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Update topology/system particle bookkeeping in OpenMM #1051

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Update topology/system particle bookkeeping in OpenMM #1051

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Commits on Sep 17, 2024

  1. TST: Reproduce issue #1049

    @mattwthompson
    mattwthompson committed Sep 17, 2024
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  2. API: De-collate virtual sites with OpenMM

    @mattwthompson
    mattwthompson committed Sep 17, 2024
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  3. DOC: Update example for virtual site change

    @mattwthompson
    mattwthompson committed Sep 17, 2024
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  4. DOC: Update docstrings and user guide

    @mattwthompson
    mattwthompson committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. TST: Test collating in to_openmm_topology

    @mattwthompson
    mattwthompson committed Sep 18, 2024
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  2. DOC: Update PDB docstring, release history

    @mattwthompson
    mattwthompson committed Sep 18, 2024
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