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Orientational Entropy for Molecules Other Than Water #27

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#294
Closed
Orientational Entropy for Molecules Other Than Water#27
#294
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feature requestNew feature or request
Milestone
v2.1.0

Description

@ioanaapapa
ioanaapapa
opened on Jan 30, 2025

Orientational entropy of molecules other than water - orientational entropy is only implemented for interfacial water molecules at present.

  • find neighbours per residue using RAD
  • implement orientational entropy for proteins/ligands using eq. from Higham et al.,2018 (10.1080/00268976.2018.1459002)

Activity

  1. ioanaapapa
    self-assigned this
    on Jan 30, 2025
  2. ioanaapapa
    added
    feature requestNew feature or request
    WP2
    on Jan 30, 2025
  3. jimboid
    added this to the milestone on Feb 3, 2025
  4. jimboid
    removed
    WP2
    on Feb 3, 2025

  5. jkalayan commented on Feb 5, 2025

    @jkalayan
    jkalayan
    on Feb 5, 2025
    Collaborator

    RAD shell entropy code can be imported from the waterEntropy package. Have a look at source code and docs for this here: https://waterentropy.readthedocs.io/en/latest/_modules/waterEntropy/neighbours/RAD.html#get_RAD_shell
    This can be extended for use with larger molecules and currently, RAD is used at the united-atom level.

  6. harryswift01
    closed this as completedon Mar 12, 2025
  7. skfegan
    reopened this on Mar 12, 2025
  8. jimboid
    removed this from the milestone on Jun 10, 2025
  9. harryswift01
    added this to the v1.2.0 milestone on Feb 2, 2026
  10. ioanaapapa
    removed their assignment
    on Feb 26, 2026
  11. skfegan
    linked a pull request that will close this issueIntroduce Basic Orientational Entropy Calculations #294on Mar 2, 2026
  12. skfegan
    closed this as completedin #294on Mar 13, 2026
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