[2] Coord gen new #29
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| from polyply.src.generate_templates import (_atoms_in_node, find_atoms, | ||
| _expand_inital_coords, | ||
| compute_volume, map_from_CoG, | ||
| extract_block, GenerateTemplates) |
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from ... import (
_atoms_in_node, ...
)
| del interaction.parameters[-1] | ||
| for param in values: | ||
| interaction.parameters.append(param) | ||
| interaction.parameters[:] = new_parameters[:] |
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This requires interaction.parameters to always be a list (and not e.g. a tuple). I'm not sure we can make that guarantee.
You can use interaction._replace [1] to create a new interaction with the parameters replaced. You'd then still need to replace the interaction with the new one, but that is guaranteed to be a list.
[1] https://docs.python.org/2/library/collections.html#collections.somenamedtuple._replace
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I think we can. It is for sure a list as it comes out of the topology parser and the namedtuple clearly is setting the attribute as list. So it would be problematic when a programmer uses the function in their own code assuming it can be something else than a list. Although this can happen I think the chance is fairly small here. Let's put this up as an issue for enhancement, because using the replace doesn't propagate as easily all the way back. You need to replace and delete all old interaction lists and then all blocks in the force-field. I wish the named tuple had a replace function.
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Tuples are immutable, so that makes sense.
What I meant is that Molecule.interactions is guaranteed a dict[str, list]. So you could do something like my_block.interactions[idx] = interaction._replace(parameters=new_parameters). But it's also fine to leave this until it breaks. Be sure to test this behaviour though!
| comb_funcs = {1.0: lorentz_berthelot_rule, | ||
| 2.0: geometric_rule, | ||
| 3.0: lorentz_berthelot_rule} |
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I still don't know why these are floats.
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Because the gromacs default section allows the combination rule number to either be a float or an int. I don't want to type cast them as int in the parser on the one hand as this does not adhere to what is actually written in the file and on the other hand it saves some lines in the parser. I put a comment though.
…node-key, more tests
[2] Coord gen new
Hi,
This is part two of the coordinate generator namely the actual coord generator.
Enjoy!
Fabian