Python StructureBuilder.init_atom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_atom [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.........