Lester Hedges

For reference, this is using Python 3.7 for both OSes. I'll try with a different variant too.

Performance is also bad on Python 3.9: ``` Unpickling BioSimSpace sysem took 4.09103798866272 seconds Pickling BioSimSpace system took 78.69318914413452 seconds Unpickling BioSimSpace sysem took 4.513953924179077 seconds Pickling BioSimSpace system took...

Hi @cespos. Thanks for your query, this is really helpful. The `leap_commands` feature was added to solve a particular problem, i.e. the addition of custom parameters, and we obviously didn't...

We should easily be able to detect the present of disulphide bonds using Sire, then generate the correct `LEaP` bond command strings. For example, we could do something like following...

Okay, I've got this working on the [feature-disulphide](https://github.com/michellab/BioSimSpace/tree/feature-disulphide) branch. The actual function that generates the records is [here](https://github.com/michellab/BioSimSpace/blob/a0736b21452d23af9990efa27b4ed98ebb5a9541/python/BioSimSpace/Parameters/Protocol/_protocol.py#L567), which is basically the same as above with the addition of generating...

I had a quick Google and found a file with the same name in an AMBER tutorial [here](https://ambermd.org/tutorials/advanced/tutorial18/section1.htm). Using this, I only generate two bond records, i.e.: ```python import BioSimSpace...

I can get it to work by tuning the tolerance, but since the bond hunter is based on _covalent_ bonds, then I also need to tweak the maximum bond limit....

Thanks, that is also an option. To date we haven't parsed those records since they are often missing or incomplete, so it's hard to detect when things are wrong. Since...

Ah, didn't realise that Sire also has a `ChemicalBondHunter`. This appears to work perfectly (for this PDB) with the default settings. Perhaps we could autodetect things if `CONECT` records aren't...

I've made some edits to Sire to make the bond searching more flexible. The user can now specify the maximum search distance and a tolerance to use when comparing equilibrium...