jnwei
c587b06e8a
add Open In Colab banner to notebook.
2025-04-25 20:07:32 -05:00
jnwei
50a2e756e7
Update OpenFold notebook to updated pytorch2 commit
2025-04-25 20:02:11 -05:00
jnwei
97dae6c68a
Updates biopython version to 1.83 in colab notebook, which seems to work better
2024-05-13 16:33:50 +07:00
jnwei
ffc9b3f65a
updates biopython version to 1.80 in colab notebook
2024-05-13 16:22:15 +07:00
Jennifer Wei
6706864754
Merge branch 'main' into setup-improvements
2024-05-13 15:35:03 +07:00
Jennifer Wei
a3c131904b
Update OpenFold.ipynb to newest pl_upgrades commit
2024-05-13 15:13:55 +07:00
jnwei
0ba7e7f9b5
removes outputs from OpenFold.ipynb
2024-05-02 02:53:35 -04:00
jnwei
638fbaf600
Updates commit value for OpenFold notebook.
2024-05-02 02:36:13 -04:00
jnwei
521bc6e910
removes outputs from OpenFold.ipynb
2024-05-02 02:36:12 -04:00
jnwei
08276f0faa
Updates commit value for OpenFold notebook.
2024-05-02 02:36:12 -04:00
Vaclav Hanzl
30813a36b6
Fix Colab by using OF commit from pl_upgrades
...
The commit used so far now fails with Colab's numpy.
(Commit from current main does not work either.)
2024-04-27 19:45:44 +02:00
jnwei
5e0616b641
edit starting sequence in notebook
2024-02-07 22:57:37 +07:00
jnwei
94a3b18e23
Adding multimer support to OpenFold notebook
2024-02-07 22:57:37 +07:00
Jennifer Wei
4384ac083a
Update OpenFold.ipynb
...
fix small typo on button.
2023-11-21 16:10:44 -05:00
Jennifer Wei
59be42ca7b
Update OpenFold.ipynb
...
Adds cell to add a button to launch colab from github.
2023-11-21 16:09:25 -05:00
Jennifer Wei
6f10686bcd
Includes button for colab link and specifies GPU type
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Edits colab metadata
2023-11-21 15:59:27 -05:00
jnwei
e09dd313f2
Fixes imports to colab notebook.
2023-11-21 15:49:06 -05:00
Vaclav Hanzl
410e829466
Fix Colab: Install all conda packages together
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Later on the conda setup is likely broken by pip.
2023-05-18 16:53:18 +02:00
Vaclav Hanzl
35b1c4e15c
Null change just to re-run integration test
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Sorry, I have no other way to re-run the Docker build test.
Changed one space.
2023-05-16 08:23:11 -04:00
Vaclav Hanzl
71d7bd5d52
Update openmm to 7.7.0, patch not needed anymore, update pdbfixer
2023-05-09 21:16:56 +02:00
Vaclav Hanzl
8b36691f73
Improve notebook: Automate tracking of the python version in Colab
2023-04-25 15:51:38 +02:00
Vaclav Hanzl
b95099bb66
Fix notebook: Colab now has python 3.9, bump it in our tricks
2023-04-25 14:11:26 +02:00
Vaclav Hanzl
5700d8cabe
Fix notebook: Add new modelcif dependency
2023-04-25 14:07:07 +02:00
Vaclav Hanzl
1fafb86898
Improve notebook: Make install/import independent of relax_prediction
...
This way user can repeat just the first and last cell to get both versions.
2023-03-06 17:54:11 +01:00
Vaclav Hanzl
007ab6f35b
Fix notebook: Also save the protein to zip when relaxation is off
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Previously protein got computed and shown in both cases but only
saved to the downloaded zip when relaxation was done.
2023-03-06 13:53:26 +01:00
Vaclav Hanzl
c84fd44340
Fix notebook: Better mitigation of the ANSI_X3.4-1968 problem in Colab
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Colab is easily broken by openmm and other software messing with locale.
This mitigation patch lets the %shell and ! work again.
It is much stronger solution than just avoiding shell when making zip.
2023-03-06 11:10:57 +01:00
Vaclav Hanzl
9c38e9587e
Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 glitch
...
* Python 3.8 is now what we get in Colab, use it in our Conda as well
* Fix imports, make some unconditional - chain of depencencies makes them
needed even for relax_prediction==False
* Mitigate spurious error "A UTF-8 locale is required. Got ANSI_X3.4-1968"
which makes all shell commands defunct - use shutil.make_archive()
2023-03-05 17:23:45 +01:00
Gustaf Ahdritz
a83fcc016f
Fix Colab title
2022-07-19 16:50:07 -04:00
Gustaf Ahdritz
bbb9c9fd37
Revamp Colab
2022-07-19 16:47:26 -04:00
Gustaf Ahdritz
592bcdd9a2
Fix notebook
2022-07-17 06:57:36 -04:00
Gustaf Ahdritz
e6852aee50
Fix notebook again
2022-07-15 15:18:43 -04:00
Gustaf Ahdritz
892adf48d9
Fix notebook
2022-07-15 15:16:09 -04:00
Gustaf Ahdritz
c401749f2c
Fix git-lfs in Colab
2022-06-23 12:56:07 -04:00
Gustaf Ahdritz
8057eb848c
Fix another notebook bug
2022-06-23 00:20:04 -04:00
Gustaf Ahdritz
42a89f8cbe
Fix typo in notebook
2022-06-22 23:33:24 -04:00
Gustaf Ahdritz
a48860cba2
Switch source of OF parameters to HuggingFace
2022-06-22 15:48:28 -04:00
Gustaf Ahdritz
7a3a2ed343
Update Colab
2022-06-22 01:04:23 -04:00
Gustaf Ahdritz
7f9f5326be
Finish updating license info
2022-02-04 15:29:17 -05:00
Gustaf Ahdritz
3bfe6f995c
Update param license in notebook
2022-02-04 15:27:32 -05:00
Gustaf Ahdritz
9a0c9e1c1c
Fix notebook
2022-02-04 14:20:55 -05:00
Gustaf Ahdritz
721e43be8d
Add GPU relaxation
2022-02-03 22:50:34 -05:00
Gustaf Ahdritz
8e908c0fa9
Update Colab
2022-02-01 20:23:17 -05:00
Gustaf Ahdritz
9c8f2356c1
Update notebook
2021-11-12 10:53:15 -05:00
Gustaf Ahdritz
98d42cf734
Update config reference in notebook
2021-11-12 01:57:53 -05:00
Gustaf Ahdritz
57cb093ef3
Update notebook
2021-11-12 00:56:40 -05:00
Gustaf Ahdritz
2d6ef1fb52
Add Colab notebook
2021-10-21 20:20:40 -04:00
