Python StructureBuilder.StructureBuilder类代码示例

    def __init__(self, structure_builder=None, QUIET=False):
        """Create a FastMMCIFParser object.

        The mmCIF parser calls a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instanciated by the
        parser object itself, but if the user provides his/her own
        StructureBuilder object, the latter is used instead.

        The main difference between this class and the regular MMCIFParser is
        that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
        interested only in coordinate information.

        Arguments:
         - structure_builder - an optional user implemented StructureBuilder class.
         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the mmCIF file!

        """
        if structure_builder is not None:
            self._structure_builder = structure_builder
        else:
            self._structure_builder = StructureBuilder()

        self.line_counter = 0
        self.build_structure = None
        self.QUIET = bool(QUIET)

    def __init__(self, PERMISSIVE=True, get_header=False,
                 structure_builder=None, QUIET=False):
        """Create a PDBParser object.

        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/her own
        StructureBuilder object, the latter is used instead.

        Arguments:
         - 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!.
         - structure_builder - an optional user implemented StructureBuilder class.
         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the PDB file!
        """
        if structure_builder is not 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 residues_to_struct(name_residues_list, structID):
    """
    Build a structure from a list of (chain name, residues) - each as
    a chain.
    """
    
    builder = StructureBuilder()
    builder.init_structure(structID)
    builder.init_model(0)

    for (name, residues) in name_residues_list:
        builder.init_chain(name)
        for res in residues:
            builder.chain.add(res)

    return builder.get_structure()

    def init_structure(self, total_num_bonds, total_num_atoms, total_num_groups, total_num_chains, total_num_models, structure_id):
        """Initialise the structure object.

        :param total_num_bonds: the number of bonds in the structure
        :param total_num_atoms: the number of atoms in the structure
        :param total_num_groups: the number of groups in the structure
        :param total_num_chains: the number of chains in the structure
        :param total_num_models: the number of models in the structure
        :param structure_id the: id of the structure (e.g. PDB id)
        """
        self.structure_bulder = StructureBuilder()
        self.structure_bulder.init_structure(structure_id=structure_id)
        self.chain_index_to_type_map = {}
        self.chain_index_to_seq_map = {}
        self.chain_index_to_description_map = {}
        self.chain_counter = 0

 def __init__(self, structure_builder=None, QUIET=False):
     """Create a PDBParser object.
     The PDB parser call a number of standard methods in an aggregated
     StructureBuilder object. Normally this object is instanciated by the
     MMCIParser object itself, but if the user provides his/her own
     StructureBuilder object, the latter is used instead.
     Arguments:
      - structure_builder - an optional user implemented StructureBuilder class.
      - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
        the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
        These warnings might be indicative of problems in the PDB file!
     """
     if structure_builder is not None:
         self._structure_builder = structure_builder
     else:
         self._structure_builder = StructureBuilder()
     # self.header = None
     # self.trailer = None
     self.line_counter = 0
     self.build_structure = None
     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 MMCIFParser(object):
    """Parse a PDB file and return a Structure object."""

    def __init__(self, structure_builder=None, QUIET=False):
        """Create a PDBParser object.

        The PDB parser call a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instanciated by the
        MMCIParser object itself, but if the user provides his/her own
        StructureBuilder object, the latter is used instead.

        Arguments:
         - structure_builder - an optional user implemented StructureBuilder class.
         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the PDB file!
        """
        if structure_builder is not None:
            self._structure_builder = structure_builder
        else:
            self._structure_builder = StructureBuilder()
        # self.header = None
        # self.trailer = None
        self.line_counter = 0
        self.build_structure = None
        self.QUIET = bool(QUIET)

    # Public methods

    def get_structure(self, structure_id, filename):
        """Return the structure.

        Arguments:
         - structure_id - string, the id that will be used for the structure
         - filename - name of the mmCIF file OR an open filehandle
        """
        with warnings.catch_warnings():
            if self.QUIET:
                warnings.filterwarnings("ignore", category=PDBConstructionWarning)
        self._mmcif_dict = MMCIF2Dict(filename)
        self._build_structure(structure_id)
        return self._structure_builder.get_structure()

    # Private methods

    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"]
        try:
            element_list = mmcif_dict["_atom_site.type_symbol"]
        except KeyError:
            element_list = None
        seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
        chain_id_list = mmcif_dict["_atom_site.label_asym_id"]
        x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
        y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
        z_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_z"]]
        alt_list = mmcif_dict["_atom_site.label_alt_id"]
        icode_list = mmcif_dict["_atom_site.pdbx_PDB_ins_code"]
        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:
            serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
        except KeyError:
            # No model number column
            serial_list = None
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number")
        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 "_atom_site.auth_seq_id" in mmcif_dict:
            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
        structure_builder = self._structure_builder
        structure_builder.init_structure(structure_id)
        structure_builder.init_seg(" ")
        # Historically, Biopython PDB parser uses model_id to mean array index
        # so serial_id means the Model ID specified in the file
        current_model_id = -1
        current_serial_id = 0
        for i in range(0, len(atom_id_list)):

#.........这里部分代码省略.........

 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(object):
    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"]
        try:
            element_list = mmcif_dict["_atom_site.type_symbol"]
        except KeyError:
            element_list = None
        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:
            serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
        except KeyError:
            # No model number column
            serial_list = None
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number")
        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 "_atom_site.auth_seq_id" in mmcif_dict:
            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
        structure_builder=self._structure_builder
        structure_builder.init_structure(structure_id)
        structure_builder.init_seg(" ")
        # Historically, Biopython PDB parser uses model_id to mean array index
        # so serial_id means the Model ID specified in the file
        current_model_id = 0
        current_serial_id = 0
        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]
            # occupancy & B factor
            try:
                tempfactor=float(b_factor_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing B factor")
            try:
                occupancy=float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy")
            fieldname=fieldname_list[i]
            if fieldname=="HETATM":
                hetatm_flag="H"
            else:
                hetatm_flag=" "
            if serial_list is not None:
                # model column exists; use it
                serial_id = serial_list[i]
                if current_serial_id != serial_id:
                    # if serial changes, update it and start new model
                    current_serial_id = serial_id
                    structure_builder.init_model(current_model_id, current_serial_id)
                    current_model_id += 1
            else:
                # no explicit model column; initialize single model
                structure_builder.init_model(current_model_id)
            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)
#.........这里部分代码省略.........

class StructureDecoder(object):
    """Class to pass the data from mmtf-python into a Biopython data structure."""

    def __init__(self):
        """Initialize the class."""
        self.this_type = ""

    def init_structure(self, total_num_bonds, total_num_atoms,
                       total_num_groups, total_num_chains, total_num_models,
                       structure_id):
        """Initialize the structure object.

        :param total_num_bonds: the number of bonds in the structure
        :param total_num_atoms: the number of atoms in the structure
        :param total_num_groups: the number of groups in the structure
        :param total_num_chains: the number of chains in the structure
        :param total_num_models: the number of models in the structure
        :param structure_id: the id of the structure (e.g. PDB id)

        """
        self.structure_bulder = StructureBuilder()
        self.structure_bulder.init_structure(structure_id=structure_id)
        self.chain_index_to_type_map = {}
        self.chain_index_to_seq_map = {}
        self.chain_index_to_description_map = {}
        self.chain_counter = 0

    def set_atom_info(self, atom_name, serial_number, alternative_location_id,
                      x, y, z, occupancy, temperature_factor, element, charge):
        """Create an atom object an set the information.

        :param atom_name: the atom name, e.g. CA for this atom
        :param serial_number: the serial id of the atom (e.g. 1)
        :param alternative_location_id: the alternative location id for the atom, if present
        :param x: the x coordiante of the atom
        :param y: the y coordinate of the atom
        :param z: the z coordinate of the atom
        :param occupancy: the occupancy of the atom
        :param temperature_factor: the temperature factor of the atom
        :param element: the element of the atom, e.g. C for carbon. According to IUPAC. Calcium  is Ca
        :param charge: the formal atomic charge of the atom

        """
        # MMTF uses "\x00" (the NUL character) to indicate to altloc, so convert
        # that to the space required by StructureBuilder
        if alternative_location_id == "\x00":
            alternative_location_id = " "

        # Atom_name is in twice - the full_name is with spaces
        self.structure_bulder.init_atom(str(atom_name), [x, y, z],
                                        temperature_factor, occupancy,
                                        alternative_location_id, str(atom_name),
                                        serial_number=serial_number,
                                        element=str(element).upper())

    def set_chain_info(self, chain_id, chain_name, num_groups):
        """Set the chain information.

        :param chain_id: the asym chain id from mmCIF
        :param chain_name: the auth chain id from mmCIF
        :param num_groups: the number of groups this chain has

        """
        # A Bradley - chose to use chain_name (auth_id) as it complies
        # with current Biopython. Chain_id might be better.
        self.structure_bulder.init_chain(chain_id=chain_name)
        if self.chain_index_to_type_map[self.chain_counter] == "polymer":
            self.this_type = " "
        elif self.chain_index_to_type_map[self.chain_counter] == "non-polymer":
            self.this_type = "H"
        elif self.chain_index_to_type_map[self.chain_counter] == "water":
            self.this_type = "W"
        self.chain_counter += 1

    def set_entity_info(self, chain_indices, sequence, description, entity_type):
        """Set the entity level information for the structure.

        :param chain_indices: the indices of the chains for this entity
        :param sequence: the one letter code sequence for this entity
        :param description: the description for this entity
        :param entity_type: the entity type (polymer,non-polymer,water)

        """
        for chain_ind in chain_indices:
            self.chain_index_to_type_map[chain_ind] = entity_type
            self.chain_index_to_seq_map[chain_ind] = sequence
            self.chain_index_to_description_map[chain_ind] = description

    def set_group_info(self, group_name, group_number, insertion_code,
                       group_type, atom_count, bond_count, single_letter_code,
                       sequence_index, secondary_structure_type):
        """Set the information for a group

        :param group_name: the name of this group, e.g. LYS
        :param group_number: the residue number of this group
        :param insertion_code: the insertion code for this group
        :param group_type: a string indicating the type of group (as found in the chemcomp dictionary.
            Empty string if none available.
        :param atom_count: the number of atoms in the group
        :param bond_count: the number of unique bonds in the group
#.........这里部分代码省略.........

class FastMMCIFParser(object):
    """Parse an MMCIF file and return a Structure object."""

    def __init__(self, structure_builder=None, QUIET=False):
        """Create a FastMMCIFParser object.

        The mmCIF parser calls a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instanciated by the
        parser object itself, but if the user provides his/her own
        StructureBuilder object, the latter is used instead.

        The main difference between this class and the regular MMCIFParser is
        that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
        interested only in coordinate information.

        Arguments:
         - structure_builder - an optional user implemented StructureBuilder class.
         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the mmCIF file!

        """
        if structure_builder is not None:
            self._structure_builder = structure_builder
        else:
            self._structure_builder = StructureBuilder()

        self.line_counter = 0
        self.build_structure = None
        self.QUIET = bool(QUIET)

    # Public methods

    def get_structure(self, structure_id, filename):
        """Return the structure.

        Arguments:
         - structure_id - string, the id that will be used for the structure
         - filename - name of the mmCIF file OR an open filehandle

        """
        with warnings.catch_warnings():
            if self.QUIET:
                warnings.filterwarnings("ignore", category=PDBConstructionWarning)
            with as_handle(filename) as handle:
                self._build_structure(structure_id, handle)

        return self._structure_builder.get_structure()

    # Private methods

    def _build_structure(self, structure_id, filehandle):

        # two special chars as placeholders in the mmCIF format
        # for item values that cannot be explicitly assigned
        # see: pdbx/mmcif syntax web page
        _unassigned = set(('.', '?'))

        # Read only _atom_site. and atom_site_anisotrop entries
        read_atom, read_aniso = False, False
        _fields, _records = [], []
        _anisof, _anisors = [], []
        for line in filehandle:
            if line.startswith('_atom_site.'):
                read_atom = True
                _fields.append(line.strip())
            elif line.startswith('_atom_site_anisotrop.'):
                read_aniso = True
                _anisof.append(line.strip())
            elif read_atom and line.startswith('#'):
                read_atom = False
            elif read_aniso and line.startswith('#'):
                read_aniso = False
            elif read_atom:
                _records.append(line.strip())
            elif read_aniso:
                _anisors.append(line.strip())

        # Dumping the shlex module here since this particular
        # category should be rather straightforward.
        # Quite a performance boost..
        _record_tbl = zip(*map(str.split, _records))
        _anisob_tbl = zip(*map(str.split, _anisors))

        mmcif_dict = dict(zip(_fields, _record_tbl))
        mmcif_dict.update(dict(zip(_anisof, _anisob_tbl)))

        # Build structure object
        atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
        residue_id_list = mmcif_dict["_atom_site.label_comp_id"]

        try:
            element_list = mmcif_dict["_atom_site.type_symbol"]
        except KeyError:
            element_list = None

        chain_id_list = mmcif_dict["_atom_site.auth_asym_id"]

        x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
        y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
#.........这里部分代码省略.........

    def set_structure(self, pdb_object):
        """Check what the user is providing and build a structure."""
        if pdb_object.level == "S":
            structure = pdb_object
        else:
            sb = StructureBuilder()
            sb.init_structure('pdb')
            sb.init_seg(' ')
            # Build parts as necessary
            if pdb_object.level == "M":
                sb.structure.add(pdb_object.copy())
                self.structure = sb.structure
            else:
                sb.init_model(0)
                if pdb_object.level == "C":
                    sb.structure[0].add(pdb_object.copy())
                else:
                    sb.init_chain('A')
                    if pdb_object.level == "R":
                        try:
                            parent_id = pdb_object.parent.id
                            sb.structure[0]['A'].id = parent_id
                        except Exception:
                            pass
                        sb.structure[0]['A'].add(pdb_object.copy())
                    else:
                        # Atom
                        sb.init_residue('DUM', ' ', 1, ' ')
                        try:
                            parent_id = pdb_object.parent.parent.id
                            sb.structure[0]['A'].id = parent_id
                        except Exception:
                            pass
                        sb.structure[0]['A'].child_list[0].add(pdb_object.copy())

            # Return structure
            structure = sb.structure
        self.structure = structure

    def set_structure(self, pdb_object):
        # Check what the user is providing and build a structure appropriately
        if pdb_object.level == "S":
            structure = pdb_object
        else:
            sb = StructureBuilder()
            sb.init_structure("pdb")
            sb.init_seg(" ")
            # Build parts as necessary
            if pdb_object.level == "M":
                sb.structure.add(pdb_object)
                self.structure = sb.structure
            else:
                sb.init_model(0)
                if pdb_object.level == "C":
                    sb.structure[0].add(pdb_object)
                else:
                    sb.init_chain("A")
                    if pdb_object.level == "R":
                        try:
                            parent_id = pdb_object.parent.id
                            sb.structure[0]["A"].id = parent_id
                        except Exception:
                            pass
                        sb.structure[0]["A"].add(pdb_object)
                    else:
                        # Atom
                        sb.init_residue("DUM", " ", 1, " ")
                        try:
                            parent_id = pdb_object.parent.parent.id
                            sb.structure[0]["A"].id = parent_id
                        except Exception:
                            pass
                        sb.structure[0]["A"].child_list[0].add(pdb_object)

            # Return structure
            structure = sb.structure
        self.structure = structure

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):
        """Create a PDBParser object.

        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/her own
        StructureBuilder object, the latter is used instead.

        Arguments:
         - 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!.
         - structure_builder - an optional user implemented StructureBuilder class.
         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the PDB file!
        """
        if structure_builder is not 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:
         - id - string, the id that will be used for the structure
         - file - name of the PDB file OR an open filehandle
        """
        with warnings.catch_warnings():
            if self.QUIET:
                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)

            with as_handle(file, mode='rU') as handle:
                self._parse(handle.readlines())

            self.structure_builder.set_header(self.header)
            # Return the Structure instance
            structure = self.structure_builder.get_structure()

        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 (PRIVATE)."""
        # 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 (PRIVATE)."""
        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 (PRIVATE)."""
        local_line_counter = 0
        structure_builder = self.structure_builder
        current_model_id = 0
        # Flag we have an open model
        model_open = 0
#.........这里部分代码省略.........

class MMCIFParser(object):
    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 "_atom_site.auth_seq_id" in mmcif_dict:
            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
#.........这里部分代码省略.........