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Expand library of predefined solvents #4

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1 of 9 tasks
timbernat opened this issue Nov 17, 2023 · 0 comments
Open
1 of 9 tasks

Expand library of predefined solvents #4

timbernat opened this issue Nov 17, 2023 · 0 comments
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@timbernat
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enhancement New feature or request good first issue Good for newcomers planned-feature Changes or additons which are planned by the developer(s) priority:low Low-to-no urgency on a fix, issue is minor and pinned for awareness

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timbernat commented Nov 17, 2023 •
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Currently, the only solvent defined in openfftools.solvation.solvents is TIP3P water; would like to expand this library in the future to include charged structural SDF files for many common small-molecule solvents (e.g. ethanol, DCM, toluene, etc)

  • Introduce templates for common solvents
    • One-time setup for each solvent:
      • Obtain SMILES
      • Embed conformers
      • Charge w/ AM1-BCC-ELF10
      • Write to SDF files in openfftools.solvations.solvents
  • Implement more robust plugin system
    • Ship SDF files within package data
    • Find way to compile registry of available solvents/make accessible from within code
@timbernat timbernat added enhancement New feature or request planned-feature Changes or additons which are planned by the developer(s) labels Nov 17, 2023
@timbernat timbernat self-assigned this Nov 17, 2023
@timbernat timbernat added the good first issue Good for newcomers label Oct 18, 2024
@timbernat timbernat added the priority:low Low-to-no urgency on a fix, issue is minor and pinned for awareness label Dec 12, 2024
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enhancement New feature or request good first issue Good for newcomers planned-feature Changes or additons which are planned by the developer(s) priority:low Low-to-no urgency on a fix, issue is minor and pinned for awareness
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