示例#1
0
文件: offlib.py 项目: xy21hb/ParmEd
    def _parse_residue(fileobj, name):
        """
        Parses the residue information out of the OFF file assuming the file
        is pointed at the first line of an atoms table section of the OFF file

        Parameters
        ----------
        fileobj : file-like
            Assumed to be open for read, this file is parsed until the *next*
            atom table is read
        name : str
            The name of the residue being processed right now
        """
        container = ResidueTemplateContainer(name)
        nres = 1
        templ = ResidueTemplate(name)
        line = fileobj.readline()
        while line[0] != '!':
            nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
            nam = _strip_enveloping_quotes(nam)
            typ = _strip_enveloping_quotes(typ)
            typx = int(typx)
            resx = int(resx)
            flags = int(flags)
            seq = int(seq)
            elmnt = int(elmnt)
            chg = float(chg)
            atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
            if resx == nres + 1:
                container.append(templ)
                nres += 1
                templ = ResidueTemplate(name)
            templ.add_atom(atom)
            line = fileobj.readline()
            # Skip blank lines
            while line and not line.strip():
                line = fileobj.readline()
        container.append(templ)
        if nres > 1:
            start_atoms = []
            runsum = 0
            for res in container:
                start_atoms.append(runsum)
                runsum += len(res)
        # Make sure we get the next section
        rematch = AmberOFFLibrary._sec2re.match(line)
        if not rematch:
            raise RuntimeError('Expected pertinfo table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        line = fileobj.readline()
        while line[0] != '!':
            if not line:
                raise RuntimeError('Unexpected EOF in Amber OFF library')
            # Not used, just skip
            # TODO sanity check
            line = fileobj.readline()
        rematch = AmberOFFLibrary._sec3re.match(line)
        if not rematch:
            raise RuntimeError('Expected boundbox table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        # Only 5 lines
        try:
            hasbox = float(fileobj.readline().strip())
            angle = float(fileobj.readline().strip())
            a = float(fileobj.readline().strip())
            b = float(fileobj.readline().strip())
            c = float(fileobj.readline().strip())
        except ValueError:
            raise RuntimeError('Error processing boundbox table entries')
        else:
            if hasbox > 0:
                if angle < 3.15:
                    # No box is this acute -- must be in radians
                    angle *= RAD_TO_DEG
                container.box = [a, b, c, angle, angle, angle]
        # Get the child sequence entry
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec4re.match(line)
        if not rematch:
            raise RuntimeError('Expected childsequence table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        n = int(fileobj.readline().strip())
        if nres + 1 != n:
            warnings.warn('Unexpected childsequence (%d); expected %d for '
                          'residue %s' % (n, nres+1, name), AmberWarning)
        elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
            raise RuntimeError('child sequence must be 1 greater than the '
                               'number of residues in the unit')
        # Get the CONNECT array to set head and tail
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec5re.match(line)
        if not rematch:
            raise RuntimeError('Expected connect array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        try:
            head = int(fileobj.readline().strip())
            tail = int(fileobj.readline().strip())
        except ValueError:
            raise RuntimeError('Error processing connect table entries')
        if head > 0 and nres == 1:
            templ.head = templ[head-1]
        elif head > 0 and nres > 1:
            if head < sum((len(r) for r in container)):
                raise RuntimeError('HEAD on multi-residue unit not supported')
        if tail > 0 and nres == 1:
            templ.tail = templ[tail-1]
        elif tail > 0 and nres > 1:
            if tail < sum((len(r) for r in container)):
                warnings.warn('TAIL on multi-residue unit not supported (%s). '
                              'Ignored...' % name, AmberWarning)
        # Get the connectivity array to set bonds
        line = fileobj.readline()
        if len(templ.atoms) > 1:
            rematch = AmberOFFLibrary._sec6re.match(line)
            if not rematch:
                raise RuntimeError('Expected connectivity table not found')
            elif rematch.groups()[0] != name:
                raise RuntimeError('Found residue %s while processing residue %s' %
                                   (rematch.groups()[0], name))
            line = fileobj.readline()
            while line[0] != '!':
                i, j, flag = line.split()
                line = fileobj.readline()
                if nres > 1:
                    # Find which residue we belong in
                    i = int(i) - 1
                    j = int(j) - 1
                    for ii, idx in enumerate(start_atoms):
                        if idx > i:
                            ii -= 1
                            break
                    start_idx = start_atoms[ii]
                    container[ii].add_bond(i-start_idx, j-start_idx)
                else:
                    templ.add_bond(int(i)-1, int(j)-1)
        # Get the hierarchy table
        rematch = AmberOFFLibrary._sec7re.match(line)
        if not rematch:
            raise RuntimeError('Expected hierarchy table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        line = fileobj.readline()
        while line[0] != '!':
            # Skip this section... not used
            # TODO turn this into a sanity check
            line = fileobj.readline()
        # Get the unit name
        rematch = AmberOFFLibrary._sec8re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit name string not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        fileobj.readline() # Skip this... not used
        line = fileobj.readline()
        # Get the atomic positions
        rematch = AmberOFFLibrary._sec9re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit positions table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for res in container:
            for atom in res:
                x, y, z = fileobj.readline().split()
                atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
        line = fileobj.readline()
        # Get the residueconnect table
        rematch = AmberOFFLibrary._sec10re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit residueconnect table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            c1,c2,c3,c4,c5,c6 = (int(x) for x in fileobj.readline().split())
            if (c1 > 0 and templ.head is not None and
                    templ.head is not templ[c1-1]):
                raise RuntimeError('HEAD atom is not connect0')
            if (c2 > 0 and templ.tail is not None and
                    templ.tail is not templ[c2-1]):
                raise RuntimeError('TAIL atom is not connect1')
            for i in (c3, c4, c5, c6):
                if i == 0: continue
                templ.connections.append(templ[i-1])
        # Get the residues table
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec11re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit residues table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            resname, id, next, start, typ, img = fileobj.readline().split()
            resname = _strip_enveloping_quotes(resname)
            id = int(id)
            start = int(start)
            next = int(next)
            typ = _strip_enveloping_quotes(typ)
            img = int(img)
            if next - start != len(container[i]):
                warnings.warn('residue table predicted %d, not %d atoms for '
                              'residue %s' % (next-start, len(container[i]),
                              name), AmberWarning)
            if typ == 'p':
                container[i].type = PROTEIN
            elif typ == 'n':
                container[i].type = NUCLEIC
            elif typ == 'w':
                container[i].type = SOLVENT
            elif typ != '?':
                warnings.warn('Unknown residue type "%s"' % typ, AmberWarning)
            if nres > 1:
                container[i].name = resname
        # Get the residues sequence table
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec12re.match(line)
        if not rematch:
            raise RuntimeError('Expected residue sequence number not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            #TODO sanity check
            fileobj.readline()
        line = fileobj.readline()
        # Get the solventcap array
        rematch = AmberOFFLibrary._sec13re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit solventcap array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        # Ignore the solvent cap
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        # Velocities
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec14re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit solventcap array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for res in container:
            for atom in res:
                vx, vy, vz = (float(x) for x in fileobj.readline().split())
                atom.vx, atom.vy, atom.vz = vx, vy, vz

        if nres > 1:
            return container
        return templ
示例#2
0
文件: offlib.py 项目: drroe/ParmEd
    def _parse_residue(fileobj, name):
        """
        Parses the residue information out of the OFF file assuming the file
        is pointed at the first line of an atoms table section of the OFF file

        Parameters
        ----------
        fileobj : file-like
            Assumed to be open for read, this file is parsed until the *next*
            atom table is read
        name : str
            The name of the residue being processed right now
        """
        container = ResidueTemplateContainer(name)
        nres = 1
        templ = ResidueTemplate(name)
        line = fileobj.readline()
        while line[0] != '!':
            nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
            nam = _strip_enveloping_quotes(nam)
            typ = _strip_enveloping_quotes(typ)
            typx = int(typx)
            resx = int(resx)
            flags = int(flags)
            seq = int(seq)
            elmnt = int(elmnt)
            chg = float(chg)
            atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
            if resx == nres + 1:
                container.append(templ)
                nres += 1
                templ = ResidueTemplate(name)
            templ.add_atom(atom)
            line = fileobj.readline()
        container.append(templ)
        if nres > 1:
            start_atoms = []
            runsum = 0
            for res in container:
                start_atoms.append(runsum)
                runsum += len(res)
        # Make sure we get the next section
        rematch = AmberOFFLibrary._sec2re.match(line)
        if not rematch:
            raise RuntimeError('Expected pertinfo table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        line = fileobj.readline()
        while line[0] != '!':
            if not line:
                raise RuntimeError('Unexpected EOF in Amber OFF library')
            # Not used, just skip
            # TODO sanity check
            line = fileobj.readline()
        rematch = AmberOFFLibrary._sec3re.match(line)
        if not rematch:
            raise RuntimeError('Expected boundbox table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        # Only 5 lines
        try:
            hasbox = float(fileobj.readline().strip())
            angle = float(fileobj.readline().strip())
            a = float(fileobj.readline().strip())
            b = float(fileobj.readline().strip())
            c = float(fileobj.readline().strip())
        except ValueError:
            raise RuntimeError('Error processing boundbox table entries')
        else:
            if hasbox > 0:
                angle *= RAD_TO_DEG
                container.box = [a, b, c, angle, angle, angle]
        # Get the child sequence entry
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec4re.match(line)
        if not rematch:
            raise RuntimeError('Expected childsequence table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        n = int(fileobj.readline().strip())
        if nres + 1 != n:
            warnings.warn('Unexpected childsequence (%d); expected %d for '
                          'residue %s' % (n, nres+1, name), AmberWarning)
        elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
            raise RuntimeError('child sequence must be 1 greater than the '
                               'number of residues in the unit')
        # Get the CONNECT array to set head and tail
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec5re.match(line)
        if not rematch:
            raise RuntimeError('Expected connect array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        try:
            head = int(fileobj.readline().strip())
            tail = int(fileobj.readline().strip())
        except ValueError:
            raise RuntimeError('Error processing connect table entries')
        if head > 0 and nres == 1:
            templ.head = templ[head-1]
        elif head > 0 and nres > 1:
            if head < sum([len(r) for r in container]):
                raise RuntimeError('HEAD on multi-residue unit not supported')
        if tail > 0 and nres == 1:
            templ.tail = templ[tail-1]
        elif tail > 0 and nres > 1:
            if tail < sum([len(r) for r in container]):
                warnings.warn('TAIL on multi-residue unit not supported (%s). '
                              'Ignored...' % name, AmberWarning)
        # Get the connectivity array to set bonds
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec6re.match(line)
        if not rematch:
            raise RuntimeError('Expected connectivity table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        line = fileobj.readline()
        while line[0] != '!':
            i, j, flag = line.split()
            line = fileobj.readline()
            if nres > 1:
                # Find which residue we belong in
                i = int(i) - 1
                j = int(j) - 1
                for ii, idx in enumerate(start_atoms):
                    if idx > i:
                        ii -= 1
                        break
                start_idx = start_atoms[ii]
                container[ii].add_bond(i-start_idx, j-start_idx)
            else:
                templ.add_bond(int(i)-1, int(j)-1)
        # Get the hierarchy table
        rematch = AmberOFFLibrary._sec7re.match(line)
        if not rematch:
            raise RuntimeError('Expected hierarchy table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        line = fileobj.readline()
        while line[0] != '!':
            # Skip this section... not used
            # TODO turn this into a sanity check
            line = fileobj.readline()
        # Get the unit name
        rematch = AmberOFFLibrary._sec8re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit name string not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        fileobj.readline() # Skip this... not used
        line = fileobj.readline()
        # Get the atomic positions
        rematch = AmberOFFLibrary._sec9re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit positions table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for res in container:
            for atom in res:
                x, y, z = fileobj.readline().split()
                atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
        line = fileobj.readline()
        # Get the residueconnect table
        rematch = AmberOFFLibrary._sec10re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit residueconnect table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            c1,c2,c3,c4,c5,c6 = [int(x) for x in fileobj.readline().split()]
            if templ.head is not None and templ.head is not templ[c1-1]:
                warnings.warn('HEAD atom is not connect0')
            if templ.tail is not None and templ.tail is not templ[c2-1]:
                warnings.warn('TAIL atom is not connect1')
            for i in (c3, c4, c5, c6):
                if i == 0: continue
                templ.connections.append(templ[i-1])
        # Get the residues table
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec11re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit residues table not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            resname, id, next, start, typ, img = fileobj.readline().split()
            resname = _strip_enveloping_quotes(resname)
            id = int(id)
            start = int(start)
            next = int(next)
            typ = _strip_enveloping_quotes(typ)
            img = int(img)
            if next - start != len(container[i]):
                warnings.warn('residue table predicted %d, not %d atoms for '
                              'residue %s' % (next-start, len(container[i]),
                              name), AmberWarning)
            if typ == 'p':
                container[i].type = PROTEIN
            elif typ == 'n':
                container[i].type = NUCLEIC
            elif typ == 'w':
                container[i].type = SOLVENT
            elif typ != '?':
                warnings.warn('Unknown residue type "%s"' % typ,
                              AmberWarning)
            if nres > 1:
                container[i].name = resname
        # Get the residues sequence table
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec12re.match(line)
        if not rematch:
            raise RuntimeError('Expected residue sequence number not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for i in range(nres):
            #TODO sanity check
            fileobj.readline()
        line = fileobj.readline()
        # Get the solventcap array
        rematch = AmberOFFLibrary._sec13re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit solventcap array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        # Ignore the solvent cap
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        fileobj.readline()
        # Velocities
        line = fileobj.readline()
        rematch = AmberOFFLibrary._sec14re.match(line)
        if not rematch:
            raise RuntimeError('Expected unit solventcap array not found')
        elif rematch.groups()[0] != name:
            raise RuntimeError('Found residue %s while processing residue %s' %
                               (rematch.groups()[0], name))
        for res in container:
            for atom in res:
                vx, vy, vz = [float(x) for x in fileobj.readline().split()]
                atom.vx, atom.vy, atom.vz = vx, vy, vz

        if nres > 1:
            return container
        return templ
示例#3
0
文件: mol2.py 项目: pengfeili1/ParmEd
    def parse(filename, structure=False):
        """ Parses a mol2 file (or mol3) file

        Parameters
        ----------
        filename : str or file-like
            Name of the file to parse or file-like object to parse from
        structure : bool, optional
            If True, the return value is a :class:`Structure` instance. If
            False, it is either a :class:`ResidueTemplate` or
            :class:`ResidueTemplateContainter` instance, depending on whether
            there is one or more than one residue defined in it. Default is
            False

        Returns
        -------
        molecule : :class:`Structure`, :class:`ResidueTemplate`, or
                   :class:`ResidueTemplateContainer`
            The molecule defined by this mol2 file

        Raises
        ------
        Mol2Error
            If the file format is not recognized or non-numeric values are
            present where integers or floating point numbers are expected. Also
            raises Mol2Error if you try to parse a mol2 file that has multiple
            @<MOLECULE> entries with ``structure=True``.
        """
        if isinstance(filename, string_types):
            f = genopen(filename, 'r')
            own_handle = True
        else:
            f = filename
            own_handle = False
        rescont = ResidueTemplateContainer()
        struct = Structure()
        restemp = ResidueTemplate()
        mol_info = []
        multires_structure = False
        try:
            section = None
            last_residue = None
            headtail = 'head'
            molecule_number = 0
            for line in f:
                if line.startswith('#'): continue
                if not line.strip() and section is None: continue
                if line.startswith('@<TRIPOS>'):
                    section = line[9:].strip()
                    if section == 'MOLECULE' and (restemp.atoms or rescont):
                        if structure:
                            raise Mol2Error('Cannot convert MOL2 with multiple '
                                            '@<MOLECULE>s to a Structure')
                        # Set the residue name from the MOL2 title if the
                        # molecule had only 1 residue and it was given a name in
                        # the title
                        if not multires_structure and mol_info[0]:
                            restemp.name = mol_info[0]
                        multires_structure = False
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        struct = Structure()
                        last_residue = None
                        molecule_number += 1
                        mol_info = []
                    continue
                if section is None:
                    raise Mol2Error('Bad mol2 file format')
                if section == 'MOLECULE':
                    # Section formatted as follows:
                    #   mol_name
                    #   num_atoms [num_bonds [num_substr [num_feat [num_sets]]]]
                    #   mol_type
                    #   charge_type
                    #   [status_bits]
                    #   [mol_comment]
                    # TODO: Do something with the name.
                    if len(mol_info) == 0:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 1:
                        mol_info.append([int(x) for x in line.split()])
                    elif len(mol_info) == 2:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 3:
                        mol_info.append(line.strip())
                    # Ignore the rest
                    continue
                if section == 'ATOM':
                    # Section formatted as follows:
                    #   atom_id -- serial number of atom
                    #   atom_name -- name of the atom
                    #   x -- X-coordinate of the atom
                    #   y -- Y-coordinate of the atom
                    #   z -- Z-coordinate of the atom
                    #   atom_type -- type of the atom
                    #   subst_id -- Residue serial number
                    #   subst_name -- Residue name
                    #   charge -- partial atomic charge
                    #   status_bit -- ignored
                    words = line.split()
                    id = int(words[0])
                    name = words[1]
                    x = float(words[2])
                    y = float(words[3])
                    z = float(words[4])
                    typ = words[5]
                    try:
                        resid = int(words[6])
                    except IndexError:
                        resid = 0
                    try:
                        resname = words[7]
                    except IndexError:
                        resname = 'UNK'
                    if 'NO_CHARGES' not in mol_info:
                        try:
                            charge = float(words[8])
                        except IndexError:
                            charge = 0
                    else:
                        charge = 0
                    if last_residue is None:
                        last_residue = (resid, resname)
                        restemp.name = resname
                    atom = Atom(name=name, type=typ, number=id, charge=charge)
                    atom.xx, atom.xy, atom.xz = x, y, z
                    struct.add_atom(atom, resname, resid)
                    if last_residue != (resid, resname):
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        restemp.name = resname
                        last_residue = (resid, resname)
                        multires_structure = True
                    try:
                        restemp.add_atom(copy.copy(atom))
                    except ValueError:
                        # Allow mol2 files being parsed as a Structure to have
                        # duplicate atom names
                        if not structure:
                            raise
                    continue
                if section == 'BOND':
                    # Section formatted as follows:
                    #   bond_id -- serial number of bond (ignored)
                    #   origin_atom_id -- serial number of first atom in bond
                    #   target_atom_id -- serial number of other atom in bond
                    #   bond_type -- string describing bond type (ignored)
                    #   status_bits -- ignored
                    words = line.split()
                    int(words[0]) # Bond serial number... redundant and ignored
                    a1 = int(words[1])
                    a2 = int(words[2])
                    atom1 = struct.atoms.find_original_index(a1)
                    atom2 = struct.atoms.find_original_index(a2)
                    struct.bonds.append(Bond(atom1, atom2))
                    # Now add it to our residue container
                    # See if it's a head/tail connection
                    if atom1.residue is not atom2.residue:
                        if atom1.residue.idx == len(rescont):
                            res1 = restemp
                        elif atom1.residue.idx < len(rescont):
                            res1 = rescont[atom1.residue.idx]
                        assert atom.residue.idx <= len(rescont), 'Bad bond!'
                        if atom2.residue.idx == len(rescont):
                            res2 = restemp
                        elif atom2.residue.idx < len(rescont):
                            res2 = rescont[atom2.residue.idx]
                        assert atom.residue.idx <= len(rescont), 'Bad bond!'
                        assert res1 is not res2, 'BAD identical residues'
                        idx1 = atom1.idx - atom1.residue[0].idx
                        idx2 = atom2.idx - atom2.residue[0].idx
                        if atom1.residue.idx < atom2.residue.idx:
                            res1.tail = res1[idx1]
                            res2.head = res2[idx2]
                        else:
                            res1.head = res1[idx1]
                            res2.tail = res2[idx2]
                    elif not multires_structure:
                        if not structure:
                            restemp.add_bond(a1-1, a2-1)
                    else:
                        # Same residue, add the bond
                        offset = atom1.residue[0].idx
                        if atom1.residue.idx == len(rescont):
                            res = restemp
                        else:
                            res = rescont[atom1.residue.idx]
                        res.add_bond(atom1.idx-offset, atom2.idx-offset)
                    continue
                if section == 'CRYSIN':
                    # Section formatted as follows:
                    #   a -- length of first unit cell vector
                    #   b -- length of second unit cell vector
                    #   c -- length of third unit cell vector
                    #   alpha -- angle b/w b and c
                    #   beta -- angle b/w a and c
                    #   gamma -- angle b/w a and b
                    #   space group -- number of space group (ignored)
                    #   space group setting -- ignored
                    words = line.split()
                    box = [float(w) for w in words[:6]]
                    if len(box) != 6:
                        raise ValueError('%d box dimensions found; needed 6' %
                                         len(box))
                    struct.box = copy.copy(box)
                    rescont.box = copy.copy(box)
                    continue
                if section == 'SUBSTRUCTURE':
                    # Section formatted as follows:
                    #   subst_id -- residue number
                    #   subst_name -- residue name
                    #   root_atom -- first atom of residue
                    #   subst_type -- ignored (usually 'RESIDUE')
                    #   dict_type -- type of substructure (ignored)
                    #   chain -- chain ID of residue
                    #   sub_type -- type of the chain
                    #   inter_bonds -- # of inter-substructure bonds
                    #   status -- ignored
                    #   comment -- ignored
                    words = line.split()
                    if not words: continue
                    id = int(words[0])
                    resname = words[1]
                    try:
                        chain = words[5]
                    except IndexError:
                        chain = ''
                    # Set the chain ID
                    for res in struct.residues:
                        if res.number == id and res.name == resname:
                            res.chain = chain
                    continue
                # MOL3 sections
                if section == 'HEADTAIL':
                    atname, residx = line.split()
                    residx = int(residx)
                    if residx in (0, 1) or residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in head/tail')
                    for atom in res:
                        if atom.name == atname:
                            if headtail == 'head':
                                res.head = atom
                                headtail = 'tail'
                            else:
                                res.tail = atom
                                headtail = 'head'
                            break
                    else:
                        if headtail == 'head':
                            headtail = 'tail'
                        else:
                            headtail = 'head'
                    continue
                if section == 'RESIDUECONNECT':
                    words = line.split()
                    residx = int(words[0])
                    if residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in '
                                        'residueconnect')
                    for a in words[3:]:
                        if a == '0': continue
                        for atom in res:
                            if atom.name == a:
                                res.connections.append(atom)
                                break
                        else:
                            raise Mol2Error('Residue connection atom %s not '
                                            'found in residue %d' % (a, residx))
            if structure:
                return struct
            elif len(rescont) > 0:
                if not multires_structure and mol_info[0]:
                    restemp.name = mol_info[0]
                rescont.append(restemp)
                return rescont
            else:
                return restemp
        except ValueError as e:
            raise Mol2Error('String conversion trouble: %s' % e)
        finally:
            if own_handle: f.close()