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milot-mirdita

Update notebooks for numpy 2 changes

Mar 18, 2025

b119520 · Mar 18, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
AlphaFold2_advanced.ipynb		AlphaFold2_advanced.ipynb	v2.3.1 - merge 'beta' into 'main' (#371)	Feb 5, 2023
AlphaFold2_advanced_beta.ipynb		AlphaFold2_advanced_beta.ipynb	Created using Colaboratory	Nov 14, 2021
AlphaFold2_advanced_old.ipynb		AlphaFold2_advanced_old.ipynb	Don't hardcode openmm dependency to python 3.7	Dec 1, 2022
AlphaFold2_complexes.ipynb		AlphaFold2_complexes.ipynb	v2.3.1 - merge 'beta' into 'main' (#371)	Feb 5, 2023
AlphaFold_wJackhmmer.ipynb		AlphaFold_wJackhmmer.ipynb	Don't hardcode openmm dependency to python 3.7	Dec 1, 2022
Alphafold_single.ipynb		Alphafold_single.ipynb	changing default recycles to 2	Sep 16, 2021
ESMFold.ipynb		ESMFold.ipynb	pin version of openfold ESMFold	May 10, 2023
ESMFold_advanced.ipynb		ESMFold_advanced.ipynb	fixing esmfold_advanced to use pytorch2/cuda12	Dec 28, 2023
ESMFold_api.ipynb		ESMFold_api.ipynb	fixing esmfold api	Feb 25, 2024
RoseTTAFold.ipynb		RoseTTAFold.ipynb	fixing torch version	Jun 1, 2022
RoseTTAFold__network__Refine_module.patch		RoseTTAFold__network__Refine_module.patch	Add files via upload	Aug 4, 2021
RoseTTAFold_install.sh		RoseTTAFold_install.sh	Allow running the RoseTTAfold notebook locally with papermill	Feb 4, 2022
RoseTTAFold_run.sh		RoseTTAFold_run.sh	Allow running the RoseTTAfold notebook locally with papermill	Feb 4, 2022
alphafold_output_at_each_recycle.ipynb		alphafold_output_at_each_recycle.ipynb	fixing notebook to use old version of alphafold	Nov 17, 2021
colabfold.py		colabfold.py	np.float -> float	Mar 3, 2023
colabfold_alphafold.py		colabfold_alphafold.py	Update colabfold_alphafold.py	Nov 14, 2021
config.patch		config.patch	Add files via upload	Aug 1, 2021
convert_256_to_384_rep.ipynb		convert_256_to_384_rep.ipynb	fix for multimer representation	Nov 1, 2023
folding.patch		folding.patch	updating advanced patches to reduce compile time	Jun 16, 2022
mapping.patch		mapping.patch	patching advanced notebook	Sep 6, 2022
model.patch		model.patch	bugfix for alphafold_advanced model.patch	Jun 21, 2022
modules.patch		modules.patch	updating advanced patches to reduce compile time	Jun 16, 2022
omegafold.ipynb		omegafold.ipynb	specify biopython==1.81 version while installing (#622)	May 12, 2024
omegafold_hacks.ipynb		omegafold_hacks.ipynb	omegafold_hacks: clearing output	Aug 6, 2022
pairmsa.py		pairmsa.py	make compatible w/ latest colabfold db	Apr 12, 2022
protein.patch		protein.patch	Update protein.patch	Aug 10, 2021
recycle_0.patch		recycle_0.patch	Add files via upload	Mar 23, 2022
relax_amber.ipynb		relax_amber.ipynb	Update notebooks for numpy 2 changes	Mar 18, 2025
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