Support for non-atomistic force fields about foyer HOT 10 CLOSED

I think an easy way would be to add an optional flag to this that dictates whether elements should be assigned or the name taken as is.

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It could be as easy as changing
element = elem.Element.getBySymbol(mb_particle.name)
to

try:
    element = elem.Element.getBySymbol(mb_particle.name)
except KeyError:
    element = mb_particle.name

From some quick testing it looks that openmm Atoms can have arbitrary element names.

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True, but we don't want to fail silently.

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We could include a flag in the except block that raises a warning after the topology has been built that warns the user that the element names for some particles could not be interpreted

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That should also be ok. Make sure you actually create a new OpenMM Atom object though instead of just using the string.

Also I would recommend adding a little cache like here so that the user doesn't get spammed with warnings for every instance of a missing atom name.

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Right, I was planning on just providing a single warning after the topology has been built.

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Any ideas on how to load a force field with atomtypes that contain non-periodic table element names? I think I've almost got it working if I can figure that part out.

It looks like atomtypes are loaded using this function, which calls a function of the same name in OpenMM. Currently if an atomtype is not one of those in the periodic table, then a KeyError is generated when a periodic table look-up is attempted by OpenMM.

My current line of thinking is doing something like this

def registerAtomType(self, parameters):
    actual_element = parameters['element']
    parameters['element'] = 'H'
    super(Forcefield, self).registerAtomType(parameters)
    # Somehow access the atomtype we just loaded in and change the element name to actual_element

I'm just not sure how to access the atomtype that has just been loaded to change the element name.

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This is the OpenMM function where that happens. You can either replicate this function entirely on our end and remove the super() or see if you can edit self._atomTypes and change the name of the specific one after creation.

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Cool, yeah it looks like editing self._atomTypes[parameters['name']].element should do the trick

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Preliminarily implemented

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