Biounits¶

Biological assemblies, i.e. biounits, are an integral part of mmCIF files and their construction is fully defined in ost.io.MMCifInfoBioUnit. ost.io.MMCifInfoBioUnit.PDBize() provides one possibility to construct such biounits with compatibility with the PDB format in mind. That is single character chain names, dumping all ligands in one chain etc. Here we provide a more mmCIF-style way of constructing biounits. This can either be done starting from a ost.io.MMCifInfoBioUnit or the derived ost.mol.alg.BUInfo. The latter is a minimalistic representation of ost.io.MMCifInfoBioUnit and can be serialized to a byte string.

BUInfo(mmcif_buinfo):

Preprocesses data from ost.io.MMCifInfoBioUnit that are required to construct a biounit from an assymetric unit. Can be serialized.

Parameters:

mmcif_buinfo (ost.io.MMCifInfoBioUnit) – Biounit definition

ToBytes()¶

Returns:

A byte string from which the object can be reconstructed.

static FromBytes(byte_string)¶

Parameters:

byte_string – Can be created with ToBytes()

Returns:

A BUInfo object

CreateBU(asu, bu_info)¶

Constructs a biounit given an assymetric unit and transformation information. The following properties are copied from the assymetric unit and are expected to be set (this is the case if you use ost.io.LoadMMCIF() for the assymetric unit):

• Chain level:

  • Chain type (see ost.mol.ChainHandle.type)

• Residue level:

  • Chem type (see ost.mol.ResidueHandle.chem_type)

  • Chem class (ost.mol.ResidueHandle.chem_class)

  • One letter code (see ost.mol.ResidueHandle.one_letter_code)

  • Secondary structure (see ost.mol.ResidueHandle.sec_structure)

  • IsProtein and IsLigand properties (see ost.mol.ResidueHandle.is_protein/ost.mol.ResidueHandle.is_ligand)

Each chain in the returned biounit can be referenced back to the assymetric unit as they follow a standardised naming scheme: <idx>.<asu_cname>, where asu_cname is the chain name in the assymetric unit and idx is the nth occurence of that chain in the biounit with one based indexing. There is a quirk though. An index of 1, for example 1.A, is reserved for the original AU chain with identity transform (read: no transform) applied. If a certain AU chain only occurs with an actual transform applied, numbering starts at 2.

Warning

There is the (rare) possibility that a AU chain that has only identity transform applied is not named 1.<au_cname>. As of january 2024, there are 3 pdb entries (8qn6, 8x1h, 2c0x) where the same AU chain with identity transform occurs several times in the same biounit. This is likely an error in the respective mmCIF files as the resulting chains sit on top of each other. OST just names the FIRST occurence as 1.<au_cname>.

Parameters:

• asu (ost.mol.EntityHandle) – The assymetric unit

• bu_info (MMCifInfoBioUnit/BUInfo) – Info object

Returns:

A ost.mol.EntityHandle of the requested biounit