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Residue Bonded Axes - #319

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ioanaapapa wants to merge 69 commits into

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26-residue-bonded-axes

Commits on Mar 12, 2026
- data_container at UA level is now formed of a residue group and customised axes for rotation at residue level are introduced
  ioanaapapa
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  9920253
Commits on Mar 17, 2026
- update from main
  ioanaapapa
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  4e230ec
Commits on Mar 25, 2026
- added new functions to find custom backbone
  ioanaapapa
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  f1de766
Commits on Mar 31, 2026
- match backbone of last residue to that of previous residue
  ioanaapapa
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  aa9a523
- fix getting name of second to last terminal atom
  ioanaapapa
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  138e770
- fix getting name of second to last terminal atom
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  9e1a3b0
- fix getting backbone for last residue
  ioanaapapa
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  3fba88e
Commits on Apr 1, 2026
- backbone is now returned as MDAnalysis atom group; backbone COM is used as center rather than average position of atoms
  ioanaapapa
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  e3f4eaf
Commits on Apr 15, 2026
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  c2c1e2a
Commits on Apr 17, 2026
- draft new function to compute residue axes independent of residue neighbours
  ioanaapapa
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  a366d9a
- residue rotation axes are determined from center of rotation + two edge atoms
  ioanaapapa
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  bd9d6f6
Commits on Apr 20, 2026
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  ca38da3
Commits on Apr 22, 2026
- tidied up
  ioanaapapa
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  11b726c
- tidied up
  ioanaapapa
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  d989636
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  b5340fc
- corrections to get_residue_custom_axes
  ioanaapapa
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  9d7948b
- removed debugging print statements
  ioanaapapa
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  64a5187
Commits on Apr 24, 2026
Commits on Apr 27, 2026
- removed duplicate return statement
  ioanaapapa
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  3052c66
Commits on Apr 28, 2026
- changed tests to include res_position
  ioanaapapa
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  4fe8f26
- added comments to described new axis method
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  a939741
- O
  ioanaapapa
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  03351d9
Commits on Apr 30, 2026
- fix for 1 heavy atom case
  ioanaapapa
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  9f15b7e
- changed tests to match code changes
  ioanaapapa
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  5da1d6a
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  94cf45c
Commits on May 1, 2026
- fixed translation centre for single heavy atom case
  ioanaapapa
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  af80571
Commits on May 11, 2026
- changed test_get_UA_axes_raises_when_bonded_axes_fail
  ioanaapapa
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  9d1e3b7
Commits on Jun 1, 2026
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
  committed
  6a5e44a
Commits on Jun 8, 2026
- correction for single heavy atom case
  ioanaapapa
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  9694ad1
Commits on Jun 9, 2026
- changed residue level test for vanilla axes
  ioanaapapa
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  f5d5431
Commits on Jun 10, 2026
- updated tests and removed redundant 1 heavy atom code
  ioanaapapa
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  9a8aae0
- updated unit tests
  ioanaapapa
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  6b4a2d8
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  7c782cd
- modified dna regression tests to match results with new custom axes
  ioanaapapa
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  620c22d
- changed dna selection subset regression test
  ioanaapapa
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  246c72b
Commits on Jun 11, 2026
- changed residue axes to match NCC for proteins
  ioanaapapa
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  6be94e6
Commits on Jun 12, 2026
- axes change to make more similar to NCC
  ioanaapapa
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  1f47e6b
- corrected center of mass
  ioanaapapa
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  25d0150
- centre of rotation correction
  ioanaapapa
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  e9d3cfc
- centre of rotation correction
  ioanaapapa
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  828bde0
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  b46263a
Commits on Jun 22, 2026
- fix atom is not subscriptable error
  ioanaapapa
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  d8fe042
- updates baselines
  ioanaapapa
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  ec0c030
- updated baselines
  ioanaapapa
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  950e411
- will add unit tests for new lines of code
  ioanaapapa
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  d8be74d
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
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  d7dac35
- updated tests
  ioanaapapa
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  166937f
- updated unit tests
  ioanaapapa
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  c7eac7d
- update covariance unit tests
  ioanaapapa
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  9c1ec28
- fix test for building ua vectors with vanilla axes
  ioanaapapa
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  5987746
Commits on Jun 29, 2026
- updated documentation
  ioanaapapa
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  1e6cd56
Commits on Jul 1, 2026
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
  authored
  0c69554
Commits on Jul 2, 2026
Commits on Jul 3, 2026
- bug fixes for atom selection when atom selection does not start from resindex 0
  ioanaapapa
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  99b6a68
Commits on Jul 10, 2026
- added unit test for get_UA_axes
  ioanaapapa
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  759dbed
- matched tests to relative residue position
  ioanaapapa
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  d8389b5
Commits on Jul 22, 2026
- removed redundant conversion into atom group
  ioanaapapa
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  3e115bb
- updated baselines for regression test
  ioanaapapa
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  72841b7
- update regression tests to match new axes
  ioanaapapa
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  dcb04d1
Commits on Jul 24, 2026
- remove forgotten debug print statement
  ioanaapapa
  committed
  c28a351
- Merge branch 'main' into 26-residue-bonded-axes
  ioanaapapa
  committed
  8fe405c

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