def __init__(self,
PERMISSIVE=True,
get_header=False,
structure_builder=None,
QUIET=False):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
o QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be supressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = bool(PERMISSIVE)
self.QUIET = bool(QUIET)
def __init__(self, PERMISSIVE=True, get_header=False,
structure_builder=None, QUIET=False):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
o QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be supressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder!=None:
self.structure_builder=structure_builder
else:
self.structure_builder=StructureBuilder()
self.header=None
self.trailer=None
self.line_counter=0
self.PERMISSIVE=bool(PERMISSIVE)
self.QUIET=bool(QUIET)
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
if structure_builder!=None:
self.structure_builder=structure_builder
else:
self.structure_builder=StructureBuilder()
self.header=None
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
class PDBParser(object):
"""
Parse a PDB file and return a Structure object.
"""
def __init__(self,
PERMISSIVE=True,
get_header=False,
structure_builder=None,
QUIET=False):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
o QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be supressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = bool(PERMISSIVE)
self.QUIET = bool(QUIET)
# Public methods
def get_structure(self, id, file):
"""Return the structure.
Arguments:
o id - string, the id that will be used for the structure
o file - name of the PDB file OR an open filehandle
"""
if self.QUIET:
warning_list = warnings.filters[:]
warnings.filterwarnings('ignore', category=PDBConstructionWarning)
self.header = None
self.trailer = None
# Make a StructureBuilder instance (pass id of structure as parameter)
self.structure_builder.init_structure(id)
handle_close = False
if isinstance(file, basestring):
file = open(file)
handle_close = True
self._parse(file.readlines())
self.structure_builder.set_header(self.header)
# Return the Structure instance
structure = self.structure_builder.get_structure()
if handle_close:
file.close()
if self.QUIET:
warnings.filters = warning_list
return structure
def get_header(self):
"Return the header."
return self.header
def get_trailer(self):
"Return the trailer."
return self.trailer
# Private methods
def _parse(self, header_coords_trailer):
"Parse the PDB file."
# Extract the header; return the rest of the file
self.header, coords_trailer = self._get_header(header_coords_trailer)
# Parse the atomic data; return the PDB file trailer
self.trailer = self._parse_coordinates(coords_trailer)
def _get_header(self, header_coords_trailer):
"Get the header of the PDB file, return the rest."
structure_builder = self.structure_builder
i = 0
for i in range(0, len(header_coords_trailer)):
structure_builder.set_line_counter(i + 1)
line = header_coords_trailer[i]
record_type = line[0:6]
if (record_type == 'ATOM ' or record_type == 'HETATM'
or record_type == 'MODEL '):
break
header = header_coords_trailer[0:i]
# Return the rest of the coords+trailer for further processing
self.line_counter = i
coords_trailer = header_coords_trailer[i:]
header_dict = _parse_pdb_header_list(header)
return header_dict, coords_trailer
def _parse_coordinates(self, coords_trailer):
"Parse the atomic data in the PDB file."
local_line_counter = 0
structure_builder = self.structure_builder
current_model_id = 0
# Flag we have an open model
model_open = 0
current_chain_id = None
current_segid = None
current_residue_id = None
current_resname = None
for i in range(0, len(coords_trailer)):
line = coords_trailer[i]
record_type = line[0:6]
global_line_counter = self.line_counter + local_line_counter + 1
structure_builder.set_line_counter(global_line_counter)
if (record_type == 'ATOM ' or record_type == 'HETATM'):
# Initialize the Model - there was no explicit MODEL record
if not model_open:
structure_builder.init_model(current_model_id)
current_model_id += 1
model_open = 1
fullname = line[12:16]
# get rid of whitespace in atom names
split_list = fullname.split()
if len(split_list) != 1:
# atom name has internal spaces, e.g. " N B ", so
# we do not strip spaces
name = fullname
else:
# atom name is like " CA ", so we can strip spaces
name = split_list[0]
altloc = line[16:17]
resname = line[17:20]
chainid = line[21:22]
try:
serial_number = int(line[6:11])
except:
serial_number = 0
resseq = int(line[22:26].split()[0]) # sequence identifier
icode = line[26:27] # insertion code
if record_type == 'HETATM': # hetero atom flag
if resname == "HOH" or resname == "WAT":
hetero_flag = "W"
else:
hetero_flag = "H"
else:
hetero_flag = " "
residue_id = (hetero_flag, resseq, icode)
# atomic coordinates
try:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
except:
#Should we allow parsing to continue in permissive mode?
#If so what coordindates should we default to? Easier to abort!
raise PDBConstructionException(\
"Invalid or missing coordinate(s) at line %i." \
% global_line_counter)
coord = numpy.array((x, y, z), 'f')
# occupancy & B factor
try:
occupancy = float(line[54:60])
except:
self._handle_PDB_exception("Invalid or missing occupancy",
global_line_counter)
occupancy = 0.0 #Is one or zero a good default?
try:
bfactor = float(line[60:66])
except:
self._handle_PDB_exception("Invalid or missing B factor",
global_line_counter)
bfactor = 0.0 #The PDB use a default of zero if the data is missing
segid = line[72:76]
element = line[76:78].strip()
if current_segid != segid:
current_segid = segid
structure_builder.init_seg(current_segid)
if current_chain_id != chainid:
current_chain_id = chainid
structure_builder.init_chain(current_chain_id)
current_residue_id = residue_id
current_resname = resname
try:
structure_builder.init_residue(resname, hetero_flag,
resseq, icode)
except PDBConstructionException, message:
self._handle_PDB_exception(message,
global_line_counter)
elif current_residue_id != residue_id or current_resname != resname:
current_residue_id = residue_id
current_resname = resname
try:
structure_builder.init_residue(resname, hetero_flag,
resseq, icode)
except PDBConstructionException, message:
self._handle_PDB_exception(message,
global_line_counter)
# init atom
try:
structure_builder.init_atom(name, coord, bfactor,
occupancy, altloc, fullname,
serial_number, element)
except PDBConstructionException, message:
self._handle_PDB_exception(message, global_line_counter)
class PDBParser:
"""
Parse a PDB file and return a Structure object.
"""
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
if structure_builder!=None:
self.structure_builder=structure_builder
else:
self.structure_builder=StructureBuilder()
self.header=None
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
# Public methods
def get_structure(self, id, file):
"""Return the structure.
Arguments:
o id - string, the id that will be used for the structure
o file - name of the PDB file OR an open filehandle
"""
self.header=None
self.trailer=None
# Make a StructureBuilder instance (pass id of structure as parameter)
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file=open(file)
self._parse(file.readlines())
self.structure_builder.set_header(self.header)
# Return the Structure instance
return self.structure_builder.get_structure()
def get_header(self):
"Return the header."
return self.header
def get_trailer(self):
"Return the trailer."
return self.trailer
# Private methods
def _parse(self, header_coords_trailer):
"Parse the PDB file."
# Extract the header; return the rest of the file
self.header, coords_trailer=self._get_header(header_coords_trailer)
# Parse the atomic data; return the PDB file trailer
self.trailer=self._parse_coordinates(coords_trailer)
def _get_header(self, header_coords_trailer):
"Get the header of the PDB file, return the rest."
structure_builder=self.structure_builder
for i in range(0, len(header_coords_trailer)):
structure_builder.set_line_counter(i+1)
line=header_coords_trailer[i]
record_type=line[0:6]
if(record_type=='ATOM ' or record_type=='HETATM' or record_type=='MODEL '):
break
header=header_coords_trailer[0:i]
# Return the rest of the coords+trailer for further processing
self.line_counter=i
coords_trailer=header_coords_trailer[i:]
header_dict=_parse_pdb_header_list(header)
return header_dict, coords_trailer
def _parse_coordinates(self, coords_trailer):
"Parse the atomic data in the PDB file."
local_line_counter=0
structure_builder=self.structure_builder
current_model_id=0
# Flag we have an open model
model_open=0
current_chain_id=None
current_segid=None
current_residue_id=None
current_resname=None
for i in range(0, len(coords_trailer)):
line=coords_trailer[i]
record_type=line[0:6]
global_line_counter=self.line_counter+local_line_counter+1
structure_builder.set_line_counter(global_line_counter)
if(record_type=='ATOM ' or record_type=='HETATM'):
# Initialize the Model - there was no explicit MODEL record
if not model_open:
structure_builder.init_model(current_model_id)
current_model_id+=1
model_open=1
fullname=line[12:16]
# get rid of whitespace in atom names
split_list=fullname.split()
if len(split_list)!=1:
# atom name has internal spaces, e.g. " N B ", so
# we do not strip spaces
name=fullname
else:
# atom name is like " CA ", so we can strip spaces
name=split_list[0]
altloc=line[16:17]
resname=line[17:20]
chainid=line[21:22]
try:
serial_number=int(line[6:11])
except:
serial_number=0
resseq=int(line[22:26].split()[0]) # sequence identifier
icode=line[26:27] # insertion code
if record_type=='HETATM': # hetero atom flag
if resname=="HOH" or resname=="WAT":
hetero_flag="W"
else:
hetero_flag="H"
else:
hetero_flag=" "
residue_id=(hetero_flag, resseq, icode)
# atomic coordinates
try:
x=float(line[30:38])
y=float(line[38:46])
z=float(line[46:54])
except:
#Should we allow parsing to continue in permissive mode?
#If so what coordindates should we default to? Easier to abort!
raise PDBContructionError("Invalid or missing coordinate(s) at line %i." \
% global_line_counter)
coord=numpy.array((x, y, z), 'f')
# occupancy & B factor
try:
occupancy=float(line[54:60])
except:
self._handle_PDB_exception("Invalid or missing occupancy",
global_line_counter)
occupancy = 0.0 #Is one or zero a good default?
try:
bfactor=float(line[60:66])
except:
self._handle_PDB_exception("Invalid or missing B factor",
global_line_counter)
bfactor = 0.0 #The PDB use a default of zero if the data is missing
segid=line[72:76]
element=line[76:78].strip()
if current_segid!=segid:
current_segid=segid
structure_builder.init_seg(current_segid)
if current_chain_id!=chainid:
current_chain_id=chainid
structure_builder.init_chain(current_chain_id)
current_residue_id=residue_id
current_resname=resname
try:
structure_builder.init_residue(resname, hetero_flag, resseq, icode)
except PDBConstructionException, message:
self._handle_PDB_exception(message, global_line_counter)
elif current_residue_id!=residue_id or current_resname!=resname:
current_residue_id=residue_id
current_resname=resname
try:
structure_builder.init_residue(resname, hetero_flag, resseq, icode)
except PDBConstructionException, message:
self._handle_PDB_exception(message, global_line_counter)
# init atom
try:
structure_builder.init_atom(name, coord, bfactor, occupancy, altloc,
fullname, serial_number, element)
except PDBConstructionException, message:
self._handle_PDB_exception(message, global_line_counter)
def get_structure(self, structure_id, filename):
self._mmcif_dict=MMCIF2Dict(filename)
self._structure_builder=StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
class MMCIFParser:
def get_structure(self, structure_id, filename):
self._mmcif_dict=MMCIF2Dict(filename)
self._structure_builder=StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
def _build_structure(self, structure_id):
mmcif_dict=self._mmcif_dict
atom_id_list=mmcif_dict["_atom_site.label_atom_id"]
residue_id_list=mmcif_dict["_atom_site.label_comp_id"]
seq_id_list=mmcif_dict["_atom_site.label_seq_id"]
chain_id_list=mmcif_dict["_atom_site.label_asym_id"]
x_list=map(float, mmcif_dict["_atom_site.Cartn_x"])
y_list=map(float, mmcif_dict["_atom_site.Cartn_y"])
z_list=map(float, mmcif_dict["_atom_site.Cartn_z"])
alt_list=mmcif_dict["_atom_site.label_alt_id"]
b_factor_list=mmcif_dict["_atom_site.B_iso_or_equiv"]
occupancy_list=mmcif_dict["_atom_site.occupancy"]
fieldname_list=mmcif_dict["_atom_site.group_PDB"]
try:
aniso_u11=mmcif_dict["_atom_site.aniso_U[1][1]"]
aniso_u12=mmcif_dict["_atom_site.aniso_U[1][2]"]
aniso_u13=mmcif_dict["_atom_site.aniso_U[1][3]"]
aniso_u22=mmcif_dict["_atom_site.aniso_U[2][2]"]
aniso_u23=mmcif_dict["_atom_site.aniso_U[2][3]"]
aniso_u33=mmcif_dict["_atom_site.aniso_U[3][3]"]
aniso_flag=1
except KeyError:
# no anisotropic B factors
aniso_flag=0
# if auth_seq_id is present, we use this.
# Otherwise label_seq_id is used.
if mmcif_dict.has_key("_atom_site.auth_seq_id"):
seq_id_list=mmcif_dict["_atom_site.auth_seq_id"]
else:
seq_id_list=mmcif_dict["_atom_site.label_seq_id"]
# Now loop over atoms and build the structure
current_chain_id=None
current_residue_id=None
current_model_id=0
structure_builder=self._structure_builder
structure_builder.init_structure(structure_id)
structure_builder.init_model(current_model_id)
structure_builder.init_seg(" ")
for i in xrange(0, len(atom_id_list)):
x=x_list[i]
y=y_list[i]
z=z_list[i]
resname=residue_id_list[i]
chainid=chain_id_list[i]
altloc=alt_list[i]
if altloc==".":
altloc=" "
resseq=seq_id_list[i]
name=atom_id_list[i]
tempfactor=b_factor_list[i]
occupancy=occupancy_list[i]
fieldname=fieldname_list[i]
if fieldname=="HETATM":
hetatm_flag="H"
else:
hetatm_flag=" "
if current_chain_id!=chainid:
current_chain_id=chainid
structure_builder.init_chain(current_chain_id)
current_residue_id=resseq
icode, int_resseq=self._get_icode(resseq)
structure_builder.init_residue(resname, hetatm_flag, int_resseq,
icode)
elif current_residue_id!=resseq:
current_residue_id=resseq
icode, int_resseq=self._get_icode(resseq)
structure_builder.init_residue(resname, hetatm_flag, int_resseq,
icode)
coord=numpy.array((x, y, z), 'f')
structure_builder.init_atom(name, coord, tempfactor, occupancy, altloc,
name)
if aniso_flag==1:
u=(aniso_u11[i], aniso_u12[i], aniso_u13[i],
aniso_u22[i], aniso_u23[i], aniso_u33[i])
mapped_anisou=map(float, u)
anisou_array=numpy.array(mapped_anisou, 'f')
structure_builder.set_anisou(anisou_array)
# Now try to set the cell
try:
a=float(mmcif_dict["_cell.length_a"])
b=float(mmcif_dict["_cell.length_b"])
c=float(mmcif_dict["_cell.length_c"])
alpha=float(mmcif_dict["_cell.angle_alpha"])
beta=float(mmcif_dict["_cell.angle_beta"])
gamma=float(mmcif_dict["_cell.angle_gamma"])
cell=numpy.array((a, b, c, alpha, beta, gamma), 'f')
spacegroup=mmcif_dict["_symmetry.space_group_name_H-M"]
spacegroup=spacegroup[1:-1] # get rid of quotes!!
if spacegroup==None:
raise Exception
structure_builder.set_symmetry(spacegroup, cell)
except:
pass # no cell found, so just ignore
def _get_icode(self, resseq):
"""Tries to return the icode. In MMCIF files this is just part of
resseq! In PDB files, it's a separate field."""
last_resseq_char=resseq[-1]
if last_resseq_char in letters:
icode=last_resseq_char
int_resseq=int(resseq[0:-1])
else:
icode=" "
int_resseq=int(resseq)
return icode, int_resseq
def get_structure(self, structure_id, filename):
self._mmcif_dict = MMCIF2Dict(filename)
self._structure_builder = StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
class MMCIFParser:
def get_structure(self, structure_id, filename):
self._mmcif_dict = MMCIF2Dict(filename)
self._structure_builder = StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
def _build_structure(self, structure_id):
mmcif_dict = self._mmcif_dict
atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
residue_id_list = mmcif_dict["_atom_site.label_comp_id"]
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
chain_id_list = mmcif_dict["_atom_site.label_asym_id"]
x_list = map(float, mmcif_dict["_atom_site.Cartn_x"])
y_list = map(float, mmcif_dict["_atom_site.Cartn_y"])
z_list = map(float, mmcif_dict["_atom_site.Cartn_z"])
alt_list = mmcif_dict["_atom_site.label_alt_id"]
b_factor_list = mmcif_dict["_atom_site.B_iso_or_equiv"]
occupancy_list = mmcif_dict["_atom_site.occupancy"]
fieldname_list = mmcif_dict["_atom_site.group_PDB"]
try:
aniso_u11 = mmcif_dict["_atom_site.aniso_U[1][1]"]
aniso_u12 = mmcif_dict["_atom_site.aniso_U[1][2]"]
aniso_u13 = mmcif_dict["_atom_site.aniso_U[1][3]"]
aniso_u22 = mmcif_dict["_atom_site.aniso_U[2][2]"]
aniso_u23 = mmcif_dict["_atom_site.aniso_U[2][3]"]
aniso_u33 = mmcif_dict["_atom_site.aniso_U[3][3]"]
aniso_flag = 1
except KeyError:
# no anisotropic B factors
aniso_flag = 0
# if auth_seq_id is present, we use this.
# Otherwise label_seq_id is used.
if mmcif_dict.has_key("_atom_site.auth_seq_id"):
seq_id_list = mmcif_dict["_atom_site.auth_seq_id"]
else:
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
# Now loop over atoms and build the structure
current_chain_id = None
current_residue_id = None
current_model_id = 0
structure_builder = self._structure_builder
structure_builder.init_structure(structure_id)
structure_builder.init_model(current_model_id)
structure_builder.init_seg(" ")
for i in xrange(0, len(atom_id_list)):
x = x_list[i]
y = y_list[i]
z = z_list[i]
resname = residue_id_list[i]
chainid = chain_id_list[i]
altloc = alt_list[i]
if altloc == ".":
altloc = " "
resseq = seq_id_list[i]
name = atom_id_list[i]
tempfactor = b_factor_list[i]
occupancy = occupancy_list[i]
fieldname = fieldname_list[i]
if fieldname == "HETATM":
hetatm_flag = "H"
else:
hetatm_flag = " "
if current_chain_id != chainid:
current_chain_id = chainid
structure_builder.init_chain(current_chain_id)
current_residue_id = resseq
icode, int_resseq = self._get_icode(resseq)
structure_builder.init_residue(resname, hetatm_flag,
int_resseq, icode)
elif current_residue_id != resseq:
current_residue_id = resseq
icode, int_resseq = self._get_icode(resseq)
structure_builder.init_residue(resname, hetatm_flag,
int_resseq, icode)
coord = numpy.array((x, y, z), 'f')
structure_builder.init_atom(name, coord, tempfactor, occupancy,
altloc, name)
if aniso_flag == 1:
u = (aniso_u11[i], aniso_u12[i], aniso_u13[i], aniso_u22[i],
aniso_u23[i], aniso_u33[i])
mapped_anisou = map(float, u)
anisou_array = numpy.array(mapped_anisou, 'f')
structure_builder.set_anisou(anisou_array)
# Now try to set the cell
try:
a = float(mmcif_dict["_cell.length_a"])
b = float(mmcif_dict["_cell.length_b"])
c = float(mmcif_dict["_cell.length_c"])
alpha = float(mmcif_dict["_cell.angle_alpha"])
beta = float(mmcif_dict["_cell.angle_beta"])
gamma = float(mmcif_dict["_cell.angle_gamma"])
cell = numpy.array((a, b, c, alpha, beta, gamma), 'f')
spacegroup = mmcif_dict["_symmetry.space_group_name_H-M"]
spacegroup = spacegroup[1:-1] # get rid of quotes!!
if spacegroup == None:
raise Exception
structure_builder.set_symmetry(spacegroup, cell)
except:
pass # no cell found, so just ignore
def _get_icode(self, resseq):
"""Tries to return the icode. In MMCIF files this is just part of
resseq! In PDB files, it's a separate field."""
last_resseq_char = resseq[-1]
if last_resseq_char in letters:
icode = last_resseq_char
int_resseq = int(resseq[0:-1])
else:
icode = " "
int_resseq = int(resseq)
return icode, int_resseq