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Analysis scripts for bioarxiv#38

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JatGreer merged 86 commits intomainccpem/roodmus:mainfrom developmentccpem/roodmus:developmentCopy head branch name to clipboardApr 28, 2024

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Commits

Commits on Oct 18, 2023

• First draft exploring MD heterogeneity quantisation workflows

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Commits on Oct 30, 2023

• linked up workflow. Now need to add/confirm conformation tracing and plotting before comparing ensembles

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Commits on Oct 31, 2023

• Should think about updating to mdtraj rmsd if possible in future. Ignores light atoms now#

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• diversified hier cluster algs and added embedding

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Commits on Nov 8, 2023

• rdy to add ica, umap, hd and js

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Commits on Nov 9, 2023

• updating with compatible embeddings

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• identified applicable range of cluster algs

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Commits on Nov 10, 2023

• updated scikit learn version and added range of clustering/gmm and updated workflow running

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• umap library version and updated parser help

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• plot naming

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• removing gmm for now

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Commits on Nov 13, 2023

• nopkl options as they can be large

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• init merge complaint

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• Merge branch 'jgreer/het_metrics' of gitlab.tudelft.nl:aj-lab/roodmus into jgreer/het_metrics

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• checking if het metrics affect analysis tests

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• Some fixes for newly tested DRs and CAs

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Commits on Dec 5, 2023

• added het_metrics test and updated toml

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• Added het_metrics utilities for test pypi publish

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Commits on Jan 3, 2024

• Updated error messages for het metrics and added ipynb for checking contents of workflow pkl file(s)

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Commits on Jan 8, 2024

• Moved heterogeneity code over from mjoosten branch for latent variables

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Commits on Jan 9, 2024

• Added code for latent clustering without testing

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Commits on Jan 11, 2024

• Next step in the extract ensembles from entire MDA Universe and implement the CES, DRES and maybe HES. Possibly also JS on conformation indices in future

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Commits on Jan 15, 2024

• just need to add class for JS-divergence pkl heatmap plotting and test

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Commits on Jan 16, 2024

• Added class to handle ces (and eventually other) outputs to save to pkl and plot heatmap with labels. Next step is testing scripts

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Commits on Jan 17, 2024

• making notebooks to plot panels for all figures in the manuscript

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• added plotting script for figure 2

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Commits on Jan 18, 2024

• added plotting of panels for figure 4

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Commits on Jan 21, 2024

• Added new heterogeneity scritps to roodmus utilities callable

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Commits on Jan 23, 2024

• CES calculation of JS-d is implemented with plotting. Works on tests up to 1000 conformations via MD to MD. Next step is testing with latent-space-derived clustering workflows. Then test MD vs late…

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Commits on Jan 24, 2024

• Tests 1 and 2 working for MD to MD JS-divergence calculation. Added TODO for latent clustering output plot which has useless labels. Next will fix hetenseble when applied to latent-space-derived en…

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Commits on Jan 27, 2024

• updating plotting notebooks

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Commits on Jan 30, 2024

• Should work for het_ensemblecomparison of latent and MD dervied ensembles. Testing on 2vs2. Need to add profiling to deterine where slowness is occurring

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Commits on Feb 2, 2024

• supplementary figure 3DFlex covid spike monomer steered MD

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Commits on Feb 4, 2024

• Fixed and tested JD-d calculation for n subsets of clustering workflow derived ensembles. Good to scale up and add avg+err calcs to class next

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Commits on Feb 6, 2024

• Addded dres and avg+stddev for ces and dres with automated plotting. Testing in progress

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• fixing the avg and stddev auto heatmap plotting

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Commits on Feb 9, 2024

• fixing avg + stddev autoplotting

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• updating code for supplementary figures

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Commits on Feb 12, 2024

• MD vs latent JSD comparisons all make sense. NExt investigating parameter space

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Commits on Feb 26, 2024

• Updated to include mdanalysis and mdtraj versions

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Commits on Feb 29, 2024

• adding startfile writing utility

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• updated .csv files for test

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Commits on Mar 1, 2024

• looking into CTF plotting

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• looking into CTF plotting

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• updating integration test output label_truth

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• updating unit test

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• updated integration tests

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• re-enabled simulation test

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Commits on Mar 3, 2024

• added progressbar to sampling. Renamed trajfile_dir_path topfile_path to trajfile_dir and topfile

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Commits on Mar 5, 2024

• Analysis notebook for raddmg movie dataset

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• Allowing choice of DRES dimensions

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• Merge branch 'jgreer/het_metrics' of github.com:ccpem/roodmus into jgreer/het_metrics

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• fixed df comparison issue in analysis tests

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Commits on Mar 6, 2024

• Merge branch 'jgreer/het_metrics' into mjoosten/bugfixing

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• updating the version

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• Merge branch 'mjoosten/paper_figures' into mjoosten/bugfixing

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Commits on Mar 7, 2024

• sphinx docs files and basic template for docs

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• removed pycache , added gitignores and improved timestamp removal in tests

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• disabled waymarking in trajectory module

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• version bump after pycache fix

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• Merge branch 'development' into jgreer/het_metrics

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• bump version

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• trying to fix sphinx_rtd_theme error

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Commits on Mar 8, 2024

• Merge branch 'mjoosten/issue_1' into development

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• updated starfile writing script to output particle_data starfiles

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Commits on Mar 14, 2024

• updating orientation distribution plots

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Commits on Mar 26, 2024

• Updated conformation file reading and sorting. Also added functionality for removing hydrogens from conformation files

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Commits on Mar 27, 2024

• merging hydrogen removal script and updates to heterogeneity file organisation

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Commits on Apr 6, 2024

• updated figure 2 plotting

  MJoosten

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• updated plotting functions

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• updated plotting functions

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• updated plotting functions

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• updated plotting functions

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Commits on Apr 10, 2024

• fix lack of dimensions passing to workflow bug

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Commits on Apr 11, 2024

• Added prototype 1to1 matching prec/recall calculation for figure7. Next will functionise and add as option for analysis utils

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Commits on Apr 12, 2024

• updated plotting for supplementary figure

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• updated write_starfile utility

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• 1to1 matching precision calculation - also added to paper/figure_2.ipynb

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Commits on Apr 17, 2024

• added integration test for write_starfile utility

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• Merge branch 'jgreer/1to1matchmetrics' into mjoosten/issue_4

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Commits on Apr 19, 2024

• updated plotting and fixed bug in precision calc

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Commits on Apr 28, 2024

• Merge branch 'jgreer/het_metrics' of github.com:ccpem/roodmus into jgreer/het_metrics

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• Merge branch 'mjoosten/issue_4' into development

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• forgot to commit hydrogen removal script

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• Merge branch 'jgreer/het_metrics' into development

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• Version bump

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