Python StructureBuilder.init_model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_model [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_model [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_model [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_model [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_model [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_model [as 别名]

#.........这里部分代码省略.........
        """
        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
        :param single_letter_code: the single letter code of the group
        :param sequence_index: the index of this group in the sequence defined by the entity
        :param secondary_structure_type: the type of secondary structure used
            (types are according to DSSP and number to type mappings are defined in the specification)

        """
        # MMTF uses a NUL character to indicate a blank insertion code, but
        # StructureBuilder expects a space instead.
        if insertion_code == "\x00":
            insertion_code = " "

        self.structure_bulder.init_seg(' ')
        self.structure_bulder.init_residue(group_name, self.this_type,
                                           group_number, insertion_code)

    def set_model_info(self, model_id, chain_count):
        """Set the information for a model.

        :param model_id: the index for the model
        :param chain_count: the number of chains in the model

        """
        self.structure_bulder.init_model(model_id)

    def set_xtal_info(self, space_group, unit_cell):
        """Set the crystallographic information for the structure.

        :param space_group: the space group name, e.g. "P 21 21 21"
        :param unit_cell: an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma

        """
        self.structure_bulder.set_symmetry(space_group, unit_cell)

    def set_header_info(self, r_free, r_work, resolution, title,
                        deposition_date, release_date, experimnetal_methods):
        """Sets the header information.

        :param r_free: the measured R-Free for the structure
        :param r_work: the measure R-Work for the structure
        :param resolution: the resolution of the structure
        :param title: the title of the structure
        :param deposition_date: the deposition date of the structure
        :param release_date: the release date of the structure
        :param experimnetal_methods: the list of experimental methods in the structure

        """
        pass

    def set_bio_assembly_trans(self, bio_assembly_index, input_chain_indices,
                               input_transform):
        """Set the Bioassembly transformation information. A single bioassembly can have multiple transforms.

        :param bio_assembly_index: the integer index of the bioassembly
        :param input_chain_indices: the list of integer indices for the chains of this bioassembly
        :param input_transform: the list of doubles for  the transform of this bioassmbly transform.

        """
        pass

    def finalize_structure(self):
        """Any functions needed to cleanup the structure."""
        pass

    def set_group_bond(self, atom_index_one, atom_index_two, bond_order):
        """Add bonds within a group.

        :param atom_index_one: the integer atom index (in the group) of the first partner in the bond
        :param atom_index_two: the integer atom index (in the group) of the second partner in the bond
        :param bond_order: the integer bond order

        """
        pass

    def set_inter_group_bond(self, atom_index_one, atom_index_two, bond_order):
        """Add bonds between groups.

        :param atom_index_one: the integer atom index (in the structure) of the first partner in the bond
        :param atom_index_two: the integer atom index (in the structure) of the second partner in the bond
        :param bond_order: the bond order

        """
        pass