# 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 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_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 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_builder.init_atom( str(atom_name), numpy.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 """ 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