notebooks/transformations/on-the-fly-transformations.ipynb

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    "# Using the on-the-fly trajectory transformations in MDAnalysis\n",
    "\n",
    "On-the-fly transformations have been introduced in version 0.18.1 of MDAnalysis. This long awaited feature brings to MDAnalysis a whole new level of functionality, allowing for more efficient workflows when analyzing and visualizing simulation trajectories.\n",
    "\n",
    "_Note:_ This notebook demonstrates some transformations that appear in MDAnalysis 0.20.0.\n",
    "\n",
    "## Why do we need transformations?\n",
    "When visualizing and analyzing trajectories from molecular dynamics simulations, some prior modifications are often required.\n",
    "Examples of the most usual modifications or transformations are removing artifacts from periodic boundary conditions, which cause some issues with some molecular viewers (PyMol for example), removing the rotation and translation of a particular molecule and/or centering it in the unit cell, which helps focus on the its actual conformational changes by removing their natural movement in solution.\n",
    "These transformations help us better identifying patterns in the behavior of our biological systems, and, more importantly, showing them to the world.\n",
    "\n",
    "## The advantage of using MDAnalysis for trajectory transformations\n",
    "Each simulation package is often bundled with tools to transform and analyze trajectories, such as GROMACS' `trjconv`. However, most of the times, the user is required to apply all the intended transformations to the whole trajectory (or the portion of interest) prior to visualization and analysis. This often requires processing huge files, sometimes more than once. Moreover, some tools such as `trjconv` do not support frame indexing for the most popular trajectory formats, requiring iterating over frames that are not needed for that particular analysis. \n",
    "Trajectory transformations in MDAnalysis, on the other end, have one great advantage - they are performed on-the-fly. This means that, after loading the trajectory file, the user adds a transformation workflow and the transformations are applied to each frame that is read. There is no need to iterate over the whole trajectory before performing other analysis, and, with the frame indexing provided by MDAnalysis, only the frames of interest are processed. Moreover, the way the transformations API is implemented makes it really easy to add custom transformations.\n",
    "Another things that really makes the \"on-the-fly\" aspect of the MDAnalysis transformations really shine is coupling it to a visualization widget such as [NGL Viewer](http://nglviewer.org/ngl/api/index.html)."
   ]
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    "## Using MDAnalysis transformations\n",
    "Now it's time to learn how to use the trajectory transformations in MDAnalysis. During the following steps, we will apply some transformations on a 1 ns trajectory of a simple 19-residue peptide embeded in a 128-DMPC membrane, showing the GROMACS `trjconv` command and the equivalent MDAnalysis code and output. To keep thinks lightweight, frames are were taken every 100 ps, and water molecules were removed.\n",
    "\n",
    "Note that in order to use the transformations in the `MDAnalysis.transformations` module we have to explicitly import it; we can then access the, say, `translate` transformation as `MDAnalysis.transformations.translate` or also as `mda.transformations.translate` if we first ran `import MDAnalysis as mda`."
   ]
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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
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   "source": [
    "import MDAnalysis as mda\n",
    "import MDAnalysis.transformations\n",
    "\n",
    "import nglview as nv\n",
    "\n",
    "# suppress harmless warnings when using nglview and trajectories\n",
    "# (such as the ones used here) that do not contain attributes defined\n",
    "# in the PDB standard\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore') # some attributes are missing "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Load a test trajectory (the [membrane peptide dataset](https://www.mdanalysis.org/MDAnalysisData/membrane_peptide.html)):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
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   "source": [
    "from MDAnalysisData.datasets import fetch_membrane_peptide\n",
    "data = fetch_membrane_peptide()\n",
    "\n",
    "u = mda.Universe(data.topology, data.trajectory)"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "### Example 1: making everything whole again\n",
    "When performing MD simulations using periodic boundary conditions, molecules will often cross the limits of the unit cell. When this happens, some atoms of the molecule will show up on the the opposing side of the unit cell and some molecular viewers will show stretched bonds and other visual artifacts depending on the visual representation of the system. \n",
    "This is the case of our system. Without any modifications, when we look at the trajectory of our system, things will become very ugly, very fast:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
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   "source": [
    "nv.show_mdanalysis(u)"
   ]
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   "cell_type": "markdown",
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    "Using `trjconv`, one way to may every molecules whole again would be:\n",
    "\n",
    "    gmx trjconv -f pept_in_memb.xtc -s pept_in_memb.tpr -pbc mol -o output.xtc\n",
    "    \n",
    "In MDAnalysis this can be done with the `unwrap` transformation, which takes an AtomGroup as argument. This can be done as follows:"
   ]
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    "# a custom atom group can be passed as an argument. In this case we will use all the atoms\n",
    "# in the Universe u\n",
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "ag = u.atoms\n",
    "\n",
    "# we define the transformation\n",
    "transformation = mda.transformations.unwrap(ag)\n",
    "\n",
    "# we add the transformation to the trajectory in it will be applied everytime we read a frame\n",
    "u.trajectory.add_transformations(transformation)\n",
    "\n",
    "# we can do other things with the trajectory without having to generate a file with the transformed\n",
    "# trajectory\n",
    "# for ts in u.trajectory:\n",
    "#     analysis1()\n",
    "#     analysis2()\n",
    "nv.show_mdanalysis(u)"
   ]
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    "as you can see, the artifacts caused by the atoms crossing the boundaries of the unit cell are now gone.\n",
    "\n",
    "### Example 2: what if we also want to center the peptide in the unit cell?\n",
    "In that case, using `trjconv` we would do something like this:\n",
    "   \n",
    "    gmx trjconv -f pept_in_memb.xtc -s pept_in_memb.tpr -pbc mol -center -o output.xtc\n",
    "\n",
    "And we choose `Protein` as the group to be centered.\n",
    "\n",
    "In MDAnalysis we use the `center_in_box` transformation. This function takes an AtomGroup as a mandatory argument. Optional arguments include `weights`, which is used to calculate the weighted center of the given AtomGroup (if weights='mass' then the center of mass is calculated), `center_to` which is used when the user needs to center the AtomGroup in a custom point instead of the center of the unit cell, and `wrap` which, if `True`, causes all the atoms of the AtomGroup to be moved to the unit cell before calculating the weighted center.\n",
    "This transformation can be performed as follows:"
   ]
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   "cell_type": "code",
   "execution_count": null,
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   "source": [
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "prot = u.select_atoms(\"protein\")\n",
    "ag = u.atoms\n",
    "\n",
    "# we will use mass as weights for the center calculation\n",
    "transformations = (mda.transformations.unwrap(ag),\n",
    "                   mda.transformations.center_in_box(prot, weights='mass'),\n",
    "                   mda.transformations.wrap(ag, compound='fragments'))\n",
    "u.trajectory.add_transformations(*transformations)\n",
    "\n",
    "nv.show_mdanalysis(u)"
   ]
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   "cell_type": "markdown",
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    "You can see that the `transformations` workflow above has three steps:\n",
    " - make everything molecule whole again with `unwrap` ;\n",
    " - center the protein in the unit cell with `center_in_box` - this causes some of the phospholipids to fall outside the unit cell ;\n",
    " - shift the molecules (`fragments`) back to the unit cell using `wrap`\n",
    " \n",
    "Two other centering transformations are availabe - `center_in_plane` and `center_in_axis` - and just as the names say, they are used to center molecules in the `xy`, `xz` and `yz` planes, and the `x`, `y` and `z` axes, respectively.\n",
    " \n",
    "### Example 3: what if we want to do a fitting of the protein?\n",
    "Fitting is useful when processing trajectories for visualization and analyses - it removes the translations and rotations of the molecule, allowing us to have a better look at the structural changes that happen in our simulations.\n",
    "If we want to do this using `trjconv` we would do have to do this in two steps:\n",
    "\n",
    "     gmx trjconv -f pept_in_memb.xtc -s pept_in_memb.tpr -pbc mol -center -o midstep.xtc\n",
    "    \n",
    "     gmx trjconv -f midstep.xtc -s pept_in_memb.tpr -fit rot+trans -o output.xtc\n",
    "\n",
    "And we choose `Protein` as the group to be centered and for the least squares fitting.\n",
    "\n",
    "In MDAnalysis we just add another transformation to our workflow - `fit_rot_trans`. This transformation takes the AtomGroup to be fitted as argument, an AtomGroup to be used as reference and, by default, it behaves just as the option `-fit rot+trans`. If given a `plane` argument, the fitting is performed on a given plane. If `plane=xy` then the transformation will behave as `-fit rotxy+transxy`, but the `xz` and `yz` planes are also supported. Just as in `center_in_box`, a `weights` argument can be passed to the function, and it will dictate how much each atom of the molecule contributes to the least squares fitting. \n",
    "Here's what the workflow looks like:"
   ]
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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "prot = u.select_atoms(\"protein\")\n",
    "\n",
    "# we load another universe to define the reference\n",
    "# it uses the same input files, but this doesn't have to be always the case\n",
    "ref_u = mda.Universe(data.topology, data.trajectory)\n",
    "reference = ref_u.select_atoms(\"protein\")\n",
    "ag = u.atoms\n",
    "\n",
    "transformations = (mda.transformations.unwrap(ag),\n",
    "                   mda.transformations.center_in_box(prot, weights='mass'),\n",
    "                   mda.transformations.wrap(ag, compound='fragments'),\n",
    "                   mda.transformations.fit_rot_trans(prot, reference))\n",
    "u.trajectory.add_transformations(*transformations)\n",
    "\n",
    "nv.show_mdanalysis(u)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It looks a bit confusing with the membrane..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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    "scrolled": true
   },
   "outputs": [],
   "source": [
    "t = nv.MDAnalysisTrajectory(prot)\n",
    "w = nv.NGLWidget(t)\n",
    "w.add_line()\n",
    "w"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This transformations is good when we want to see how the conformation of the protein evolves with time. \n",
    "\n",
    "But, in this case, we also have a membrane. How does the protein behave in the membrane? Doing a least squares fitting in the `xy` plane can help us have a better look. Here's how it goes:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "prot = u.select_atoms(\"protein\")\n",
    "ref_u = mda.Universe(data.topology, data.trajectory)\n",
    "reference = ref_u.select_atoms(\"protein\")\n",
    "ag = u.atoms\n",
    "\n",
    "transformations = (mda.transformations.unwrap(ag),\n",
    "                   mda.transformations.center_in_box(prot),\n",
    "                   mda.transformations.wrap(ag, compound='fragments'),\n",
    "                   mda.transformations.fit_rot_trans(prot, reference, plane='xy', weights=\"mass\"))\n",
    "u.trajectory.add_transformations(*transformations)\n",
    "\n",
    "# let's hide the lipid tails to have a better view\n",
    "view_selection = u.select_atoms(\"protein or name P\")\n",
    "t = nv.MDAnalysisTrajectory(view_selection)\n",
    "w = nv.NGLWidget(t)\n",
    "w.add_line()\n",
    "w"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This transformation keeps the membrane horizontal, while the protein rotation in the z-axis is removed. This becomes particularly useful when observing protein insertion.\n",
    "\n",
    "### Example 4: I want to do my own transformations...\n",
    "The beauty of MDAnalysis transformations is the ability to easily create custom transformations. All transformations must have the following structure:\n",
    "    \n",
    "```Python\n",
    "def custom_transform(args): # arguments at this point are not mandatory\n",
    "    #do some things\n",
    "        \n",
    "    def wrapped(ts): \n",
    "        # this wrapped function must only take a Timestep as argument\n",
    "        # this is where the actual changes to the timestep must be done\n",
    "            \n",
    "        return ts\n",
    "        \n",
    "    return wrapped\n",
    "```\n",
    "       \n",
    "Let's create one here:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def up_by_2():\n",
    "    \n",
    "    def wrapped(ts):\n",
    "        # here's where the magic happens \n",
    "        # we create a numpy float32 array to avoid reduce floating\n",
    "        # point errors\n",
    "        ts.positions += np.asarray([0,0,20])\n",
    "        \n",
    "        return ts\n",
    "    \n",
    "    return wrapped"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now lets add our transformation to a workflow.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "\n",
    "# loading another universe to better see the changes made by our transformation\n",
    "previous = mda.Universe('pept_in_memb.tpr', 'pept_in_memb.xtc')\n",
    "# making the unmodified universe whole accross the trajectory\n",
    "previous.trajectory.add_transformations(mda.transformations.unwrap(previous.atoms))\n",
    "\n",
    "ag = u.atoms\n",
    "\n",
    "transformations = (mda.transformations.unwrap(ag),\n",
    "                   up_by_2())\n",
    "u.trajectory.add_transformations(*transformations)\n",
    "\n",
    "# visualization\n",
    "view_selection = previous.select_atoms(\"protein or name P\")\n",
    "t = nv.MDAnalysisTrajectory(view_selection)\n",
    "w = nv.NGLWidget(t)\n",
    "w.add_line()\n",
    "w.add_trajectory(u)\n",
    "w"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As you can see, the atoms in the `u` Universe have been shift up by 20 angstroms.\n",
    "\n",
    "The transformations can accept arguments. Let's modify `up_by_2` so that only the peptide is translated in the z coordinate:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def protein_up_by_2(agroup):\n",
    "    \n",
    "    def wrapped(ts):\n",
    "        # here's where the magic happens \n",
    "        # we create a numpy float32 array to avoid reduce floating\n",
    "        # point errors\n",
    "        agroup.positions += np.asarray([0,0,20])\n",
    "        \n",
    "        return ts\n",
    "    \n",
    "    return wrapped"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And we'll see what happens. Now is a good opportunity to showcase the `center_in_axis` transformation. The `center_in_axis` transformation snaps the the weighted center of the Atomgroup to the chosen axis. This is useful to visualize particle insertion in membranes, for example."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe(data.topology, data.trajectory)\n",
    "ag = u.atoms\n",
    "prot = u.select_atoms(\"protein\")\n",
    "\n",
    "transformations = (mda.transformations.unwrap(ag),\n",
    "                   protein_up_by_2(prot),\n",
    "                   mda.transformations.center_in_axis(prot, axis=\"z\", weights='mass'),\n",
    "                   mda.transformations.wrap(ag, compound='fragments'))\n",
    "u.trajectory.add_transformations(*transformations)\n",
    "\n",
    "nv.show_mdanalysis(u)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The two examples of custom transformations show here are very simple. But more complex things can be done, and we encourage you to try them!\n",
    "\n",
    "This has been a quick demonstration on the power of the new on-the-fly transformations of MDAnalysis. There are more transformations available for you to explore and a whole lot more for you to create for your own molecular system."
   ]
  }
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