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Issue 409

1

Fixes issue #409 - Changed url from `uniprot` to `uniprotkb` - In `search()`, changed parameter `limit` to new `size` @padix-key can you have a look?

MaxGreil

RCSB API group by function

1

Would it be possible to implement the group_by function of the RCSB API in the search command? This would allow for retrieval of grouped PDB IDs based on Uniprot accession...

jlefebre

The *UniProt KB* has revamped its REST API, with a new URL and changed parameter names (https://www.uniprot.org/help/api). While fetching entries still works (for now), the doctests and tests involving `search()`...

padix-key

pdbx get_structure with use_author_fields gives different results

1

On 7yxg, if we load the CIF file with `pdbx.get_structure(file, use_author_fields=False)` vs `pdbx.get_structure(file, use_author_fields=True)`, we get a different number of atoms. I believe this is because the author residue index...

ebetica

Difficult to select a specific chain from an assembly

3

Thanks for the help on the previous issue. Playing around with the assembly loading further, it seems to be very difficult to determine which symmetry a given atom belongs to....

rmrao

Pin version of uniprot database

1

Hi- I just discovered biotite and it looks like a great project - thanks! I need to query UniProt to get proteins for a given taxonomy and containing a certain...

dariober

When a `Tree` is created from a large number of sequences, the following error occurs: ``` src/biotite/sequence/phylo/tree.pyx:323: in biotite.sequence.phylo.tree.Tree.from_newick root, distance = TreeNode.from_newick(newick, labels) src/biotite/sequence/phylo/tree.pyx:921: in biotite.sequence.phylo.tree.TreeNode.from_newick child, dist =...

padix-key

foldx Buildmodel mutation interfact - convenience interface

3

Not sure this is interesting to you.

Mojusko

Custom-height letters

1

Hi! This is a great package and I would definitely use it a lot. I have a question: is there any way to provide custom-height metric to sequence logos? Like...

gezmi

Support writing multiple `AtomArray` to structure file

5

The pdb specification allows pdb files with multiple different models. biotite can read these files, but there is no way to write them.

dnlbauer