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
#513 - Add Python 3.12 build
Pull Request -
State: closed - Opened by padix-key 7 months ago
#512 - Allow 5 characters residue names
Pull Request -
State: closed - Opened by padix-key 7 months ago
#511 - Add workflow for building the docs
Pull Request -
State: closed - Opened by padix-key 7 months ago
#510 - Implement k-mer subsetting methods
Pull Request -
State: closed - Opened by padix-key 7 months ago
#509 - Amend: Increase performance of fetching via sra-tools (#504)
Pull Request -
State: closed - Opened by padix-key 7 months ago
#508 - Cleaning up documentation
Issue -
State: closed - Opened by padix-key 7 months ago
#507 - Getting CIGAR string of an alignment
Issue -
State: closed - Opened by padix-key 7 months ago
- 2 comments
Labels: enhancement, good first issue
#506 - Clearer error message, if `Application` instance method is called without instance
Pull Request -
State: closed - Opened by padix-key 7 months ago
#505 - Update tests to changes in databases
Pull Request -
State: closed - Opened by padix-key 8 months ago
#504 - Increase performance of fetching via sra-tools
Pull Request -
State: closed - Opened by padix-key 8 months ago
#503 - Feature Request: Option to translate NucleotideSequences with ambiguous alphabets
Issue -
State: open - Opened by ncoish 8 months ago
#502 - Misaligned code highlighting in API reference
Issue -
State: closed - Opened by padix-key 8 months ago
Labels: bug
#500 - Support 5 characters in residue names
Issue -
State: closed - Opened by padix-key 9 months ago
- 4 comments
#499 - Allow 5 characters residue names from CIF files.
Issue -
State: closed - Opened by xvlaurent 9 months ago
- 1 comment
#498 - Allow 5 characters residune names.
Pull Request -
State: closed - Opened by xvlaurent 9 months ago
- 2 comments
#497 - How to write custom annotation into pdb file?
Issue -
State: closed - Opened by diyang1354 10 months ago
- 1 comment
#496 - Update tests to current Pubchem version
Pull Request -
State: closed - Opened by padix-key 10 months ago
#495 - Update tests to current PDB version
Pull Request -
State: closed - Opened by padix-key 10 months ago
#494 - RDF: AtomArray + (3,3)-shaped box as arguments.
Pull Request -
State: closed - Opened by JHKru 10 months ago
#493 - Move to Cython 3.x
Pull Request -
State: closed - Opened by padix-key 10 months ago
#492 - Add fetching from the AlphaFold structure database
Pull Request -
State: open - Opened by dacarlin 11 months ago
#491 - struc.rdf doesn't work with custom box
Issue -
State: closed - Opened by entropybit 11 months ago
- 3 comments
#490 - Move to Cython 3.0
Issue -
State: closed - Opened by padix-key 11 months ago
#489 - AtomArrayStack with varying annotations per model
Issue -
State: open - Opened by entropybit 11 months ago
- 1 comment
Labels: enhancement
#488 - Getting biological assemblies for MMTF files
Issue -
State: closed - Opened by ljmartin 11 months ago
- 5 comments
Labels: enhancement
#487 - How to write b_factors?
Issue -
State: closed - Opened by uros-sipetic 12 months ago
- 9 comments
#486 - GenBank LOCUS parser is overly restrictive on the locus id
Issue -
State: open - Opened by tfenne 12 months ago
- 4 comments
Labels: bug, good first issue
#485 - added ArrayPloter and plotepiscan into Biotite
Pull Request -
State: closed - Opened by ferrervi 12 months ago
- 6 comments
#484 - Computation of Masses
Issue -
State: open - Opened by t0mdavid-m 12 months ago
- 1 comment
#481 - Adapt tests to changes in PDB and PubChem databases
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#480 - Fix MOL file parsing for more than 100 bonds
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#479 - Fix annotated sequence slicing bug
Pull Request -
State: closed - Opened by ANaka about 1 year ago
- 1 comment
#478 - Add manual seq type
Pull Request -
State: closed - Opened by t0mdavid-m about 1 year ago
- 2 comments
#477 - No way to force the sequence type when loading a FASTA file
Issue -
State: closed - Opened by gezmi about 1 year ago
- 4 comments
Labels: enhancement, good first issue
#476 - Issue with Reading PDB Files Using Biotite
Issue -
State: closed - Opened by sirius777coder about 1 year ago
- 4 comments
#475 - Faster continuous k-mer decomposition
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#474 - Deprecate `atom_mask` parameter in `connect_via_xxx()` functions
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#473 - Tweaks to BondList merging
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#472 - Add PubChem interface
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#471 - Support common database name in Entrez search
Pull Request -
State: closed - Opened by padix-key about 1 year ago
#470 - Disregarding gaps in building a sequence logo
Issue -
State: closed - Opened by Pinok-io about 1 year ago
- 3 comments
#469 - Refactor `PDBFile` and add `get_b_factor()`
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#468 - Support chemical component parsing in `PDBxFile`
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#467 - Support for `AtomArray`parsing from PDBx `chem_comp_atom`
Issue -
State: closed - Opened by padix-key over 1 year ago
Labels: enhancement
#466 - Refactor interface to RCSB search API
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#465 - fetch data from EBI AlphaFold database
Pull Request -
State: closed - Opened by jonfunk21 over 1 year ago
- 5 comments
#464 - Feature Request: Residue Depth MSMS application integration
Issue -
State: open - Opened by ncoish over 1 year ago
- 3 comments
Labels: enhancement
#463 - Error in Bond Types from PDB File
Issue -
State: closed - Opened by BradyAJohnston over 1 year ago
- 2 comments
#462 - using Alignment model to get an alignment object artificially
Issue -
State: closed - Opened by sirius777coder over 1 year ago
- 3 comments
Labels: question
#461 - Move more attributes to pyproject.toml
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#460 - Refactor `remove_pbc()`
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#459 - Rotate/extend label radius to prevent overlaps
Issue -
State: open - Opened by bhagesh-codebeast over 1 year ago
- 5 comments
#458 - Fix #456
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#457 - Fix remark parsing for remark numbers < 100
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#456 - Parsing error with PDB index beyond "99999"
Issue -
State: closed - Opened by heejongkim over 1 year ago
- 3 comments
Labels: bug
#455 - Fix RCSB PDB test
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#454 - Fix reading remarks with number < 100
Pull Request -
State: closed - Opened by padix-key over 1 year ago
- 1 comment
#453 - Fix line length of 'CRYST1' record
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#452 - Performance improvement in `translate()`
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#451 - Refactored CI with Python 3.11 support
Pull Request -
State: closed - Opened by danpf over 1 year ago
- 21 comments
#450 - Read assemblies from PDB/MMTF files and symmetry mates from PDB files
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#449 - Multi-model PDB takes `b_factor` from first model
Issue -
State: closed - Opened by BradyAJohnston over 1 year ago
- 2 comments
Labels: enhancement
#448 - Refactor `DSSPApp` and `annotate_sse()`
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#447 - Adding a temp_dir parameter to the VinaApp
Pull Request -
State: closed - Opened by entropybit over 1 year ago
- 2 comments
#446 - `TantanApp` is able to process multiple sequences in a single run.
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#445 - `TantanApp` is only able to process a single sequence
Issue -
State: closed - Opened by padix-key over 1 year ago
Labels: enhancement
#444 - `annotate_sse()` only works for single chains
Issue -
State: closed - Opened by padix-key over 1 year ago
Labels: bug, enhancement
#443 - update username
Pull Request -
State: closed - Opened by t0mdavid-m over 1 year ago
#442 - Update CONTRIB.rst
Pull Request -
State: closed - Opened by dnlbauer over 1 year ago
#441 - Add RMSD for atom-pair distances; tests for 'compare.py'
Pull Request -
State: closed - Opened by JHKru over 1 year ago
- 2 comments
#440 - Testing of RMSD/RMSF needs improvement
Issue -
State: closed - Opened by padix-key over 1 year ago
#439 - Add rounding to newick strings
Pull Request -
State: closed - Opened by t0mdavid-m over 1 year ago
- 1 comment
#438 - Support for AlphaFold database
Issue -
State: open - Opened by sirius777coder over 1 year ago
- 14 comments
Labels: enhancement
#437 - how can i get second structure with application.viennarna.rnaalifold
Issue -
State: closed - Opened by virgo777 over 1 year ago
- 2 comments
#436 - Add `filter_polymer()`
Pull Request -
State: closed - Opened by edikedik over 1 year ago
- 5 comments
#435 - Refactor ViennaRNA interfaces
Pull Request -
State: closed - Opened by padix-key over 1 year ago
- 1 comment
#434 - Fix typo in base_stacking()
Pull Request -
State: closed - Opened by t0mdavid-m over 1 year ago
- 1 comment
#433 - Fix static alignment function for Muscle5
Pull Request -
State: closed - Opened by padix-key over 1 year ago
#432 - Potentially wrong angle in `base_stacking()`
Issue -
State: closed - Opened by padix-key over 1 year ago
- 1 comment
#431 - remove incomplete residues
Issue -
State: closed - Opened by andreassteffen almost 2 years ago
- 2 comments
#430 - Refactoring `check_bond_continuity`
Pull Request -
State: closed - Opened by edikedik almost 2 years ago
- 4 comments
#429 - `get_chain_starts()` leads to duplicated chains and breaks chain continuity
Issue -
State: closed - Opened by edikedik almost 2 years ago
- 2 comments
#428 - Update gallery
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#427 - Fix #426
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#426 - Consistency Issues with PDB & MMTF IO for structure 5EIL
Issue -
State: closed - Opened by t0mdavid-m almost 2 years ago
#425 - Improve filters for nucleotides, amino acids and add filter for carbohydrates.
Pull Request -
State: closed - Opened by t0mdavid-m almost 2 years ago
- 5 comments
#424 - fixed list of amino acid three-letter codes may lead to unexpected results
Issue -
State: closed - Opened by edikedik almost 2 years ago
- 10 comments
#423 - support for Path objects
Pull Request -
State: closed - Opened by edikedik almost 2 years ago
- 3 comments
#422 - fix(pdbparsing): parse "+X" and "X+" charges
Pull Request -
State: closed - Opened by aurelg almost 2 years ago
- 1 comment
#421 - PDB parsing fails if the charge is specified as "+X" instead of "X+"
Issue -
State: closed - Opened by aurelg almost 2 years ago
#420 - Support stack-wise iteration over trajectory files
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#419 - Chunkwise iterator with read_iter/read_iter_structure for MD trajectory files
Issue -
State: closed - Opened by JHKru almost 2 years ago
#418 - Mol2, SDF and XYZ File Parsers
Pull Request -
State: open - Opened by entropybit almost 2 years ago
- 2 comments
#417 - Minor cleanup
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#416 - Fix Vina not recognizing metal elements
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#414 - Fix #413
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#413 - `structure.io.pdb.get_structure` incorrectly converts all chain IDs to upper case
Issue -
State: closed - Opened by naailkhan28 almost 2 years ago
- 1 comment
#412 - Issue 409
Pull Request -
State: closed - Opened by MaxGreil almost 2 years ago
- 3 comments
#411 - RCSB API group by function
Issue -
State: closed - Opened by jlefebre almost 2 years ago
- 3 comments
Labels: enhancement, good first issue
#410 - Amendment to #408
Pull Request -
State: closed - Opened by padix-key almost 2 years ago