first draft of martinize2 command tutorials

marrink-lab · Oct 9, 2024 · 5ba58d8 · 5ba58d8
2 parents 38fa6e2 + 5fb0154
commit 5ba58d8
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -14,26 +14,25 @@ env:
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
 
     strategy:
       matrix:
-       py_version: ["3.8", "3.9", "3.10", "3.11"]
+       py_version: ["3.9", "3.10", "3.11", "3.12"]
        include:
-         - py_version: "3.8"
-           WITH_CODECOV: true
          - py_version: "3.9"
            WITH_CODECOV: true
          - py_version: "3.10"
            WITH_CODECOV: true
          - py_version: "3.11"
            WITH_CODECOV: true
+         - py_version: "3.12"
+           WITH_CODECOV: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.py_version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.py_version }}
         cache: pip
@@ -54,6 +53,7 @@ jobs:
       run: |
         coverage run $(which pytest) -vv --hypothesis-show-statistics
         coverage report --omit='*/bin/pytest'
+        coverage xml
         
     - if: ${{ matrix.WITH_CODECOV }}
       name: Upload coverage codecov   
@@ -68,11 +68,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
@@ -93,11 +93,11 @@ jobs:
       runs-on: ubuntu-latest
 
       steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-           python-version: '3.11'
+           python-version: '3.x'
            cache: pip
            cache-dependency-path: |
              **/setup.cfg
@@ -118,37 +118,33 @@ jobs:
   deploy:
     needs: [build, lint, docs]
     runs-on: ubuntu-latest
-
+    environment:
+      name: pypi
+      url: https://pypi.org/p/vermouth
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+      with:
+        fetch-tags: true
+        fetch-depth: 0
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
           **/requirements-*.txt
           **/pyproject.toml
-        
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools pip
+        pip install --upgrade .
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-        pip install pbr
-         
+      run: |
+        python3 -m pip install build pbr --user
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        
-    - name: Publish package to PyPI
+      run: python3 -m build --sdist --wheel --outdir dist/
+    - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -16,26 +16,25 @@ env:
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
 
     strategy:
       matrix:
-       py_version: ["3.8", "3.9", "3.10", "3.11"]
+       py_version: ["3.9", "3.10", "3.11", "3.12"]
        include:
-         - py_version: "3.8"
-           WITH_CODECOV: true
          - py_version: "3.9"
            WITH_CODECOV: true
          - py_version: "3.10"
            WITH_CODECOV: true
          - py_version: "3.11"
            WITH_CODECOV: true
+         - py_version: "3.12"
+           WITH_CODECOV: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.py_version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.py_version }}
         cache: pip
@@ -71,11 +70,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
@@ -96,11 +95,11 @@ jobs:
       runs-on: ubuntu-latest
 
       steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-           python-version: '3.11'
+           python-version: '3.x'
            cache: pip
            cache-dependency-path: |
              **/setup.cfg
@@ -116,3 +115,39 @@ jobs:
         run: | 
           mkdir -p doc/source/_static
           sphinx-build -EnW -b html doc/source/ doc/build/html
+
+  deploy:
+    needs: [build, lint, docs]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/vermouth
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-tags: true
+        fetch-depth: 0
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: pip
+        cache-dependency-path: |
+          **/setup.cfg
+          **/requirements-*.txt
+          **/pyproject.toml
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools pip
+        pip install --upgrade .
+    - name: Install pypa/build
+      run: |
+        python3 -m pip install build pbr --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build --sdist --wheel --outdir dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
diff --git a/doc/source/martinize2_tutorials/basic_usage.rst b/doc/source/martinize2_tutorials/basic_usage.rst
@@ -1,6 +1,6 @@
-==========
+===========
 Basic usage
-==========
+===========
 
 Overly basic usage
 ==================

diff --git a/doc/source/martinize2_tutorials/elastic_networks.rst b/doc/source/martinize2_tutorials/elastic_networks.rst
@@ -1,4 +1,6 @@
-# Elastic Networks
+================
+Elastic Networks
+================
 
 The first method applied to maintain the secondary and tertiary structure
 of Martini proteins was `Elastic Networks <https://doi.org/10.1021/ct9002114>`_.

diff --git a/doc/source/martinize2_tutorials/go_models.rst b/doc/source/martinize2_tutorials/go_models.rst
@@ -1,6 +1,6 @@
-=======
+=========
 Go models
-=======
+=========
 
 GoMartini is a popular method for retaining the secondary and tertiary structures of proteins originating from the lab
 of `Adolfo Poma <https://pubs.acs.org/doi/full/10.1021/acs.jctc.6b00986>`_. In contrast to an elastic network, the Go

diff --git a/doc/source/martinize2_tutorials/index.rst b/doc/source/martinize2_tutorials/index.rst
@@ -12,4 +12,6 @@ repository: https://github.com/marrink-lab/martinize-examples
 
 .. toctree::
     basic_usage
-    7_adding_modifications/index
+    elastic_networks
+    go_models
+    mutmod
diff --git a/doc/source/martinize2_tutorials/mutmod.rst → ...tutorials/mutations_and_modifications.rst b/doc/source/martinize2_tutorials/mutmod.rst → ...tutorials/mutations_and_modifications.rst
@@ -1,6 +1,6 @@
-======
+===========================
 Mutations and modifications
-======
+===========================
 
 Martinize2 facilitates a powerful syntax for defining mutations and modifications to your input protein structure.
 Here we'll look at some of the options for how your protein can be changed during the coarse graining process. While

diff --git a/doc/source/martinize2_tutorials/water_biasing.rst b/doc/source/martinize2_tutorials/water_biasing.rst
@@ -1,6 +1,6 @@
-=========
+=============
 Water biasing
-=========
+=============
 
 One feature associated with the latest version of the
 `Go model <https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1>`_ is the ability to

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,6 +4,7 @@ requires = [
         "setuptools >= 30.3.0",
         "pbr",
     ]
+build-backend = "pbr.build"
 
 [tool.pytest.ini_options]
 addopts = "--import-mode=importlib"

diff --git a/setup.cfg b/setup.cfg
@@ -17,10 +17,10 @@ classifier =
     License :: OSI Approved :: Apache Software License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Scientific/Engineering :: Chemistry
 keywords = martini MD martinize

diff --git a/vermouth/data/mappings/his.charmm.mapping b/vermouth/data/mappings/his.charmm.mapping
@@ -0,0 +1,30 @@
+[ block ]
+[ from ]
+charmm
+[ to ]
+martini22
+
+[ from blocks ]
+HIS
+
+[ to blocks ]
+HSE
+
+[ mapping ]
+  N    BB
+ HN    BB
+ CA    BB
+ HA    BB
+ CB   SC1
+HB1   SC1
+HB2   SC1
+CD2   SC2
+HD2   SC2
+ CG   SC1
+NE2   SC2
+HE2   SC2
+ND1   SC3
+CE1   SC3
+HE1   SC3
+  C    BB
+  O    BB
diff --git a/vermouth/data/mappings/his.gromos.mapping b/vermouth/data/mappings/his.gromos.mapping
@@ -0,0 +1,27 @@
+[ block ]
+[ from ]
+gromos
+[ to ]
+martini22
+
+[ from blocks ]
+HIS
+
+[ to blocks ]
+HSE
+
+[ mapping ]
+  N    BB
+  H    BB
+ CA    BB
+ CB   SC1
+ CG   SC1
+ND1   SC3
+HD1   SC3
+CD2   SC2
+HD2   SC2
+CE1   SC3
+HE1   SC3
+NE2   SC2
+  C    BB
+  O    BB
diff --git a/vermouth/processors/annotate_mut_mod.py b/vermouth/processors/annotate_mut_mod.py
@@ -252,10 +252,9 @@ def annotate_modifications(molecule, modifications, mutations, resspec_counts):
     # Get the name of the chain in the molecule that we're looking at
     residue = {key: residue_graph.nodes[0].get(key)
                for key in 'chain resid resname insertion_code'.split()}
-    chain = residue['chain']
-    extra = False
     for mutmod, key, library in associations:
         for resspec, mod in mutmod:
+            extra = False
             mod_found = _resiter(mod, residue_graph, resspec, library, key, molecule)
             if not mod_found:
                 #if no mod found, return that there's a problem