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
#179 - Duplicated to_bio?
Issue -
State: closed - Opened by jkosinski about 1 year ago
- 3 comments
#178 - Move it out of create_arguments() function
Issue -
State: closed - Opened by jkosinski about 1 year ago
- 1 comment
#177 - Add mmseqs2 info
Issue -
State: closed - Opened by jkosinski about 1 year ago
- 5 comments
Labels: enhancement
#176 - Add Alphapulldown token to mmseqs2 request
Issue -
State: closed - Opened by jkosinski about 1 year ago
- 1 comment
Labels: enhancement
#175 - Database description difference APD vs. AF
Issue -
State: closed - Opened by SchwarzMarek about 1 year ago
- 2 comments
#174 - Too many atoms?
Issue -
State: closed - Opened by mbaddoo about 1 year ago
- 3 comments
#173 - alpha-analysis.sif - no csv output
Issue -
State: closed - Opened by JtheBAB about 1 year ago
- 7 comments
Labels: enhancement
#172 - issue on running mmseqs2 remotely
Issue -
State: closed - Opened by teaninja about 1 year ago
- 1 comment
#171 - '4fxg.cif' is obsliterated at 01-MAR-23 in OBSLTE.dat file, so how to handle the following problem
Issue -
State: closed - Opened by liusfore about 1 year ago
- 1 comment
#170 - Output.ipynb does not work
Issue -
State: closed - Opened by Amin-Debabeche about 1 year ago
- 1 comment
#169 - error encountered with alpha-analysis.sif
Issue -
State: closed - Opened by mbaddoo about 1 year ago
- 6 comments
#167 - True multimer
Pull Request -
State: closed - Opened by DimaMolod about 1 year ago
Labels: enhancement
#165 - Error in the execution of Feature 2
Issue -
State: closed - Opened by Resram about 1 year ago
- 4 comments
#164 - "af2_plots @ b5b96c8" seems inaccessible
Issue -
State: closed - Opened by kimcho452 about 1 year ago
- 5 comments
#163 - Dealing with disordered proteins
Issue -
State: closed - Opened by 0Telepathetic0 about 1 year ago
- 1 comment
#162 - Problem Creating CSV Output: KeyError 'jobs'
Issue -
State: closed - Opened by teaninja about 1 year ago
- 17 comments
#161 - KeyError: 'P78344.pkl'
Issue -
State: closed - Opened by RogerLang about 1 year ago
- 2 comments
#158 - Index error when running alpha-analysis.sif (solved in updated version of the singularity image. Please download again)
Issue -
State: closed - Opened by aham41 about 1 year ago
- 6 comments
#156 - Run using only mmseqs/colabfold
Issue -
State: closed - Opened by susiegriggo about 1 year ago
- 4 comments
#155 - Proper naming for alpha-analysis.sif
Issue -
State: open - Opened by Pooryamb about 1 year ago
#154 - "Could not find the template sequence" and "must be real number, not NoneType"
Issue -
State: closed - Opened by nduan1 over 1 year ago
- 4 comments
#153 - Save mmCIF output files
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: enhancement
#152 - Alphafold databases when running mmseqs2 locally
Issue -
State: closed - Opened by susiegriggo over 1 year ago
- 8 comments
#151 - Develop readme
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
#150 - Create Developing.md
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
#149 - Move and organize readme files and png files in a doc directory
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: documentation
#148 - Add remote jupyter server link
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: documentation
#147 - Updating AlphaPulldown
Issue -
State: closed - Opened by mpm896 over 1 year ago
- 1 comment
#146 - missing information in notebook file
Issue -
State: closed - Opened by mbaddoo over 1 year ago
- 2 comments
#145 - Installation does not work on Macbook with M2
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 2 comments
Labels: bug
#144 - The jupyter notebook created does not work because I get the error "analysis_pipeline not found".
Issue -
State: closed - Opened by mbaddoo over 1 year ago
- 11 comments
#143 - Merged main
Pull Request -
State: closed - Opened by dingquanyu over 1 year ago
#142 - fixed ranked plddt error
Pull Request -
State: closed - Opened by dingquanyu over 1 year ago
#141 - Plotting interaction network
Issue -
State: open - Opened by mpm896 over 1 year ago
- 1 comment
Labels: enhancement
#140 - seq_index Error
Issue -
State: closed - Opened by mbaddoo over 1 year ago
- 5 comments
#139 - Update README.md
Pull Request -
State: closed - Opened by dingquanyu over 1 year ago
#138 - Update the add-unifold branch
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#137 - af2plots missing and not installed?
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 3 comments
Labels: bug
#136 - Fix paths in test_predict_structure.py
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
#135 - Fix random seed
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
#134 - Organise submodules
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#133 - Adding pulldown mode running on CPU
Issue -
State: closed - Opened by remybonnav over 1 year ago
- 3 comments
#132 - Running on low VRAM (8GB) GPU
Issue -
State: closed - Opened by remybonnav over 1 year ago
- 1 comment
#131 - Pulldown error on WSL2
Issue -
State: closed - Opened by remybonnav over 1 year ago
- 2 comments
#130 - Independently run MSA prediction?
Issue -
State: closed - Opened by remybonnav over 1 year ago
- 2 comments
#129 - np.int and np.object error
Issue -
State: closed - Opened by remybonnav over 1 year ago
- 9 comments
#128 - Fix 120
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#127 - How to run Pulldown on defined "candidates" list without AlphaFold Directory
Issue -
State: closed - Opened by HollyAnd over 1 year ago
- 1 comment
#126 - tensorflow problem
Issue -
State: closed - Opened by Tosfly over 1 year ago
- 2 comments
#125 - How to evaluate interaction for more than two proteins
Issue -
State: closed - Opened by SchwarzMarek over 1 year ago
- 5 comments
Labels: enhancement
#124 - Singularity image does not work with alphafold results.
Issue -
State: closed - Opened by tony9959 over 1 year ago
- 1 comment
#123 - Recommend more specific version of `PDBfixer`
Issue -
State: closed - Opened by deniskristak over 1 year ago
- 1 comment
Labels: documentation
#122 - Fix relax and resume
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
#121 - Fix relax and add multimer job resume
Pull Request -
State: closed - Opened by jkosinski over 1 year ago
#120 - KeyError: 'template_confidence_scores'
Issue -
State: closed - Opened by Pooryamb over 1 year ago
- 7 comments
Labels: bug
#119 - fixed #117
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#118 - Issue with run_multimer_jobs
Issue -
State: closed - Opened by sarahemooneyy over 1 year ago
- 2 comments
Labels: question
#117 - Fail to align to templates
Issue -
State: closed - Opened by Pooryamb over 1 year ago
- 2 comments
#116 - Unable to run the singularity image
Issue -
State: closed - Opened by matthieu-haudiquet over 1 year ago
- 1 comment
#115 - Use obsolete_pdbs_path when using mmseqs2
Pull Request -
State: closed - Opened by kttn8769 over 1 year ago
- 1 comment
#114 - About protein interface site
Issue -
State: closed - Opened by wangxuann1995 over 1 year ago
- 1 comment
Labels: question
#113 - Add unittest
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#112 - About reduced db
Issue -
State: closed - Opened by Aaronro16 over 1 year ago
- 3 comments
#111 - Generating the MSAs by Colabfold
Issue -
State: closed - Opened by Pooryamb over 1 year ago
- 4 comments
#110 - Handel empty template
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#109 - images of structures not rendering in jupyter
Issue -
State: closed - Opened by lauradunphy over 1 year ago
- 3 comments
Labels: bug
#108 - Fix for custom job creation
Pull Request -
State: closed - Opened by dennissv over 1 year ago
- 6 comments
#106 - ValueError when calculating some PI-scores
Issue -
State: closed - Opened by EricLMiller over 1 year ago
- 6 comments
#105 - Implement --restart option for run_multimer_jobs.py
Issue -
State: closed - Opened by jkosinski over 1 year ago
Labels: enhancement
#104 - Add options for changing msa depth
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: enhancement
#103 - Add ability of skipping templates
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 3 comments
Labels: enhancement
#102 - Enable modeling of monomers and their fragments
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: enhancement
#101 - Add option to skip pairing
Issue -
State: closed - Opened by jkosinski over 1 year ago
- 1 comment
Labels: enhancement
#100 - Alphafold 2.3.0
Pull Request -
State: closed - Opened by henrywotton over 1 year ago
#99 - Custom model homodimer interaction with other protein input specification
Issue -
State: closed - Opened by SchwarzMarek over 1 year ago
- 2 comments
#98 - AlphaPulldown 0.22.3 can't run with Alphafold database in Version 2.3.0
Issue -
State: closed - Opened by lorethan22 over 1 year ago
- 3 comments
#97 - Error with create_indivisual_features.py
Issue -
State: closed - Opened by YyMsd almost 2 years ago
#96 - Interpretation of mpDockQ/pDockQ
Issue -
State: closed - Opened by CelineGrech almost 2 years ago
- 6 comments
#95 - Improve metadata recording
Issue -
State: closed - Opened by jkosinski almost 2 years ago
- 2 comments
#94 - Unable to generate .pkl (example 1, 1st step)
Issue -
State: closed - Opened by ZackLi1984 almost 2 years ago
#93 - Feature request: only run 1 set of model params instead of all 5?
Issue -
State: closed - Opened by rlawr almost 2 years ago
- 7 comments
#92 - cannot find .cif file during feature generation
Issue -
State: closed - Opened by rlawr almost 2 years ago
- 2 comments
#91 - Improve flags handling?
Issue -
State: closed - Opened by jkosinski almost 2 years ago
- 1 comment
#90 - output_dir is merged with protein description?
Issue -
State: closed - Opened by DimaMolod almost 2 years ago
- 5 comments
#89 - FileNotFoundError: [Errno 2] No such file or directory: 'hhsearch': 'hhsearch'
Issue -
State: closed - Opened by sarahemooneyy almost 2 years ago
- 2 comments
#88 - fixed #82
Pull Request -
State: closed - Opened by henrywotton almost 2 years ago
#87 - run_get_good_pae.sh "jobs" data missing when computing pi_score
Issue -
State: closed - Opened by SchwarzMarek almost 2 years ago
- 11 comments
#86 - TypeError: cannot unpack non-iterable DataPipeline object while using create_individual_features.py
Issue -
State: closed - Opened by lorethan22 almost 2 years ago
- 4 comments
#85 - Pvalue in output csv table
Issue -
State: closed - Opened by nduan1 almost 2 years ago
- 2 comments
#84 - GPU usage in create_individual_features.py
Issue -
State: closed - Opened by phpeters almost 2 years ago
- 2 comments
#83 - Issue 72
Pull Request -
State: closed - Opened by henrywotton almost 2 years ago
#82 - Improve auto-creating output directory in check_output_dir
Issue -
State: closed - Opened by jkosinski almost 2 years ago
#81 - Very slow compile error
Issue -
State: closed - Opened by mpm896 almost 2 years ago
- 7 comments
#80 - Error with run_multimer_jobs.py
Issue -
State: closed - Opened by mpm896 almost 2 years ago
- 5 comments
#79 - Modeling entire protein chain based on fragment multimer model
Issue -
State: closed - Opened by mpm896 almost 2 years ago
- 1 comment
#78 - added a try-exception block fixe #71
Pull Request -
State: closed - Opened by henrywotton almost 2 years ago
#77 - Error with run_multimer_jobs.py when using MMseqs2
Issue -
State: closed - Opened by gretabellinzona almost 2 years ago
- 10 comments
#76 - unable to execute create_individual_features.py to compute MSA
Issue -
State: closed - Opened by sarbanid almost 2 years ago
- 6 comments
#75 - why python==3.7.* ?
Issue -
State: closed - Opened by schluenz almost 2 years ago
- 2 comments
#74 - When I create predictions_with_good_interpae.csv, there is some problems
Issue -
State: closed - Opened by yaober almost 2 years ago
- 2 comments