Day2-Session2-Lecture/universe_creation_and_manipulation-lecture.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "d0cb32fa",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Universe creation and manipulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "509605b7",
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [
    {
     "data": {
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       "model_id": "c382fa720ea84195b09b9cad6464b200",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "_ColormakerRegistry()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import MDAnalysis as mda\n",
    "import nglview as nv\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c8a1d6b1",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "* There is more than one way of creating a `Universe` depending on the needs;\n",
    "* The content of a `Universe` can be altered;\n",
    "* MDAnalysis can talk with other libraries."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "188ac2e9",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Creating a `Universe`"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "968ef82b",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### The boring way"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "ac8587fd",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 47681 atoms>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from MDAnalysis.tests.datafiles import TPR, XTC\n",
    "u = mda.Universe(TPR, XTC)\n",
    "u"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb8afedf",
   "metadata": {},
   "source": [
    "```python\n",
    "mda.Universe(topology, trajectory)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "afecfab1",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### From a numpy array"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0af5b8f1",
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "positions = u.atoms.positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "9786a89e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[ 52.02       43.560005   31.550003 ]\n",
      " [ 51.190002   44.11       31.720001 ]\n",
      " [ 51.550003   42.83       31.04     ]\n",
      " ...\n",
      " [105.340004   74.07001    40.989998 ]\n",
      " [ 57.68       35.32       14.8      ]\n",
      " [ 62.960007   47.240005    3.7500002]]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<Universe with 47681 atoms>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(positions)\n",
    "u = mda.Universe(TPR, positions)\n",
    "u"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e1ee7b75",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### From scratch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "0806e17b",
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "water_positions = u.select_atoms('resname SOL').residues[:2].atoms.select_atoms(\"not name MW\").positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c8b3444f",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "u = mda.Universe.empty(\n",
    "    n_atoms=6, n_residues=2, n_segments=1,\n",
    "    atom_resindex=[0, 0, 0, 1, 1, 1],\n",
    "    residue_segindex=[0, 0],\n",
    "    trajectory=True\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9e1bf40e",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "u.add_TopologyAttr('names', ['O', 'H1', 'H2'] * 2)\n",
    "u.add_TopologyAttr('elements', ['O', 'H', 'H'] * 2)\n",
    "u.add_TopologyAttr('resnames', ['HOH', 'HOH'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "ae9392c7",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.add_bonds([(0, 1), (0, 2), (3, 4), (3, 5)])\n",
    "u.add_angles([(1, 0, 2), (4, 3, 5)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "1d88fb03",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[21.44      26.970001   3.5000002]\n",
      " [21.81      26.160002   3.14     ]\n",
      " [21.470001  27.59       2.77     ]\n",
      " [41.45      43.95      47.210003 ]\n",
      " [40.71      44.31      46.720005 ]\n",
      " [42.210003  44.14      46.670002 ]]\n"
     ]
    }
   ],
   "source": [
    "print(water_positions)\n",
    "u.atoms.positions = water_positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "92ac1a7c",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "990652ad5dc5417eb532ce21c0e2a7f0",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "nv.show_mdanalysis(u)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22737364",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### By copying another `Universe`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "ed5df1a4",
   "metadata": {},
   "outputs": [],
   "source": [
    "u2 = u.copy()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "621f0291",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### By merging atom groups"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "91155fef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 12 atoms>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u3 = mda.Merge(u.atoms, u2.atoms)\n",
    "u3"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3498364e",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Moving atoms"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5b10557c",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Setting atom positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "32bc9ed2",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.positions = np.array(...)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b11bf285",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Be careful! `AtomGroup.positions` returns a copy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "e9363cf3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Before [[21.44      26.970001   3.5000002]\n",
      " [21.81      26.160002   3.14     ]\n",
      " [21.470001  27.59       2.77     ]\n",
      " [41.45      43.95      47.210003 ]\n",
      " [40.71      44.31      46.720005 ]\n",
      " [42.210003  44.14      46.670002 ]]\n",
      "After [[21.44      26.970001   3.5000002]\n",
      " [21.81      26.160002   3.14     ]\n",
      " [21.470001  27.59       2.77     ]\n",
      " [41.45      43.95      47.210003 ]\n",
      " [40.71      44.31      46.720005 ]\n",
      " [42.210003  44.14      46.670002 ]]\n"
     ]
    }
   ],
   "source": [
    "print('Before', u.atoms.positions)\n",
    "positions = u.atoms.positions\n",
    "positions += 10\n",
    "print('After', u.atoms.positions)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2bf5983e",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Translation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ff3a8543",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.positions += ..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f5326634",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.translate(...)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "281a9033",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "48bb6948e56a4c7f9509bffd8b85b9b3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from MDAnalysis.tests.datafiles import fullerene\n",
    "template = mda.Universe(fullerene)\n",
    "template.atoms.translate(-template.atoms.center_of_mass())\n",
    "nv.show_mdanalysis(template)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "c075b615",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>,\n",
       " <AtomGroup with 60 atoms>]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "distance = 10.0 * np.sqrt(2)  # sqrt(2) nm in Å\n",
    "all_fullerenes = []\n",
    "for i in range(5):\n",
    "    for j in range(5):\n",
    "        for k in range(5):\n",
    "            vector = np.array([i / 2, j / 2, k]) * distance\n",
    "            if i % 2 == 0 and j %2 != 0:\n",
    "                vector += [0.0, 0.0, distance / 2]\n",
    "            if i % 2 != 0 and j % 2 == 0:\n",
    "                vector += [0.0, 0.0, distance / 2]\n",
    "            fullerene_copy = template.copy()\n",
    "            fullerene_copy.atoms.translate(vector)\n",
    "            all_fullerenes.append(fullerene_copy.atoms)\n",
    "all_fullerenes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "c0ed1dd1",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b39407a127b8435596bcaa7bc06e98f1",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "crystal = mda.Merge(*all_fullerenes)\n",
    "v = nv.show_mdanalysis(crystal)\n",
    "#v.camera = 'orthographic'\n",
    "v"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5fe7fe33",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Rotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7cee5446",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.rotate(...)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "84921cdd",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.rotateby(...)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "def9fc3b",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.align_principal_axis(...)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d5d65d08",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Geometric transformations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fb6f733c",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.transform(...)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ca9baff4",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Periodic boundary conditions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e3b1bb79",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.unwrap(...)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "73adc7bf",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.wrap(...)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2f3a9b46",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.pack_into_box(...)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "f9d2f109",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
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       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from MDAnalysis.tests.datafiles import TPR, GRO\n",
    "u = mda.Universe(TPR, GRO)\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v.add_ball_and_stick('SOL')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "3a57e370",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "59929fdd230a435cbddfa5a4e0ef7730",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "protein = u.select_atoms('protein')\n",
    "protein.unwrap(compound='residues')\n",
    "\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v.add_ball_and_stick('protein')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "65bad8ec",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "11d31138ec474be48a7bf57088a0b8cd",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "protein = u.select_atoms('protein')\n",
    "protein.unwrap(compound='segments')\n",
    "\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "fb644eac",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "4f12736deeef400d9153089097022770",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "protein = u.select_atoms('protein')\n",
    "protein.wrap()\n",
    "\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "8519513e",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a7e4195fd7ae4dd495927902f36121e7",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v.add_ball_and_stick('SOL')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "fd4bb2ff",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "1edd66c91b0c429aad67d3354d4ea3eb",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "water = u.select_atoms('resname SOL')\n",
    "water.wrap(compound='residues')\n",
    "\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v.add_ball_and_stick('SOL')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "c4dd3e6a",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "8f766130a5ec47b0b75fd0b9f4d38f85",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "water = u.select_atoms('resname SOL')\n",
    "water.pack_into_box()\n",
    "\n",
    "v = nv.show_mdanalysis(u)\n",
    "v.add_unitcell()\n",
    "v.add_ball_and_stick('SOL')\n",
    "v"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "16930c44",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Be careful! Changes may not be permanent!"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "edfaa6be",
   "metadata": {},
   "source": [
    "Tomorrow: on-the-fly transformations"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6f36b58f",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Talking to other libraries"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9640ab09",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Using files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ddb62f61",
   "metadata": {},
   "outputs": [],
   "source": [
    "u.atoms.write(...)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "412b24c0",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Parmed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "f3d203bc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Structure 1164 atoms; 274 residues; 1043 bonds; PBC (triclinic); NOT parametrized>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import parmed as pmd\n",
    "pmd.download_CIF('4lzt').save('4lzt.cif', overwrite=True)\n",
    "parmed_structure = pmd.load_file('4lzt.cif')\n",
    "parmed_structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "afdb0c56",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 1164 atoms>"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u = mda.Universe(parmed_structure)\n",
    "u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "5d95e0ab",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Structure 7500 atoms; 1 residues; 11250 bonds; PBC (triclinic); NOT parametrized>"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "parmed_crystal = crystal.atoms.convert_to.parmed()\n",
    "parmed_crystal"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "04603354",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### RDKit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "20389e4f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x27eca478170>"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "imatinib = Chem.MolFromSmiles('C1N(CCN(C1)Cc1ccc(cc1)C(Nc1cc(c(cc1)C)Nc1nccc(n1)c1cccnc1)=O)C ')\n",
    "Chem.AllChem.EmbedMolecule(imatinib)\n",
    "imatinib = Chem.AddHs(imatinib, addCoords=True)\n",
    "imatinib"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "be135980",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 68 atoms>"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u = mda.Universe(imatinib)\n",
    "u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "33cf1c22",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AtomGroup with 4 atoms>"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "selection = u.select_atoms('smarts cC(=O)N')\n",
    "selection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "9f2af1e6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a52ab1e0cc3945c78b98d41ee54a2307",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "nv.show_mdanalysis(selection)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "f6a52007",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x27ed07e34e0>"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdkit_fullerene = crystal.residues[0].atoms.convert_to.rdkit(NoImplicit=False)\n",
    "rdkit_fullerene"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "55dcf07f",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### OpenMM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "a5ff81a9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<simtk.openmm.app.pdbxfile.PDBxFile at 0x27ece717c08>"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from simtk.openmm import app\n",
    "structure = app.PDBxFile('4lzt.cif')\n",
    "structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "13a56668",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 1164 atoms>"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u = mda.Universe(structure)\n",
    "u"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e4557791",
   "metadata": {},
   "source": [
    "This works on [`Topology`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.topology.Topology.html), [`PDBFile`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.pdbfile.PDBFile.html#), [`PDBxFile`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.pdbxfile.PDBxFile.html#), [`Modeller`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.modeller.Modeller.html#), and [`Simulation`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.simulation.Simulation.html#) objects."
   ]
  }
 ],
 "metadata": {
  "celltoolbar": "Slideshow",
  "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": "3.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}