Ecosyste.ms: Issues

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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

#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

#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

#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