Code

Feature Multiple Distance Restraints#178

Code

Merged

lohedges merged 25 commits intoOpenBioSim:develOpenBioSim/biosimspace:develfrom fjclark:feature_mdrfjclark/biosimspace-openbiosim:feature_mdrCopy head branch name to clipboardDec 4, 2023

+2,013-236

Commits

Commits on Aug 8, 2023

• Update _restraint.py to handle multiple distance restraints

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  fjclark

  committed
  6bae2d5

• Update names of all Boresch restraint tests

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  0c78c6b

• Check correct keys in multiple distance restraints dict

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  64dd2aa

• Add tests for multiple distance restraints and fix bugs this revealed

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  fd400b8

• Write input files for multiple distance restraints

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  fjclark

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  6d9b629

Commits on Aug 9, 2023

• Change access of pandas series to avoid deprecation warning

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  5dc9585

Commits on Aug 10, 2023

• Add first version of multiple distance restraints derivation algorithm

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  67b4382

Commits on Aug 15, 2023

• Ensure that atom record is always written

  

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  8cd3986

Commits on Sep 1, 2023

• Correct SOMD pert files

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  eb41a90

• Merge branch 'devel' into feature_mdr

  

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  8d89a05

• Fix sandpit CI

  

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  0fe2fe4

• Fix issue with checking alchemlyb version number

  

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  8e722eb

Commits on Sep 21, 2023

• Make restraint search more robust for multiple distance restraints

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  514370e

Commits on Oct 2, 2023

• Add more tests of mdr restraint search algorithm

  

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  f5d1743

• Merge branch 'devel' into feature_mdr

  

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  16d00d0

Commits on Nov 8, 2023

• Merge branch 'devel' into feature_mdr

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  a61bbc0

Commits on Nov 14, 2023

• Add tests for MDR restraints dict

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  9971a7b

• Implement multiple distance restraints for GROMACS

  Show description for edf8294
  fjclark

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  edf8294

• Merge branch 'feature_mdr' of https://github.com/fjclark/biosimspace-openbiosim into feature_mdr

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  f8098bf

• Merge branch 'feature_mdr_gromacs' into feature_mdr

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  a8aeb71

• Merge branch 'devel' into feature_mdr

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  35b237f

• Require that gromacs process is passed free energy protocol if restraint is supplied

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  e33539f

• Update changelog with MDR implementation

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  a8b56d0

Commits on Nov 18, 2023

• Add warning about SOMD instabilities with decoupled ligands [ci skip]

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  6655bfd

Commits on Nov 21, 2023

• Remove duplicate mention of scikit-learn in dependencies [ci skip]

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  8025d4a