biotite-dev biotite issues

biotite-dev / biotite

A comprehensive library for computational molecular biology

https://www.biotite-python.org

BSD 3-Clause "New" or "Revised" License

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issues

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Implement structural superimposition and TM-score

#705 padix-key opened 2 days ago
1
Add example for structure search based on 3Di alphabet

#704 padix-key opened 4 days ago
1
Make `EValueEstimator` accept a `Generator`

#703 padix-key opened 1 week ago
0
Expand tutorial about position specific scoring matrices

#702 padix-key opened 1 week ago
1
Temporarily revert DSSP version in environment

#701 padix-key closed 1 week ago
1
disambiguate assembly chains by appending assembly id

#700 alex-hh opened 1 week ago
5
Add support for lDDT computation

#699 padix-key opened 2 weeks ago
1
Residue-wise lDDT of an AlphaFold DB protein against a reference from PDB

#698 padix-key opened 2 weeks ago
0
Sequence profile alignment

#697 padix-key opened 2 weeks ago
0
Detect membrane embedded region of a protein sequence

#696 padix-key opened 2 weeks ago
0
Assembly of a DNA double helix structure

#695 padix-key opened 2 weeks ago
0
Refactor test parametrization

#694 padix-key opened 2 weeks ago
0
Add @althonos to `CONTRIB.rst`

#693 althonos closed 2 weeks ago
1
Add gallery example for profile alignments

#692 padix-key opened 2 weeks ago
0
Refactor some examples

#691 padix-key closed 2 weeks ago
1
Edit the structure annotation using an atom

#690 dargen3 opened 2 weeks ago
2
Carry through space group information when reading and writing pdb files

#689 zanebeckwith opened 3 weeks ago
3
Introducing Rust code into Biotite

#688 padix-key opened 3 weeks ago
3
Refactor internal CCD

#687 padix-key closed 2 weeks ago
1
Update _split_one_line and remove whitespace parameter

#686 xvlaurent closed 4 days ago
7
Support computation of lDDT

#685 padix-key opened 1 month ago
2
Bonds cannot be found for alternative atom names

#684 padix-key opened 1 month ago
1
Do not try integer packing for huge values

#683 padix-key closed 4 weeks ago
1
Integrate structural alphabets better into Biotite

#682 padix-key closed 2 weeks ago
1
Add CLePAPS structural alphabet

#681 padix-key opened 1 month ago
0
Allow failing PubChem tests due to busy server

#680 padix-key closed 1 month ago
1
Avoid deserialization of PDBx data in `__contains__()`

#679 padix-key closed 1 month ago
0
Omit 'standard' bonds when writing `struct_conn` category

#678 padix-key closed 1 month ago
0
Improve performance of `pdbx.compress()`

#677 padix-key closed 1 month ago
2
Add Protein Blocks structural alphabet

#676 padix-key closed 2 weeks ago
1
Vectorize apply_residue_wise

#675 alex-hh closed 1 month ago
2
Add `compress()` function to decrease the file size of BinaryCIF files

#674 padix-key closed 1 month ago
1
Enable quoted string with whitespace in CIF file 'atom_site' category.

#673 xvlaurent opened 1 month ago
2
Docstrings for 'set_annotation': Remove 'None' as input type for 'array'.

#672 JHKru closed 1 month ago
2
Use PCM annotation for finding inter-residue bonds

#671 padix-key opened 1 month ago
0
Allow loading computationally predicted cif files, which may not have certain custom annotations

#670 Croydon-Brixton closed 1 month ago
8
Allow writing out custom annotation fields to cif files

#669 Croydon-Brixton closed 1 month ago
6
Micro-PR to add `alt_atom_id` to Biotite's internal CCD

#668 Croydon-Brixton closed 1 month ago
13
Fasta reader seemingly not working in Biotite 1.0.1

#667 JHKru closed 1 month ago
1
Add support for structural alphabets

#666 padix-key closed 2 weeks ago
0
Add 3di encoding to `biotite.structure`

#665 althonos closed 2 weeks ago
11
Improve performance of pickling `KmerTable`

#664 padix-key closed 2 months ago
1
Add k-mer functionality benchmarks

#663 padix-key closed 2 months ago
1
Loading old npz files

#662 ljmartin closed 2 months ago
2
Support Python 3.13

#661 padix-key closed 1 month ago
1
From cif to unit cell coordinates

#660 Heisenburger2020 opened 2 months ago
3
Fix invalid CIF/BCIF files created when file is edited

#659 padix-key closed 2 months ago
1
The format of the mmCIF file after changing the block and saving is broken

#658 dargen3 closed 2 months ago
3
Improve performance of BinaryCIF deserialization

#657 padix-key closed 2 months ago
1
ImportError: cannot import name 'filter_backbone' from 'biotite.structure'

#656 marjanUofT closed 2 months ago
1