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Expose molecule-virtual site map #1076

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mattwthompson opened this issue Oct 9, 2024 · 1 comment
Open

Expose molecule-virtual site map #1076

mattwthompson opened this issue Oct 9, 2024 · 1 comment
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enhancement New feature or request

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@mattwthompson
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Description
Please describe the behavior you would like added to Interchange.

#1051 (comment)

(Need to add more context)

@mattwthompson
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Not finalized, but in #1081 I'm exposing a mapping (dict[int, list[_BaseVirtualSiteKey]]) between molecule indices and the virtual sites included in them. Here's an example of a TIP4P dimer:

In [7]: imported.topology._molecule_virtual_site_map
Out[7]:
defaultdict(list,
            {0: [ImportedVirtualSiteKey with orientation atom indices (0, 1, 2)],
             1: [ImportedVirtualSiteKey with orientation atom indices (3, 4, 5)]})

In English: molecules 0 and 1 each have (1-length) lists of virtual sites, each list containing some information about the atoms they're associated with.

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