Academic Year 22-23 cleanup

.gitignore

@@ -6,3 +6,4 @@ init*.*
 tmp
 __pycache__
 hints.txt
+.idea

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.2.2
+  rev: "1.5.2"
   hooks:
-    - id: nbqa-autopep8
-      args: [--nbqa-skip-celltags=before-import]
+    - id: nbqa-black
+      args: ["--nbqa-skip-celltags=before-import"]
     - id: nbqa-pyupgrade
-      args: [--py36-plus]
+      args: ["--py39-plus"]
     - id: nbqa-isort
-      args: [--nbqa-skip-celltags=before-import]
+      args: ["--nbqa-skip-celltags=before-import"]
     - id: nbqa-check-ast
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: "v4.3.0"
   hooks:
     - id: check-yaml
     - id: check-ast
@@ -26,10 +26,24 @@ repos:
             .*\.prmtop
         )$
 - repo: https://github.com/kynan/nbstripout.git
-  rev: 0.5.0
+  rev: "0.6.0"
   hooks:
     - id: nbstripout
 - repo: https://github.com/psf/black
-  rev: 21.12b0
+  rev: "22.8.0"
   hooks:
     - id: black
+- repo: https://github.com/pycqa/isort
+  rev: "5.10.1"
+  hooks:
+    - id: isort
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: "v1.9.0"
+  hooks:
+    - id: python-no-eval
+    - id: python-use-type-annotations
+- repo: https://github.com/asottile/pyupgrade
+  rev: "v2.38.0"
+  hooks:
+    - id: pyupgrade
+      args: ["--py39-plus"]

01_first_steps/01_water.ipynb

@@ -172,21 +172,26 @@
    "outputs": [],
    "source": [
     "# a. Select the TIP3P-FB force field.\n",
-    "forcefield = ForceField('amber14/tip3pfb.xml')\n",
+    "forcefield = ForceField(\"amber14/tip3pfb.xml\")\n",
     "\n",
     "# b. Create an object to compute energies and forces for our topology.\n",
-    "system = forcefield.createSystem(topology, nonbondedCutoff=1*nanometer)\n",
+    "system = forcefield.createSystem(topology, nonbondedCutoff=1 * nanometer)\n",
     "\n",
     "# c. Definition an integrator, mandatory.\n",
     "integrator = VerletIntegrator(1 * femtoseconds)\n",
     "\n",
     "# d. A simulation object in OpenMM combines topology, system and integrator.\n",
     "simulation = Simulation(topology, system, integrator)\n",
-    "simulation.context.setPositions(np.array([\n",
-    "    [0.0, 0.0, 0.0],\n",
-    "    [0.0, 0.0, 1.0],\n",
-    "    [0.0, 1.0, 0.0],\n",
-    "]) * angstroms)"
+    "simulation.context.setPositions(\n",
+    "    np.array(\n",
+    "        [\n",
+    "            [0.0, 0.0, 0.0],\n",
+    "            [0.0, 0.0, 1.0],\n",
+    "            [0.0, 1.0, 0.0],\n",
+    "        ]\n",
+    "    )\n",
+    "    * angstroms\n",
+    ")"
    ]
   },
   {
@@ -258,8 +263,7 @@
     "    # with all attributes, useful to explore undocumented\n",
     "    # attributes.\n",
     "    # print(vars(atom))\n",
-    "    print(\"Name and mass of atom {}: {}, {}\".format(\n",
-    "        iatom, atom.name, atom.element.mass))"
+    "    print(f\"Name and mass of atom {iatom}: {atom.name}, {atom.element.mass}\")"
    ]
   },
   {
@@ -334,8 +338,7 @@
    "outputs": [],
    "source": [
     "# Simply extract and print information\n",
-    "state = simulation.context.getState(\n",
-    "    getPositions=True, getForces=True, getEnergy=True)\n",
+    "state = simulation.context.getState(getPositions=True, getForces=True, getEnergy=True)\n",
     "print(\"Potential energy: \", state.getPotentialEnergy())\n",
     "print()\n",
     "print(\"Atomic positions\")\n",
@@ -364,7 +367,7 @@
     "d01 /= np.linalg.norm(d01)\n",
     "d02 /= np.linalg.norm(d02)\n",
     "cosine = np.dot(d01, d02)\n",
-    "print(np.arccos(cosine)*180/np.pi)"
+    "print(np.arccos(cosine) * 180 / np.pi)"
    ]
   },
   {
@@ -385,10 +388,10 @@
     "# NGLView is a structure and trajectory visualization that integrates well with Jupyter Notebooks.\n",
     "\n",
     "# Write out a PDB file\n",
-    "with open('water.pdb', 'w') as outfile:\n",
+    "with open(\"water.pdb\", \"w\") as outfile:\n",
     "    PDBFile.writeFile(topology, pos, outfile)\n",
     "# Visualize\n",
-    "nglview.show_mdtraj(mdtraj.load('water.pdb'))"
+    "nglview.show_mdtraj(mdtraj.load(\"water.pdb\"))"
    ]
   },
   {
@@ -433,24 +436,24 @@
     "simulation.reporters = []\n",
     "\n",
     "# Write a frame to the PDB trajectory every step.\n",
-    "simulation.reporters.append(PDBReporter('traj.pdb', 1))\n",
+    "simulation.reporters.append(PDBReporter(\"traj.pdb\", 1))\n",
     "\n",
     "# Write scalar properties to a CSV file every step.\n",
-    "simulation.reporters.append(StateDataReporter(\n",
-    "    \"scalars.csv\",\n",
-    "    1,\n",
-    "    time=True,\n",
-    "    potentialEnergy=True,\n",
-    "    totalEnergy=True,\n",
-    "    temperature=True))\n",
+    "simulation.reporters.append(\n",
+    "    StateDataReporter(\n",
+    "        \"scalars.csv\",\n",
+    "        1,\n",
+    "        time=True,\n",
+    "        potentialEnergy=True,\n",
+    "        totalEnergy=True,\n",
+    "        temperature=True,\n",
+    "    )\n",
+    ")\n",
     "\n",
     "# Write scalar properties to screen every 100 steps.\n",
-    "simulation.reporters.append(StateDataReporter(\n",
-    "    stdout,\n",
-    "    100,\n",
-    "    step=True,\n",
-    "    totalEnergy=True,\n",
-    "    temperature=True))\n",
+    "simulation.reporters.append(\n",
+    "    StateDataReporter(stdout, 100, step=True, totalEnergy=True, temperature=True)\n",
+    ")\n",
     "\n",
     "# Actually run the molecular dynamics simulation.\n",
     "simulation.step(1000)"
@@ -469,7 +472,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nglview.show_mdtraj(mdtraj.load('traj.pdb'))"
+    "nglview.show_mdtraj(mdtraj.load(\"traj.pdb\"))"
    ]
   },
   {
@@ -490,7 +493,6 @@
    "outputs": [],
    "source": [
     "# The following line is needed to obtain an interactive plot.\n",
-    "%matplotlib widget\n",
     "df = pandas.read_csv(\"scalars.csv\")\n",
     "# To show the contents of a Pandas Dataframe, just put\n",
     "# the variable on the last line.\n",
@@ -505,8 +507,8 @@
    "source": [
     "# Plot the potential and total energy as function of time.\n",
     "ax = plt.gca()\n",
-    "df.plot(kind='line', x='#\"Time (ps)\"', y='Potential Energy (kJ/mole)', ax=ax)\n",
-    "df.plot(kind='line', x='#\"Time (ps)\"', y='Total Energy (kJ/mole)', ax=ax)"
+    "df.plot(kind=\"line\", x='#\"Time (ps)\"', y=\"Potential Energy (kJ/mole)\", ax=ax)\n",
+    "df.plot(kind=\"line\", x='#\"Time (ps)\"', y=\"Total Energy (kJ/mole)\", ax=ax)"
    ]
   },
   {
@@ -515,7 +517,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df.plot(kind='line', x='#\"Time (ps)\"', y='Temperature (K)')"
+    "df.plot(kind=\"line\", x='#\"Time (ps)\"', y=\"Temperature (K)\")"
    ]
   },
   {

01_first_steps/02_lennard_jones.ipynb

@@ -142,16 +142,15 @@
    "outputs": [],
    "source": [
     "# Define the ensemble to be simulated in.\n",
-    "integrator = LangevinIntegrator(temperature, 1/picosecond, 2*femtoseconds)\n",
+    "integrator = LangevinIntegrator(temperature, 1 / picosecond, 2 * femtoseconds)\n",
     "system.addForce(MonteCarloBarostat(pressure, temperature))\n",
     "\n",
     "# Define a simulation object.\n",
     "simulation = Simulation(topology, system, integrator)\n",
     "\n",
     "# Initialization steps before MD.\n",
     "# - Asign random positions\n",
-    "simulation.context.setPositions(np.random.uniform(\n",
-    "    0, box_size/angstrom, (natom, 3))*angstrom)\n",
+    "simulation.context.setPositions(np.random.uniform(0, box_size / angstrom, (natom, 3)) * angstrom)\n",
     "# - Minimize the energy\n",
     "simulation.minimizeEnergy()\n",
     "# - Initialize velocities with random values at 300K.\n",
@@ -176,29 +175,29 @@
     "\n",
     "# Write the initial geometry as a PDB file.\n",
     "positions = simulation.context.getState(getPositions=True).getPositions()\n",
-    "with open('ljinit.pdb', 'w') as f:\n",
+    "with open(\"ljinit.pdb\", \"w\") as f:\n",
     "    PDBFile.writeFile(simulation.topology, positions, f)\n",
     "\n",
     "# Write a frame to the DCD trajectory every 100 steps.\n",
-    "simulation.reporters.append(DCDReporter('ljtraj.dcd', 100))\n",
+    "simulation.reporters.append(DCDReporter(\"ljtraj.dcd\", 100))\n",
     "\n",
     "# Write scalar properties to a CSV file every 10 steps.\n",
-    "simulation.reporters.append(StateDataReporter(\n",
-    "    \"ljscalars.csv\",\n",
-    "    10,\n",
-    "    time=True,\n",
-    "    potentialEnergy=True,\n",
-    "    totalEnergy=True,\n",
-    "    temperature=True,\n",
-    "    volume=True))\n",
+    "simulation.reporters.append(\n",
+    "    StateDataReporter(\n",
+    "        \"ljscalars.csv\",\n",
+    "        10,\n",
+    "        time=True,\n",
+    "        potentialEnergy=True,\n",
+    "        totalEnergy=True,\n",
+    "        temperature=True,\n",
+    "        volume=True,\n",
+    "    )\n",
+    ")\n",
     "\n",
     "# Write scalar properties to screen every 1000 steps.\n",
-    "simulation.reporters.append(StateDataReporter(\n",
-    "    stdout,\n",
-    "    1000,\n",
-    "    step=True,\n",
-    "    temperature=True,\n",
-    "    volume=True))\n",
+    "simulation.reporters.append(\n",
+    "    StateDataReporter(stdout, 1000, step=True, temperature=True, volume=True)\n",
+    ")\n",
     "\n",
     "# Actually run the molecular dynamics simulation.\n",
     "simulation.step(30000)\n",
@@ -249,8 +248,8 @@
    "outputs": [],
    "source": [
     "df = pandas.read_csv(\"ljscalars.csv\")\n",
-    "df.plot(kind='line', x='#\"Time (ps)\"', y='Temperature (K)')\n",
-    "df.plot(kind='line', x='#\"Time (ps)\"', y='Box Volume (nm^3)')"
+    "df.plot(kind=\"line\", x='#\"Time (ps)\"', y=\"Temperature (K)\")\n",
+    "df.plot(kind=\"line\", x='#\"Time (ps)\"', y=\"Box Volume (nm^3)\")"
    ]
   },
   {