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
#287 - ValueError: operands could not be broadcast together
Issue -
State: closed - Opened by Stigimoloch 7 months ago
- 5 comments
#286 - Merge pull request #284 from KosinskiLab/update-unittest-objects
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
#285 - Reorganise structure of the package
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
- 15 comments
#284 - Update objects.py and unittest on objects.py
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
#283 - Rebase update-truemultimer
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
#282 - FLAGS.use_gpu_relax not passed to predict()
Issue -
State: closed - Opened by jkosinski 7 months ago
#281 - Merging error if pair_msa=False when executing pair_and_merge
Issue -
State: closed - Opened by dingquanyu 7 months ago
Labels: bug
#280 - New.
Pull Request -
State: closed - Opened by DimaMolod 7 months ago
- 2 comments
#279 - KeyError when executing run_get_good_pae.sh
Issue -
State: closed - Opened by maurerv 7 months ago
- 1 comment
Labels: bug
#278 - Update predict_structure.py
Pull Request -
State: closed - Opened by DimaMolod 7 months ago
- 1 comment
#277 - Fix 9
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
- 1 comment
#276 - Consider removing extra information from model pkl immediately before saving them
Issue -
State: closed - Opened by jkosinski 7 months ago
- 2 comments
Labels: enhancement
#275 - Parallise analysis pipeline
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
- 2 comments
Labels: enhancement
#274 - mpDockQ/pDockQ scores seem >1 for 3-protein complexes
Issue -
State: closed - Opened by niradsp 7 months ago
- 6 comments
#273 - fixed the sorting and now it sorts numerically
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
#272 - IndexError when predicting monomers with more than 3 recycles
Issue -
State: closed - Opened by maurerv 7 months ago
- 3 comments
#271 - Update example_1.md
Pull Request -
State: closed - Opened by DimaMolod 7 months ago
Labels: documentation
#270 - Fix mmseqs issue60 issue176 issue177
Pull Request -
State: closed - Opened by dingquanyu 7 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: closed - Opened by sophiaaredas 7 months ago
- 7 comments
#268 - Update truemultimer
Pull Request -
State: closed - Opened by dingquanyu 7 months ago
- 1 comment
#267 - create_individual_features.py: command not found
Issue -
State: closed - Opened by sophiaaredas 7 months ago
- 2 comments
#266 - Create feats merged
Pull Request -
State: closed - Opened by DimaMolod 7 months ago
- 2 comments
#265 - convert_to_modelcif on top directory scenario
Issue -
State: closed - Opened by jkosinski 7 months ago
- 2 comments
Labels: enhancement
#264 - check_predict_structure.py not passing
Issue -
State: closed - Opened by jkosinski 7 months ago
- 1 comment
Labels: bug
#263 - Fix versions in example 1
Pull Request -
State: closed - Opened by jkosinski 7 months ago
- 1 comment
#262 - Crashing because of missing stereo_chemical_props.txt
Issue -
State: closed - Opened by jkosinski 7 months ago
Labels: help wanted
#261 - Update example_1.md
Pull Request -
State: closed - Opened by jkosinski 7 months ago
#260 - Update Developing.md
Pull Request -
State: closed - Opened by jkosinski 7 months ago
- 3 comments
#259 - Is this file committed to test/ by mistake?
Issue -
State: closed - Opened by jkosinski 7 months ago
#258 - Add an analysis script to draw MSA coverage, pLDDT plots, and distograms
Issue -
State: open - Opened by jkosinski 7 months ago
- 1 comment
#257 - Addition of flag (-save-pae-json) resulting in output of seperate pae.json files linked to predicted structures
Issue -
State: closed - Opened by jkosinski 8 months ago
- 2 comments
Labels: enhancement
#256 - Generate Distogram and MSA coverage
Issue -
State: open - Opened by Qrouger 8 months ago
- 7 comments
#255 - How to run multimer_jobs.py with relaxed model option?
Issue -
State: closed - Opened by herman-einstein 8 months ago
- 1 comment
#254 - Autormsd
Pull Request -
State: closed - Opened by DimaMolod 8 months ago
#253 - CPU part silently failing for a particular protein
Issue -
State: closed - Opened by sroet 8 months ago
- 2 comments
#252 - Link to an existing AlphaFold2 installation
Issue -
State: closed - Opened by nmarounina 8 months ago
- 2 comments
#251 - May I know how to execute run_multimer_jobs.py with CPU
Issue -
State: closed - Opened by herman-einstein 8 months ago
- 8 comments
#250 - No module named 'alphafold.version'
Issue -
State: closed - Opened by cmwilson252 8 months ago
- 3 comments
#247 - Make fasta parser work with default uniprot descriptions
Issue -
State: closed - Opened by DimaMolod 8 months ago
- 1 comment
Labels: bug
#246 - Update example_3.md
Pull Request -
State: closed - Opened by jkosinski 8 months ago
#245 - maxres and maxfilt flags not working
Issue -
State: closed - Opened by BelminLeiden 8 months ago
- 3 comments
#244 - Modelcif conversion
Pull Request -
State: closed - Opened by bienchen 9 months ago
- 1 comment
Labels: enhancement
#243 - alpha_analysis_jax_0.4.sif python issue
Issue -
State: closed - Opened by BobCoelingh 9 months ago
- 9 comments
#242 - Merge newest AlphaFold
Issue -
State: closed - Opened by jkosinski 9 months ago
- 1 comment
#241 - allow_resume can be very slow
Issue -
State: open - Opened by jkosinski 9 months ago
#240 - modeling json with flags/versions
Pull Request -
State: closed - Opened by DimaMolod 9 months ago
#239 - Modelcif
Pull Request -
State: closed - Opened by DimaMolod 9 months ago
- 1 comment
#238 - update to main
Pull Request -
State: closed - Opened by DimaMolod 9 months ago
#237 - fail to initialise cuda backend
Issue -
State: closed - Opened by grandrea 9 months ago
- 3 comments
#236 - fixed links, typos, md formatting
Pull Request -
State: closed - Opened by quantixed 9 months ago
- 1 comment
#235 - Add option of using mmseqs2 template search instead of hmmer for template search
Issue -
State: closed - Opened by jkosinski 9 months ago
- 1 comment
Labels: enhancement
#234 - Fresh install fails SCOPData from Bio.Data import
Issue -
State: closed - Opened by grandrea 9 months ago
- 2 comments
#233 - Error for specific proteins
Issue -
State: closed - Opened by roderickslieker 9 months ago
- 31 comments
Labels: help wanted
#232 - create features scripts crash in the newest version
Issue -
State: closed - Opened by aokosinska 9 months ago
- 3 comments
Labels: bug
#231 - create_individual_features_with_templates.py doesn't work with the latest Biopython
Issue -
State: closed - Opened by aokosinska 9 months ago
Labels: documentation
#229 - Add matplotlib.pyplot.close() to plot_pae.py?
Issue -
State: closed - Opened by jkosinski 9 months ago
#228 - Update example_3.md
Pull Request -
State: closed - Opened by jkosinski 9 months ago
- 2 comments
#227 - notebook autosave off not working?
Issue -
State: open - Opened by jkosinski 9 months ago
- 2 comments
Labels: bug
#226 - Add how to install analysis_pipeline in developer mode
Issue -
State: closed - Opened by jkosinski 9 months ago
- 2 comments
Labels: documentation
#225 - update setup.cfg fixed #224
Pull Request -
State: closed - Opened by dingquanyu 9 months ago
#224 - AlphaLink2 submodule not correctly installed
Issue -
State: closed - Opened by dingquanyu 9 months ago
- 3 comments
Labels: bug
#223 - Add option of using hhsearch instead of hmmer for template search
Issue -
State: closed - Opened by jkosinski 10 months ago
- 1 comment
Labels: enhancement
#222 - Print which templates are used
Issue -
State: closed - Opened by jkosinski 10 months ago
- 1 comment
Labels: enhancement
#221 - Cicd user and developer
Pull Request -
State: closed - Opened by DimaMolod 10 months ago
#220 - Move analysis installation instruction to the main readme?
Issue -
State: closed - Opened by jkosinski 10 months ago
- 1 comment
#219 - Fix checking for pkl files across multiple directories
Pull Request -
State: closed - Opened by jkosinski 10 months ago
- 2 comments
#218 - Update Developing.md
Pull Request -
State: closed - Opened by jkosinski 10 months ago
#217 - Update README.md
Pull Request -
State: closed - Opened by jkosinski 10 months ago
- 8 comments
#216 - The link does not work anymore
Issue -
State: closed - Opened by jkosinski 10 months ago
#214 - Detail of AlphaPulldown dependencies
Issue -
State: closed - Opened by nmarounina 10 months ago
- 1 comment
#213 - alphalink2 example
Issue -
State: open - Opened by grandrea 10 months ago
- 4 comments
Labels: question
#211 - Unable to create Jupyter notebook due too compression of pickle files
Issue -
State: closed - Opened by B0r1sD 10 months ago
- 2 comments
Labels: bug
#210 - Running a oligomer with a monomer together
Issue -
State: closed - Opened by RenhaoL 10 months ago
- 3 comments
Labels: question
#209 - Don't import AF flags if there are already imported
Pull Request -
State: closed - Opened by DimaMolod 10 months ago
#207 - Fix #195
Pull Request -
State: closed - Opened by dingquanyu 10 months ago
#206 - Interpreting predictions_with_good_interpae.csv
Issue -
State: closed - Opened by calebmallery 11 months ago
Labels: question
#204 - Implement VoroIF-GNN scoring of interfaces
Issue -
State: open - Opened by jkosinski 11 months ago
Labels: enhancement
#203 - Inquiry about difference in tool results
Issue -
State: closed - Opened by lw78943 11 months ago
- 4 comments
#202 - update unifold submodule
Pull Request -
State: closed - Opened by dingquanyu 11 months ago
#201 - Update alphalink2 inference integration
Pull Request -
State: closed - Opened by dingquanyu 11 months ago
#200 - Integrated AlphaLink2 with AlphaPulldown
Pull Request -
State: closed - Opened by dingquanyu 11 months ago
#199 - alpha-analysis.sif
Issue -
State: closed - Opened by calebmallery 11 months ago
- 4 comments
#198 - get_good_inter_pae.py fails at pDockQ
Issue -
State: closed - Opened by grandrea 11 months ago
- 6 comments
#197 - Test for gappy pdb
Pull Request -
State: closed - Opened by jkosinski 11 months ago
#196 - Compute multiple sequence alignment (MSA) using multiple pbd templates
Issue -
State: closed - Opened by jflucier 11 months ago
- 1 comment
#195 - Pickle file size
Issue -
State: closed - Opened by matthieu-haudiquet 11 months ago
- 2 comments
#194 - create_individual_features.py specify number of cpu
Issue -
State: closed - Opened by jflucier 11 months ago
- 1 comment
#193 - Merge updated main README to add-unifold branch
Pull Request -
State: closed - Opened by dingquanyu 11 months ago
#191 - Error: Could not find HHBlits database
Issue -
State: closed - Opened by theabhirath 11 months ago
- 1 comment
#190 - True multimer
Pull Request -
State: closed - Opened by DimaMolod 12 months ago
#189 - Questions about the mpDockQ/pDockQ column in csv table
Issue -
State: closed - Opened by teaninja 12 months ago
- 4 comments
#188 - Option to run Bait as a homo-dimer?
Issue -
State: closed - Opened by calebmallery 12 months ago
- 3 comments
#187 - empty commit to bypass main branch protection
Pull Request -
State: closed - Opened by DimaMolod 12 months ago
#186 - True multimer
Pull Request -
State: closed - Opened by DimaMolod 12 months ago
#185 - Output notebook: models ranking and coloring
Issue -
State: closed - Opened by gilep 12 months ago
- 13 comments
Labels: bug
#184 - CI/CD
Pull Request -
State: closed - Opened by DimaMolod 12 months ago
#183 - isssue with running Alphapulldown in PBS array HPC
Issue -
State: closed - Opened by MuthusaravananS 12 months ago
- 1 comment
#182 - missing output in the jupyter notebook
Issue -
State: closed - Opened by Qmi3 12 months ago
#181 - Save full cif file in a temporary pathname
Issue -
State: closed - Opened by jkosinski 12 months ago
- 1 comment
#180 - Error: kalign failed
Issue -
State: closed - Opened by th-of about 1 year ago
- 1 comment