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DefaultParser.py
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DefaultParser.py
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# Copyright 2016 Anthony Bradley. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code handle loading mmtf-python into Biopython's structures."""
from Bio.PDB.StructureBuilder import StructureBuilder
import numpy as np
class StructureDecoder:
"""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_builder = StructureBuilder()
self.structure_builder.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 coordinate 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_builder.init_atom(
str(atom_name),
np.array((x, y, z), "f"),
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_builder.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
: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_builder.init_seg(" ")
self.structure_builder.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_builder.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_builder.set_symmetry(space_group, unit_cell)
def set_header_info(
self,
r_free,
r_work,
resolution,
title,
deposition_date,
release_date,
experimnetal_methods,
):
"""Set 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
"""
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.
"""
def finalize_structure(self):
"""Any functions needed to cleanup the structure."""
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
"""
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
"""