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
...
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
...
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
...
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
...
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
...
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
7ad8058904
Pare down notebook requirements
2022-07-19 11:06:26 -04:00
Gustaf Ahdritz
1779d15a83
Add notebook-specific environment.yml
2022-07-19 10:58:11 -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
