Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / biotite-dev/biotite issues and pull requests
#615 - Road to Biotite 1.0
Issue -
State: open - Opened by padix-key 4 days ago
Labels: major release
#614 - Removal of deprecated functionalities
Issue -
State: open - Opened by padix-key 4 days ago
Labels: major release
#613 - Implementing TRR/XTC support
Issue -
State: open - Opened by padix-key 4 days ago
Labels: major release
#612 - mdtraj 1.10 incompatibility
Pull Request -
State: closed - Opened by tjmier 8 days ago
#611 - pdbx get_sequence return dict of seq
Pull Request -
State: open - Opened by tjmier 8 days ago
- 2 comments
#610 - Fix indexing with inverse slices
Pull Request -
State: closed - Opened by padix-key 8 days ago
#609 - Indexing BondList with inverse slice does not preserve order
Issue -
State: closed - Opened by padix-key 8 days ago
Labels: bug
#608 - Fix artifact name for source distribution
Pull Request -
State: closed - Opened by padix-key 9 days ago
#607 - Biotite dssp not running! Subprocess error: code 6
Issue -
State: open - Opened by padix-key 10 days ago
- 5 comments
Labels: bug
#605 - biotite 0.41.1 `.whl` not available for MacOS ARM
Issue -
State: open - Opened by BradyAJohnston 10 days ago
- 2 comments
#604 - Fix `Atom` `__repr__()` (#602)
Pull Request -
State: closed - Opened by ljarosch 15 days ago
- 4 comments
#603 - Updated platform and tooling versions in CI
Pull Request -
State: closed - Opened by padix-key 15 days ago
#602 - Custom annotations do not appear in Atom `__repr__()`
Issue -
State: closed - Opened by ljarosch 15 days ago
- 1 comment
Labels: bug
#601 - `Numpy 2.0` is used when installing `Biotite`via pip.
Pull Request -
State: closed - Opened by t0mdavid-m 15 days ago
- 1 comment
#600 - chain id parameter for structure.io.pdbx.get_sequence
Pull Request -
State: closed - Opened by tjmier 16 days ago
- 8 comments
#599 - Add chain id specifier to pdbx.get_sequence
Issue -
State: closed - Opened by tjmier 18 days ago
- 3 comments
#598 - Move build backend to 'hatch'
Pull Request -
State: closed - Opened by padix-key 19 days ago
#597 - Make ThrottleStatus a data class
Pull Request -
State: closed - Opened by padix-key 19 days ago
#596 - PubChem throttle control does not properly work
Issue -
State: open - Opened by padix-key 19 days ago
Labels: bug, good first issue
#595 - get_structures not returning extra fields
Issue -
State: closed - Opened by tjmier 20 days ago
- 2 comments
#594 - Allow SD files without terminal delimiter
Pull Request -
State: closed - Opened by padix-key 21 days ago
#593 - Fix bond inference for structures with insertion codes
Pull Request -
State: closed - Opened by padix-key 21 days ago
#592 - [BUG] Biotite's bond inference seems broken for some structures with specific insertion codes
Issue -
State: closed - Opened by ljarosch 22 days ago
- 3 comments
Labels: bug
#591 - Enable use of specific local CCD version
Issue -
State: closed - Opened by ljarosch 22 days ago
- 2 comments
#590 - Adopt a code formatter and linter
Issue -
State: open - Opened by 0ut0fcontrol 26 days ago
- 2 comments
Labels: major release
#589 - Support multi-entry SDF files
Pull Request -
State: closed - Opened by padix-key 27 days ago
#588 - Ensure PDB columns are not exceeded
Pull Request -
State: closed - Opened by padix-key 27 days ago
#587 - Add superimposition method for homologous sequences
Pull Request -
State: closed - Opened by padix-key 27 days ago
#586 - Fix setting empty columns
Pull Request -
State: closed - Opened by padix-key 28 days ago
#585 - Stabilize test_pubchem/test_search_simple
Pull Request -
State: closed - Opened by tcjaffe 28 days ago
#584 - fix: typos
Pull Request -
State: closed - Opened by Croydon-Brixton 29 days ago
- 1 comment
#583 - Fixed long locus ID issue in GB parser
Pull Request -
State: closed - Opened by tcjaffe 29 days ago
- 3 comments
#582 - Passing empty array leads to malformed PDBx file
Issue -
State: closed - Opened by padix-key 29 days ago
#581 - Add `create_atom_names()`
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#580 - Add more descriptive error message for `residue()`
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#579 - Fix warning and error message in `get_structure()`
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#578 - Issue retrieving residue info for 3UQ
Issue -
State: closed - Opened by xvlaurent about 1 month ago
- 2 comments
Labels: bug
#577 - Fix slicing with annotation on minus strand
Pull Request -
State: closed - Opened by trichter about 1 month ago
#576 - Add repair functions
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#575 - Support V3000 CTAB
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#574 - Get 4x4 transformation matrix from `AffineTransform`
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#573 - Return empty dot bracket notation when no basepairs are found
Pull Request -
State: closed - Opened by t0mdavid-m about 1 month ago
- 1 comment
#572 - Add `one_letter_code()`
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#571 - Implement NEP 29
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#570 - Failed to deserialize category 'entity' with ValueError: No closing quotation
Issue -
State: open - Opened by 0ut0fcontrol about 1 month ago
- 3 comments
Labels: bug
#569 - Make `flower` color scheme the default
Issue -
State: open - Opened by padix-key about 1 month ago
Labels: enhancement, major release
#568 - Determinism when resolving atom alternative locations
Issue -
State: open - Opened by nscorley about 1 month ago
- 2 comments
Labels: bug
#567 - Support reading and writing intra-residue bonds in PDBx files
Pull Request -
State: closed - Opened by padix-key about 1 month ago
- 3 comments
#566 - Full support of SDFiles
Issue -
State: closed - Opened by padix-key about 1 month ago
- 4 comments
Labels: enhancement
#565 - Use Hatch as build backend
Issue -
State: closed - Opened by padix-key about 1 month ago
Labels: enhancement, good first issue
#564 - Adapt tests to changed database response
Pull Request -
State: closed - Opened by padix-key about 1 month ago
#563 - Add `include_terminal_gaps` parameter
Pull Request -
State: closed - Opened by padix-key about 2 months ago
#562 - strucio.save_structure rips up structure from MD containing ligand
Issue -
State: closed - Opened by entropybit about 2 months ago
- 2 comments
#561 - Support V3000 CTAB
Issue -
State: closed - Opened by padix-key about 2 months ago
Labels: enhancement
#560 - Allow including terminal gaps in `write_alignment_to_cigar()`
Issue -
State: closed - Opened by padix-key about 2 months ago
Labels: enhancement
#559 - Float columns in `PDBFile.set_structure()` are not bounded
Issue -
State: closed - Opened by padix-key about 2 months ago
Labels: bug
#558 - Trajectory_sse.py: Not working
Issue -
State: closed - Opened by vaibhavanand1 2 months ago
- 2 comments
#557 - Allow chain IDs with more than one character in PDB structures
Pull Request -
State: closed - Opened by GabiAxel 2 months ago
- 4 comments
#556 - little bug of `biotite.structure.dot_bracket_from_structure`
Issue -
State: closed - Opened by flyfyyfyy 2 months ago
- 1 comment
#555 - Fix two bugs in assembly generation
Pull Request -
State: closed - Opened by 0ut0fcontrol 3 months ago
- 2 comments
#554 - DeserializationError: Failed to deserialize category 'pdbx_struct_assembly_gen'
Issue -
State: closed - Opened by 0ut0fcontrol 3 months ago
- 2 comments
#553 - missing bonds if use_author_fields=False when two same CCD together in wwPDB .cif file
Issue -
State: open - Opened by 0ut0fcontrol 3 months ago
- 3 comments
Labels: bug
#552 - Revamp documentation
Pull Request -
State: closed - Opened by padix-key 3 months ago
- 2 comments
#551 - Revamp documentation
Issue -
State: closed - Opened by padix-key 3 months ago
#550 - Migrate remaining content of `biotite-util` repository to `biotite`
Pull Request -
State: closed - Opened by padix-key 3 months ago
- 3 comments
#548 - Bump minor version
Pull Request -
State: closed - Opened by padix-key 3 months ago
#547 - Fix minor issues in documentation
Pull Request -
State: closed - Opened by padix-key 3 months ago
#546 - Propagate `include_bonds` parameter to `get_assembly()`
Pull Request -
State: closed - Opened by padix-key 3 months ago
#545 - pdbx.get_assembly` does not support multiple operation in one line?
Issue -
State: closed - Opened by 0ut0fcontrol 3 months ago
- 2 comments
#544 - Remove MMTF usage
Pull Request -
State: closed - Opened by padix-key 3 months ago
#543 - Put CCD subset under regular Git
Pull Request -
State: closed - Opened by padix-key 3 months ago
#542 - CCD build on install
Pull Request -
State: closed - Opened by padix-key 3 months ago
- 1 comment
#541 - Add job to periodically update the CCD
Pull Request -
State: closed - Opened by padix-key 3 months ago
- 1 comment
#540 - Save datasets in `structure.info` as BinaryCIF
Pull Request -
State: closed - Opened by padix-key 3 months ago
#539 - Implement `include_bonds` for PDBx
Pull Request -
State: closed - Opened by padix-key 4 months ago
#538 - Fix artifact upload
Pull Request -
State: closed - Opened by padix-key 4 months ago
#537 - Restrict NumPy to 1.x
Pull Request -
State: closed - Opened by padix-key 4 months ago
#536 - Fix CI
Pull Request -
State: closed - Opened by padix-key 4 months ago
#535 - Replace MMTF usage in example gallery
Issue -
State: closed - Opened by padix-key 5 months ago
#534 - Add function to parse secondary structure elements from PDBx
Issue -
State: open - Opened by padix-key 5 months ago
Labels: enhancement, good first issue
#533 - Read bonds from PDBx files
Issue -
State: closed - Opened by padix-key 5 months ago
Labels: enhancement, good first issue
#532 - Support compressed download in `database.rcsb.fetch()`
Issue -
State: open - Opened by padix-key 5 months ago
- 3 comments
Labels: enhancement, good first issue
#531 - Support `BinaryCIF` file format
Pull Request -
State: closed - Opened by padix-key 5 months ago
#530 - Add CI job for updating `structure.info`
Issue -
State: closed - Opened by padix-key 5 months ago
- 1 comment
Labels: wontfix
#529 - Update to NumPy 2.0
Pull Request -
State: open - Opened by padix-key 5 months ago
Labels: major release
#528 - PDBxFile is not writing _atom_site.id to CIF file
Issue -
State: closed - Opened by andrejberg 5 months ago
- 1 comment
#527 - Feature request: protein structure alignment
Issue -
State: closed - Opened by pengtb 5 months ago
- 2 comments
#526 - Refactor `superimpose()`
Pull Request -
State: closed - Opened by padix-key 5 months ago
#525 - `mmtf` being officiallity deprecated & not served.
Issue -
State: closed - Opened by BradyAJohnston 6 months ago
- 3 comments
#524 - kabsch alignment algorithm swapped mobile and fixed when creating rotation matrix
Issue -
State: closed - Opened by jonathanking-absci 6 months ago
- 3 comments
Labels: bug
#523 - Handle invalid `CRYST1` records correctly
Pull Request -
State: closed - Opened by padix-key 6 months ago
#522 - Fail to load RCSB structure 1fs4
Issue -
State: closed - Opened by xvlaurent 6 months ago
- 1 comment
Labels: bug
#521 - Second attempt on image scraper fixing
Pull Request -
State: closed - Opened by padix-key 6 months ago
#520 - Fix ignored image scrapers in gallery
Pull Request -
State: closed - Opened by padix-key 6 months ago
#519 - Update documentation
Pull Request -
State: closed - Opened by padix-key 6 months ago
#518 - Support changes in Matplotlib API
Pull Request -
State: closed - Opened by padix-key 7 months ago
#517 - Use ellipsis in doctests
Pull Request -
State: closed - Opened by padix-key 7 months ago
#516 - Support alignment conversion from/to CIGAR
Pull Request -
State: closed - Opened by padix-key 7 months ago
#515 - Structure `environment.yml`
Pull Request -
State: closed - Opened by padix-key 7 months ago
#514 - Support NCBI API keys
Pull Request -
State: closed - Opened by padix-key 7 months ago