Code

Release 2023.5.0#228

Code

Merged

lohedges merged 96 commits intomainOpenBioSim/biosimspace:mainfrom release_2023.5.0OpenBioSim/biosimspace:release_2023.5.0Copy head branch name to clipboardDec 16, 2023

+2,883-640

Commits

Commits on Aug 8, 2023

• Update _restraint.py to handle multiple distance restraints

  Show description for 6bae2d5
  fjclark

  committed
  6bae2d5

• Update names of all Boresch restraint tests

  fjclark

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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

  fjclark

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  fd400b8

• Write input files for multiple distance restraints

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  fjclark

  committed
  6d9b629

Commits on Aug 9, 2023

• Change access of pandas series to avoid deprecation warning

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  committed
  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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  Finlay Clark

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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 Oct 13, 2023

• Update Sire version.

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  f4fdf3e

Commits on Oct 18, 2023

• Add support for restraining backbone atoms in nucleic acids

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  a593b35

• Merge branch 'devel' into feature_rna_backbone

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  e098add

• Correct names of nucleic acid backbone atoms

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  d3fcd46

Commits on Oct 22, 2023

• Use regex mode to allow searching for atom names containing '

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  fjclark

  committed
  4ff8e23

Commits on Oct 23, 2023

• Ensure that amber restraint mask only contains atoms present in the

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  fjclark

  committed
  7f5fc87

• Pass match_water through to specialised water model functions.

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  lohedges

  committed
  3d3ed62

• Test generic solvate function as well as specialised tip3p function.

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  d55d93f

• Use sandpit conftest.

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  222f2c8

Commits on Oct 24, 2023

• Hide residue name lists and improve search functions

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  fjclark

  committed
  fe68da3

• Add tests for RNA backbone restraint functionality

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  429dfc6

• Copy nucleic acid backbone restraint functionality to Sandpit

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  committed
  98ec277

• Merge pull request #190 from OpenBioSim/fix_185_devel

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  lohedges

  authored
  0095314

• Test return type of residue searches [ci skip]

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  committed
  609cca8

• Ensure that residue search functions always return residues [ci skip]

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  fjclark

  committed
  0ae9a3d

• Merge pull request #189 from fjclark/feature_rna_backbone

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  lohedges

  authored
  cb92227

Commits on Oct 27, 2023

• Check perturbable molecules for velocity property. [closes #192]

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  f234669

• Remove end-state velocity property from perturbable molecules.

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  accc097

Commits on Oct 31, 2023

• Merge pull request #193 from OpenBioSim/fix_192

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  lohedges

  authored
  4b0ba24

Commits on Nov 7, 2023

• Handle multiple velocity properties per molecule. [closes #196]

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  7d35a09

• Can now use inequality operator.

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  946c009

• Add test for property preservation during water topology swap.

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  lohedges

  committed
  cc40607

• Only try to remove perturbable velocities if they are present.

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  ae1be67

Commits on Nov 8, 2023

• Fix parameterisation function used for crystal waters. [ci skip]

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  9ca43e4

• Merge pull request #197 from OpenBioSim/fix_196

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  lohedges

  authored
  7b77a26

• Merge branch 'devel' into feature_mdr

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  committed
  a61bbc0

Commits on Nov 10, 2023

• Remove redundant __ne__ operator. [closes #200]

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  e58a9c8

• Rename test.

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  7d9fe7a

• Merge pull request #201 from OpenBioSim/fix_200

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  lohedges

  authored
  621149b

Commits on Nov 13, 2023

• Sire.IO.AmberRst7.box_angles now returns correct units.

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  lohedges

  committed
  c011e22

• Now cursor.rotate rotates velocities too.

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  lohedges

  committed
  84660b2

• Still need to apply units to angles.

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  90c476f

• Avoid inserting pair into boresch_dof_data until after try except block

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  fjclark

  committed
  bf82a68

• Update changelog with restraint bugfix PR [ci skip]

  fjclark

  committed
  ec6306e

• Merge pull request #203 from OpenBioSim/fix_sire_api_updates

  Show description for d1d0acb
  lohedges

  authored
  d1d0acb

Commits on Nov 14, 2023

• Add tests for MDR restraints dict

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  committed
  9971a7b

• Add missing rotate_velocities=False.

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  2f7f76e

• Merge pull request #204 from fjclark/devel

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  lohedges

  authored
  66512f2

• Add devel section to CHANGELOG with upcoming changes. [ci skip]

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  92999ad

• Implement multiple distance restraints for GROMACS

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  fjclark

  committed
  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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• 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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  committed
  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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• Merge remote-tracking branch 'upstream/main' into feat_2023.4

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• Sire 2023.4

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  08d9f85

Commits on Nov 22, 2023

• Fix renumber option in extract method. [closes #208]

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  f5ac207

Commits on Nov 27, 2023

• Merge pull request #31 from Exscientia/feat_2023.4

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  xiki-tempula

  authored
  3c19b75

Commits on Dec 1, 2023

• Reconstruct intrascale matrices using the GroTop parser. [closes #213]

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  committed
  645ad53

Commits on Dec 4, 2023

• Merge pull request #178 from fjclark/feature_mdr

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  lohedges

  authored
  755103e

• Merge branch 'devel' into fix_208

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  committed
  27f137a

• Update CHANGELOG. [ci skip]

  lohedges

  committed
  943ea5c

• Merge pull request #210 from OpenBioSim/fix_208

  Show description for fe41a76
  lohedges

  authored
  fe41a76

Commits on Dec 6, 2023

• Fix imports in metadynamics driver script. [closes #215]

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  3ca9d3f

• Make sure force constant parameters have unique names. [closes #216]

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  committed
  407835f

Commits on Dec 7, 2023

• Use existing backend to get the trajectory from the process.

  Show description for d3e74dd
  lohedges

  committed
  d3e74dd

Commits on Dec 8, 2023

• bugfix: addtoconfig is not a function in _amber.py, add to protocol dict instead

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  0348d07

• Merge pull request #220 from annamherz/devel

  Show description for c46fd7c
  lohedges

  authored
  c46fd7c

• Match all atom names starting with H. [closes #221]

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  committed
  122f9fb

• Merge pull request #217 from OpenBioSim/fix_215_216

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  authored
  d9569df

• Merge pull request #219 from OpenBioSim/fix_218

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  authored
  3976503

Commits on Dec 11, 2023

• Merge pull request #222 from OpenBioSim/fix_221

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  lohedges

  authored
  7869803

• Make sure disulphide search is converted to a SelectorBond.

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  lohedges

  committed
  bb6b27b

• Fix custom parameters for AMBER protein force fields. [closes #225]

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  c6a271b

• Update docstrings.

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  68e5cb6

Commits on Dec 12, 2023

• Split into pre_mol_commands and post_mol_commands.

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  committed
  5ce764f

• Merge pull request #224 from OpenBioSim/fix_223

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  lohedges

  authored
  d86dc9f

• Merge branch 'devel' into fix_225

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  committed
  02ca3bf

Commits on Dec 14, 2023

• Merge pull request #226 from OpenBioSim/fix_225

  Show description for b17b7c2
  lohedges

  authored
  b17b7c2

• Update CHANGELOG. [ci skip]

  lohedges

  committed
  2920392

• Update example use of additional LEaP commands. [ci skip]

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  committed
  233d87e

Commits on Dec 15, 2023

• Merge tag '2023.4.1' into feat_update

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  committed
  1527a6b

• Merge pull request #32 from Exscientia/feat_update

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  xiki-tempula

  authored
  5654db4

• Merge remote-tracking branch 'exscientia/devel' into sync_exscientia

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  3147810

• Fix typo in test name.

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  2cb6535

• Merge pull request #227 from OpenBioSim/sync_exscientia

  Show description for 2bc01f2
  lohedges

  authored
  2bc01f2

Commits on Dec 16, 2023

• Update Sire version.

  lohedges

  committed
  bf7e151

• Update CHANGELOG for the 2023.5.0 release.

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  committed
  85d609a