def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
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
self.structure_reference = {}
self.authors = {}
self.current_model_id = 0
self.current_chain_id = 0
self.current_residue_id = 0
self.current_atom_id = 0
self.header_dict = {
"name": "",
"head": "",
"deposition_date": "1900-01-01",
"release_date": "1909-01-08",
"structure_method": "unknown",
"resolution": None,
"structure_reference": "unknown",
"journal_reference": "unknown",
"journal": "unknown",
"keywords": "",
"author": "", # andere Anordnung im als im normalen PDB-File, gruening, b.a. <-> b.a.gruening
"compound": {"1": {"misc": ""}},
"source": {"1": {"misc": ""}},
}
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
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
self.structure_reference = {}
self.authors = {}
self.current_model_id = 0
self.current_chain_id = 0
self.current_residue_id = 0
self.current_atom_id = 0
self.header_dict = {
'name': "",
'head': '',
'deposition_date': "1900-01-01",
'release_date': "1909-01-08",
'structure_method': "unknown",
'resolution': None,
'structure_reference': "unknown",
'journal_reference': "unknown",
'journal': "unknown",
'keywords': "",
'author':
"", #andere Anordnung im als im normalen PDB-File, gruening, b.a. <-> b.a.gruening
'compound': {
'1': {
'misc': ''
}
},
'source': {
'1': {
'misc': ''
}
},
}
class PDBMLParser:
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
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
self.structure_reference = {}
self.authors = {}
self.current_model_id = 0
self.current_chain_id = 0
self.current_residue_id = 0
self.current_atom_id = 0
self.header_dict = {
"name": "",
"head": "",
"deposition_date": "1900-01-01",
"release_date": "1909-01-08",
"structure_method": "unknown",
"resolution": None,
"structure_reference": "unknown",
"journal_reference": "unknown",
"journal": "unknown",
"keywords": "",
"author": "", # andere Anordnung im als im normalen PDB-File, gruening, b.a. <-> b.a.gruening
"compound": {"1": {"misc": ""}},
"source": {"1": {"misc": ""}},
}
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)
self._parse(file)
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 _parse(self, filepath):
# get an iterable
context = etree.iterparse(filepath, events=("start", "end"))
structure_builder = self.structure_builder
# turn it into an iterator
context = iter(context)
# get the root element
event, root = context.next()
header_only = False
# TODO: its not a good solution :(
# Save the structure state for each atom, its used to add anisotrop properties afterwards
atom_id_structure_mapping = {}
for event, elem in context:
if event == "end": # and elem.tag == "record":
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_siteCategory":
elem.tail = None
elem.clear()
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_site_anisotrop":
# res = chain.__getitem__(("", id, ""))
# atom = res.__getitem__()
pass
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_site":
if header_only:
elem.clear()
else:
atom_id = int(elem.get("id"))
# SET the AtomID as line_counter
structure_builder.set_line_counter(atom_id)
resname = elem.find("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_comp_id").text
if elem.find("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}group_PDB").text == "ATOM":
if resname == "HOH" or resname == "WAT":
hetero_flag = "W"
else:
hetero_flag = "H"
else:
hetero_flag = " "
sequence_identifier = elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_seq_id")
model = int(elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_PDB_model_num"))
if self.current_model_id != model:
self.current_model_id = model
structure_builder.init_model(self.current_model_id)
self.current_chain_id = 0
seg_id = elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_seq_id")
structure_builder.init_seg(seg_id)
chain = elem.find("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_asym_id").text
if self.current_chain_id != chain:
self.current_chain_id = chain
structure_builder.init_chain(self.current_chain_id)
self.current_residue_id = 0
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if self.current_residue_id != sequence_identifier:
self.current_residue_id = sequence_identifier
try:
structure_builder.init_residue(resname, hetero_flag, sequence_identifier, " ")
except PDBConstructionException, message:
self._handle_PDB_exception(message, atom_id)
residue_container = (resname, hetero_flag, sequence_identifier, " ")
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
"""
name = elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_atom_id")
x, y, z = (
float(elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_x")),
float(elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_y")),
float(elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_z")),
)
coord = numpy.array((x, y, z), "f")
b_factor = float(
elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}B_iso_or_equiv", "0.0")
)
occupancy = float(elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}occupancy", "0.0"))
altloc = elem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_alt_id")
if not altloc:
altloc = ""
fullname = name
# TODO: current_atom_id wird nicht gespeichert
if not name:
print "Error: no name"
sys.exit()
try:
structure_builder.init_atom(
name, coord, b_factor, occupancy, altloc, fullname, serial_number=atom_id
)
except PDBConstructionException, message:
self._handle_PDB_exception(message, atom_id)
atom_container = (name, coord, b_factor, occupancy, altloc, fullname, atom_id)
elem.clear()
elem.tail = None
atom_id_structure_mapping[atom_id] = {
"model": self.current_model_id,
"seg_id": seg_id,
"chain_id": self.current_chain_id,
"residue": residue_container,
"atom": atom_container,
}
"""
# TODO:
recordtype ANISOU
anisou=map(float, (line[28:35], line[35:42], line[43:49], line[49:56], line[56:63], line[63:70]))
# U's are scaled by 10^4
anisou_array=(numpy.array(anisou, 'f')/10000.0).astype('f')
structure_builder.set_anisou(anisou_array)
recordtype SIGUIJ
# standard deviation of anisotropic B factor
siguij=map(float, (line[28:35], line[35:42], line[42:49], line[49:56], line[56:63], line[63:70]))
# U sigma's are scaled by 10^4
siguij_array=(numpy.array(siguij, 'f')/10000.0).astype('f')
structure_builder.set_siguij(siguij_array)
recordtype SIGATM
# standard deviation of atomic positions
sigatm=map(float, (line[30:38], line[38:45], line[46:54], line[54:60], line[60:66]))
sigatm_array=numpy.array(sigatm, 'f')
structure_builder.set_sigatm(sigatm_array)
"""
elif elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity_polyCategory":
for sub in elem.findall("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity_poly"):
self.header_dict["compound"][sub.get("entity_id", "primary")].update(
{"chain": sub.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_strand_id").lower()}
)
elem.clear()
elif elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entityCategory":
for subelem in elem.findall("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity"):
cid = subelem.get("id")
if self.header_dict["compound"].has_key(cid):
self.header_dict["compound"][cid].update(
{
"molecule": subelem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_description"
).lower()
}
)
else:
self.header_dict["compound"][cid] = {"misc": ""}
self.header_dict["compound"][cid].update(
{
"molecule": subelem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_description"
).lower()
}
)
temp = subelem.findtext("{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_mutation")
if temp:
self.header_dict["compound"][cid].update({"mutation": temp.lower()})
elem.clear()
class PDBMLParser:
def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
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
self.structure_reference = {}
self.authors = {}
self.current_model_id = 0
self.current_chain_id = 0
self.current_residue_id = 0
self.current_atom_id = 0
self.header_dict = {
'name': "",
'head': '',
'deposition_date': "1900-01-01",
'release_date': "1909-01-08",
'structure_method': "unknown",
'resolution': None,
'structure_reference': "unknown",
'journal_reference': "unknown",
'journal': "unknown",
'keywords': "",
'author':
"", #andere Anordnung im als im normalen PDB-File, gruening, b.a. <-> b.a.gruening
'compound': {
'1': {
'misc': ''
}
},
'source': {
'1': {
'misc': ''
}
},
}
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)
self._parse(file)
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 _parse(self, filepath):
# get an iterable
context = etree.iterparse(filepath, events=("start", "end"))
structure_builder = self.structure_builder
# turn it into an iterator
context = iter(context)
# get the root element
event, root = context.next()
header_only = False
# TODO: its not a good solution :(
# Save the structure state for each atom, its used to add anisotrop properties afterwards
atom_id_structure_mapping = {}
for event, elem in context:
if event == "end": # and elem.tag == "record":
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_siteCategory":
elem.tail = None
elem.clear()
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_site_anisotrop":
#res = chain.__getitem__(("", id, ""))
#atom = res.__getitem__()
pass
if elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}atom_site":
if header_only:
elem.clear()
else:
atom_id = int(elem.get("id"))
# SET the AtomID as line_counter
structure_builder.set_line_counter(atom_id)
resname = elem.find(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_comp_id"
).text
if elem.find(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}group_PDB"
).text == "ATOM":
if resname == "HOH" or resname == "WAT":
hetero_flag = "W"
else:
hetero_flag = "H"
else:
hetero_flag = " "
sequence_identifier = elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_seq_id"
)
model = int(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_PDB_model_num"
))
if self.current_model_id != model:
self.current_model_id = model
structure_builder.init_model(self.current_model_id)
self.current_chain_id = 0
seg_id = elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_seq_id"
)
structure_builder.init_seg(seg_id)
chain = elem.find(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}auth_asym_id"
).text
if self.current_chain_id != chain:
self.current_chain_id = chain
structure_builder.init_chain(self.current_chain_id)
self.current_residue_id = 0
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if self.current_residue_id != sequence_identifier:
self.current_residue_id = sequence_identifier
try:
structure_builder.init_residue(
resname, hetero_flag, sequence_identifier,
" ")
except PDBConstructionException, message:
self._handle_PDB_exception(message, atom_id)
residue_container = (resname, hetero_flag,
sequence_identifier, " ")
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
"""
name = elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_atom_id"
)
x, y, z = float(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_x"
)
), float(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_y"
)
), float(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}Cartn_z"
))
coord = numpy.array((x, y, z), 'f')
b_factor = float(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}B_iso_or_equiv",
"0.0"))
occupancy = float(
elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}occupancy",
"0.0"))
altloc = elem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}label_alt_id"
)
if not altloc:
altloc = ""
fullname = name
#TODO: current_atom_id wird nicht gespeichert
if not name:
print "Error: no name"
sys.exit()
try:
structure_builder.init_atom(name,
coord,
b_factor,
occupancy,
altloc,
fullname,
serial_number=atom_id)
except PDBConstructionException, message:
self._handle_PDB_exception(message, atom_id)
atom_container = (name, coord, b_factor, occupancy,
altloc, fullname, atom_id)
elem.clear()
elem.tail = None
atom_id_structure_mapping[atom_id] = {
"model": self.current_model_id,
"seg_id": seg_id,
"chain_id": self.current_chain_id,
"residue": residue_container,
"atom": atom_container
}
"""
# TODO:
recordtype ANISOU
anisou=map(float, (line[28:35], line[35:42], line[43:49], line[49:56], line[56:63], line[63:70]))
# U's are scaled by 10^4
anisou_array=(numpy.array(anisou, 'f')/10000.0).astype('f')
structure_builder.set_anisou(anisou_array)
recordtype SIGUIJ
# standard deviation of anisotropic B factor
siguij=map(float, (line[28:35], line[35:42], line[42:49], line[49:56], line[56:63], line[63:70]))
# U sigma's are scaled by 10^4
siguij_array=(numpy.array(siguij, 'f')/10000.0).astype('f')
structure_builder.set_siguij(siguij_array)
recordtype SIGATM
# standard deviation of atomic positions
sigatm=map(float, (line[30:38], line[38:45], line[46:54], line[54:60], line[60:66]))
sigatm_array=numpy.array(sigatm, 'f')
structure_builder.set_sigatm(sigatm_array)
"""
elif elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity_polyCategory":
for sub in elem.findall(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity_poly"
):
self.header_dict["compound"][sub.get(
"entity_id", "primary"
)].update({
"chain":
sub.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_strand_id"
).lower()
})
elem.clear()
elif elem.tag == "{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entityCategory":
for subelem in elem.findall(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}entity"
):
cid = subelem.get("id")
if self.header_dict["compound"].has_key(cid):
self.header_dict["compound"][cid].update({
"molecule":
subelem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_description"
).lower()
})
else:
self.header_dict["compound"][cid] = {"misc": ''}
self.header_dict["compound"][cid].update({
"molecule":
subelem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_description"
).lower()
})
temp = subelem.findtext(
"{http://pdbml.pdb.org/schema/pdbx-v32.xsd}pdbx_mutation"
)
if temp:
self.header_dict["compound"][cid].update(
{"mutation": temp.lower()})
elem.clear()