issues Search Results · repo:microsoft/bioemu language:Python
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inmicrosoft/bioemu (press backspace or delete to remove)Hello the bio-emu team,
thank you very much for the great tool!
Is it possible to sample conformational space for multi-chain proteins? Is there a dedicated input mode available for
such cases? If not, ...
genesup
- 1
- Opened 7 hours ago
- #67
I run model inference on HPC environment by the following command:
python -m bioemu.sample --ckpt_path ./bioemu/models/checkpoint.ckpt --model_config_path ./bioemu/models/config.yaml --sequence ./1ake/features/A.a3m ...
PKUfjh
- 3
- Opened 3 days ago
- #66
bioemu requires python version to be 3.10 python 3.10 needs numpy version to be 1.20 but there is an error which shows
that numpy.int is deprecated from = 1.20
AttributeError: module numpy has no attribute ...
- 1
- Opened 4 days ago
- #65
As described in README, I m doing (with uv instead of pip for speed):
uv venv uv pip install bioemu
uv run python -m bioemu.sample --sequence ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV ...
marinegor
- 6
- Opened 5 days ago
- #63
Thank you very much for this great work.
Do you have any plans to release the training data or is it available by request? Specifically, I am interested in the
~50k clusters you get from AFDB after the ...
MatthewMasters
- 2
- Opened 7 days ago
- #62
I am having problems with reconstructing the full-atom models, in particular, the MD-optimization step.
I run this command python -m bioemu.sidechain_relax ...
The first step (reconstruction of sidechains ...
- Opened 8 days ago
- #61
Thanks for making this great tool available!
While experimenting with a few proteins I have noticed that bioemu seems very averse to unraveling local secondary
structure. When partially unfolded states ...
patwin2
- 1
- Opened 10 days ago
- #58
Hi! I m working on an open-source open-science platform for scientific collaboration and rich data communication. I
integrated your model so that users can put your model in their workflows much easier: ...
dionjwa
- Opened 11 days ago
- #57
Hi! I was trying out the model and I installed BioEmu as the directions suggested, and then I ran the example script:
python -m bioemu.sample --sequence GYDPETGTWG --num_samples 10 --output_dir ~/test-chignolin ...
alexberlaga
- 7
- Opened 11 days ago
- #55
I have encountered a problem during the side-chain construction using hpacker.
reconstructing side-chains: 0%| | 0/10 [00:00 ?, ?it/s]Traceback (most recent call last):
File /opt/conda/envs/bioemu/lib/python3.10/site-packages/bioemu/run_hpacker.py ...
duynth29
- Opened 12 days ago
- #54
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