Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#368 - Fix 367

Pull Request - State: closed - Opened by dingquanyu 11 days ago - 6 comments

#367 - 'ranking_confidence' is not in the result.pkl file after the update

Issue - State: closed - Opened by DimaMolod 14 days ago - 10 comments

#366 - Rearange backend initialisation

Pull Request - State: closed - Opened by dingquanyu 15 days ago - 2 comments

#365 - Convert predicted models to modelcif

Pull Request - State: closed - Opened by DimaMolod 15 days ago

#364 - Update libffi version

Pull Request - State: closed - Opened by dingquanyu 15 days ago - 4 comments

#363 - Clean duplicating functions/ redundant code

Issue - State: open - Opened by DimaMolod 16 days ago

#362 - Use DEFINE_list for model_names flag

Issue - State: open - Opened by DimaMolod 16 days ago - 3 comments

#361 - Fix 344

Pull Request - State: closed - Opened by dingquanyu 18 days ago

#360 - Updated container creation scheme

Pull Request - State: closed - Opened by maurerv 18 days ago - 2 comments

#359 - Runtime of each prediction

Issue - State: closed - Opened by what-is-what 21 days ago - 1 comment

#358 - GPU seems not working when run_multimer_jobs.py

Issue - State: closed - Opened by HUST6324 22 days ago - 5 comments

#356 - More exception in analysis pipeline

Pull Request - State: closed - Opened by dingquanyu 22 days ago

#355 - Improve resume predictions

Pull Request - State: closed - Opened by DimaMolod 24 days ago - 4 comments

#354 - 343 replace this with non cctbx solution

Pull Request - State: open - Opened by gchojnowski 25 days ago

#353 - Improve resume predictions

Issue - State: closed - Opened by DimaMolod 28 days ago - 1 comment

#352 - Multiple feature directories

Issue - State: closed - Opened by DimaMolod 28 days ago - 2 comments

#351 - Update example_1.md

Pull Request - State: closed - Opened by B0r1sD 28 days ago - 2 comments

#350 - jackhammer error running test

Issue - State: closed - Opened by Clockris about 1 month ago - 3 comments

#349 - Add again --dry_run flag

Pull Request - State: closed - Opened by DimaMolod about 1 month ago - 1 comment

#347 - Now allow it to parse pLDDT values from bfactor

Pull Request - State: closed - Opened by dingquanyu about 1 month ago

#346 - Group unittests

Pull Request - State: open - Opened by dingquanyu about 1 month ago - 1 comment

#345 - Update alphalink backend

Pull Request - State: closed - Opened by dingquanyu about 1 month ago

#344 - singularity error

Issue - State: closed - Opened by polya18 about 1 month ago - 20 comments

#343 - Replace this with non-cctbx solution

Issue - State: open - Opened by jkosinski about 1 month ago - 7 comments

#342 - run_multimer_jobs issue

Issue - State: closed - Opened by J-Held about 1 month ago - 5 comments

#341 - Running calculate_mpdockq.py with only PDB

Issue - State: closed - Opened by busrasavas about 1 month ago - 1 comment

#340 - Add dropout

Issue - State: open - Opened by jkosinski about 1 month ago

#339 - GPU not working when run_multimer_jobs.py

Issue - State: open - Opened by polya18 about 2 months ago - 3 comments

#338 - Update documentation request

Issue - State: open - Opened by Clockris about 2 months ago

#337 - Too many proteins in one interaction ?

Issue - State: open - Opened by Qrouger about 2 months ago - 2 comments

#336 - Add generation of JSON for AlphaFold server

Issue - State: open - Opened by jkosinski about 2 months ago
Labels: enhancement

#334 - using several GPUs on a single workstation

Issue - State: open - Opened by errinaceus about 2 months ago

#333 - Improve pdb_analyser.py

Pull Request - State: closed - Opened by DimaMolod about 2 months ago - 2 comments

#330 - Fix interface measurements in the analysis pipeline

Pull Request - State: closed - Opened by dingquanyu about 2 months ago - 3 comments

#329 - pi-score outputs

Issue - State: closed - Opened by salomonssonj about 2 months ago - 7 comments

#328 - Multiple mmts

Pull Request - State: closed - Opened by DimaMolod about 2 months ago - 3 comments

#327 - Fix 292 and singularity image

Pull Request - State: closed - Opened by dingquanyu about 2 months ago

#324 - alphapulldown.utils.process_files automatically excludes permutation of the input elements

Pull Request - State: closed - Opened by maurerv about 2 months ago - 1 comment

#323 - predictions_with_good_interpae.csv

Issue - State: closed - Opened by DimaMolod about 2 months ago
Labels: bug

#322 - Different behavior of the all_vs_all mode in AlphaPulldown 2.0.0 beta v2?

Issue - State: closed - Opened by TM-Hamm about 2 months ago - 9 comments

#321 - update tests and fixed create_notebook

Pull Request - State: closed - Opened by dingquanyu 2 months ago

#320 - Flash attention?

Issue - State: open - Opened by jkosinski 2 months ago
Labels: enhancement

#319 - operands could not be broadcast together with shapes - MMSEQ2

Issue - State: open - Opened by rukibuki 2 months ago - 2 comments

#318 - Update tests

Pull Request - State: closed - Opened by dingquanyu 2 months ago

#317 - Snakemake docker

Pull Request - State: closed - Opened by DimaMolod 2 months ago

#316 - Path output alpha-analysis.sif

Issue - State: open - Opened by JtheBAB 2 months ago - 3 comments

#313 - Version2

Pull Request - State: closed - Opened by DimaMolod 2 months ago - 9 comments

#312 - Version2 beta v1 issues

Issue - State: closed - Opened by dingquanyu 2 months ago

#311 - Add interface PAE and plddt calculation to anlaysis pipeline

Pull Request - State: closed - Opened by dingquanyu 3 months ago - 4 comments

#310 - database setup - HHblits reference

Issue - State: closed - Opened by WardDeb 3 months ago - 2 comments

#309 - rebase openfold branch

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#308 - Manuals 2.0 beta

Pull Request - State: closed - Opened by dingquanyu 3 months ago - 5 comments

#307 - Fix292, update analysis pipeline singularity files

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#306 - Update alphafold_backend.py

Pull Request - State: closed - Opened by DimaMolod 3 months ago

#305 - Fix padding

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#304 - fixed an issue in af2-like coloring by plddt

Pull Request - State: closed - Opened by gchojnowski 3 months ago

#303 - Backend revision

Pull Request - State: closed - Opened by dingquanyu 3 months ago - 6 comments

#301 - merge updates on indents and function cleaning

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#300 - Merge Dima patches to jit-jobs first

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#299 - Pad input features from different prediction jobs to a universal desired shapes

Pull Request - State: closed - Opened by dingquanyu 3 months ago - 4 comments

#298 - Update setup.cfg: setting tensorflow>=2.14.0 leads to incompatible cuda

Pull Request - State: closed - Opened by kashyapchhatbar 3 months ago - 1 comment

#297 - Reopening PR

Pull Request - State: closed - Opened by DimaMolod 3 months ago - 3 comments

#296 - Setting tensorflow>=2.14.0 leads to incompatible cuda

Issue - State: closed - Opened by kashyapchhatbar 3 months ago - 1 comment

#295 - Revert "Dima small patches"

Pull Request - State: closed - Opened by dingquanyu 3 months ago

#294 - num_predictions_per_model

Issue - State: closed - Opened by hqdream 3 months ago - 3 comments

#293 - How to run with reduced_dbs

Issue - State: open - Opened by fteufel 3 months ago - 2 comments

#292 - KeyError: 'template_confidence_scores'

Issue - State: closed - Opened by Qrouger 3 months ago - 13 comments

#291 - Dima small patches

Pull Request - State: closed - Opened by DimaMolod 3 months ago - 7 comments

#290 - alpha-analysis.sif can not process larger models

Issue - State: open - Opened by teaninja 4 months ago - 2 comments

#289 - added standard alphafold database coloring to notebook displays

Pull Request - State: closed - Opened by dingquanyu 4 months ago

#288 - Fix 223 282

Pull Request - State: closed - Opened by dingquanyu 4 months ago - 1 comment

#287 - ValueError: operands could not be broadcast together

Issue - State: open - Opened by Stigimoloch 4 months ago - 4 comments

#285 - Reorganise structure of the package

Pull Request - State: closed - Opened by dingquanyu 4 months ago - 15 comments

#284 - Update objects.py and unittest on objects.py

Pull Request - State: closed - Opened by dingquanyu 4 months ago

#283 - Rebase update-truemultimer

Pull Request - State: closed - Opened by dingquanyu 4 months ago

#282 - FLAGS.use_gpu_relax not passed to predict()

Issue - State: closed - Opened by jkosinski 4 months ago

#281 - Merging error if pair_msa=False when executing pair_and_merge

Issue - State: closed - Opened by dingquanyu 4 months ago
Labels: bug

#280 - New.

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 2 comments

#279 - KeyError when executing run_get_good_pae.sh

Issue - State: closed - Opened by maurerv 4 months ago - 1 comment
Labels: bug

#278 - Update predict_structure.py

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 1 comment

#277 - Fix 9

Pull Request - State: closed - Opened by dingquanyu 4 months ago - 1 comment

#276 - Consider removing extra information from model pkl immediately before saving them

Issue - State: open - Opened by jkosinski 4 months ago
Labels: enhancement

#275 - Parallise analysis pipeline

Pull Request - State: open - Opened by dingquanyu 4 months ago - 1 comment
Labels: enhancement

#274 - mpDockQ/pDockQ scores seem >1 for 3-protein complexes

Issue - State: closed - Opened by niradsp 4 months ago - 6 comments

#273 - fixed the sorting and now it sorts numerically

Pull Request - State: closed - Opened by dingquanyu 4 months ago

#272 - IndexError when predicting monomers with more than 3 recycles

Issue - State: closed - Opened by maurerv 4 months ago - 3 comments

#271 - Update example_1.md

Pull Request - State: closed - Opened by DimaMolod 4 months ago
Labels: documentation

#270 - Fix mmseqs issue60 issue176 issue177

Pull Request - State: closed - Opened by dingquanyu 4 months ago

#268 - Update truemultimer

Pull Request - State: closed - Opened by dingquanyu 4 months ago - 1 comment

#267 - create_individual_features.py: command not found

Issue - State: closed - Opened by sophiaaredas 4 months ago - 2 comments

#266 - Create feats merged

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 2 comments

#265 - convert_to_modelcif on top directory scenario

Issue - State: closed - Opened by jkosinski 4 months ago - 2 comments
Labels: enhancement

#264 - check_predict_structure.py not passing

Issue - State: closed - Opened by jkosinski 4 months ago - 1 comment
Labels: bug

#263 - Fix versions in example 1

Pull Request - State: closed - Opened by jkosinski 4 months ago - 1 comment

#262 - Crashing because of missing stereo_chemical_props.txt

Issue - State: closed - Opened by jkosinski 4 months ago
Labels: help wanted