Ecosyste.ms: Issues

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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

#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

#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