def __init__(self, id, serial_num=None):
ProteinEntity.__init__(self, 'MODEL', id)
if serial_num is None:
self.__serial_num = id
else:
self.__serial_num = serial_num
def __init__(self, id, name, segid=''):
ProteinEntity.__init__(self, 'RESIDUE', id)
self.__direct_parent = None
self.__disordered = 0
self.__name = name
self.__segid = segid
def __init__(self, id, name, segid=''):
ProteinEntity.__init__(self, 'RESIDUE', id)
self.__direct_parent = None
self.__disordered = 0
self.__name = name
self.__segid = segid
def __init__(self, serial_number, name, coords, element=None):
ProteinEntity.__init__(self, 'ATOM', name.upper())
self.__direct_parent = None
self.__name = name.upper() # eg. CA, spaces are removed from atom name
self.__serial_number = serial_number
self.__coords = coords
self.__element = self.__derive_element(name, element)
self.__bfactor = 0
self.__occupancy = 1.0
self.__altloc = ''
self.__fullname = ''
self.__disordered_flag = 0
self.__anisou_array = None
self.__siguij_array = None
self.__sigatm_array = None
def __init__(self, serial_number, name, coords, element=None):
ProteinEntity.__init__(self, 'ATOM', name.upper())
self.__direct_parent = None
self.__name = name.upper() # eg. CA, spaces are removed from atom name
self.__serial_number = serial_number
self.__coords = coords
self.__element = self.__derive_element(name, element)
self.__bfactor = 0
self.__occupancy = 1.0
self.__altloc = ''
self.__fullname = ''
self.__disordered_flag = 0
self.__anisou_array = None
self.__siguij_array = None
self.__sigatm_array = None
def __init__(self, filename, id=None):
# Extract the protein id from file
assert(isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
def __init__(self, filename, id=None):
# Extract the protein id from file
assert (isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
