Python StructureBuilder.init_chain方法代码示例

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
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()

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
class XBGFParser:
    def __init__(self, PERMISSIVE=1, structure_builder=None):
        if structure_builder != None:
            self.structure_builder = structure_builder
        else:
            self.structure_builder = StructureBuilder()
        self.PERMISSIVE = PERMISSIVE

    # public interface

    def parse(self, id, file):
        self.structure_builder.init_structure(id)
        if isinstance(file, basestring):
            file=open(file)
        self.charges = dict()
        self.chain_suffix = 0
        self._parse(file.readlines())
        self.structure = self.structure_builder.get_structure()
        return self._process_structure()

    # private methods

    def _parse(self, lines):
        self.structure_builder.init_model(0)
        self.structure_builder.init_seg("")
        self.current_chain_id = None
        self.current_residue_id = None
        self.current_resname = None
        for i in range(0, len(lines)):
            self.line_counter = i + 1
            self.structure_builder.set_line_counter(self.line_counter)
            line = lines[i]
            if line[0:6] == 'ATOM  ':
                self._update_atom(line)

    def _update_chain(self, line):
        chain_id = self._extract_chain(line)
        if self.current_chain_id != chain_id:
            try:
                self.structure_builder.init_chain(chain_id)
                self.current_chain_id = chain_id
                self.current_residue_id = None
                self.current_resname = None
            except PDBConstructionException, message:
                self._handle_PDB_exception(message) 

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
    def set_structure(self, pdb_object):
        """Check what object the user is providing and build a structure."""
        # This is duplicated from the PDBIO class
        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 ValueError:
                            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 ValueError:
                            pass
                        sb.structure[0]['A'].child_list[0].add(pdb_object)

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

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
    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

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
    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

# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import init_chain [as 别名]
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.........