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Fix issue #284 #287

Merged
merged 2 commits into from
May 16, 2024
Merged

Fix issue #284 #287

merged 2 commits into from
May 16, 2024

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lohedges
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@lohedges lohedges commented May 7, 2024

This PR closes #284 by using SDF as the intermediate format for antechamber if the original molecule was loaded from that format, otherwise PDB is used. This mirrors the functionality used for the OpenFF protocol. A more general solution could be to allow the user to specify the intermediate format, but I'm not sure if this is needed at this time.

The fix has been tested by the author of issue #284. They are unable to share the molecule in question so I haven't added a unit test at this time.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

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@chryswoods

@lohedges lohedges added the bug Something isn't working label May 7, 2024
@lohedges lohedges requested a review from chryswoods May 7, 2024 17:19
@lohedges lohedges temporarily deployed to biosimspace-build May 7, 2024 17:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build May 7, 2024 17:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build May 7, 2024 17:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build May 7, 2024 17:19 — with GitHub Actions Inactive
@lohedges lohedges mentioned this pull request May 13, 2024
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👍

@lohedges lohedges merged commit aae9347 into devel May 16, 2024
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@lohedges lohedges deleted the fix_284 branch May 16, 2024 11:33
lohedges added a commit that referenced this pull request May 16, 2024
lohedges added a commit that referenced this pull request May 16, 2024
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Option to write parameterisation intermediary file in SDF format to retain bond information
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