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T019: Fix atom unit conversion #306

Merged
merged 6 commits into from
Dec 28, 2022
Merged

T019: Fix atom unit conversion #306

merged 6 commits into from
Dec 28, 2022

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dominiquesydow
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@dominiquesydow dominiquesydow commented Dec 28, 2022 •
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Description

Fix problem as described in #298

Todos

  • Change atom.unit to atom.units
  • Fix Angström to nm conversion with pint(mol_positions.to("nanometers"))
  • Also: fix openmm warning - import simtk.openmm is now `openmm``
  • Also: Add MacOS/M1 conda note (CONDA_SUBDIR=osx=64)
  • Also: T019 runs for ages (>12 min) in CI!!!! Try using mamba instead of conda to install openmmforcefield within T019 > it seems to have worked, now only 2 min!!
  • Test only T019 (for now) - revert back to all notebooks in T019: Fix "No template found for residue 444 (03P)" #308

Status

  • Ready to go

@dominiquesydow dominiquesydow self-assigned this Dec 28, 2022
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@dominiquesydow dominiquesydow added the bug Something isn't working label Dec 28, 2022
@dominiquesydow dominiquesydow changed the title T019 openmm unit T019: Change atom.unit to atom.units Dec 28, 2022
@dominiquesydow dominiquesydow linked an issue Dec 28, 2022 that may be closed by this pull request
T019: AttributeError: 'numpy.ndarray' object has no attribute 'unit' #298
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@dominiquesydow dominiquesydow mentioned this pull request Dec 28, 2022
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@dominiquesydow dominiquesydow merged commit cec5d3b into base-ci-env-fix Dec 28, 2022
@dominiquesydow dominiquesydow deleted the t019-openmm-unit branch December 28, 2022 22:59
@dominiquesydow dominiquesydow changed the title T019: Change atom.unit to atom.units T019: Fix atom unit conversion Dec 28, 2022
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T019: AttributeError: 'numpy.ndarray' object has no attribute 'unit'
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