Merge pull request #571 from marrink-lab/issue570

Log a helpful message when an element is not present in the ATOM_MASS dict

.github/workflows/deploy.yml

@@ -52,7 +52,7 @@ jobs:
         
     - name: Run pytest with codecoverage
       run: |
-        coverage run --source=vermouth $(which pytest) -vv vermouth --hypothesis-show-statistics
+        coverage run $(which pytest) -vv --hypothesis-show-statistics
         coverage report --omit='*/bin/pytest'
         
     - if: ${{ matrix.WITH_CODECOV }}

.github/workflows/run_tests.yml

@@ -53,7 +53,11 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run:  pytest vermouth --cov=vermouth --cov-report=xml --hypothesis-show-statistics
+      run: |
+        coverage run $(which pytest) -vv --hypothesis-show-statistics
+        coverage report
+        coverage xml 
+
     - if: ${{ matrix.WITH_CODECOV }}
       name: Upload coverage codecov   
       uses: codecov/codecov-action@v3 

pyproject.toml

@@ -4,3 +4,13 @@ requires = [
         "setuptools >= 30.3.0",
         "pbr",
     ]
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+testpaths = ["vermouth/tests"]
+python_files = "test_*.py"
+
+[tool.coverage.run]
+branch = true
+omit = ["vermouth/tests/*", "vermouth/redistributed/*", '*/bin/pytest']
+source_pkgs = ["vermouth"]

vermouth/processors/attach_mass.py

@@ -18,10 +18,13 @@
 
 
 from .processor import Processor
+from ..log_helpers import StyleAdapter, get_logger
 
-# TODO: make the masses part of the forcefield
-ATOM_MASSES = {'H': 1, 'C': 12, 'N': 14, 'O': 16, 'S': 32, 'P': 31, 'M': 0}
+LOGGER = StyleAdapter(get_logger(__name__))
 
+# TODO: make the masses part of the forcefield
+ATOM_MASSES = {'H': 1, 'C': 12, 'N': 14, 'O': 16, 'S': 32, 'P': 31}
+DEFAULT_MASS = 30
 
 def attach_mass(molecule, attribute='mass'):
     """
@@ -36,7 +39,11 @@ def attach_mass(molecule, attribute='mass'):
         The attribute the mass is assigned to.
     """
     for node in molecule.nodes.values():
-        node[attribute] = ATOM_MASSES[node['element']]
+        element = node['element']
+        if element not in ATOM_MASSES:
+            LOGGER.info("Cannot find a mass for element {}. We assume it's some"
+                        " metal, and will set its mass to {} amu.", element, DEFAULT_MASS)
+        node[attribute] = ATOM_MASSES.get(node['element'], DEFAULT_MASS)
 
 
 class AttachMass(Processor):