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.
- mutadock-1.1/.github/workflows/python-package.yml +41 -0
- mutadock-1.1/.gitignore +4 -0
- mutadock-1.1/.readthedocs.yaml +28 -0
- mutadock-1.1/LICENSE +674 -0
- mutadock-1.1/PKG-INFO +95 -0
- mutadock-1.1/README.md +67 -0
- mutadock-1.1/docs/Makefile +20 -0
- mutadock-1.1/docs/_build/doctrees/environment.pickle +0 -0
- mutadock-1.1/docs/_build/doctrees/index.doctree +0 -0
- mutadock-1.1/docs/_build/html/.buildinfo +4 -0
- mutadock-1.1/docs/_build/html/_sources/index.rst.txt +106 -0
- mutadock-1.1/docs/_build/html/_static/alabaster.css +663 -0
- mutadock-1.1/docs/_build/html/_static/basic.css +925 -0
- mutadock-1.1/docs/_build/html/_static/custom.css +1 -0
- mutadock-1.1/docs/_build/html/_static/doctools.js +156 -0
- mutadock-1.1/docs/_build/html/_static/documentation_options.js +13 -0
- mutadock-1.1/docs/_build/html/_static/file.png +0 -0
- mutadock-1.1/docs/_build/html/_static/github-banner.svg +5 -0
- mutadock-1.1/docs/_build/html/_static/language_data.js +199 -0
- mutadock-1.1/docs/_build/html/_static/minus.png +0 -0
- mutadock-1.1/docs/_build/html/_static/plus.png +0 -0
- mutadock-1.1/docs/_build/html/_static/pygments.css +84 -0
- mutadock-1.1/docs/_build/html/_static/searchtools.js +620 -0
- mutadock-1.1/docs/_build/html/_static/sphinx_highlight.js +154 -0
- mutadock-1.1/docs/_build/html/genindex.html +99 -0
- mutadock-1.1/docs/_build/html/index.html +189 -0
- mutadock-1.1/docs/_build/html/objects.inv +0 -0
- mutadock-1.1/docs/_build/html/search.html +117 -0
- mutadock-1.1/docs/_build/html/searchindex.js +1 -0
- mutadock-1.1/docs/conf.py +27 -0
- mutadock-1.1/docs/index.rst +106 -0
- mutadock-1.1/docs/make.bat +35 -0
- mutadock-1.1/install.sh +3 -0
- mutadock-1.1/pyproject.toml +60 -0
- mutadock-1.1/requirements.txt +9 -0
- mutadock-1.1/src/docking/__init__.py +40 -0
- mutadock-1.1/src/docking/np_docking.py +205 -0
- mutadock-1.1/src/docking/vina_dock.py +83 -0
- mutadock-1.1/src/docking/vina_helper.py +340 -0
- mutadock-1.1/src/mutation/Amino.py +559 -0
- mutadock-1.1/src/mutation/__init__.py +40 -0
- mutadock-1.1/src/mutation/csv_generator.py +156 -0
- mutadock-1.1/src/mutation/csv_sort.py +110 -0
- mutadock-1.1/src/mutation/ddg_calc.py +135 -0
- mutadock-1.1/src/mutation/ddg_calc_double.py +179 -0
- mutadock-1.1/src/mutation/ddg_calc_triple.py +204 -0
- mutadock-1.1/src/mutation/generate_mutants.py +182 -0
- mutadock-1.1/src/mutation/helpers.py +117 -0
- mutadock-1.1/src/mutation/np_mutation.py +205 -0
- mutadock-1.1/src/mutation/predict_ddG.py +70 -0
- 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
|
mutadock-1.1/.gitignore
ADDED
|
@@ -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
|