geometricus

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Rewrite to not use dictionary or warn user if same name is used twice.

Ninjani

Ninjani

look into benchmarks and robustness of the two libraries and possibly change to biopython. * a good starting point in this [repo](https://github.com/jgreener64/pdb-benchmarks) by @jgreener64

akdel

- [ ] PDB parsing should throw sane errors and have the correct residue length - [ ] k-mer based fragments should have the right length - [ ] radius...

Ninjani

Error running shapemer from RADIUS

2

I am running the 'getting_started.ipynb' notebook. The following lines of code: `invariants, _ = get_invariants_for_structures(X_names, n_threads=4, split_infos=[SplitInfo(SplitType.RADIUS, 5)], moment_types=["O_3", "O_4", "O_5", "F"])` give the error below: `AttributeError: 'C KDTree' object...

rrw1007

How can I use geometricus to conduct t-SNE dimensionality reduction for my own pdb files?

3

Hi developer, I am a beginner in protein structure study and I read your paper "A structural biology community assessment of AlphaFold2 applications". Thank you for your nice job! I...

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