mutadock 1.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (51) hide show
  1. mutadock-1.1/.github/workflows/python-package.yml +41 -0
  2. mutadock-1.1/.gitignore +4 -0
  3. mutadock-1.1/.readthedocs.yaml +28 -0
  4. mutadock-1.1/LICENSE +674 -0
  5. mutadock-1.1/PKG-INFO +95 -0
  6. mutadock-1.1/README.md +67 -0
  7. mutadock-1.1/docs/Makefile +20 -0
  8. mutadock-1.1/docs/_build/doctrees/environment.pickle +0 -0
  9. mutadock-1.1/docs/_build/doctrees/index.doctree +0 -0
  10. mutadock-1.1/docs/_build/html/.buildinfo +4 -0
  11. mutadock-1.1/docs/_build/html/_sources/index.rst.txt +106 -0
  12. mutadock-1.1/docs/_build/html/_static/alabaster.css +663 -0
  13. mutadock-1.1/docs/_build/html/_static/basic.css +925 -0
  14. mutadock-1.1/docs/_build/html/_static/custom.css +1 -0
  15. mutadock-1.1/docs/_build/html/_static/doctools.js +156 -0
  16. mutadock-1.1/docs/_build/html/_static/documentation_options.js +13 -0
  17. mutadock-1.1/docs/_build/html/_static/file.png +0 -0
  18. mutadock-1.1/docs/_build/html/_static/github-banner.svg +5 -0
  19. mutadock-1.1/docs/_build/html/_static/language_data.js +199 -0
  20. mutadock-1.1/docs/_build/html/_static/minus.png +0 -0
  21. mutadock-1.1/docs/_build/html/_static/plus.png +0 -0
  22. mutadock-1.1/docs/_build/html/_static/pygments.css +84 -0
  23. mutadock-1.1/docs/_build/html/_static/searchtools.js +620 -0
  24. mutadock-1.1/docs/_build/html/_static/sphinx_highlight.js +154 -0
  25. mutadock-1.1/docs/_build/html/genindex.html +99 -0
  26. mutadock-1.1/docs/_build/html/index.html +189 -0
  27. mutadock-1.1/docs/_build/html/objects.inv +0 -0
  28. mutadock-1.1/docs/_build/html/search.html +117 -0
  29. mutadock-1.1/docs/_build/html/searchindex.js +1 -0
  30. mutadock-1.1/docs/conf.py +27 -0
  31. mutadock-1.1/docs/index.rst +106 -0
  32. mutadock-1.1/docs/make.bat +35 -0
  33. mutadock-1.1/install.sh +3 -0
  34. mutadock-1.1/pyproject.toml +60 -0
  35. mutadock-1.1/requirements.txt +9 -0
  36. mutadock-1.1/src/docking/__init__.py +40 -0
  37. mutadock-1.1/src/docking/np_docking.py +205 -0
  38. mutadock-1.1/src/docking/vina_dock.py +83 -0
  39. mutadock-1.1/src/docking/vina_helper.py +340 -0
  40. mutadock-1.1/src/mutation/Amino.py +559 -0
  41. mutadock-1.1/src/mutation/__init__.py +40 -0
  42. mutadock-1.1/src/mutation/csv_generator.py +156 -0
  43. mutadock-1.1/src/mutation/csv_sort.py +110 -0
  44. mutadock-1.1/src/mutation/ddg_calc.py +135 -0
  45. mutadock-1.1/src/mutation/ddg_calc_double.py +179 -0
  46. mutadock-1.1/src/mutation/ddg_calc_triple.py +204 -0
  47. mutadock-1.1/src/mutation/generate_mutants.py +182 -0
  48. mutadock-1.1/src/mutation/helpers.py +117 -0
  49. mutadock-1.1/src/mutation/np_mutation.py +205 -0
  50. mutadock-1.1/src/mutation/predict_ddG.py +70 -0
  51. mutadock-1.1/win_install.bat +8 -0
@@ -0,0 +1,41 @@
1
+ # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
2
+ # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
3
+
4
+ name: Python package
5
+
6
+ on:
7
+ push:
8
+ branches: [ "main" ]
9
+ pull_request:
10
+ branches: [ "main" ]
11
+
12
+ jobs:
13
+ build:
14
+
15
+ runs-on: ubuntu-latest
16
+ strategy:
17
+ fail-fast: false
18
+ matrix:
19
+ python-version: ["3.9", "3.10", "3.11"]
20
+
21
+ steps:
22
+ - uses: actions/checkout@v4
23
+ - name: Set up Python ${{ matrix.python-version }}
24
+ uses: actions/setup-python@v3
25
+ with:
26
+ python-version: ${{ matrix.python-version }}
27
+ - name: Install dependencies
28
+ run: |
29
+ python -m pip install --upgrade pip
30
+ python -m pip install flake8 pytest
31
+ if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
32
+ python3 -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'
33
+ - name: Lint with flake8
34
+ run: |
35
+ # stop the build if there are Python syntax errors or undefined names
36
+ flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
37
+ # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
38
+ flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
39
+ - name: Test with pytest
40
+ run: |
41
+ pytest
@@ -0,0 +1,4 @@
1
+ /myenv/
2
+ /try/
3
+ /dist/
4
+ *.pyc
@@ -0,0 +1,28 @@
1
+ # Required
2
+ version: 2
3
+
4
+ # Set the OS, Python version and other tools you might need
5
+ build:
6
+ os: ubuntu-22.04
7
+ tools:
8
+ python: "3.12"
9
+ # You can also specify other tool versions:
10
+ # nodejs: "19"
11
+ # rust: "1.64"
12
+ # golang: "1.19"
13
+
14
+ # Build documentation in the "docs/" directory with Sphinx
15
+ sphinx:
16
+ configuration: docs/conf.py
17
+
18
+ # Optionally build your docs in additional formats such as PDF and ePub
19
+ formats:
20
+ - pdf
21
+ # - epub
22
+
23
+ # Optional but recommended, declare the Python requirements required
24
+ # to build your documentation
25
+ # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
26
+ # python:
27
+ # install:
28
+ # - requirements: docs/requirements.txt