Exemplo n.º 1
0
    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
Exemplo n.º 2
0
    def __init__(self, id, name, segid=''):
        ProteinEntity.__init__(self, 'RESIDUE', id)
        self.__direct_parent = None

        self.__disordered = 0
        self.__name = name
        self.__segid = segid
Exemplo n.º 3
0
    def __init__(self, id, name, segid=''):
        ProteinEntity.__init__(self, 'RESIDUE', id)
        self.__direct_parent = None

        self.__disordered = 0
        self.__name = name
        self.__segid = segid
Exemplo n.º 4
0
Arquivo: Atom.py Projeto: q10/fiddle
    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
Exemplo n.º 5
0
Arquivo: Atom.py Projeto: q10/fiddle
    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
Exemplo n.º 6
0
    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)
Exemplo n.º 7
0
    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)