Update tutorials

paprika/restraints/openmm.py

@@ -17,13 +17,13 @@ def apply_positional_restraints(
 
     Parameters
     ----------
-    coordinate_path
+    coordinate_path : str
         The path to the coordinate file which the restraints will be applied to.
         This should contain either the host or the complex, the dummy atoms and
         and solvent.
-    system: openmm.System
+    system : openmm.System
         The system object to add the positional restraints to.
-    force_group
+    force_group : int
         The force group to add the positional restraints to.
     """
 
@@ -35,7 +35,6 @@ def apply_positional_restraints(
     for atom in structure.atoms:
 
         if atom.name == "DUM":
-
             positional_restraint = openmm.CustomExternalForce(
                 "k * ((x-x0)^2 + (y-y0)^2 + (z-z0)^2)"
             )
@@ -62,6 +61,25 @@ def apply_positional_restraints(
 def apply_dat_restraint(
     system, restraint, phase, window_number, flat_bottom=False, force_group=None
 ):
+    """A utility function which takes in pAPRika restraints and applies the
+    restraints to an OpenMM System object.
+
+    Parameters
+    ----------
+    system : openmm.System
+        The system object to add the positional restraints to.
+    restraint : list
+        List of pAPRika defined restraints
+    phase : str
+        Phase of calculation ("attach", "pull" or "release")
+    window_number : int
+        The corresponding window number of the current phase
+    flat_bottom : bool
+        Specify whether the restraint is a flat bottom potential
+    force_group : int
+        The force group to add the positional restraints to.
+
+    """
 
     from simtk import openmm, unit
 

tutorial/01-tutorial-cb6-but.ipynb

@@ -116,7 +116,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Align the pulling axis"
+    "### Align the pulling axis\n",
+    "<a id='guest'></a>"
    ]
   },
   {
@@ -490,10 +491,9 @@
    "metadata": {},
    "source": [
     "## Add restraints using pAPRika\n",
-    "\n",
+    "<a id='host_static'></a>\n",
     "`pAPRika` supports four different types of restraints:\n",
     "\n",
-    "\n",
     "- Static restraints: these six restraints keep the host and in the proper orientation during the simulation (necessary),\n",
     "- Guest restraints: these restraints pull the guest away from the host along the $z$ axis (necessary),\n",
     "- Conformational restraints: these restraints alter the conformational sampling of the host molecule (optional), and\n",
@@ -881,8 +881,9 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "from paprika.restraints.restraints import create_window_list\n",
     "\n",
-    "window_list = restraints.create_window_list(guest_restraints)\n",
+    "window_list = create_window_list(guest_restraints)\n",
     "for window in window_list:\n",
     "    os.makedirs(f\"windows/{window}\")"
    ]
@@ -914,11 +915,13 @@
    },
    "outputs": [],
    "source": [
+    "from paprika.restraints.amber import amber_restraint_line\n",
+    "\n",
     "host_guest_restraints = static_restraints + guest_restraints\n",
     "for window in window_list:\n",
     "    with open(f\"windows/{window}/disang.rest\", \"a\") as file:\n",
     "        for restraint in host_guest_restraints:\n",
-    "            string = restraints.amber_restraint_line(restraint, window)\n",
+    "            string = amber_restraint_line(restraint, window)\n",
     "            if string is not None:\n",
     "                file.write(string)"
    ]
@@ -1451,6 +1454,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "<a id='results'></a>\n",
     "There is a large uncertainty associated with this calculation because we only simulated for a very short amount of time in each window and we used a large amount of spacing between each window in the pull phase, but the uncertainty will go down with more time.\n",
     "\n",
     "The experimental value is $-RT \\ln (280*10^3 M)$ = -7.44 kcal/mol."
@@ -1466,7 +1470,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1480,9 +1484,18 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.7.8"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

tutorial/02-tutorial-cb6-but-pbc.ipynb

@@ -517,8 +517,9 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "from paprika.restraints.restraints import create_window_list\n",
     "\n",
-    "window_list = restraints.create_window_list(guest_restraints)\n",
+    "window_list = create_window_list(guest_restraints)\n",
     "for window in window_list:\n",
     "    os.makedirs(f\"windows/{window}\")"
    ]
@@ -550,11 +551,13 @@
    },
    "outputs": [],
    "source": [
+    "from paprika.restraints.amber import amber_restraint_line\n",
+    "\n",
     "host_guest_restraints = static_restraints + guest_restraints\n",
     "for window in window_list:\n",
     "    with open(f\"windows/{window}/disang.rest\", \"a\") as file:\n",
     "        for restraint in host_guest_restraints:\n",
-    "            string = restraints.amber_restraint_line(restraint, window)\n",
+    "            string = amber_restraint_line(restraint, window)\n",
     "            if string is not None:\n",
     "                file.write(string)"
    ]
@@ -1264,8 +1267,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.6.4"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}