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

#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

#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

#420 - Support stack-wise iteration over trajectory files

Pull Request - State: closed - Opened by padix-key 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

#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