Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#357 - run_structure_prediction.py accepts comma separated list of input folds and optionally dedicated output_directories for each fold
Pull Request -
State: closed - Opened by maurerv 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
#332 - Make it possible to run create_individual_features.py with multimeric tempaltes using mmseqs2
Issue -
State: open - Opened by DimaMolod about 2 months ago
#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
#315 - added distogram parser - no tests so far as the pkl files may be too …
Pull Request -
State: open - Opened by gchojnowski 2 months ago
#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
#286 - Merge pull request #284 from KosinskiLab/update-unittest-objects
Pull Request -
State: closed - Opened by dingquanyu 4 months ago
#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
#269 - The 'Bio.Data.SCOPData' module will be deprecated in a future release of Biopython in favor of 'Bio.Data.PDBData
Issue -
State: open - Opened by sophiaaredas 4 months ago
- 5 comments
#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