Smiles reader

offpele/data/ligands/ammonium.pdb

@@ -0,0 +1,7 @@
+HETATM    1  N1  UNL     1       0.002   0.023  -0.006  1.00  0.00           N1+
+HETATM    2  H1  UNL     1       0.536  -0.051   0.886  1.00  0.00           H  
+HETATM    3  H2  UNL     1      -0.644   0.846  -0.038  1.00  0.00           H  
+HETATM    4  H3  UNL     1       0.705   0.017  -0.775  1.00  0.00           H  
+HETATM    5  H4  UNL     1      -0.598  -0.835  -0.068  1.00  0.00           H  
+CONECT    1    2    3    4    5
+END

offpele/data/ligands/malonate.pdb

@@ -0,0 +1,16 @@
+HETATM    1  O1  UNL     1      -1.598  -1.076   1.038  1.00  0.00           O  
+HETATM    2  C1  UNL     1      -1.509  -0.220   0.134  1.00  0.00           C  
+HETATM    3  O2  UNL     1      -2.594   0.553  -0.220  1.00  0.00           O1-
+HETATM    4  C2  UNL     1      -0.228  -0.031  -0.564  1.00  0.00           C  
+HETATM    5  C3  UNL     1       0.811   0.299   0.424  1.00  0.00           C  
+HETATM    6  O3  UNL     1       2.138   0.539   0.046  1.00  0.00           O  
+HETATM    7  O4  UNL     1       0.529   0.371   1.629  1.00  0.00           O  
+HETATM    8  H1  UNL     1       0.047  -0.941  -1.147  1.00  0.00           H  
+HETATM    9  H2  UNL     1      -0.338   0.776  -1.310  1.00  0.00           H  
+HETATM   10  H3  UNL     1       2.740  -0.269  -0.031  1.00  0.00           H  
+CONECT    1    2    2
+CONECT    2    3    4
+CONECT    4    5    8    9
+CONECT    5    6    7    7
+CONECT    6   10
+END

offpele/data/ligands/trimethylglycine.pdb

@@ -0,0 +1,26 @@
+HETATM    1  C1  UNL     1      -0.071  -1.459  -0.304  1.00  0.00           C  
+HETATM    2  N1  UNL     1      -0.237  -0.057  -0.095  1.00  0.00           N1+
+HETATM    3  C2  UNL     1      -1.150   0.412  -1.153  1.00  0.00           C  
+HETATM    4  C3  UNL     1      -0.923   0.191   1.157  1.00  0.00           C  
+HETATM    5  C4  UNL     1       0.942   0.732  -0.249  1.00  0.00           C  
+HETATM    6  C5  UNL     1       2.046   0.408   0.633  1.00  0.00           C  
+HETATM    7  O1  UNL     1       3.116   1.052   0.564  1.00  0.00           O  
+HETATM    8  O2  UNL     1       1.991  -0.597   1.577  1.00  0.00           O1-
+HETATM    9  H1  UNL     1      -0.318  -1.760  -1.343  1.00  0.00           H  
+HETATM   10  H2  UNL     1      -0.821  -1.989   0.347  1.00  0.00           H  
+HETATM   11  H3  UNL     1       0.903  -1.865  -0.059  1.00  0.00           H  
+HETATM   12  H4  UNL     1      -0.567   0.400  -2.104  1.00  0.00           H  
+HETATM   13  H5  UNL     1      -2.067  -0.176  -1.186  1.00  0.00           H  
+HETATM   14  H6  UNL     1      -1.369   1.481  -0.953  1.00  0.00           H  
+HETATM   15  H7  UNL     1      -1.903   0.672   1.034  1.00  0.00           H  
+HETATM   16  H8  UNL     1      -1.108  -0.781   1.667  1.00  0.00           H  
+HETATM   17  H9  UNL     1      -0.323   0.825   1.846  1.00  0.00           H  
+HETATM   18  H10 UNL     1       1.237   0.709  -1.316  1.00  0.00           H  
+HETATM   19  H11 UNL     1       0.622   1.801  -0.063  1.00  0.00           H  
+CONECT    1    2    9   10   11
+CONECT    2    3    4    5
+CONECT    3   12   13   14
+CONECT    4   15   16   17
+CONECT    5    6   18   19
+CONECT    6    7    7    8
+END

offpele/examples/Molecule.ipynb

@@ -0,0 +1,275 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Molecule definitions\n",
+    "This notebook shows the two available methods that can be used to define a molecule object in `offpele`. It can accept either a PDB file or a SMILES tag."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from offpele.topology import Molecule\n",
+    "from offpele.utils import get_data_file_path\n",
+    "from simtk import unit"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Get paths to PDB files\n",
+    "AMMONIUM_PDB = get_data_file_path('ligands/ammonium.pdb')\n",
+    "MALONATE_PDB = get_data_file_path('ligands/malonate.pdb')\n",
+    "TRIMETHYLGLYCINE_PDB = get_data_file_path('ligands/trimethylglycine.pdb')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Ammonium"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Loading molecule from RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "6ef432604fce46449cb01163a0d80937",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(AMMONIUM_PDB)\n",
+    "m.off_molecule"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Constructing molecule from a SMILES tag with RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "9ef8a6bcb4604a36841e2cba619021f4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(smiles='[NH4+]')\n",
+    "m.off_molecule"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Malonate"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Loading molecule from RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "d9d06088dca545eba8264513d0a5d583",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(MALONATE_PDB)\n",
+    "m.off_molecule"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Constructing molecule from a SMILES tag with RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "8e39907d119c4d8ca34aeb94cceb5b4d",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(smiles='O=C([O-])CC(O)=O')\n",
+    "m.off_molecule"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Trimethylglycine"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Loading molecule from RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "61d2fc78a8884bb0911e2b081ead9bcc",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(TRIMETHYLGLYCINE_PDB)\n",
+    "m.off_molecule"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " - Constructing molecule from a SMILES tag with RDKit\n",
+      " - Generating rotamer library\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "a252655daacb45188dae2ab895febc58",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(smiles='C[N+](C)(C)CC(=O)[O-]')\n",
+    "m.off_molecule"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}