Merge branch 'main' into skip-failing-notebooks

Author: Yoshanuikabundi

source/_ext/cookbook/globals_.py

@@ -92,7 +92,8 @@
 """
 
 OPTIONAL_NOTEBOOKS: list[str] = [
-    ".*/experimental/.*",
+    # ".*/experimental/.*",
+    "openforcefield/openff-interchange/experimental/openmmforcefields/gaff.ipynb",
 ]
 """
 Notebooks whose execution failure will not cause notebook processing to fail.

source/install.md

@@ -44,7 +44,7 @@ If you have an existing Mamba installation, skip steps 1 and 2 below. If you hav
     $ conda activate openff
     $ openff-toolkit-examples --target offtk-examples
     $ cd offtk-examples/toolkit_showcase
-    $ jupyter notebook toolkit_showcase.ipynb
+    $ jupyter-lab toolkit_showcase.ipynb
     ```
 
 If that worked, you're all set! The rest of this page covers corner cases and how to manage Conda environments. For package-specific installation instructions, please see the individual [project docs].
@@ -150,7 +150,7 @@ Any time you want to use software installed in an environment you have created,
 
 ```shell-session
 $ conda activate <name>
-$ jupyter notebook .
+$ jupyter-lab .
 ```
 
 [virtual environments]: inv:conda#user-guide/concepts/environments

source/workshops/2024/protein_prep.md

@@ -7,11 +7,11 @@ This workshop covers the preparation of a protein system from a structure downlo
 First session
 : [Feb 27 23:00 UTC](https://time.is/1000_28_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?Protein_Prep_OpenFF_Workshop)
 
-: [💨 Join on Zoom](https://us06web.zoom.us/j/84928391532?pwd=ZJoPVISZzA1LHo3mvfxbg1zug26Gas.1)
-
 Second Session
 : [Apr 17 12:00 UTC](https://time.is/2200_17_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Protein_Prep_OpenFF_Workshop)
 
+: [💨 Join on Zoom](https://us06web.zoom.us/j/85120722786?pwd=Hb4mp4gOkNnjyarG4RLsoR9ClEPDDC.1)
+
 Zoom links will be published here 24 hours before the sessions begin.
 
 Materials and Google Colab links can be found below.

source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip

@@ -11,14 +11,12 @@ dependencies:
     - packaging
     # Examples
     - openff-toolkit-examples>=0.15.2
-    - openff-interchange>=0.3.7
-    - openff-nagl
+    - openff-interchange>=0.3.25
+    - openff-nagl >=0.3.7
     # - openff-bespokefit
     # - openff-fragmenter
     # - openff-qcsubmit
     # - openff-recharge
-    - gromacs >=2021=nompi*
-    - lammps
     - rich
     - jax
     - dgl

source/workshops/2024/protein_prep/colab-env.yml

@@ -56,6 +56,8 @@
    "source": [
     "The point of this workshop is to demonstrate what is possible entirely with Open Source tools, and to provide a framework for semi-interactive preparation of chemical systems in Jupyter.\n",
     "\n",
+    "This workflow does not reflect a routine or highly tested or maintained procedure for protein preparation, and is intended as a jumping off point to emphasise the capabilities of FOSS tools and to demonstrate how OpenFF tools might be used in a broader workflow.\n",
+    "\n",
     "What can we do?\n",
     "\n",
     "- Repair proteins with missing loops, residues, atoms\n",
@@ -75,7 +77,7 @@
     " \n",
     "What can't we do?\n",
     "\n",
-    "- Non-standard amino acids and PTMs (see \"Things to make and do\"!)\n",
+    "- Non-standard amino acids and PTMs (see \"[Things to make and do]\"!)\n",
     "- Metalloproteins\n",
     "- Biopolymers other than proteins\n",
     "- Lipids\n",
@@ -86,7 +88,8 @@
     "    - Disulfide bonds in the PDB CONECT records are used\n",
     "    - Disulfide bonds not in the PDB CONECT records may be detected from proximity\n",
     "\n",
-    "[substitution table]: https://github.com/openmm/pdbfixer/blob/6bf10e138f6475f6f1850dae78d7bf1b420a1612/pdbfixer/pdbfixer.py#L67\n"
+    "[substitution table]: https://github.com/openmm/pdbfixer/blob/6bf10e138f6475f6f1850dae78d7bf1b420a1612/pdbfixer/pdbfixer.py#L67\n",
+    "[Things to make and do]: https://docs.openforcefield.org/workshops/2024/vignettes.html"
    ]
   },
   {
@@ -919,15 +922,15 @@
     "\n",
     "Sage currently supports and is recommended for:\n",
     "\n",
-    "- Small molecules and ions composed of the elements C, H, O, N, P, and S\n",
+    "- Small molecules and ions composed of the elements C, H, O, N, P, S, F, Cl, Br, and I\n",
     "- Water (TIP3P)\n",
     "- Common monatomic, monovalent ions: Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I-\n",
     "- Monatomic xenon\n",
     "\n",
     "Sage does not yet support (though it may or may not be able to parametrize):\n",
     "\n",
-    "- Bonds involving elements other than CHONPS\n",
-    "- Most monatomic ions (these will fail to parametrize)\n",
+    "- Bonds involving elements other than C, H, O, N, P, S, F, Cl, Br, and I\n",
+    "- Other monatomic ions (these will fail to parametrize)\n",
     "- Proteins and other biopolymers\n",
     "- Lipid membranes\n",
     "\n",

source/workshops/2024/protein_prep/colab-protein_prep.ipynb

@@ -7,11 +7,11 @@ This workshop introduces the SMIRNOFF format to familiar MD practitioners and de
 First Session
 : [Feb 20 23:00 UTC](https://time.is/1000_21_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?SMIRNOFF_OpenFF_Workshop)
 
-: [💨 Join on Zoom](https://us06web.zoom.us/j/81208498403?pwd=m17ZJnzLDwXvLbInqDKdGoeImro0cC.1)
-
 Second Session
 : [Apr 10 12:00 UTC](https://time.is/2200_10_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?SMIRNOFF_OpenFF_Workshop)
 
+: [💨 Join on Zoom](https://us06web.zoom.us/j/87669037455?pwd=CK8ETt2HwXJe7h9rM42JbFzaU9RJFJ.1)
+
 Zoom links will be published here 24 hours before the sessions begin.
 
 Materials and Google Colab links can be found below.

source/workshops/2024/smirnoff.md

@@ -320,10 +320,10 @@
         <Proper smirks="[*:1]-[*:2]#[*:3]-[*:4]" periodicity1="1" phase1="0.0 * degree ** 1" id="t165" k1="0.0 * mole ** -1 * kilocalorie ** 1" idivf1="1.0"></Proper>
         <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>
         <Proper smirks="[*:1]~[*:2]=[#6,#7,#16,#15;X2:3]=[*:4]" periodicity1="1" phase1="0.0 * degree ** 1" id="t167" k1="0.0 * mole ** -1 * kilocalorie ** 1" idivf1="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="2.339482342559e-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>
     </ProperTorsions>
     <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>

source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip

@@ -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

source/workshops/2024/smirnoff/bespokefit-hexanoic-acid.offxml

@@ -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": {},

source/workshops/2024/smirnoff/colab-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