biotite

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Currently the CIF and BinaryCIF container classes use the default *mixin* implementation of `__contains__()`. However, this default implementation uses ```python try: self[key]: except KeyError: return False return True ``` Hence,...

padix-key

This PR increases the speed in which PDBx files with structure + bonds written by Biotite can be read: Currently, `pdbx.set_structure(include_bonds=True)` writes **all** inter-residue bonds, to be sure that all...

padix-key

Improve performance of `pdbx.compress()`

2

padix-key

Add 3di encoding to `biotite.structure`

7

Hi Patrick, As discussed here is the encoder as taken (and slightly updated) from `mini3di`. I am not familiar with the biotite API that much but I tried doing some...

althonos

Add positional substitution matrices

1

This PR adds functionality for creating positional substitution matrices, i.e. matrices that have a score for each position in a sequence. This allows position-specific sequence alignments, such as algorithms like...

padix-key

Enable quoted string with whitespace in CIF file 'atom_site' category.

1

I have to work with in-house CIF files that have label_atom_id including whitespaces (which is allowed by the official[ mmCIF dictionary](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_atom_id.html)), but I found that biotite [does not expect whitespaces...

xvlaurent

The PDB annotates now protein chemical modifications (PCMs) in the CCD (https://www.wwpdb.org/news/news?year=2024#662fa1a565d8a8cacaf76f9c). These annotation describe also where such PCMs bind to a protein chain via `pdbx_chem_comp_pcm.comp_id_linking_atom` and `pdbx_chem_comp_pcm.modified_residue_id_linking_atom`. We could...

padix-key

From cif to unit cell coordinates

3

Dear Sir/Madams, I wonder if biotitie could calculate the unit cell configuration(not bio assembly) of protein from a mmcif file with the space group, unit cell shape and asymmetry unit...

Heisenburger2020

Add CI job for uploading built documentation to website

1

padix-key