Ecosyste.ms: Issues

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GitHub / aqlaboratory/openfold issues and pull requests

#337 - Fix multimer boolean tensor error

Pull Request - State: closed - Opened by dingquanyu over 1 year ago

#335 - few updates - returning mmcif dict to avoid double parsing

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#335 - few updates - returning mmcif dict to avoid double parsing

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#334 - setup.py error

Issue - State: open - Opened by xianruizhong over 1 year ago

#334 - setup.py error

Issue - State: open - Opened by xianruizhong over 1 year ago

#333 - Add utils to export weights to jax format

Issue - State: closed - Opened by Luofan-KK over 1 year ago - 1 comment

#333 - Add utils to export weights to jax format

Issue - State: closed - Opened by Luofan-KK over 1 year ago - 1 comment

#332 - Update uniref download link

Pull Request - State: open - Opened by empyriumz over 1 year ago

#332 - Update uniref download link

Pull Request - State: open - Opened by empyriumz over 1 year ago

#331 - Multimer

Pull Request - State: closed - Opened by dingquanyu over 1 year ago

#331 - Multimer

Pull Request - State: closed - Opened by dingquanyu over 1 year ago

#329 - No module named 'scripts.utils'

Issue - State: closed - Opened by evancollins1 over 1 year ago - 1 comment

#329 - No module named 'scripts.utils'

Issue - State: closed - Opened by evancollins1 over 1 year ago - 2 comments

#328 - Improve comments

Pull Request - State: open - Opened by kfeng123 over 1 year ago

#328 - Improve comments

Pull Request - State: open - Opened by kfeng123 over 1 year ago

#326 - System Requirements

Issue - State: closed - Opened by sr5434 over 1 year ago - 2 comments

#325 - several improvements

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#325 - several improvements

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#324 - Notebook working off run_pretrained_openfold.py output

Issue - State: closed - Opened by roivant-matts over 1 year ago - 1 comment

#324 - Notebook working off run_pretrained_openfold.py output

Issue - State: closed - Opened by roivant-matts over 1 year ago - 1 comment

#323 - Epitope vis

Pull Request - State: closed - Opened by michalozeryflato over 1 year ago

#323 - Epitope vis

Pull Request - State: closed - Opened by michalozeryflato over 1 year ago

#322 - Validation set used in the OpenFold paper

Issue - State: closed - Opened by meneshail over 1 year ago - 1 comment

#322 - Validation set used in the OpenFold paper

Issue - State: closed - Opened by meneshail over 1 year ago - 1 comment

#321 - Running inference

Issue - State: closed - Opened by roivant-matts over 1 year ago

#320 - Fix Colab: Install all conda packages together

Pull Request - State: closed - Opened by vaclavhanzl over 1 year ago

#318 - Run "scripts/precompute_alignments_mmseqs.py" Error

Issue - State: open - Opened by Luofan-KK over 1 year ago - 1 comment

#317 - Unable to downgrade g++

Issue - State: open - Opened by GiammaFer75 over 1 year ago - 1 comment

#316 - Aqlaboratory/multimer

Pull Request - State: closed - Opened by conradry over 1 year ago

#314 - add comment about the interpretation of ambiguous atoms

Pull Request - State: closed - Opened by luwei0917 over 1 year ago - 1 comment

#312 - Running inference using MultiGPU

Issue - State: open - Opened by chinmayraneQ over 1 year ago - 6 comments

#311 - Docker build broken

Issue - State: closed - Opened by vaclavhanzl over 1 year ago - 1 comment

#310 - Third track

Pull Request - State: closed - Opened by lucasgascon over 1 year ago - 1 comment

#309 - Advance python version to 3.9 to build docker in Ubuntu Lunar Lobster

Pull Request - State: closed - Opened by vaclavhanzl over 1 year ago - 4 comments

#308 - Fix Colab again after ModelCIF merge and python version change in Colab

Pull Request - State: closed - Opened by vaclavhanzl over 1 year ago - 8 comments

#307 - suporting newer numpy

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago - 1 comment

#306 - code uses np.object, which is deprecated in numpy version 1.24

Issue - State: open - Opened by michalozeryflato over 1 year ago - 1 comment

#305 - unit-tests not passing

Issue - State: closed - Opened by Pellarin over 1 year ago - 1 comment

#304 - Unused import?

Issue - State: open - Opened by amorehead over 1 year ago

#303 - Inference with mixed precision

Issue - State: open - Opened by soumyadipghosh over 1 year ago - 1 comment

#302 - predicted_aligned_error (PAE) output error

Issue - State: closed - Opened by ToHanwei over 1 year ago - 2 comments

#301 - error when running python setup.py install

Issue - State: open - Opened by d-mz over 1 year ago - 1 comment

#300 - Multimer branch question

Issue - State: open - Opened by shruthivis over 1 year ago

#299 - Error in precompute_alignments_mmseqs.py

Issue - State: open - Opened by lzhangUT over 1 year ago

#298 - Support mmseqs server?

Issue - State: open - Opened by gezmi over 1 year ago

#297 - installation issues - scripts/install_third_party_dependencies.sh

Issue - State: open - Opened by chewyalvin over 1 year ago - 3 comments

#295 - Improve TriangularMultiplicativeUpdate stability in fp16 mode

Pull Request - State: closed - Opened by nikitos9000 over 1 year ago - 1 comment

#294 - CASP 15 results

Issue - State: closed - Opened by empyriumz over 1 year ago - 3 comments

#293 - RuntimeError: attn_softmax_inplace_forward_ not implemented on CPU

Issue - State: open - Opened by ToHanwei over 1 year ago - 6 comments

#292 - Fix comparison for max_seqlen when downloading CAMEO.

Pull Request - State: closed - Opened by jonathanking over 1 year ago - 1 comment

#291 - Question regarding the training loss

Issue - State: closed - Opened by meneshail over 1 year ago - 4 comments

#290 - Add missing warmup_num_steps parameters to DeepSpeed config generation script.

Pull Request - State: closed - Opened by jonathanking over 1 year ago - 1 comment

#289 - Tmp

Pull Request - State: closed - Opened by moritzschaefer over 1 year ago

#288 - Cpu support

Pull Request - State: closed - Opened by MarcoMorik over 1 year ago

#287 - New option to output in ModelCIF format instead of PDB format

Pull Request - State: closed - Opened by josemduarte over 1 year ago - 1 comment

#286 - Colab notebook not working

Issue - State: closed - Opened by vaclavhanzl over 1 year ago - 9 comments

#285 - Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 glitch

Pull Request - State: closed - Opened by vaclavhanzl over 1 year ago - 4 comments

#284 - ModelCIF output

Issue - State: closed - Opened by josemduarte over 1 year ago - 5 comments

#283 - New option to output in ModelCIF format instead of PDB format

Pull Request - State: closed - Opened by josemduarte over 1 year ago

#282 - Support latest version of Lightning

Issue - State: open - Opened by awaelchli over 1 year ago - 2 comments

#281 - ValueError: Could not find HHBlits database path/uniclust30_2018_08

Issue - State: open - Opened by ArsLeicholt over 1 year ago - 6 comments

#280 - Unable to achieve the expected training accuracy

Issue - State: open - Opened by llwx593 over 1 year ago - 1 comment

#279 - Add a .gitignore file

Pull Request - State: closed - Opened by awaelchli over 1 year ago

#278 - Fix `--cpus_per_task` argument in README

Pull Request - State: closed - Opened by awaelchli over 1 year ago

#277 - download_roda_pdbs.sh doesn't download any files from server

Issue - State: open - Opened by awaelchli over 1 year ago - 2 comments

#276 - Upgrade DeepSpeed version?

Issue - State: open - Opened by Zhang690683220 over 1 year ago - 4 comments

#275 - Resolving torch cuda availability for cpu-only installation

Pull Request - State: closed - Opened by zrqiao almost 2 years ago - 1 comment

#273 - Can't obtain grad in the openfold model

Issue - State: open - Opened by sgyersula almost 2 years ago

#272 - Inject rigids

Pull Request - State: closed - Opened by moritzschaefer almost 2 years ago

#271 - Where are the numbered algorithms explained?

Issue - State: closed - Opened by tonydavis629 almost 2 years ago - 1 comment

#270 - The timings are not written into timings.json

Issue - State: open - Opened by carlmensch almost 2 years ago

#269 - Error when running unit_test

Issue - State: open - Opened by SingL3 almost 2 years ago

#269 - Error when running unit_test

Issue - State: open - Opened by SingL3 almost 2 years ago

#268 - Flash Attention seems broken

Issue - State: open - Opened by tanhevg almost 2 years ago - 4 comments

#267 - do we have small or middle size dataset to train openfold?

Issue - State: closed - Opened by chrjxj almost 2 years ago - 2 comments

#266 - No error but also no output ("Successfully loaded params ...")

Issue - State: open - Opened by ecfischer almost 2 years ago - 4 comments

#266 - No error but also no output ("Successfully loaded params ...")

Issue - State: open - Opened by ecfischer almost 2 years ago - 4 comments

#265 - Which Python versions this package supports? Only Python 3.7?

Issue - State: open - Opened by rfilgueiras almost 2 years ago - 4 comments

#264 - Obsolete parsing and File not found fix

Pull Request - State: closed - Opened by l-bick almost 2 years ago - 1 comment

#264 - Obsolete parsing and File not found fix

Pull Request - State: closed - Opened by l-bick almost 2 years ago - 1 comment

#263 - Load pretrained jax weights

Pull Request - State: closed - Opened by l-bick almost 2 years ago - 3 comments

#262 - Problem on scripts/install_third_party_dependencies.sh

Issue - State: open - Opened by tryumanshow almost 2 years ago - 4 comments

#262 - Problem on scripts/install_third_party_dependencies.sh

Issue - State: open - Opened by tryumanshow almost 2 years ago - 4 comments

#261 - Why is `use_memory_efficient_kernel` always set to `False`

Issue - State: closed - Opened by RuiWang1998 almost 2 years ago - 1 comment

#261 - Why is `use_memory_efficient_kernel` always set to `False`

Issue - State: closed - Opened by RuiWang1998 almost 2 years ago - 1 comment

#260 - Dockerfile that has mmseq2 installed

Issue - State: open - Opened by rrw1007 almost 2 years ago - 2 comments

#260 - Dockerfile that has mmseq2 installed

Issue - State: open - Opened by rrw1007 almost 2 years ago - 2 comments

#259 - ModuleNotFoundError: No module named 'attn_core_inplace_cuda'

Issue - State: open - Opened by SimonKitSangChu almost 2 years ago - 2 comments

#259 - ModuleNotFoundError: No module named 'attn_core_inplace_cuda'

Issue - State: open - Opened by SimonKitSangChu almost 2 years ago - 5 comments