Commits · d755f53e75b12a450a7ffc5a8bf1bc28fe7b916d · Martin Larralde / peptides.py · GitLab

26 Oct, 2021 1 commit
- Fix missing publication year in docs `index.rst` [ci skip] · d755f53e
  Martin Larralde authored Oct 26, 2021
  
  d755f53e
25 Oct, 2021 7 commits
- Release v0.2.0 · 88983a8d
  Martin Larralde authored Oct 25, 2021
  
  88983a8d
- Rewrite `auto_correlation` and `hydrophobicity` using vectorized code · bb116938
  Martin Larralde authored Oct 25, 2021
  
  bb116938
- Rewrite some `Peptide` methods to use `numpy` or pseudovectorization with `array.array` · 08df9ca4
  Martin Larralde authored Oct 25, 2021
  
  08df9ca4
- Improve `README.md` with list of features and reference to documentation · 2b1e7997
  Martin Larralde authored Oct 25, 2021
  
  2b1e7997
- Add some JS scripts to improve the styling of the documentation · a5efc8a6
  Martin Larralde authored Oct 25, 2021
  
  a5efc8a6
- Fix broken links in documentation index · f4956f27
  Martin Larralde authored Oct 25, 2021
  
  f4956f27
- Use `sphinx.ext.extlinks` to provide publication links via DOI and PMID · bed751e6
  Martin Larralde authored Oct 25, 2021
  
  bed751e6
24 Oct, 2021 7 commits
- Add support for Bayes discriminant distance in `Peptide.structural_class` · a525c537
  Martin Larralde authored Oct 24, 2021
  
  a525c537
- Add eigendecomposition tables for Nakashima (1986) dataset · a44ef145
  Martin Larralde authored Oct 24, 2021
  
  a44ef145
- Implement the Mahalanobis distance prediction of structural class from Chou & Zhang (1995) · 667f7c55
  Martin Larralde authored Oct 24, 2021
  
  667f7c55
- Rewrite AST generation code to be generic over the literal type · 7631e195
  Martin Larralde authored Oct 24, 2021
  
  7631e195
- Reorganise data tables location and storage management · e5ba847c
  Martin Larralde authored Oct 24, 2021
  
  e5ba847c
- Add a *To-Do* section to `Peptides.structural_property` · 30f88bea
  Martin Larralde authored Oct 24, 2021
  
  30f88bea
- Add method to predict the structural class of a peptide · 9eb6fd7b
  Martin Larralde authored Oct 24, 2021
  
  9eb6fd7b
23 Oct, 2021 18 commits
- Add vectors described in Sneath (1966) · 76840b5a
  Martin Larralde authored Oct 24, 2021
  
  76840b5a
- Add the hydrophilicity scale and descriptors from Barley (2018) · a89c16a0
  Martin Larralde authored Oct 23, 2021
  
  a89c16a0
- Mention EMBOSS, ExPASy and Rcpi as code and data sources in docs · 33913667
  Martin Larralde authored Oct 23, 2021
  
  33913667
- Add PCP descriptors from Venkatarajan *et al.* (2001) · 8db5dc62
  Martin Larralde authored Oct 23, 2021
  
  8db5dc62
- Fix path to CSS stylesheets in `docs/conf.py` · e1536a98
  Martin Larralde authored Oct 23, 2021
  
  e1536a98
- Add a docstring to the `Peptide.__init__` method · 2dfc146c
  Martin Larralde authored Oct 23, 2021
  
  2dfc146c
- Fix some documentation styling issues in the CSS · 6f01cfbc
  Martin Larralde authored Oct 23, 2021
  
  6f01cfbc
- Add missing syntax-highlighting dependencies to `docs/requirements.txt` · 96d0ac7b
  Martin Larralde authored Oct 23, 2021
  
  96d0ac7b
- Fix build of documentation in ReadTheDocs environment · 9e195a4c
  Martin Larralde authored Oct 23, 2021
  
  9e195a4c
- Fix code generation in `setup.py` to work with older Python versions · 452863a0
  Martin Larralde authored Oct 23, 2021
  
  452863a0
- Add `astor` to the documentation dependencies · cd6d27b1
  Martin Larralde authored Oct 23, 2021
  
  cd6d27b1
- Add Sphinx configuration files to build the project documentation · f720d063
  Martin Larralde authored Oct 23, 2021
  
  f720d063
- Update `setup.py` to generate `array` look-up tables instead of using `dict` tables · c6340958
  Martin Larralde authored Oct 23, 2021
  
  c6340958
- Swap order of `Peptide.hydrophobic_moment` for consistency with profile methods · a530e3ef
  Martin Larralde authored Oct 23, 2021
  
  a530e3ef
- Add methods to get the occurrences and frequencies of amino acids in a `Peptide` · f17721db
  Martin Larralde authored Oct 23, 2021
  
  f17721db
- Update `Peptide.aliphatic_index` to support unknown Leu/Ile residues (code J) · 2ed5b2c6
  Martin Larralde authored Oct 23, 2021
  
  2ed5b2c6
- Update all methods to support unknown amino-acids in input sequences · a8458c33
  Martin Larralde authored Oct 23, 2021
  
  a8458c33
- Add class method to generate a random `Peptide` with fixed AA frequencies · a0f5563a
  Martin Larralde authored Oct 23, 2021
  
  a0f5563a
22 Oct, 2021 2 commits
- Add documentation and references to all the descriptor methods · 9c6f8e11
  Martin Larralde authored Oct 22, 2021
  
  9c6f8e11
- Add more documentation and references to the methods for physical properties · ae06648a
  Martin Larralde authored Oct 22, 2021
  
  ae06648a
21 Oct, 2021 5 commits
- Release v0.1.0 · b045c0d2
  Martin Larralde authored Oct 21, 2021
  
  b045c0d2
- Reformat `peptides/__init__.py` code with `black` · 4562d25c
  Martin Larralde authored Oct 21, 2021
  
  4562d25c
- Add remaining missing type hints to `peptides/__init__.py` · 0a7b93c2
  Martin Larralde authored Oct 21, 2021
  
  0a7b93c2
- Implement methods computing several profiles for the whole peptide · 28104f14
  Martin Larralde authored Oct 21, 2021
  
  28104f14
- Add a `py.typed` marker file to the `peptides` module · 24bea734
  Martin Larralde authored Oct 21, 2021
  
  24bea734