Merge pull request #730 from chrisiacovella/master

updated docs to reflect refactoring and remove use of depricated func…
mosdef-hub · May 21, 2020 · 4b60ced · 4b60ced
2 parents 60711ff + 04e6178
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diff --git a/docs/tutorials/ethane.mol2 b/docs/tutorials/ethane.mol2
@@ -15,12 +15,12 @@ NO_CHARGES
        7 H           -0.3570     0.7690     0.6530 H             1 RES     
        8 H           -0.3570     0.1810    -0.9930 H             1 RES     
 @<TRIPOS>BOND
-       1        6        5 1
-       2        8        5 1
-       3        3        1 1
-       4        1        2 1
+       1        8        5 1
+       2        1        2 1
+       3        6        5 1
+       4        4        1 1
        5        7        5 1
-       6        1        5 1
-       7        4        1 1
+       6        5        1 1
+       7        3        1 1
 @<TRIPOS>SUBSTRUCTURE
        1 RES             1 RESIDUE    0 **** ROOT      0
diff --git a/docs/tutorials/tutorial_methane.ipynb b/docs/tutorials/tutorial_methane.ipynb
@@ -164,7 +164,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.7"
   },
   "widgets": {
    "state": {

diff --git a/docs/tutorials/tutorial_monolayer.ipynb b/docs/tutorials/tutorial_monolayer.ipynb
@@ -24,7 +24,7 @@
    "source": [
     "import mbuild as mb\n",
     "\n",
-    "from mbuild.examples import Alkane\n",
+    "from mbuild.lib.recipes import Alkane\n",
     "from mbuild.lib.moieties import Silane\n",
     "\n",
     "\n",
@@ -116,10 +116,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Also note the `backfill` optional argument which allows you to place a different compound on any unused ports. In this case we want to backfill with hydrogen atoms on every port without a chain.\n",
-    "\n",
-    "\n",
-    "And that's it! Check out `examples.alkane_monolayer` for the fully wrapped class."
+    "Also note the `backfill` optional argument which allows you to place a different compound on any unused ports. In this case we want to backfill with hydrogen atoms on every port without a chain."
    ]
   },
   {
@@ -141,6 +138,34 @@
     "# Save as .mol2 file\n",
     "monolayer.save('monolayer.mol2', overwrite=True)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "`lib.recipes.monolayer.py` wraps many these functions into a simple, general class for generating the monolayers, as shown below:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mbuild.lib.recipes import Monolayer\n",
+    "\n",
+    "monolayer = Monolayer(fractions=[1.0], chains=alkylsilane, backfill=hydrogen, \n",
+    "                      pattern=mb.Grid2DPattern(n=8, m=8), \n",
+    "                      surface=surface, tile_x=2, tile_y=1)\n",
+    "monolayer.visualize()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -159,7 +184,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/tutorial_polymers.ipynb b/docs/tutorials/tutorial_polymers.ipynb
@@ -39,19 +39,24 @@
     "class CH2(mb.Compound):\n",
     "    def __init__(self):\n",
     "        super(CH2, self).__init__()\n",
+    "        # Add carbon        \n",
     "        self.add(mb.Particle(name='C', pos=[0,0,0]), label='C[$]')\n",
     "        \n",
     "        # Add hydrogens \n",
     "        self.add(mb.Particle(name='H', pos=[-0.109, 0, 0.0]), label='HC[$]')    \n",
     "        self.add(mb.Particle(name='H', pos=[0.109, 0, 0.0]), label='HC[$]')\n",
     "        \n",
+    "        # Add bonds between the atoms\n",
+    "        self.add_bond((self['C'][0], self['HC'][0]))\n",
+    "        self.add_bond((self['C'][0], self['HC'][1]))\n",
+    "        \n",
     "        # Add ports anchored to the carbon\n",
     "        self.add(mb.Port(anchor=self[0]), label='up')\n",
     "        self.add(mb.Port(anchor=self[0]), label='down')\n",
     "        \n",
     "        # Move the ports approximately half a C-C bond length away from the carbon\n",
-    "        mb.translate(self['up'], [0, -0.154/2, 0]) \n",
-    "        mb.translate(self['down'], [0, 0.154/2, 0]) \n",
+    "        self['up'].translate([0, -0.154/2, 0]) \n",
+    "        self['down'].translate([0, 0.154/2, 0]) \n",
     "\n",
     "monomer = CH2()\n",
     "monomer.visualize(show_ports=True)"
@@ -78,19 +83,32 @@
     "class CH2(mb.Compound):\n",
     "    def __init__(self):\n",
     "        super(CH2, self).__init__()\n",
+    "        # Add carbon\n",
     "        self.add(mb.Particle(name='C', pos=[0,0,0]), label='C[$]')\n",
+    "        \n",
+    "        # Add hydrogens \n",
     "        self.add(mb.Particle(name='H', pos=[-0.109, 0, 0.0]), label='HC[$]')    \n",
     "        self.add(mb.Particle(name='H', pos=[0.109, 0, 0.0]), label='HC[$]')\n",
+    "        \n",
+    "        # Rotate the hydrogens\n",
     "        theta = 0.5 * (180 - 109.5) * np.pi / 180\n",
-    "        mb.rotate(self['HC'][0], theta, around=[0, 1, 0])\n",
-    "        mb.rotate(self['HC'][1], -theta, around=[0, 1, 0])\n",
+    "        #mb.rotate(self['HC'][0], theta, around=[0, 1, 0])\n",
+    "        #mb.rotate(self['HC'][1], -theta, around=[0, 1, 0])\n",
+    "        self['HC'][0].rotate( theta, around=[0, 1, 0])\n",
+    "        self['HC'][1].rotate(-theta, around=[0, 1, 0])\n",
     "        \n",
+    "        # Add bonds between the atoms\n",
+    "        self.add_bond((self['C'][0], self['HC'][0]))\n",
+    "        self.add_bond((self['C'][0], self['HC'][1]))\n",
+    "        \n",
+    "        # Add the ports and appropriately rotate them\n",
     "        self.add(mb.Port(anchor=self[0]), label='up')\n",
-    "        mb.translate(self['up'], [0, -0.154/2, 0]) \n",
-    "        mb.rotate(self['up'], theta, around=[1, 0, 0])\n",
+    "        self['up'].translate([0, -0.154/2, 0]) \n",
+    "        self['up'].rotate(theta, around=[1, 0, 0])\n",
+    "        \n",
     "        self.add(mb.Port(anchor=self[0]), label='down')\n",
-    "        mb.translate(self['down'], [0, 0.154/2, 0]) \n",
-    "        mb.rotate(self['down'], -theta, around=[1, 0, 0]) \n",
+    "        self['down'].translate([0, 0.154/2, 0]) \n",
+    "        self['down'].rotate(-theta, around=[1, 0, 0]) \n",
     "\n",
     "monomer = CH2()\n",
     "monomer.visualize(show_ports=True)"
@@ -137,7 +155,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Visualization of this structure demonstrates a problem; the polymer curls up on itself.  This is a result of the fact that ports not only define the location in space, but also an orientation. This can be trivially fixed, by first rotating the port 180&deg; around the y-axis.  \n",
+    "Visualization of this structure demonstrates a problem; the polymer curls up on itself.  This is a result of the fact that ports not only define the location in space, but also an orientation. This can be trivially fixed, by  rotating the down port 180&deg; around the y-axis.  \n",
     "\n",
     "We can also add a variable ```chain_length``` both to the for loop and ```init```  that will allow the length of the polymer to be adjusted when the class is instantiated.  "
    ]
@@ -154,20 +172,29 @@
     "class CH2(mb.Compound):\n",
     "    def __init__(self):\n",
     "        super(CH2, self).__init__()\n",
+    "         # Add carbons and hydrogens\n",
     "        self.add(mb.Particle(name='C', pos=[0,0,0]), label='C[$]')\n",
     "        self.add(mb.Particle(name='H', pos=[-0.109, 0, 0.0]), label='HC[$]')    \n",
     "        self.add(mb.Particle(name='H', pos=[0.109, 0, 0.0]), label='HC[$]')\n",
+    "  \n",
+    "        # rotate hydrogens\n",
     "        theta = 0.5 * (180 - 109.5) * np.pi / 180\n",
-    "        mb.rotate(self['HC'][0], theta, around=[0, 1, 0])\n",
-    "        mb.rotate(self['HC'][1], -theta, around=[0, 1, 0])\n",
+    "        self['HC'][0].rotate(theta, around=[0, 1, 0])\n",
+    "        self['HC'][1].rotate(-theta, around=[0, 1, 0])\n",
+    "        \n",
+    "        # Add bonds between the atoms\n",
+    "        self.add_bond((self['C'][0], self['HC'][0]))\n",
+    "        self.add_bond((self['C'][0], self['HC'][1]))\n",
     "        \n",
+    "        # Add ports\n",
     "        self.add(mb.Port(anchor=self[0]), label='up')\n",
-    "        mb.translate(self['up'], [0, -0.154/2, 0]) \n",
-    "        mb.rotate(self['up'], theta, around=[1, 0, 0])\n",
+    "        self['up'].translate([0, -0.154/2, 0]) \n",
+    "        self['up'].rotate(theta, around=[1, 0, 0])\n",
+    "        \n",
     "        self.add(mb.Port(anchor=self[0]), label='down')\n",
-    "        mb.translate(self['down'], [0, 0.154/2, 0])\n",
-    "        mb.rotate(self['down'], np.pi, [0, 1, 0])\n",
-    "        mb.rotate(self['down'], -theta, around=[1, 0, 0]) \n",
+    "        self['down'].translate([0, 0.154/2, 0])\n",
+    "        self['down'].rotate(np.pi, [0, 1, 0])\n",
+    "        self['down'].rotate(-theta, around=[1, 0, 0]) \n",
     "\n",
     "\n",
     "class AlkanePolymer(mb.Compound):\n",
@@ -248,7 +275,7 @@
     "\n",
     "# the pattern we generate puts points in the xy-plane, so we'll rotate the polymer\n",
     "# so that it is oriented normal to the xy-plane\n",
-    "mb.rotate(polymer, np.pi/2, [1, 0, 0])\n",
+    "polymer.rotate(np.pi/2, [1, 0, 0])\n",
     "\n",
     "# define a compound to hold all the polymers\n",
     "system = mb.Compound()\n",
@@ -262,7 +289,7 @@
     "# now clone the polymer and move it to the points in the pattern\n",
     "for pos in pattern_disk:\n",
     "    current_polymer = mb.clone(polymer)\n",
-    "    mb.translate(current_polymer, pos)\n",
+    "    current_polymer.translate(pos)\n",
     "    system.add(current_polymer)\n",
     "    \n",
     "system.visualize()"
@@ -287,16 +314,16 @@
     "\n",
     "polymer = mb.lib.recipes.Polymer(CH2(), 10, port_labels=('up', 'down'))\n",
     "system = mb.Compound()\n",
-    "mb.rotate(polymer, np.pi/2, [1, 0, 0])\n",
+    "polymer.rotate(np.pi/2, [1, 0, 0])\n",
     "\n",
     "pattern_disk = mb.Grid3DPattern(5, 5, 5)\n",
     "pattern_disk.scale(8.0)\n",
     "    \n",
     "for pos in pattern_disk:\n",
     "    current_polymer = mb.clone(polymer)\n",
     "    for around in [(1, 0, 0), (0, 1, 0), (0, 0, 1)]:  # rotate around x, y, and z\n",
-    "        mb.rotate(current_polymer, random.uniform(0, np.pi), around)\n",
-    "    mb.translate(current_polymer, pos)\n",
+    "        current_polymer.rotate(random.uniform(0, np.pi), around)\n",
+    "    current_polymer.translate(pos)\n",
     "    system.add(current_polymer)\n",
     "\n",
     "system.visualize()"
@@ -353,13 +380,13 @@
     "        super(AlkanePolymer, self).__init__()\n",
     "        monomer_proto = CH2()\n",
     "        last_monomer = CH2()\n",
-    "        mb.rotate(last_monomer['down'], random.uniform(-delta,delta), [1, 0, 0])\n",
-    "        mb.rotate(last_monomer['down'], random.uniform(-delta,delta), [0, 1, 0])\n",
+    "        last_monomer['down'].rotate(random.uniform(-delta,delta), [1, 0, 0])\n",
+    "        last_monomer['down'].rotate(random.uniform(-delta,delta), [0, 1, 0])\n",
     "        self.add(last_monomer)\n",
     "        for i in range(chain_length-1):\n",
     "            current_monomer = mb.clone(monomer_proto)\n",
-    "            mb.rotate(current_monomer['down'], random.uniform(-delta,delta), [1, 0, 0])\n",
-    "            mb.rotate(current_monomer['down'], random.uniform(-delta,delta), [0, 1, 0])\n",
+    "            current_monomer['down'].rotate(random.uniform(-delta,delta), [1, 0, 0])\n",
+    "            current_monomer['down'].rotate(random.uniform(-delta,delta), [0, 1, 0])\n",
     "            mb.force_overlap(move_this=current_monomer, \n",
     "                             from_positions=current_monomer['up'], \n",
     "                             to_positions=last_monomer['down'])\n",
@@ -369,6 +396,13 @@
     "polymer = AlkanePolymer(chain_length = 200, delta=0.4)\n",
     "polymer.visualize()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -387,7 +421,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.7"
   },
   "widgets": {
    "state": {