biotite

biotite copied to clipboard

Support compressed download in `database.rcsb.fetch()`

3

The RCSB PDB provides all files also in gzipped format. Therefore, to improve download times in `database.rcsb.fetch()`, one could optionally download the gzipped files and and unzip the HTTP response...

padix-key

NumPy 2.0 will be released soon (https://github.com/numpy/numpy/issues/24300), bringing some deprecated functionalities and breaking changes with it. This PR aims to make Biotite ready for usage with NumPy 2.0.

padix-key

The *Chemical Component Dictionary* (CCD) is heavily used inside `biotite.structure.info`, e.g. for finding bonds in an `AtomArray`. The data in `biotite.structure.info` is updated using functionalities from https://github.com/biotite-dev/biotite-util. The CCD is...

padix-key

`mmtf` being officiallity deprecated & not served.

1

`bcif` is the replacement for `mmtf`, and some databases such as RCSB are going to stop serving `mmtf` later this year. https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c

BradyAJohnston

kabsch alignment algorithm swapped mobile and fixed when creating rotation matrix

2

Hello, I'm working on some code that suggests that when creating the rotation matrix via `superimpose`, the kabsch algorithm implementation simply has `fixed` and `mobile` swapped as in `superimpose.py:_superimpose()`. Do...

jonathanking-absci

This issue tracks small tasks, that would improve the look-and-feel of the documentation: - [x] Update `sphinx-gallery` version - [ ] Fix missing *Fork me on GitHub* image - [...

padix-key

The `translate` method on NucleotideSequence is very useful when you have an unambiguous sequence, but if the sequence contains symbols from the extended ambiguous alphabet, calling the `translate` method results...

ncoish

This PR adds the ability to fetch databases from the AlphaFold structure database by querying on UniProt accession - new functionality in `biotite.database.alphafold` module for fetching structures via UniProt accession...

dacarlin

Support for AlphaFold database

14

Hi, I think Biotite is a really useful tool when I deal with a lot of biological data. Do your team has any plan to integrate AlphaFold database into the...

sirius777coder

AtomArrayStack with varying annotations per model

1

Based on comment from @padix-key on #487 I opened this issue. The problem is that currently it is not possible to manage a collection of models with different annotations on...

entropybit