Weird behaviour when PDB input files have no chainID

[amjjbonvin]

In the topoaa module, when an input PDB file has no chainID/segID defined the module puts $PRO as segid which causes problems downstream. No segIDs were defined in the config files since those are in principle defined in the default.cfg file of the module.

This does not happen when a PDB input has the chainID present.

In default.cfg there are default segIDs defined for each molecule. Those should be used.

[joaomcteixeira]

Is it correct to say that each input PDB file must have a single chain?

[joaomcteixeira]

I am working on this right now.
If we have two input structures. One with chainID A and the other without chainID/segID (bugged). Which letter should we assign to the second structure? A or B? In other words, should the chainID/segID added to the structures with this information missing follow the IDs of the ones which have, or can they be independent?

[rvhonorato]

Since I was assigned first, I already fixed this :)

[rvhonorato]

I am working on this right now. If we have two input structures. One with chainID A and the other without chainID/segID (bugged). Which letter should we assign to the second structure? A or B? In other words, should the chainID/segID added to the structures with this information missing follow the IDs of the ones which have, or can they be independent?

Basically needs to be the same as for 2.x

[rvhonorato]

I won't have any more time this week to clean and PR this one, so probably better if you go ahead @joaomcteixeira

[amjjbonvin]

In 2.4 the chains are assigned in the order of the input molecules (if not specified). For 3.0 I would do the same, first molecule gets A, second B and so on, unless overwritten by parameters in the config file

[joaomcteixeira]

Will address this as part of a sanitization process for all PDBs entering the haddock3 pipeline.

[rvhonorato]

Would be nice to have this PDBHandler part as an independent library so we could also use it in the webserver; check what it does now.

[rvhonorato]

Is this one still relevant?

[joaomcteixeira]

Yes, it's relevant. It's solved in #144. But I need to finish that PR.

[rvhonorato]

Apparently it was fixed in #144