Add function for structural alignments via least-squares fit

[rasbt]

A staticmethod least-squares superposition. We could call it align and implement it with similar parameters as the rmsd function. In addition, it would be nice to have a substructure parameter for substructure alignment -- maybe accepting an iterable of residue numbers here.

[universvm]

Hi @rasbt ,

I wonder if it'd be worth integrating a library like this one: https://github.com/charnley/rmsd rather than implementing the algorithm from scratch.

Alternatively another method could be to call biopython align the objects, save to a temp file and reload them into an array.

What do you think?

[rasbt]

Sure, that makes a lot of sense. I see that the rmsd package is also under BSD licence, and we could add it to biopandas.externals (similar to how scikit-learn does it) and then modify it to our needs -- with the respective copyright notice of course & citation in the docs.

It looks like rmsd is meant as a command line tool, so we would have to adjust it a little.

Regarding biopython, that's another option, but to be honest, I would favor the rmsd package because biopython is quite a bloated library and it would add a big dependency.

[universvm]

I'd agree with steering away from biopython.

I'll look into it but not sure when I'll have an ETA. Nevertheless I might contact you again about code style etc...

:)

[rasbt]

No pressure. This is a hobby project, so whenever you have time and feel like it :)