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uibcdf · Aug 13, 2024 · b4175d9 · b4175d9
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diff --git a/docs/contents/user/tools/build/add_bonds.ipynb b/docs/contents/user/tools/build/add_bonds.ipynb
@@ -0,0 +1,198 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "3908cf62-3a4c-4c82-a061-e78f6f2f7097",
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# This cell is removed with the tag: \"remove-input\"\n",
+    "# As such, it will not be shown in documentation\n",
+    "\n",
+    "#import warnings\n",
+    "#warnings.filterwarnings('ignore')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "034d6a12-81b5-40fe-89a7-59046d378078",
+   "metadata": {},
+   "source": [
+    "(Tutorial_Add_bonds)=\n",
+    "# Add bonds\n",
+    "\n",
+    "To be written..."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "19c12010-9573-490a-89fa-f899756609d7",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "804fe4f2f91b418fbaecbfd991719a56",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import molsysmt as msm"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "7ebdbcb9-f241-472a-9a5e-63066fbb064b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "623d0cf1-e54f-438e-a7f5-fdab6e56d8af",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert(molsys)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "ec89fe3d-b83c-495b-bc29-c1c1b3f58408",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.remove_bonds(molsys)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "5357ae81-d988-48a5-9e5e-d61ce63a0dba",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.get(molsys, n_bonds=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "4ed0846f-048c-4184-96a1-07b649dcd9cf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.add_bonds(molsys, bonded_atom_pairs=[[0,1], [0,2], [1,4]])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "03abc0cd-29aa-45ac-9da3-bf470bd2d37f",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "3"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.get(molsys, n_bonds=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "1aa4d0b4-7985-43c1-a41b-d87870271e17",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "bonded_atom_pairs = msm.get(molsys, bonded_atom_pairs=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "1fa3f835-6ebc-4a17-b021-e1f4ed392785",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "bonded_atom_pairs == [[0,1], [0,2], [1,4]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ec17414f-e734-49a7-84e0-3fcde8284f4c",
+   "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": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/contents/user/tools/build/add_missing_bonds.ipynb b/docs/contents/user/tools/build/add_missing_bonds.ipynb
@@ -28,6 +28,118 @@
     "\n",
     "To be written..."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "298105c1-444e-4e94-bf44-e16ce0e5e171",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "56cb802dd5d94eff8a202610839ed1db",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import molsysmt as msm"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "cb9faa83-9dba-4e6e-8e89-ad0ae6604c80",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e0970914-34f1-4ae6-8104-76ea7394046b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert(molsys)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "fc7a3b4a-c6c8-4690-884d-ff054daddd44",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "bonded_atom_pairs = msm.get(molsys, bonded_atom_pairs=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "5218d00e-a83b-4cb8-a01f-5b0c28686bdc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.remove_bonds(molsys)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "88abb2cb-2778-4d1f-9ab5-df84d879a7ec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.add_missing_bonds(molsys)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "7c3129c2-c4c3-403b-8053-9f361371f9a2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "new_bonded_atom_pairs = msm.get(molsys, bonded_atom_pairs=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "aa10a14e-f3bf-4edb-ae1a-c648d68a7bbf",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "new_bonded_atom_pairs == bonded_atom_pairs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "00813f47-1589-43d7-8bb1-2716dda3a387",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -46,7 +158,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/contents/user/tools/build/add_missing_heavy_atoms.ipynb b/docs/contents/user/tools/build/add_missing_heavy_atoms.ipynb
@@ -667,7 +667,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/molsysmt/build/add_missing_bonds.py b/molsysmt/build/add_missing_bonds.py
@@ -21,17 +21,7 @@ def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
         return add_bonds(molecular_system, bonds, in_place=in_place, skip_digestion=True)
 
-    elif engine=="ParmEd":
-
-        raise NotImplementedError
-
-    elif engine=="pytraj":
-
-        raise NotImplementedError
-
     else:
 
         raise NotImplementedError
 
-    raise NotImplementedError
-
diff --git a/tests/build/add_bonds/test_add_bonds.py b/tests/build/add_bonds/test_add_bonds.py
@@ -0,0 +1,22 @@
+"""
+Unit and regression test for the is solvate module of the molsysmt package on molsysmt MolSys molecular
+systems.
+"""
+
+# Import package, test suite, and other packages as needed
+import pytest
+import molsysmt as msm
+from molsysmt import systems
+import numpy as np
+
+
+def test_add_bonds_molsysmt_MolSys_1():
+
+    molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']
+    molsys = msm.convert(molsys)
+    msm.build.remove_bonds(molsys)
+    msm.build.add_bonds(molsys, bonded_atom_pairs=[[0,1], [0,2], [1,4]])
+    n_bonds, bonded_atom_pairs = msm.get(molsys, n_bonds=True, bonded_atom_pairs=True)
+
+    assert n_bonds==3
+    assert bonded_atom_pairs==[[0,1], [0,2], [1,4]]
diff --git a/tests/build/add_missing_bonds/test_add_missing_bonds.py b/tests/build/add_missing_bonds/test_add_missing_bonds.py
@@ -20,3 +20,13 @@ def test_add_missing_bonds_molsysmt_MolSys_1():
 
     assert n_bonds_before==n_bonds_after
 
+def test_add_missing_bonds_molsysmt_MolSys_2():
+
+    molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']
+    molsys = msm.convert(molsys)
+    bonded_atom_pairs = msm.get(molsys, bonded_atom_pairs=True)
+    msm.build.remove_bonds(molsys)
+    msm.build.add_missing_bonds(molsys)
+    new_bonded_atom_pairs = msm.get(molsys, bonded_atom_pairs=True)
+
+    assert new_bonded_atom_pairs == bonded_atom_pairs