Read biological assembly information where available.

[BradyAJohnston]

Is your feature request related to a problem?

I would like to have access to the different symmetry operations required to build a biological assembly from a file if present. (https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies)

Describe the solution you'd like

A list or similar available which contains the different symmetry operations required to build the biological assembly.

Describe alternatives you've considered

I am not necessarily looking to build to the assembly inside of MDAnalaysis, but just have access to the information.

[richardjgowers]

So currently if you've loaded a PDB file, then any REMARK lines are accessible at Universe.trajectory.remarks, but they aren't parsed into anything better than the raw lines from the file. From a quick skim of the PDB spec, it's not clear how universal the symmetry operations are in the given PDB examples compared to PDBx format.

[IAlibay]

We could parse the BIOMT matrices if present and expose them, that should be easy enough.

[aya9aladdin]

I'm interested in working on this issue.... the solution that I'm thinking about is adding a topology attribute class BIOMT to the topologyattr module, so it will hold the assembly transformation matrix in a numpy array, with updating the PDBParser to parse the matrix. Am I on the right direction?

[IAlibay]

I don't necessarily think we need a new topology attribute for this, it's should be a single matrix for the whole system.

Probably the simplest thing here is to store the matrix under Timestep.data and then have a convenience method (probably under PDBParser) which allows you to use that matrix to yield the biological assembly. As @richardjgowers mentioned, the PDB standard is rather messy here, so there will be assumptions to be made (so we probably don't want to apply any kind of transformation by default).