Some tests added

uibcdf · Dec 23, 2024 · f0e200f · f0e200f
1 parent 3cec39f
commit f0e200f
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Showing 9 changed files with 2 additions and 28 deletions.
diff --git a/docs/contents/user/tools/element/group/get_bonded_atom_pairs.ipynb b/docs/contents/user/tools/element/group/get_bonded_atom_pairs.ipynb
@@ -20,7 +20,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "1e89da9f146c4d0fb4667d405f7e5b5c",
+       "model_id": "fc8b56fda4bd48509a680626ea2ad898",
        "version_major": 2,
        "version_minor": 0
       },
@@ -93,23 +93,6 @@
    "id": "a3d5ed12-0081-4c28-8078-5ce59947a1a8",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[autoreload of molsysmt.element.group.amino_acid.get_bonded_atom_pairs failed: Traceback (most recent call last):\n",
-      "  File \"/conda/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/IPython/extensions/autoreload.py\", line 276, in check\n",
-      "    superreload(m, reload, self.old_objects)\n",
-      "  File \"/conda/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/IPython/extensions/autoreload.py\", line 500, in superreload\n",
-      "    update_generic(old_obj, new_obj)\n",
-      "  File \"/conda/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/IPython/extensions/autoreload.py\", line 397, in update_generic\n",
-      "    update(a, b)\n",
-      "  File \"/conda/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/IPython/extensions/autoreload.py\", line 309, in update_function\n",
-      "    setattr(old, name, getattr(new, name))\n",
-      "ValueError: get_bonded_atom_pairs() requires a code object with 0 free vars, not 2\n",
-      "]\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
@@ -176,14 +159,6 @@
     "atom_indices = list(range(10, 10+len(atom_names)))\n",
     "msm.element.group.amino_acid.get_bonded_atom_pairs('VAL', atom_names, atom_indices=atom_indices)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ec9d2016-b9ae-4f7d-bfdc-5808f3d85d0b",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/molsysmt/_private/digestion/argument/bonded_atom_pairs.py b/molsysmt/_private/digestion/argument/bonded_atom_pairs.py
@@ -11,7 +11,7 @@ def digest_bonded_atom_pairs(bonded_atom_pairs, caller=None):
             for sublist in bonded_atom_pairs:
                 if not (isinstance(sublist, list) and len(sublist) == 2):
                     raise ArgumentError('bonded_atom_pairs', value=bonded_atom_pairs, caller=caller, message=None)
-                if not all(isinstance(item, int) for item in sublist):
+                if not all(isinstance(item, (int, np.integer)) for item in sublist):
                     print('aa')
                     raise ArgumentError('bonded_atom_pairs', value=bonded_atom_pairs, caller=caller, message=None)
             return np.array(bonded_atom_pairs)

diff --git a/molsysmt/build/add_missing_bonds.py b/molsysmt/build/add_missing_bonds.py
@@ -18,7 +18,6 @@ def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
         bonds = get_missing_bonds(molecular_system, threshold=threshold, selection=selection,
                                  structure_index=structure_index, syntax=syntax,
                                  skip_digestion=True)
-
         return add_bonds(molecular_system, bonds, in_place=in_place, skip_digestion=True)
 
     else:

diff --git a/.../amino_acid/test_get_bonded_atom_pairs.py → .../test_get_bonded_atom_pairs_amino_acid.py b/.../amino_acid/test_get_bonded_atom_pairs.py → .../test_get_bonded_atom_pairs_amino_acid.py
diff --git a/...ent/group/amino_acid/test_get_group_db.py → ...mino_acid/test_get_group_db_amino_acid.py b/...ent/group/amino_acid/test_get_group_db.py → ...mino_acid/test_get_group_db_amino_acid.py
diff --git a/...ment/group/amino_acid/test_group_names.py → ...amino_acid/test_group_names_amino_acid.py b/...ment/group/amino_acid/test_group_names.py → ...amino_acid/test_group_names_amino_acid.py
diff --git a/...t/group/ion/test_get_bonded_atom_pairs.py → ...oup/ion/test_get_bonded_atom_pairs_ion.py b/...t/group/ion/test_get_bonded_atom_pairs.py → ...oup/ion/test_get_bonded_atom_pairs_ion.py
diff --git a/tests/element/group/ion/test_get_group_db.py → ...lement/group/ion/test_get_group_db_ion.py b/tests/element/group/ion/test_get_group_db.py → ...lement/group/ion/test_get_group_db_ion.py
diff --git a/tests/element/group/ion/test_group_names.py → ...element/group/ion/test_group_names_ion.py b/tests/element/group/ion/test_group_names.py → ...element/group/ion/test_group_names_ion.py