code-cov pmb.setup_lj_interaction

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Switched to Ctest for testing, allowing to run the tests on paralel (#87)
 
 ### Added
+- Helper method to delete entries from `pmb.df` (#112)
 - Code of conduct of our community `CODE_OF_CONDUCT.md`, adhering to the Contributor Covenant v2.1 (#104) 
 - New optional argument `backbone_vector` enabling to build molecules along an input vector using `pmb.create_molecule` and `pmb.create_pmb_object` (#99)
 - New boolean flag `--ideal` as argparse argument of `samples/globular_protein.py` enabling to run the script without setting up interactions.
@@ -28,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Unit testing for reaction methods. (#86)
 
 ### Fixed
+- Warning handling and coverage in `setup_lj_interaction` (#112)
 - Wrong parsing in `pmb.protein_sequence_parser` of input sequences provided as a list of aminoacids using the three letter code. (#101)
 - Wrong setup of the rigid object in `pmb.enable_motion_of_rigid_object`, leading to crashes in `samples/globular_protein.py` when enabling the protein motion. (#101)
 - The argparse argument `--move_protein` of `samples/globular_protein.py` is now a boolean flag instead of taking arbitrary float values. (#101)

pyMBE.py

@@ -1670,7 +1670,19 @@ def define_residue(self, name, central_bead, side_chains):
         self.df.at [index,'pmb_type'] = 'residue'
         self.df.at [index,'central_bead'] = central_bead
         self.df.at [index,('side_chains','')] = side_chains
-        return 
+        return
+
+    def delete_entries_in_df(self, entry_name):
+        """
+        Deletes entries with name `entry_name` from the DataFrame if it exists.
+
+        Args:
+            entry_name (`str`): The name of the entry in the dataframe to delete.
+
+        """
+        if entry_name in self.df["name"].values:
+            self.df = self.df[self.df["name"] != entry_name].reset_index(drop=True)
+
 
     def destroy_pmb_object_in_system(self, name, espresso_system):
         """
@@ -3237,15 +3249,15 @@ def setup_lj_interactions(self, espresso_system, shift_potential=True, combining
 
         """
         from itertools import combinations_with_replacement
+        import warnings
         implemented_combining_rules = ['Lorentz-Berthelot']
         compulsory_parameters_in_df = ['sigma','epsilon']
         # Sanity check
         if combining_rule not in implemented_combining_rules:
             raise ValueError('In the current version of pyMBE, the only combinatorial rules implemented are ', implemented_combining_rules)
+        shift=0
         if shift_potential:
             shift="auto"
-        else:
-            shift=0
         # List which particles have sigma and epsilon values defined in pmb.df and which ones don't
         particles_types_with_LJ_parameters = []
         non_parametrized_labels= []
@@ -3293,8 +3305,8 @@ def setup_lj_interactions(self, espresso_system, shift_potential=True, combining
                                 new_value=lj_params,
                                 non_standard_value=True)
         if non_parametrized_labels and warnings:
-            print(f'WARNING: The following particles do not have a defined value of sigma or epsilon in pmb.df: {non_parametrized_labels}. No LJ interaction has been added in ESPResSo for those particles.')
-            
+            warnings.warn(f'The following particles do not have a defined value of sigma or epsilon in pmb.df: {non_parametrized_labels}. No LJ interaction has been added in ESPResSo for those particles.',UserWarning) 
+
         return
 
     def write_pmb_df (self, filename):

testsuite/delete_entries_in_df.py

@@ -0,0 +1,70 @@
+#
+# Copyright (C) 2025 pyMBE-dev team
+#
+# This file is part of pyMBE.
+#
+# pyMBE is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# pyMBE is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import pyMBE
+
+pmb = pyMBE.pymbe_library(seed=42)
+reduced_unit_set = pmb.get_reduced_units()
+particle_parameters={"S1":{"name": "S1",
+                        "sigma":0.355*pmb.units.nm, 
+                        "epsilon":1*pmb.units('reduced_energy'),
+                            "z":0},
+                    "S2":{"name": "S2",
+                        "sigma":0.355*pmb.units.nm, 
+                        "epsilon":1*pmb.units('reduced_energy'),
+                            "z":1},
+                    "S3":{"name": "S3",
+                        "sigma":0.355*pmb.units.nm, 
+                        "epsilon":1*pmb.units('reduced_energy'),
+                            "z":2}}
+
+pmb.define_particles(parameters=particle_parameters)
+
+generic_harmonic_constant = 400 * pmb.units('reduced_energy / reduced_length**2')
+generic_bond_length = 0.355*pmb.units.nm
+HARMONIC_parameters = {'r_0'    : generic_bond_length,
+                       'k'      : generic_harmonic_constant}
+pmb.define_bond(bond_type = 'harmonic',
+                        bond_parameters = HARMONIC_parameters, particle_pairs = [["S1", "S2"]])
+
+pmb.delete_entries_in_df(entry_name="S1-S2")
+assert pmb.df[pmb.df["name"]=="S1-S2"].empty
+pmb.delete_entries_in_df(entry_name="S1")
+assert pmb.df[pmb.df["name"]=="S1"].empty
+
+residue_parameters={"R1":{"name": "R1",
+                        "central_bead": "S2",
+                        "side_chains": []},
+                    "R2":{"name": "R2",
+                        "central_bead": "S2",
+                        "side_chains": ["S2","S3"]}}
+
+for parameter_set in residue_parameters.values():
+    pmb.define_residue(**parameter_set)
+
+pmb.delete_entries_in_df(entry_name="R1")
+assert pmb.df[pmb.df["name"]=="R1"].empty
+
+molecule_parameters={"M1":{"name": "M1",
+                    "residue_list": ["R2","R2","R2"]}}
+
+for parameter_set in molecule_parameters.values():
+    pmb.define_molecule(**parameter_set)
+
+pmb.delete_entries_in_df(entry_name="M1")
+assert pmb.df[pmb.df["name"]=="M1"].empty

testsuite/lj_tests.py

@@ -1,5 +1,5 @@
 #
-# Copyright (C) 2024 pyMBE-dev team
+# Copyright (C) 2024-2025 pyMBE-dev team
 #
 # This file is part of pyMBE.
 #
@@ -112,15 +112,32 @@
                 "epsilon":pmb.units.Quantity(2,"reduced_energy"), 
                 "cutoff":2*2**(1./6.)*pmb.units.nm, 
                 "offset":2*pmb.units.nm}
+X_input_parameters={"name":"X"}
+
 pmb.define_particle(**A_input_parameters)
 pmb.define_particle(**B_input_parameters)
 pmb.define_particle(**C_input_parameters)
+pmb.define_particle(**X_input_parameters)
 
 # Create a dummy instance of an espresso system
 import espressomd
 espresso_system=espressomd.System(box_l = [50]*3)
 
-# Setup LJ interactions
+with warnings.catch_warnings(record=True) as w:
+    warnings.simplefilter("always")  # Capture all warnings, even those normally ignored
+    pmb.setup_lj_interactions(espresso_system=espresso_system)
+    assert any("The following particles do not have a defined value of sigma or epsilon" in str(warning.message) for warning in w), "Expected warning was not raised!"
+
+pmb.delete_entries_in_df("X")
+
+# ValueError if combining-rule other than Lorentz_-Berthelot is used
+input_params = {"espresso_system":espresso_system, "combining_rule": "Geometric"}
+np.testing.assert_raises(ValueError, pmb.setup_lj_interactions, **input_params)
+
+# Initialized with shift=0
+pmb.setup_lj_interactions(espresso_system=espresso_system, shift_potential=False)
+
+# Setup LJ interactions shift="auto"
 pmb.setup_lj_interactions(espresso_system=espresso_system)
 
 # Check A-A LJ setup