convention for TopologyObject repr ?

[Oliver Beckstein]

Hi,

Why do we do something special to the order of atom indices in an TopologyObject when printing the repr? Namely in https://github.com/MDAnalysis/mdanalysis/blob/4f36e2a06eb2d04274dfe4510910986c2dd17681/package/MDAnalysis/core/topologyobjects.py#L118 

indices = (self.indices if self.indices[0] < self.indices[-1] else self.indices[::-1])

why do we reverse the order?

I found it quite confusing when I looked at a Dihedral object and the order of atoms was different from my carefully crafted order to define the dihedral:

>>> dih = u.atoms[[10, 0, 1, 3]].dihedral

>>> list(dih.atoms)

[<Atom 11: C5 of type opls_135 of resname V36, resid 1 and segid V36>,
 <Atom 1: C1 of type opls_465 of resname V36, resid 1 and segid V36>,
 <Atom 2: O2 of type opls_467 of resname V36, resid 1 and segid V36>,
 <Atom 4: C3 of type opls_468 of resname V36, resid 1 and segid V36>]

>>> repr(dih)

'<Dihedral between: Atom 3, Atom 1, Atom 0, Atom 10>'

I’d much rather have the actual order output, but I was wondering if there was any specific reason why we decided to manipulate the printed order?

Oliver

--

Oliver Beckstein (he/his/him)

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[hugomac...@gmail.com]

That seems strange and possibly confusing. 
With my user hat on I would want this changed, would you be able to raise an issue?

 Is the reordering only done for the `repr` of dihedral or is it some base behaviour of one of the underlying classes?

Cheers, 

Hugo. 

[Oliver Beckstein]

Hi Hugo,

I opened https://github.com/MDAnalysis/mdanalysis/issues/4181

On Jun 26, 2023, at 3:35 PM, hugomac...@gmail.com <hugomac...@gmail.com> wrote:

That seems strange and possibly confusing. 
With my user hat on I would want this changed, would you be able to raise an issue?

 Is the reordering only done for the `repr` of dihedral or is it some base behaviour of one of the underlying classes?

It looked general to me but I didn’t test it further.

Oliver