'is_crystal' prevents setup for GROMACS Relative Free Energy files

[annamherz]

Hello! When writing FE input files for GROMACS using the newest version of BSS (devel branch from 11.03.2024) and sire 2023.3.0.dev (and python version 3.9.16) it is unable to proceed. I get the error with gromacs 22 and 23.

The error is as follows:

│ /home/anna/biosimspace/python/BioSimSpace/FreeEnergy/_relative.py:333 in __init__                │
│                                                                                                  │
│    330 │   │   self.difference = self._difference                                                │
│    331 │   │                                                                                     │
│    332 │   │   # Initialise the process runner.                                                  │
│ ❱  333 │   │   self._initialise_runner(self._system)                                             │
│    334 │                                                                                         │
│    335 │   def run(self, serial=True):                                                           │
│    336 │   │   """                                                                               │
│                                                                                                  │
│ /home/anna/biosimspace/python/BioSimSpace/FreeEnergy/_relative.py:2010 in _initialise_runner     │
│                                                                                                  │
│   2007 │   │   if self._engine == "SOMD":                                                        │
│   2008 │   │   │   system._set_water_topology("AMBER", property_map=self._property_map)          │
│   2009 │   │   elif self._engine == "GROMACS":                                                   │
│ ❱ 2010 │   │   │   system._set_water_topology("GROMACS", property_map=self._property_map)        │
│   2011 │   │                                                                                     │
│   2012 │   │   # Setup all of the simulation processes for each leg.                             │
│   2013                                                                                           │
│                                                                                                  │
│ /home/anna/biosimspace/python/BioSimSpace/_SireWrappers/_system.py:2383 in _set_water_topology   │
│                                                                                                  │
│   2380 │   │   │   │   │   self._sire_object, water_model, property_map                          │
│   2381 │   │   │   │   )                                                                         │
│   2382 │   │   │   else:                                                                         │
│ ❱ 2383 │   │   │   │   self._sire_object = _SireIO.setGromacsWater(                              │
│   2384 │   │   │   │   │   self._sire_object, water_model, property_map, is_crystal              │
│   2385 │   │   │   │   )                                                                         │
│   2386                                                                                           │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ArgumentError: Python argument types in
    sire.legacy.IO._IO.setGromacsWater(System, str, dict, bool)
did not match C++ signature:
    setGromacsWater(SireMol::SelectResult molecules, QString model, SireBase::PropertyMap map={})
    setGromacsWater(SireSystem::System system, QString model, SireBase::PropertyMap map={})

This is with the following python sample script and input ligands. If I remove is_crystal from line 2384, it is able to proceed and setup the input files. I'm not really sure why this is?

Thank you!

[lohedges]

Are you sure the sire version is correct? The latest devel versoin of BioSimSpace is only compatiblle with version 2024.1.0.dev of sire?

[annamherz]

Ah that would be it! I'm so sorry I completely missed checking that. It works when it's updated!

[lohedges]

No problem. The compatibility is only checked at the conda package level, so it wouldn't throw an error if you did a source install of BioSimSpace over the top of an old sire install.