond not in existingBonds and (
                            bond[1], bond[0]) not in existingBonds:
                        top.addBond(bond[0], bond[1])
                        existingBonds.add(bond)