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View Code? Open in Web Editor NEWNotebooks demonstrating how to do simple tasks related to free energy calculations.
License: MIT License
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examplenotebooks's Issues
Make cookbook materials fetchables
Follow-up on #84: There should be a single source of truth for cookbook input files (SDFs, PDBs, etc.) instead of having a copy in, e.g., the OpenFE test suite, with a duplicate stored here.
We could then make the first line of each notebook be ! openfe fetch cookbook-files — this could be either a fetchable per-notebook or a single fetchable to download all cookbook notebooks.
This would have the advantage that even a download of a single notebook would be self-contained, instead of requiring users to download a tarball/clone of the repo.
Steps to make this happen:
- Create the fetchables in the OpenFE CLI. See fetchables.py for examples
- Cut a release of OpenFE, update ExampleNotebooks to use that OpenFE version.
- Update the cookbook notebooks here to download the required files.
Change default branch name from master to main
Reason for benchmark_demo.ipynb is unclear
From an external perspective - why should I be looking at this notebook? Why this notebook and not quickrun demo? What am I getting out of it?
rename default branch to main
For some reason we have master here, may as well be consistent
remove fetch command
In the showcase notebook there's a mda.fetch_mmtf command, but fetching from rcsb can sometimes be problematic with firewalls. Better to download and include the mmtf locally in the repo.
Set up ReviewNB?
Can we set up reviewnb or similar here? It would make reviewing these PRs a lot easier.
Showcase: Document possible options in networks
Can document the choice in network topology, show radial vs MST vs lomap topologies.
reference data for TYK2 example
Hi all,
Thank you for putting up such a nice tutorial! I'm able to run it through very smoothly. Question regarding the CLI tutorial, after the last step once the DDGBind is calculated, is the reference/experimental data available to be compared with so that I know how good the calculated DDGBind is? Thanks.
Showcase: Include energetics analysis section
should include some details on the plots produced by the RFE protocol.
Relies on #111
Add README files to all data clarifying provenance and status
We need to make sure that folks don't suddenly feel like using say the tyk2 inputs and assuming that they are synched with the PLB or even our own internal benchmark inputs.
Installation instructions
Should have a few lines on how to clone this repo, set up an appropriate environment and run the notebooks.
PDB file format issue when read in the first step (I guess )
Hey,
I tried on another dataset (cdk2) from https://github.com/openforcefield/protein-ligand-benchmark, the receptor and ligand files are located here https://github.com/openforcefield/protein-ligand-benchmark/tree/main/data/cdk2, it seems the protein residues do not start from 1 but from -1 for ACE instead, not sure if this is the reason to cause the issue when I run the first step. The error is below:
`RBFE-NETWORK PLANNER
Parsing in Files:
Got input:
Small Molecules: SmallMoleculeComponent(name=lig_20) SmallMoleculeComponent(name=lig_1oi9) SmallMoleculeComponent(name=lig_26) SmallMoleculeComponent(name=lig_1oiu) SmallMoleculeComponent(name=lig_1h1q) SmallMoleculeComponent(name=lig_21) SmallMoleculeComponent(name=lig_22) SmallMoleculeComponent(name=lig_1h1r) SmallMoleculeComponent(name=lig_17) SmallMoleculeComponent(name=lig_1oiy)
Traceback (most recent call last):
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/bin/openfe", line 10, in
sys.exit(main())
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/openfecli/utils.py", line 61, in wrapper
result = function(*args, **kwargs)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/openfecli/commands/plan_rbfe_network.py", line 136, in plan_rbfe_network
protein = PROTEIN.get(protein)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/plugcli/params.py", line 61, in get
return self.getter(user_input, context)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/plugcli/params.py", line 108, in call
found = strategy(user_input, context)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/openfecli/parameters/protein.py", line 25, in _load_protein_from_pdbx
return ProteinComponent.from_pdbx_file(user_input)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/gufe/components/proteincomponent.py", line 121, in from_pdbx_file
openmm_PDBxFile = PDBxFile(pdbx_file)
File "/hpc/users/wenchangzhou/softwares/mambaforge3/envs/openfe_env/lib/python3.10/site-packages/gufe/vendor/pdb_file/pdbxfile.py", line 83, in init
block = data[0]
IndexError: list index out of range
`
py3Dmol widgets not working
On a fresh install I get the below in the creating_networks_from_external_files notebook
# traverse through all views
edges = list(ligand_network.edges)
interact(display_edge, index=widgets.IntSlider(min=0, max=len(edges)-1, step=1))
>>> Error displaying widget
<function __main__.display_edge(index)>
Showcase: Switch to tyk2 system throughout
Currently the notebook bounces between benzene modifications in t4 and jnk1. Instead use a tyk2 system throughout (to later link up with example results data)
Rename openmm-rbfe to just relative_free_energy
Then have sub-directotries for each thing you're looking at:
- relative_free_energy
- openmm_hybrid_showcase
- notebook
- quickrun
- notebook
- blah
- foo
- openmm_hybrid_showcase
That way users cleanly know where to look for things.
Showcase: Document possible options in mapping
Can document the possibilities in choosing AtomMapper, show examples of Lomap vs Karto
Update tutorials/notebooks with new settings
E.g. the tutorial OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb is using the old setting, such as AlchemicalSamplerSettings.
Showcase: Include mention of other possible Protocols after introducing RFE
Somewhere after we've introduced the RFE Protocol we should mention that other Protocols exist. Signpost to both AFE protocol and non-eq options in development.
Notebook for AHFEs
We need a notebook to showcase how to run AHFE calculations in OpenFE
Mention of OpenFF biopolymer FF is misleading
The mention of the OpenFF biopolymer FF is confusing in ApplyingProtocolToNetworkQuickrunDemo.ipynb, especially since we don't mention FF choices (this is actually a user report).
update wget command
I think we need to cut a new release on github and maybe update the wget command
Update notebooks to work in the openfe main docs
Check and update:
- MD tutorial
- AHFE tutorial
- CInnabar tutorial
These should just need an extra "/n" at the end of the title to render properly.
Update READMEs
The main readme needs to be updated, and we need secondary readmes to explain why a notebook exists (in addition to explanation in the notebook itself).
notebook still uses `execute`, not `execute_DAG`
I'm not sure if this was maybe part of gufe 0.5, but the example notebook is currently import execute, which doesn't work in current gufe. (Via Slack from Bill Swope.)
setup unclear for a data repository
Call it data or assets?
Showcase: Include data created by execution in notebook repo
Need to put in some recent results data from tyk2 into notebook. Can probably remove the simulation.nc file for size reasons, rest should then fit in a reasonable amount of space.
Alternatively, have the showcase notebook run a special fetch command?
Dry run does not return an empty dictionary
Hasn't been the case for a while, we need to update the showcase notebook
Cookbook: Alchemical Planners
We want to mention the Alchemical Planners in the UserGuide. To do this, we should have a short cookbook that demonstrates their use with code.
Add Coverage Reports
It would be nice to make sure we are not accidentally skipping notebooks or cells we meant to test
Showcase: Cinnabar usage
Show off cinnabar usage on entire network
Feedback on OpenFE installation tutorial
I have started to review the hands on tutorial presented at the symposium. I am sharing this with you as I see an opportunity for the documentation to be further improved.
[1] The installation part is great - very slick. I managed to get it all installed and ran the tests as indicated - 549 pass but 2 fail, as they did at the symposium.
I shared these on Slack.
[2] Fetching the files needed for the tutorial works a treat
------quote------
openfe fetch rbfe-tutorial
Fetching https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/master/rbfe_tutorial/tyk2_ligands.sdf
Fetching https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/master/rbfe_tutorial/tyk2_protein.pdb
Fetching https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/master/rbfe_tutorial/cli_tutorial.md
Fetching https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/master/rbfe_tutorial/python_tutorial.ipynb
------unquote------
[3.1] I then elected to run the tutorial on my local machine with this command
jupyter notebook => select file python_tutorial.ipynb in browser
http://localhost:8888/notebooks/python_tutorial.ipynb
[3.2]
One could also just follow the commands in the file.
cli_tutorial.md
[4] It is a little glitchy in that the network diagram does not display molecules when an edge is clicked in the browser. It does actually do this in the command line variant.
[5] In the browser the tutorial ends with this statement.
-----quote-----
Each of these individual .json files contains a Transformation, which contains all the information to run the calculation. These could be farmed out as individual jobs on a HPC cluster.
-----unquote----
This is very annoying as I do not have an HPC cluster and all I want to do is run one small edge and see the RBFE between 2 molecules.
My analogy - the lovely cake is almost within reach, but not quite , it is locked away behind the glass and I need a key called HPC to open this.
So these docs are good but not great.
[6] In the CLI version of the tutorial the hapless user (myself) hits quite a similar brick wall.
---quote---
# this will take a very long time! don't actually do it!
for file in network_setup/transformations/*.json; do
relpath=${file:30} # strip off "network_setup/transformations/"
dirpath=${relpath%.*} # strip off final ".json"
openfe quickrun $file -o results/$relpath -d results/$dirpath
done
---unquote---
So again the magic of RBFE calculations remains just out of reach.
Irfan suggested that the JSON files could be written to disk allowing the
user to run just 1 edge - which is a good idea, in fact I see it as needed.
Oh can we have this in both the command line instance and the instance in the ipynb file.
[7] Final comments
This is rather complex for a beginner to run through.
I do accept that free energy calculations are complex, so maybe that is the
nature of the beast.
Notebook for RHFEs
We need a notebook where we show how to make RHFEs - particularly defining two separate Protocols for each leg of the transformation.
easy campaign scripts don't use the right molecule flag
Using -m instead of -M
Clean up casing for notebooks
We've got a weird mix of name casing for our notebooks & folders, please let's just stick to snake_case.
Showcase: Add visualisation of ligand network topology
Related to showing choice of networks (#106), can also show the shape of these visually.
`ImportError` in RBFE showcase
I probably got here from https://try.openfree.energy/
This happens at import numba which is probably called from https://github.com/choderalab/openmmtools?
I'm not sure why 0.57 is brought down ...
# packages in environment at /usr/local:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.0 py310h206695f_3 conda-forge
amberutils 21.0 pypi_0 pypi
anyio 3.7.0 pyhd8ed1ab_1 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.2 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.4 h0f2a231_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
boost 1.74.0 py310h7c3ba0c_5 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.0 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h255011f_3 conda-forge
cftime 1.6.2 py310hde88566_1 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.3 unix_pyhd8ed1ab_2 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
conda 23.5.0 py310hff52083_1 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.8.0 pyhd8ed1ab_0 conda-forge
condacolab 0.1.9 pypi_0 pypi
contourpy 1.1.0 py310hd41b1e2_0 conda-forge
coverage 7.2.7 py310h2372a71_0 conda-forge
cryptography 41.0.1 py310h75e40e8_0 conda-forge
cudatoolkit 11.8.0 h37601d7_11 conda-forge
curl 8.1.2 h409715c_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.35 py310hc6cd4ac_0 conda-forge
debugpy 1.6.7 py310heca2aa9_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge
execnet 1.9.0 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
flit-core 3.9.0 pyhd8ed1ab_0 conda-forge
fmt 9.1.0 h924138e_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.40.0 py310h2372a71_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
greenlet 2.0.2 py310hc6cd4ac_1 conda-forge
gufe 0.9.0 pyhd8ed1ab_0 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.2 nompi_h4df4325_101 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.7.0 pyha770c72_0 conda-forge
importlib_metadata 6.7.0 hd8ed1ab_0 conda-forge
importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.23.1 pyh210e3f2_0 conda-forge
ipython 8.14.0 pyh41d4057_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.5 pyhd8ed1ab_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.3.1 py310hff52083_0 conda-forge
jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge
jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.2 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.23.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.7 pyhd8ed1ab_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py310hbf28c38_1 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libarchive 3.6.2 h3d51595_0 conda-forge
libblas 3.9.0 17_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge
libcurl 8.1.2 h409715c_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.76.3 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_3 conda-forge
libmamba 1.4.4 h658169a_1 conda-forge
libmambapy 1.4.4 py310h8aae740_1 conda-forge
libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsolv 0.7.24 h3eb15da_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.0 h0b41bf4_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libxslt 1.1.37 h873f0b0_0 conda-forge
libzip 1.9.2 hc929e4a_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.40.0 py310h1b8f574_0 conda-forge
lomap2 2.3.0 pyhd8ed1ab_0 conda-forge
lxml 4.9.2 py310hbdc0903_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 1.4.4 py310h51d5547_1 conda-forge
markupsafe 2.1.3 py310h2372a71_0 conda-forge
matplotlib-base 3.7.1 py310he60537e_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdtraj 1.9.7 py310h902c554_4 conda-forge
mistune 3.0.0 pyhd8ed1ab_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.6.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.6.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.6.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.0 nompi_he1eeb6f_102 conda-forge
netcdf4 1.6.2 nompi_py310h55e1e36_100 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.5.4 pyha770c72_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numba 0.57.0 py310h0f6aa51_2 conda-forge
numexpr 2.8.4 py310h690d005_100 conda-forge
numpy 1.23.5 py310h53a5b5f_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openfe 0.10.1 pyhd8ed1ab_1 conda-forge
openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge
openff-forcefields 2023.06.0 pyh1a96a4e_0 conda-forge
openff-interchange 0.3.5 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.5 pyhd8ed1ab_0 conda-forge
openff-models 0.0.5 pyh1a96a4e_0 conda-forge
openff-toolkit 0.13.0 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.13.0 pyhd8ed1ab_0 conda-forge
openff-units 0.2.1 pyh1a96a4e_0 conda-forge
openff-utilities 0.1.8 pyh1a96a4e_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openmm 8.0.0 py310h5728c26_1 conda-forge
openmmforcefields 0.11.2 pyhd8ed1ab_2 conda-forge
openmmtools 0.23.0 pyhd8ed1ab_0 conda-forge
openssl 3.1.1 hd590300_1 conda-forge
overrides 7.3.1 pyhd8ed1ab_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.3rc0 pypi_0 pypi
pandas 2.0.2 py310h7cbd5c2_0 conda-forge
pandoc 3.1.3 h32600fe_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.7.1 pyhd8ed1ab_0 conda-forge
parmed 3.4.4 py310heca2aa9_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pbr 5.11.1 pyhd8ed1ab_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
pdbfixer 1.9 pyh1a96a4e_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.4.0 py310h023d228_1 conda-forge
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 23.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 3.6.0 pyhd8ed1ab_0 conda-forge
plugcli 0.2.0 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.38 pyha770c72_0 conda-forge
prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge
psutil 5.9.5 py310h1fa729e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycairo 1.24.0 py310hda9f760_0 conda-forge
pycosat 0.6.4 py310h5764c6d_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.9 py310h2372a71_0 conda-forge
pyedr 0.7.1 pyhd8ed1ab_0 conda-forge
pygments 2.15.1 pyhd8ed1ab_0 conda-forge
pymbar 3.1.1 py310hde88566_2 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge
pyrsistent 0.19.3 py310h1fa729e_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.7.0 py310hb60b9b2_3 conda-forge
pytest 7.3.2 pyhd8ed1ab_1 conda-forge
pytest-xdist 3.3.1 pyhd8ed1ab_0 conda-forge
python 3.10.11 he550d4f_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2023.3 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py310h5764c6d_5 conda-forge
pyzmq 25.1.0 py310h5bbb5d0_0 conda-forge
rdkit 2022.09.1 py310h10c98a6_0 conda-forge
readline 8.2 h8228510_1 conda-forge
reportlab 3.6.13 py310h1a56a1c_0 conda-forge
reproc 14.2.4 h0b41bf4_0 conda-forge
reproc-cpp 14.2.4 hcb278e6_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
ruamel.yaml 0.17.32 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge
sander 22.0 pypi_0 pypi
scipy 1.10.1 py310ha4c1d20_3 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.16 py310h2372a71_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tinydb 4.8.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.3.2 py310h2372a71_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.6.3 hd8ed1ab_0 conda-forge
typing_extensions 4.6.3 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
unicodedata2 15.0.0 py310h5764c6d_0 conda-forge
urllib3 2.0.3 pyhd8ed1ab_0 conda-forge
validators 0.20.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.6.0 pyhd8ed1ab_0 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 3.5.2 py310hff52083_1 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.3.0 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.7.0 h27087fc_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.19.0 py310hdeb6495_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge
</details>
Showcase: Write proper introduction to showcase notebook
Currently the showcase starts with some text about colab. Instead, write a paragraph of text introducing the showcase notebook and it's purpose.
use separate repo for binder definition
On reading the binder docs on why notebooks are slow to load, there's a section detailing how to use a separate repo to define the required environment. This can reduce the number of rebuilds required (as you don't rebuild for a commit in this content repo, only the binder env repo), which would increase our "uptime" and make more commits here less annoying (encouraging smaller fixes).
showcase: include Ben's HREX gif?
@RiesBen has a nice gif of HREX. Can we include this in the showcase notebook?
MD Protocol tutorial
We've got a few folks interested in using the MD protocol. A tutorial for it's use, inputs, outputs, etc.. would be useful.
Showcase: Write call to action at end of the notebook
Currently the notebook doesn't signpost future things that could follow on. Could include links to docs, full tutorial, website etc
Showcase: Better looking top matter
Make the landing page of the showcase notebook more visually appealing
CLI isn't working with environment.yaml
we're getting these errors on binder when calling openfe --help
Traceback (most recent call last):
File "/srv/conda/envs/notebook/bin/openfe", line 5, in <module>
from openfecli.cli import main
File "/srv/conda/envs/notebook/lib/python3.9/site-packages/openfecli/__init__.py", line 5, in <module>
from . import commands
ImportError: cannot import name 'commands' from partially initialized module 'openfecli' (most likely due to a circular import) (/srv/conda/envs/notebook/lib/python3.9/site-packages/openfecli/__init__.py)
Update License
We should update the license to:
- Acknowledge the use of Perses components (although they'll be moved eventually, we've got modified versions of vendored components for Perses in the openmm rbfe notebook)
- Double check that all our imports are MIT compatible
Open Free Energy Binder instance of notrebook fails to start.
Hi All. Not sure if this is appropriate as it may be a Binder issue and not an OpenFE issue. However the Binder instance of the RBFE tutorial fails to load (for me) after waiting a few hours.
The link is this one (http://try.openfree.energy/) from the project home page https://openfree.energy/
Hence I would expect this is the experience most people will see if they arrive at the project home page and click the "try it online" button.
Showcase: Include structural analysis section
relies on #111
include some examples of the structural analysis plots produced
Showcase: Document atom mapping scoring metrics
Can show off different mapping scoring options. Could compare default lomap to karto's RMSD option
Test easyCampaign
We don't test this example but we should. I'm thinking some sed modifications to reduce the time it takes and then we run the script and make sure it doesn't throw an error
Tell pytest long running cells okay to fail
We need to do something to skip cells that will take a long time to run, or something like that
https://github.com/OpenFreeEnergy/ExampleNotebooks/runs/5366811859?check_suite_focus=true#step:6:98
Choose and Configure a Protocol cookbook is out of date
There are a couple aspects to this Protocol which are out of date for the 1.0 release.
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