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Add functionality for reading and writing alignments from/to A3M format

1

Resolves #724.

padix-key

Support files formatted in general non-PDBx CIF format

2

The `CIFBlock.deserialize()` method fails to parse CIF data correctly, causing inability to access `CIFCategory` objects. Reproduction example: ```python import biotite.structure.io.pdbx as pdbx cifblock = pdbx.CIFBlock.deserialize( """ _symmetry_space_group_name_H-M 'P 1' _cell_length_a...

Alex6357

`biotite.structure.superimpose()` currently returns an `AffineTransformation`. Multiple aspects could be refactored here: - As `AffineTransformation` represents actually a *rigid transformation*, it would be renamed to `RigidTransformation` - Currently it uses two...

padix-key

Disallow redundant bonds in `BondList`

6

Linford24

Currently `filter_monoatomic_ions()` uses a very simple logic: https://github.com/biotite-dev/biotite/blob/ae894b0c6f83e769009a41c235aad84b404c1895/src/biotite/structure/filter.py#L90 This will probably fail for some ions, so there should be a more rigorous procedure.

padix-key

Add `atomworks` to extension package page

3

Recently https://github.com/RosettaCommons/atomworks was released, which uses `AtomArray` and `AtomArrayStack` as structure representation. Hence, I think it would be fitting to include it in the [list of extension packages](https://www.biotite-python.org/latest/extensions.html). @Croydon-Brixton @nscorley...

padix-key

Bond can be created of an atom to itself

2

Currently you can add a bond to `BondList`, that connects an atom with itself. This should never be possible. Tangentially, `pdbx.set_structure()` does not check atom uniqueness when writing the `chem_comp_bond`...

padix-key

Add pandas-style query functionality to `AtomArray` and `AtomArrayStack` objects

6

This pull request introduces new query capabilities to the `AtomArray` class in the `biotite.structure` module, enabling users to filter, mask, and retrieve indices of atoms based on convenient pandas-like query...

Croydon-Brixton

Resolves #688. This PR introduces Rust code into Biotite. To make it work along the existing Cython modules the build backend is switched back to `setuptools`, using `setuptools-rust` to build...

padix-key