Merge pull request #47 from openforcefield/update_smirnoff_workshop

Update SMIRNOFF workshop materials
openforcefield · Apr 9, 2024 · a8a8e32 · a8a8e32
2 parents b05c7d9 + ad5eaef
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diff --git a/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip b/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip
diff --git a/source/workshops/2024/smirnoff/bespokefit-hexanoic-acid.offxml b/source/workshops/2024/smirnoff/bespokefit-hexanoic-acid.offxml
@@ -320,10 +320,10 @@
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         <Proper smirks="[*:1]~[*:2]-[*:3]#[*:4]" periodicity1="1" phase1="0.0 * degree ** 1" id="t166" k1="0.0 * mole ** -1 * kilocalorie ** 1" idivf1="1.0"></Proper>
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-        <Proper smirks="[#6H2X4x0!r+0A:1](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](-;!@[#8H1X2x0!r+0A]-;!@[#1H0X1x0!r+0A])=;!@[#8H0X1x0!r+0A:4]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t183" k1="2.339482342559e-05 * kilocalories_per_mole ** 1" k2="-0.09629862049992 * mole ** -1 * kilocalorie ** 1" k3="1.502296337255e-06 * kilocalories_per_mole ** 1" k4="6.115051851251e-06 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
-        <Proper smirks="[#6H2X4x0!r+0A:1](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](=;!@[#8H0X1x0!r+0A])-;!@[#8H1X2x0!r+0A:4]-;!@[#1H0X1x0!r+0A]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t184" k1="-2.665103673882e-05 * kilocalories_per_mole ** 1" k2="0.570167135834 * kilocalories_per_mole ** 1" k3="0.1812559079425 * mole ** -1 * kilocalorie ** 1" k4="4.541093756891e-06 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
-        <Proper smirks="[#1H0X1x0!r+0A:1]-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](-;!@[#8H1X2x0!r+0A]-;!@[#1H0X1x0!r+0A])=;!@[#8H0X1x0!r+0A:4]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t185" k1="0.9162555051511 * mole ** -1 * kilocalorie ** 1" k2="0.2080633644506 * mole ** -1 * kilocalorie ** 1" k3="-0.1737773653881 * mole ** -1 * kilocalorie ** 1" k4="-0.004756813549828 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
-        <Proper smirks="[#1H0X1x0!r+0A:1]-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](=;!@[#8H0X1x0!r+0A])-;!@[#8H1X2x0!r+0A:4]-;!@[#1H0X1x0!r+0A]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t186" k1="0.2912505051823 * kilocalories_per_mole ** 1" k2="-1.528497551787e-05 * kilocalories_per_mole ** 1" k3="-0.2013576311107 * mole ** -1 * kilocalorie ** 1" k4="-1.188164284603e-05 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
+        <Proper smirks="[#6H2X4x0!r+0A:1](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](-;!@[#8H1X2x0!r+0A]-;!@[#1H0X1x0!r+0A])=;!@[#8H0X1x0!r+0A:4]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t183" k1="2.311750799844e-05 * kilocalories_per_mole ** 1" k2="-0.09934852329684 * mole ** -1 * kilocalorie ** 1" k3="1.505881066552e-06 * kilocalories_per_mole ** 1" k4="6.156327275483e-06 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
+        <Proper smirks="[#6H2X4x0!r+0A:1](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](=;!@[#8H0X1x0!r+0A])-;!@[#8H1X2x0!r+0A:4]-;!@[#1H0X1x0!r+0A]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t184" k1="-2.672553443299e-05 * kilocalories_per_mole ** 1" k2="0.5733687344026 * kilocalories_per_mole ** 1" k3="0.1812558882216 * mole ** -1 * kilocalorie ** 1" k4="4.510013887253e-06 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
+        <Proper smirks="[#1H0X1x0!r+0A:1]-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](-;!@[#8H1X2x0!r+0A]-;!@[#1H0X1x0!r+0A])=;!@[#8H0X1x0!r+0A:4]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t185" k1="0.9162450108759 * mole ** -1 * kilocalorie ** 1" k2="0.2080640783886 * mole ** -1 * kilocalorie ** 1" k3="-0.1737774081048 * mole ** -1 * kilocalorie ** 1" k4="-0.005008864859333 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
+        <Proper smirks="[#1H0X1x0!r+0A:1]-;!@[#6H2X4x0!r+0A:2](-;!@[#1H0X1x0!r+0A])(-;!@[#6H2X4x0!r+0A](-;!@[#1H0X1x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#6H2X4x0!r+0A,#6H3X4x0!r+0A](-;!@[#1H0X1x0!r+0A,#6H2X4x0!r+0A])(-;!@[#1H0X1x0!r+0A])-;!@[#1H0X1x0!r+0A])-;!@[#6H0X3x0!r+0A:3](=;!@[#8H0X1x0!r+0A])-;!@[#8H1X2x0!r+0A:4]-;!@[#1H0X1x0!r+0A]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0 * degree ** 1" phase2="180 * degree ** 1" phase3="0 * degree ** 1" phase4="180 * degree ** 1" id="t186" k1="0.291045899231 * kilocalories_per_mole ** 1" k2="-1.490732021763e-05 * kilocalories_per_mole ** 1" k3="-0.2013184497385 * mole ** -1 * kilocalorie ** 1" k4="-1.235976991155e-05 * kilocalories_per_mole ** 1" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"></Proper>
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     <ImproperTorsions version="0.3" potential="k*(1+cos(periodicity*theta-phase))" default_idivf="auto">
         <Improper smirks="[*:1]~[#6X3:2](~[*:3])~[*:4]" periodicity1="2" phase1="180.0 * degree ** 1" k1="5.230790565314 * mole ** -1 * kilocalorie ** 1" id="i1"></Improper>

diff --git a/source/workshops/2024/smirnoff/colab-env.yml b/source/workshops/2024/smirnoff/colab-env.yml
@@ -1,26 +1,23 @@
-name: 2024-smirnoff-workshop
+name: openff-docs-examples
 channels:
     - conda-forge
 dependencies:
-    # Notebook + runtime
+    # Colab-specific versions
     - ipywidgets=7.6.0
+    - nglview=3.0.3
     # Examples
-    - openff-toolkit-examples>=0.14.5
-    - openff-interchange>=0.3.18
-    - openff-nagl
-    - openff-bespokefit>=0.2.3
+    - openff-toolkit-examples ~=0.15.2
+    - openff-interchange ~=0.3.25
+    - openff-nagl ~=0.3.7
+    - openff-bespokefit
     - gromacs >=2021=nompi*
-    - lammps
+    - lammps >=2023.08.02
     - rich
     - jax
     - dgl
-    - nglview=3.0.3
     - xtb-python
     - pdbfixer
     - mdtraj
-    - propka
-    - pdb2pqr
     - openmmtools
     - chemper
-    - dockstring
     - mdanalysis
diff --git a/source/workshops/2024/smirnoff/colab-smirnoff.ipynb b/source/workshops/2024/smirnoff/colab-smirnoff.ipynb
@@ -1,5 +1,34 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c36c3757-9937-4265-b151-27c69acf185d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip install -U https://github.com/conda-incubator/condacolab/archive/cuda-version-12.tar.gz\n",
+    "import condacolab\n",
+    "condacolab.install_mambaforge()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a5c51ca7-b042-454c-8f06-d19225fe4acd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/utils.py\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/colab-env.yml\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/7FCX_prepped.pdb\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/smirks.png\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/interchange_vectors.png\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/bespoke_hexanoic_acid_alltorsions.offxml\n",
+    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/smirnoff/bespokefit-hexanoic-acid.offxml\n",
+    "!mamba env update -q --name=base --file=colab-env.yml"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "81036958-df15-4b2e-9c41-093ebfccaaf9",
@@ -109,37 +138,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c36c3757-9937-4265-b151-27c69acf185d",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!pip install -U https://github.com/conda-incubator/condacolab/archive/cuda-version-12.tar.gz\n",
-    "import condacolab\n",
-    "condacolab.install_mambaforge()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a5c51ca7-b042-454c-8f06-d19225fe4acd",
-   "metadata": {},
+   "id": "bc3f4e94-c626-46c9-a9fa-db2454ff892f",
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/utils.py\n",
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/colab-env.yml\n",
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/7FCX_prepped.pdb\n",
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/smirks.png\n",
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/bespoke_hexanoic_acid_alltorsions.offxml\n",
-    "!wget -qN https://raw.githubusercontent.com/openforcefield/openff-docs/2024-smirnoff-workshop/source/workshops/2024/smirnoff/bespokefit-hexanoic-acid.offxml\n",
-    "!mamba env update -q --name=base --file=colab-env.yml\n",
-    "from google.colab import output\n",
-    "output.enable_custom_widget_manager()"
+    "from utils import draw_molecule, nglview_show_openmm"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc3f4e94-c626-46c9-a9fa-db2454ff892f",
+   "id": "e090acfa-1e7f-431f-8b35-3ab282e3b259",
    "metadata": {
     "editable": true,
     "slideshow": {
@@ -149,7 +164,8 @@
    },
    "outputs": [],
    "source": [
-    "from utils import draw_molecule, nglview_show_openmm"
+    "from google.colab import output\n",
+    "output.enable_custom_widget_manager()"
    ]
   },
   {
@@ -301,7 +317,7 @@
    "id": "daa98897-edce-4830-97cb-533a335b460f",
    "metadata": {},
    "source": [
-    "<img src=\"smirks.png\" width=\"400\"/>"
+    "<img src=\"smirks.png\" width=\"600\"/>"
    ]
   },
   {
@@ -494,6 +510,14 @@
     "## Interchange's matrix representation"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "14778b26-1109-448e-b4e6-d8a87171ae92",
+   "metadata": {},
+   "source": [
+    "![Graphic depicting Interchange's matrix representation](interchange_vectors.png)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -549,6 +573,7 @@
    "outputs": [],
    "source": [
     "edited_params = hexanoic_acid_in_sage[\"Bonds\"].get_force_field_parameters()\n",
+    "# Change the first (0th) bond length (1) to 4 angstroms\n",
     "edited_params[0, 1] = 4.0\n",
     "\n",
     "hexanoic_acid_in_sage[\"Bonds\"].set_force_field_parameters(edited_params)\n",
@@ -571,11 +596,9 @@
    "id": "31a3526b-ac25-4ad3-9a4a-7218de2bc941",
    "metadata": {},
    "source": [
-    "Introduce NADP, parametrize with Sage, investigate assigned parameters, demonstrate same potential energy across different engines \n",
-    "\n",
-    "Heart-type fatty acid binding protein (hFABP) \n",
+    "I've prepared a simulation box with heart-type Fatty Acid Binding Protein (hFABP), a globular protein with a [PDB entry] including a bound hexanoic acid molecule.\n",
     "\n",
-    "https://www.rcsb.org/structure/7FCX"
+    "[PDB entry]: https://www.rcsb.org/structure/7FCX"
    ]
   },
   {
@@ -587,7 +610,6 @@
    "source": [
     "from openff.toolkit import Topology\n",
     "\n",
-    "\n",
     "topology = Topology.from_pdb(\n",
     "    \"7FCX_prepped.pdb\", \n",
     "    unique_molecules=[hexanoic_acid]\n",
@@ -943,9 +965,8 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.8"
   },
-  "orphan": true,
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
     "state": {},

diff --git a/source/workshops/2024/smirnoff/env.yml b/source/workshops/2024/smirnoff/env.yml
@@ -1,34 +1,33 @@
-name: 2024-smirnoff-workshop
+name: openff-docs-examples
 channels:
     - conda-forge
 dependencies:
-    # Notebook + runtime
     - pip
     - python>=3.10
     - jupyterlab>=4
     - ipywidgets>=8
+    - jupyterlab_execute_time
     - jupyterlab-lsp
-    - pyright
+    - jedi-language-server
     - jupyterlab_code_formatter
     - black
     - isort
     # Examples
-    - openff-toolkit-examples>=0.14.5
-    - openff-interchange>=0.3.18
-    - openff-nagl
-    - openff-bespokefit>=0.2.3
+    - openff-toolkit-examples ~=0.15.2
+    - openff-interchange ~=0.3.25
+    - openff-nagl ~=0.3.7
+    - openff-bespokefit
+    - openff-qcsubmit
     - gromacs >=2021=nompi*
-    - lammps
+    - lammps >=2023.08.02
     - rich
     - jax
     - dgl
     - nglview>=3.0.6
     - xtb-python
     - pdbfixer
     - mdtraj
-    - propka
-    - pdb2pqr
     - openmmtools
     - chemper
-    - dockstring
     - mdanalysis
+    - plotly
diff --git a/source/workshops/2024/smirnoff/interchange_vectors.png b/source/workshops/2024/smirnoff/interchange_vectors.png