Code

Feature/dssp#4304

Code

Merged

orbeckst merged 86 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom marinegor:feature/dsspmarinegor/mdanalysis:feature/dsspCopy head branch name to clipboardJun 18, 2024

+876-1

Commits

Commits on Sep 29, 2023

• Add DSSP test files

  marinegor

  committed
  5065e2d

• Add DSSP test files

  marinegor

  committed
  1dfdb29

• First implementation of DSSP class

  marinegor

  committed
  f73fcda

• Remove pydssp dependency

  marinegor

  committed
  fe66c30

• Add documentation

  marinegor

  committed
  13bc86a

• Fix hydrogen selection issue

  marinegor

  committed
  cf79a89

• Remove unnecessary print

  marinegor

  committed
  7230845

Commits on Oct 2, 2023

• Fix problem with prolines and add example with average secondary structure in trajectory

  marinegor

  committed
  929d011

• Fix pep8 formatting issues

  marinegor

  committed
  7c966d5

• Fix pep8 formatting issues

  marinegor

  committed
  a5a4891

Commits on Oct 4, 2023

• Replace ndarray in results with list, and remove unnecessary code

  marinegor

  committed
  c2a333c

• Add documentation for translate

  marinegor

  committed
  bd5ba75

Commits on Oct 11, 2023

• Added a reference to Kabsch 983 DSSP paper

  marinegor

  committed
  0d6f734

Commits on Nov 24, 2023

• Update documentation and formatting

  marinegor

  committed
  8840d9b

Commits on Jan 14, 2024

• Make numpy docstrings

  marinegor

  committed
  c6fca72

• Compress dssp pdb files

  marinegor

  committed
  20e672f

• Update documentation and add trajectory tests

  marinegor

  committed
  47c4123

• Fix pep8 in docstrings and add pydssp license info

  marinegor

  committed
  c4cf7c9

• Add versionadded

  marinegor

  committed
  de2133d

• Merge remote-tracking branch 'upstream/develop' into feature/dssp

  marinegor

  committed
  60e9f13

• Update changelog

  marinegor

  committed
  603d209

• Fix datafiles DSSP error

  marinegor

  committed
  6044372

• Add einops as dependency to analysis

  marinegor

  committed
  78b5a4f

• Move einops as required dependency

  marinegor

  committed
  2bd0af5

• Move einops to install_requires

  marinegor

  committed
  21a9403

Commits on Jan 15, 2024

• Move einops to analysis dependencies

  marinegor

  committed
  a15ed16

• Add skipped tests if einops not present

  marinegor

  committed
  8161c55

• Fix dssp test without einops

  marinegor

  committed
  b0093fe

Commits on Feb 6, 2024

• Remove _check_input function

  marinegor

  committed
  f947c04

• Rewrite get_hbond_map function

  marinegor

  committed
  3493443

• Correct helix detection but bug in loops

  marinegor

  committed
  9d34e49

• Remove unnecessary print

  marinegor

  committed
  30c958e

• Fix big with loops

  marinegor

  committed
  4c6c2a8

• Implement no-einops dssp

  marinegor

  committed
  3eb3058

• Moved dssp into separate module and separated original pydssp and my implementation

  marinegor

  committed
  a3c386a

• Add pydssp as analysis dependency

  marinegor

  committed
  1a4d4b8

• Update package/pyproject.toml

  Show description for 82334c7
  

  Egor Marin

  and

  orbeckst

  authored
  82334c7

• Add suggestions from code review

  marinegor

  committed
  edcb713

Commits on Feb 7, 2024

• Remove pydssp from pyproject.toml and add section in documentation

  marinegor

  committed
  04e33ae

• Update documentation

  marinegor

  committed
  f7e4ac0

• Merge with develop

  marinegor

  committed
  1baf1e2

• Add @Due for DSSP by Kabsch

  marinegor

  committed
  f31d6f5

Commits on Feb 23, 2024

• Update package/MDAnalysis/analysis/dssp/dssp.py

  Show description for 742e19d
  

  Egor Marin

  and

  orbeckst

  authored
  742e19d

• Update package/MDAnalysis/analysis/dssp/dssp.py

  Show description for 47ef5ad
  

  Egor Marin

  and

  orbeckst

  authored
  47ef5ad

• Fix documentation

  marinegor

  committed
  530ca0c

• Fix documentation issues

  marinegor

  committed
  c0fdd99

• Fix code formatting and add coverage exceptions

  marinegor

  committed
  118be27

• Add dssp entry for documentation

  marinegor

  committed
  8c33e83

• Add one more no cover pragma

  marinegor

  committed
  25dae6f

• Remove unnecessary get_hbond_map import

  marinegor

  committed
  ac6f063

• Move shape check to _prepare and add respective test

  marinegor

  committed
  42392f2

Commits on Feb 24, 2024

• Fix DSSP documentation issues

  marinegor

  committed
  8de3630

• Fix test for uneven number of atoms in universe

  marinegor

  committed
  5a21c9a

• Add entry for pydssp in LICENSE

  marinegor

  committed
  864a43e

Commits on Feb 26, 2024

• Merge remote-tracking branch 'upstream/develop' into feature/dssp

  marinegor

  committed
  001ce41

• Add DSSP entry to testuite/pyproject.toml

  marinegor

  committed
  5b04387

Commits on Mar 25, 2024

• Merge branch 'develop' into feature/dssp

  orbeckst

  authored
  1484c5d

Commits on Apr 8, 2024

• Apply suggestions from code review

  Show description for 9c28640
  

  3 peopleauthored
  9c28640

• Add AtomGroup to DSSP

  marinegor

  committed
  7b30cdd

• Fix documentation in pydssp_numpy

  marinegor

  committed
  2d9efec

• Add test for AtomGroup in DSSP

  marinegor

  committed
  ebaf90a

• Move functions after DSSP class

  marinegor

  committed
  5b783b3

• Fix docs in DSSP.translate

  marinegor

  committed
  e203ab8

• Fix citations

  marinegor

  committed
  579a5f0

• Fix merge conflicts

  marinegor

  committed
  81112d4

Commits on Apr 9, 2024

• Update references.bib

  yuxuanzhuang

  authored
  38d6d1f

• add reference

  yuxuanzhuang

  authored
  5c2fddf

• move functions below classes

  yuxuanzhuang

  authored
  428e892

Commits on Apr 18, 2024

• Improve selection syntax and add configurable selection names

  marinegor

  committed
  15ab7f5

• Remove unnecessary nocover pragmas

  marinegor

  committed
  dcf22fe

Commits on Apr 19, 2024

• Apply suggestions from codereview

  marinegor

  committed
  eb10f00

• Make sure I add duecredit test

  marinegor

  committed
  858bef0

• Update hydrogen_name description with a Note

  marinegor

  committed
  99b2164

• Add print line in dssp documentation

  marinegor

  committed
  58c24c1

Commits on May 3, 2024

• Merge branch 'develop' into feature/dssp

  orbeckst

  authored
  610b39f

• Delete test_dssp.py

  Show description for f50f5c3
  orbeckst

  authored
  f50f5c3

• Update testsuite/MDAnalysisTests/analysis/test_dssp.py

  orbeckst

  authored
  848060e

Commits on May 29, 2024

• Update class documentation with "hydrogen_atom" argument explanation

  marinegor

  committed
  84dd012

Commits on Jun 12, 2024

• Add check for exactly 1 hydrogen on the atom

  

  Egor Marin

  committed
  ebcab2f

• Apply suggestions from code review

  Show description for f4daa24
  

  marinegor

  and

  orbeckst

  authored
  f4daa24

• Generalize hydrogen checks

  

  Egor Marin

  committed
  2fef313

• Merge remote-tracking branch 'origin/feature/dssp' into feature/dssp

  

  Egor Marin

  committed
  daf6529

Commits on Jun 13, 2024

• minor dssp reST fixes & updates

  orbeckst

  authored
  884630d

• fix dssp doc

  orbeckst

  authored
  8d503a2

• fixed docs for DSSP.results

  Show description for 5438877
  orbeckst

  authored
  5438877

• Update dssp.py

  orbeckst

  authored
  d3d2cf2