Some tests added

docs/contents/user/tools/element/group/get_group_type.ipynb

@@ -0,0 +1,99 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "c55e0a44-c9d9-4229-9a9b-96ecd1ed9b8d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "cc4d7152-a00a-4654-be50-b421e01f584d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "83bdfff8a1d1405796d60a09d881a850",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import molsysmt as msm"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e203abd4-cf31-4dc5-afa7-b3d980bd30a9",
+   "metadata": {},
+   "source": [
+    "# Get group type\n",
+    "\n",
+    "In construction."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f5ae9d14-a25f-40cd-b895-44aade003898",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "6de8ddad-1b3d-447a-974d-eed4b4154169",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "types = msm.element.group.get_group_type(molsys, element='group', selection='all')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "877cd452-492f-4bf9-9ef5-d2ded6dcf3dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "types2 = msm.element.group.get_group_type(molsys, element='group', selection='all', redefine_types=True)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/contents/user/tools/element/group/index.md

@@ -0,0 +1,19 @@
+# Molecule
+
+
+|      |      |
+| :--- | :--- |
+| [Get bonded_atom_pairs](get_bonded_atom_pairs.ipynb) | Getting the bonded atom pairs in a group |
+| [Get group_type](get_group_type.ipynb) | Getting the group type |
+| [Is group_type](is_group_type.ipynb) | Is group type |
+
+```{eval-rst}
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   get_bonded_atom_pairs.ipynb
+   get_group_type.ipynb
+   is_group_type.ipynb
+
+```

docs/contents/user/tools/element/group/is_group_type.ipynb

@@ -0,0 +1,161 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "c55e0a44-c9d9-4229-9a9b-96ecd1ed9b8d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "cc4d7152-a00a-4654-be50-b421e01f584d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "3deb7193f94343f7b759d5efefa6b0e1",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import molsysmt as msm"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e203abd4-cf31-4dc5-afa7-b3d980bd30a9",
+   "metadata": {},
+   "source": [
+    "# Is group type\n",
+    "\n",
+    "In construction."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d02da3fc-babc-46bd-ac67-824f2ea2588a",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.element.group.is_group_type('water')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "c0af30b4-d6a0-49a8-a134-8f64fcfc6140",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.element.group.is_group_type('lipid')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "835416a3-0584-4f83-afdf-04be79129295",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.element.group.is_group_type('terminal capping')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "bc8b7376-9025-4405-a51e-4521638e56d0",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.element.group.is_group_type('amino acid')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46baffcf-b621-4b7e-ab7f-8b55721c93d0",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

molsysmt/element/group/get_group_type.py

@@ -40,11 +40,11 @@ def get_group_type(molecular_system, element='atom', selection='all', redefine_t
             unique_group_names = np.unique(group_names_from_group)
             aux_dict = {}
             for name in unique_group_names:
-                tmp_group_type = _get_group_type_from_group_name(name)
+                tmp_group_type = get_group_type_from_group_name(name)
                 if tmp_group_type == 'small molecule':
                     if _small_molecule_is_amino_acid(molecular_system, group_index):
                         tmp_group_type = 'amino acid'
-                aux_dict[name] = _get_group_type_from_group_name(name)
+                aux_dict[name] = get_group_type_from_group_name(name)
 
             output = [aux_dict[ii] for ii in group_names_from_group]
 

tests/element/group/test_get_group_type_from_molsysmt_MolSys.py

@@ -0,0 +1,39 @@
+"""
+Unit and regression test for the get_form module of the molsysmt package.
+"""
+
+# Import package, test suite, and other packages as needed
+import molsysmt as msm
+from molsysmt import systems
+import numpy as np
+
+def test_get_group_type_from_molsysmt_MolSys_1():
+
+    molsys = msm.convert(systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'])
+    types = msm.element.group.get_group_type(molsys, element='group', selection='all')
+    assert len(types) == 1273
+    assert types[0] == 'terminal capping'
+    assert all(np.array(types[1:37])=='amino acid')
+    assert types[37] == 'terminal capping'
+    assert all(np.array(types[38:-2])=='water')
+    assert all(np.array(types[-2:])=='ion')
+
+def test_get_group_type_from_molsysmt_MolSys_2():
+
+    molsys = msm.convert(systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'])
+    types = msm.element.group.get_group_type(molsys, element='atom', selection='all', redefine_types=True)
+
+    assert all(np.array(types[:6])=='terminal capping')
+    assert all(np.array(types[6:599])=='amino acid')
+    assert all(np.array(types[599:605])=='terminal capping')
+    assert all(np.array(types[605:4304])=='water')
+    assert all(np.array(types[-2:])=='ion')
+
+def test_get_group_type_from_molsysmt_MolSys_3():
+
+    molsys = msm.convert(systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'])
+    types = msm.element.group.get_group_type(molsys, element='group', selection='all')
+    types2 = msm.element.group.get_group_type(molsys, element='group', selection='all', redefine_types=True)
+
+    assert types==types2
+

tests/element/group/test_is_group_type.py

@@ -0,0 +1,35 @@
+"""
+Unit and regression test for the get_form module of the molsysmt package.
+"""
+
+# Import package, test suite, and other packages as needed
+import molsysmt as msm
+from molsysmt import systems
+import numpy as np
+
+def test_is_group_type_molsysmt_MolSys_1():
+
+    assert msm.element.group.is_group_type('water')
+    assert msm.element.group.is_group_type('ion')
+    assert msm.element.group.is_group_type('small molecule')
+    assert msm.element.group.is_group_type('amino acid')
+    assert msm.element.group.is_group_type('terminal capping')
+    assert msm.element.group.is_group_type('nucleotide')
+    assert msm.element.group.is_group_type('lipid')
+    assert msm.element.group.is_group_type('saccharide')
+    assert msm.element.group.is_group_type('oligosaccharide')
+    assert msm.element.group.is_group_type('papa')==False
+
+
+def test_is_group_type_molsysmt_MolSys_2():
+
+    assert msm.element.group.is_group_type('waters')
+    assert msm.element.group.is_group_type('ions')
+    assert msm.element.group.is_group_type('small molecules')
+    assert msm.element.group.is_group_type('amino acids')
+    assert msm.element.group.is_group_type('terminal cappings')
+    assert msm.element.group.is_group_type('nucleotides')
+    assert msm.element.group.is_group_type('lipids')
+    assert msm.element.group.is_group_type('saccharides')
+    assert msm.element.group.is_group_type('oligosaccharides')
+