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Merged
jthorton merged 3 commits into from
Sep 25, 2026
Merged

CLI settings and assorted clean up #329

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254377d
small cleanup
jthorton Sep 25, 2026
94776e9
more clean up
jthorton Sep 25, 2026
289af4a
sort protocol tutorials
jthorton Sep 25, 2026
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19 changes: 10 additions & 9 deletions rbfe_tutorial/cli_tutorial.md
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,8 @@ While less flexible than using the API, some options can be modified by providin
The default settings represented in YAML settings format is as follows:

``` yaml
mapper: kartograf
mapper:
method: kartograf
settings:
atom_max_distance: 0.95
atom_map_hydrogens: true
Expand All @@ -148,7 +149,7 @@ partial_charge:
off_toolkit_backend: ambertools
number_of_conformers: None
nagl_model: None

forcefields: None
```

Let's assume you want to exchange the kartograf atom mapper with the LOMAP atom mapper, the Minimal Spanning Tree
Expand Down Expand Up @@ -191,8 +192,8 @@ Parsing in Files:
Using Options:
Mapper: <LomapAtomMapper (time=20, threed=True, max3d=1.0, element_change=True, seed='', shift=False)>
Mapping Scorer: <function default_lomap_score at 0x166bc5300>
Network Generation: <function generate_minimal_spanning_network at 0x16a413e20>
Partial Charge Generation: am1bcc
Network Generation: <function generate_maximal_network at 0x16a413e20>
Partial Charge Generation: nagl

n_protocol_repeats=1 (1 simulation repeat(s) per transformation)
```
Expand Down Expand Up @@ -232,8 +233,8 @@ for file in network_setup/transformations/*.json; do
relpath=${file:30} # strip off "network_setup/transformations/"
dirpath=${relpath%.*} # strip off final ".json"
# loop over three repeats
for repeat in {1..3}; do
openfe quickrun $file -o results/repeat${repeat}/$relpath -d results/repeat${repeat}/$dirpath
for repeat in {0..2}; do
openfe quickrun $file -o results_$repeat/$relpath -d results_$repeat/$dirpath
done
done
```
Expand All @@ -248,9 +249,9 @@ and submit a job script for the simplest SLURM use case:
for file in network_setup/transformations/*.json; do
relpath=${file:30} # strip off "network_setup/transformations/"
dirpath=${relpath%.*} # strip off final ".json"
for repeat in {1..3}; do
for repeat in {0..2}; do
jobpath="network_setup/transformations/${dirpath}_${repeat}.job"
cmd="openfe quickrun $file -o results/repeat${repeat}/$relpath -d results/repeat${repeat}/$dirpath"
cmd="openfe quickrun $file -o results_${repeat}/$relpath -d results_${repeat}/$dirpath"

@jthorton jthorton Sep 25, 2026

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This can be reversed but I was trying to standardise how we recommend formatting the results output.

echo -e "#!/usr/bin/env bash\n${cmd}" > $jobpath
sbatch $jobpath
done
Expand All @@ -276,7 +277,7 @@ The structure should look something like this:
<!-- take the top lines from `tree results` -->
```text
results
├── replicate_0
├── results_0
│   ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex
│   │   ├── shared_RelativeHybridTopologyProtocolUnit-79c279f04ec84218b7935bc0447539a9_attempt_0
│   │   │   ├── checkpoint.nc
Expand Down
40 changes: 27 additions & 13 deletions showcase/openfe_showcase.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,11 @@
"* Scorers (for atom mappings)\n",
"* Ligand networks\n",
"\n",
"This showcase currently focuses on relative binding free energy (RBFE) calculations. However, OpenFE also provides protocols for running [absolute hydration free energy calculations](https://docs.openfree.energy/en/latest/tutorials/ahfe_tutorial.html) and [Molecular Dynamics (MD) simulations](https://docs.openfree.energy/en/latest/tutorials/md_tutorial.html). In the future, other methods will become available, such as absolute binding free energy calculations and RBFE calculations using a Separated Topologies approach.\n",
"This showcase currently focuses on relative binding free energy (RBFE) calculations using a hybrid topology approach. However, OpenFE provides a wide range of protocols for:\n",
"- [Absolute binding free energy calculations](https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html)\n",
"- [Absolute hydration free energy calculations](https://docs.openfree.energy/en/latest/tutorials/ahfe_tutorial.html)\n",
"- [Molecular Dynamics (MD) simulations](https://docs.openfree.energy/en/latest/tutorials/md_tutorial.html)\n",
"- [Relative binding free energy calculations using a Separated Topologies (SepTop) approach](https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html)\n",

@IAlibay IAlibay Sep 25, 2026

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Can you sort this alphabetically please? I.e. we want the absolutes together

"\n",
"If you are planning your own calculations, please also check out our [tutorials](https://docs.openfree.energy/en/stable/tutorials/index.html) which will walk you step-by-step through setup, execution and analysis of different protocols."
]
Expand Down Expand Up @@ -219,16 +223,16 @@
"used along the way.\n",
" \n",
"\n",
"| **Actions** | **Software** |\n",
"|:------------------------------|:-----------------------------------------------------------|\n",
"| Create OpenFE Molecules | OpenFE RDKit |\n",
"| Create Network | OpenFE Lomap, Networkx |\n",
"| Visualise Network | OpenFE NetworkX, RDKit, Matplotlib |\n",
"| Create ligand topologies | OpenFE interface - OpenFF tk |\n",
"| Create hybrid OpenMM topology | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Create Lambda Protocol | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Set up and run RBFE calculations | OpenFE interface - OpenMM + OpenMMTools |\n",
"| Analyze RBFE calculations | OpenFE interface - PyMBAR + OpenMMTools |"
"| **Actions** | **Software** |\n",
"|:------------------------------|:--------------------------------------------------------|\n",
"| Create OpenFE Molecules | OpenFE RDKit |\n",
"| Create Network | OpenFE Lomap, Kartograf, NetworkX |\n",
"| Visualise Network | OpenFE NetworkX, RDKit, Matplotlib |\n",
"| Create ligand topologies | OpenFE interface - OpenFF tk |\n",
"| Create hybrid OpenMM topology | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Create Lambda Protocol | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Set up and run RBFE calculations | OpenFE interface - OpenMM + OpenMMTools |\n",
"| Analyze RBFE calculations | OpenFE interface - PyMBAR + OpenMMTools |"
]
},
{
Expand Down Expand Up @@ -3277,7 +3281,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[?25lLoading results: ▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇ 54/54 files\u001b[?25h\n",
"\u001B[?25lLoading results: ▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇ 54/54 files\u001B[?25h\n",
"writing dg output to 'final_results.tsv'\n",
"ligand\tDG(MLE) (kcal/mol)\tuncertainty (kcal/mol)\n",
"lig_ejm_31\t-0.09\t0.06\n",
Expand Down Expand Up @@ -3399,19 +3403,29 @@
"metadata": {},
"source": [
"In our [documentation](https://docs.openfree.energy/en/latest/index.html), \n",
"we provide tutorials for ever protocol to walk you through setup, execution and analysis step by step.\n",
"we provide tutorials for every protocol to walk you through setup, execution and analysis step by step.\n",
"\n",
"* [RBFE CLI tutorial](https://docs.openfree.energy/en/latest/tutorials/rbfe_cli_tutorial.html)\n",
"* [RBFE Python tutorial](https://docs.openfree.energy/en/latest/tutorials/rbfe_python_tutorial.html)\n",
"* [AHFE tutorial](https://docs.openfree.energy/en/latest/tutorials/ahfe_tutorial.html)\n",
"* [MD tutorial](https://docs.openfree.energy/en/latest/tutorials/md_tutorial.html)\n",
"* [ABFE tutorial](https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html)\n",
"* [RBFE using a Separated Topologies (SepTop) approach tutorial](https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html)\n",
"\n",
"In addition to the tutorials, you can find [cookbooks](https://docs.openfree.energy/en/latest/cookbook/index.html), written as How-to guides on how to utilize different components of the toolkit, as well as a [User Guide](https://docs.openfree.energy/en/latest/guide/index.html) that goes into the underlying concepts of the OpenFE toolkit.\n",
"\n",
"For details about the toolkit's core methods and classes, please visit our [API Reference](https://docs.openfree.energy/en/latest/reference/index.html) or our [Github page](https://github.com/OpenFreeEnergy/openfe).\n",
"\n",
"To learn more about the project, our team and how you can get involved, please visit our [Homepage](https://openfree.energy/) or get in touch at OpenFreeEnergy@omsf.io."
]
},
{
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": "",
"id": "eb2308d6adfdda77"
}
],
"metadata": {
Expand Down
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