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
#447 - Adding a temp_dir parameter to the VinaApp
Pull Request -
State: closed - Opened by entropybit almost 2 years ago
- 2 comments
#446 - `TantanApp` is able to process multiple sequences in a single run.
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#445 - `TantanApp` is only able to process a single sequence
Issue -
State: closed - Opened by padix-key almost 2 years ago
Labels: enhancement
#444 - `annotate_sse()` only works for single chains
Issue -
State: closed - Opened by padix-key almost 2 years ago
Labels: bug, enhancement
#443 - update username
Pull Request -
State: closed - Opened by t0mdavid-m almost 2 years ago
#442 - Update CONTRIB.rst
Pull Request -
State: closed - Opened by dnlbauer almost 2 years ago
#441 - Add RMSD for atom-pair distances; tests for 'compare.py'
Pull Request -
State: closed - Opened by JHKru almost 2 years ago
- 2 comments
#440 - Testing of RMSD/RMSF needs improvement
Issue -
State: closed - Opened by padix-key almost 2 years ago
#439 - Add rounding to newick strings
Pull Request -
State: closed - Opened by t0mdavid-m almost 2 years ago
- 1 comment
#438 - Support for AlphaFold database
Issue -
State: open - Opened by sirius777coder almost 2 years ago
- 14 comments
Labels: enhancement
#437 - how can i get second structure with application.viennarna.rnaalifold
Issue -
State: closed - Opened by virgo777 almost 2 years ago
- 2 comments
#436 - Add `filter_polymer()`
Pull Request -
State: closed - Opened by edikedik almost 2 years ago
- 5 comments
#435 - Refactor ViennaRNA interfaces
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
- 1 comment
#434 - Fix typo in base_stacking()
Pull Request -
State: closed - Opened by t0mdavid-m almost 2 years ago
- 1 comment
#433 - Fix static alignment function for Muscle5
Pull Request -
State: closed - Opened by padix-key almost 2 years ago
#432 - Potentially wrong angle in `base_stacking()`
Issue -
State: closed - Opened by padix-key almost 2 years ago
- 1 comment
#431 - remove incomplete residues
Issue -
State: closed - Opened by andreassteffen about 2 years ago
- 2 comments
#430 - Refactoring `check_bond_continuity`
Pull Request -
State: closed - Opened by edikedik about 2 years ago
- 4 comments
#429 - `get_chain_starts()` leads to duplicated chains and breaks chain continuity
Issue -
State: closed - Opened by edikedik about 2 years ago
- 2 comments
#428 - Update gallery
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#427 - Fix #426
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#426 - Consistency Issues with PDB & MMTF IO for structure 5EIL
Issue -
State: closed - Opened by t0mdavid-m about 2 years ago
#425 - Improve filters for nucleotides, amino acids and add filter for carbohydrates.
Pull Request -
State: closed - Opened by t0mdavid-m about 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 about 2 years ago
- 10 comments
#423 - support for Path objects
Pull Request -
State: closed - Opened by edikedik about 2 years ago
- 3 comments
#422 - fix(pdbparsing): parse "+X" and "X+" charges
Pull Request -
State: closed - Opened by aurelg about 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 about 2 years ago
#420 - Support stack-wise iteration over trajectory files
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#419 - Chunkwise iterator with read_iter/read_iter_structure for MD trajectory files
Issue -
State: closed - Opened by JHKru about 2 years ago
#418 - Mol2, SDF and XYZ File Parsers
Pull Request -
State: open - Opened by entropybit about 2 years ago
- 2 comments
#417 - Minor cleanup
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#416 - Fix Vina not recognizing metal elements
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#414 - Fix #413
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#413 - `structure.io.pdb.get_structure` incorrectly converts all chain IDs to upper case
Issue -
State: closed - Opened by naailkhan28 about 2 years ago
- 1 comment
#412 - Issue 409
Pull Request -
State: closed - Opened by MaxGreil about 2 years ago
- 3 comments
#411 - RCSB API group by function
Issue -
State: closed - Opened by jlefebre about 2 years ago
- 3 comments
Labels: enhancement, good first issue
#410 - Amendment to #408
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#409 - Changed UniProt REST API
Issue -
State: closed - Opened by padix-key about 2 years ago
#408 - Support for RCSB PDB search API v2
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#407 - Remove unused code line
Pull Request -
State: closed - Opened by padix-key about 2 years ago
#406 - pdbx get_structure with use_author_fields gives different results
Issue -
State: closed - Opened by ebetica about 2 years ago
- 2 comments
Labels: wontfix
#405 - RCSB API v1 was exchanged for v2
Issue -
State: closed - Opened by jlefebre about 2 years ago
- 1 comment
#404 - Support superimposition of coordinates
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#403 - Coloring MSA based on R value or other arbitrary values
Issue -
State: closed - Opened by seanrjohnson over 2 years ago
- 3 comments
#402 - Pad PDB lines to 80 characters
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#401 - fix(pdb): support pdb without charge column
Pull Request -
State: closed - Opened by f-allain over 2 years ago
- 2 comments
#400 - Use rounded lines in structure plots
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#399 - Pin version of uniprot database
Issue -
State: closed - Opened by dariober over 2 years ago
- 1 comment
#398 - Fix `MafftApp` runs for more than 10 sequences
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#397 - `RecursionError` in `TreeNode.from_newick()`
Issue -
State: open - Opened by padix-key over 2 years ago
Labels: bug
#396 - Fix typo in matrix parsing
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#395 - Fix empty attribute string in GFFFile
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#394 - Add 'periodic' parameter to 'connect_via_distances()'
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#393 - 'hbond()' uses BondList to find bonded hydrogen atoms
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#392 - Add more chain-level utitlities and change chain start condition
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#391 - Fix #379
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#390 - Fix #302
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#389 - Difficult to select a specific chain from an assembly
Issue -
State: closed - Opened by rmrao over 2 years ago
- 3 comments
#388 - Fix #387
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#387 - `get_assembly` does not return both chains for 5zng
Issue -
State: closed - Opened by rmrao over 2 years ago
- 3 comments
Labels: bug
#386 - feat: propagate default_bond_type to molfile set_structure
Pull Request -
State: closed - Opened by f-allain over 2 years ago
#385 - fix: add deuterium in atom_masses
Pull Request -
State: closed - Opened by aurelg over 2 years ago
- 1 comment
#384 - sequence and secondary structure representation
Issue -
State: closed - Opened by diffracteD over 2 years ago
- 1 comment
#383 - Possibility to combine different types of plots
Issue -
State: closed - Opened by gezmi over 2 years ago
- 1 comment
#381 - Structure module patches
Pull Request -
State: closed - Opened by f-allain over 2 years ago
- 8 comments
#379 - Retrieving bond information from PDB files
Issue -
State: closed - Opened by JacobAnter over 2 years ago
- 8 comments
#374 - foldx Buildmodel mutation interfact - convenience interface
Pull Request -
State: open - Opened by Mojusko over 2 years ago
- 3 comments
#370 - Output dtype of input coordinates in 'structure.displacement()'
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#369 - Add 'writer_iter()' static method
Pull Request -
State: closed - Opened by padix-key over 2 years ago
#365 - Documentation: API reference point to the source code on GitHub
Pull Request -
State: closed - Opened by padix-key almost 3 years ago
#358 - Add example for gallery
Pull Request -
State: closed - Opened by padix-key almost 3 years ago
#321 - Wrong bonds in structures with residues sharing the same residue ID
Issue -
State: closed - Opened by padix-key over 3 years ago
- 1 comment
Labels: good first issue
#316 - 'structure.hbond()' does not use bond information
Issue -
State: closed - Opened by padix-key over 3 years ago
Labels: enhancement
#315 - [WIP] Optional brute force approach for RDF calculation
Pull Request -
State: open - Opened by padix-key over 3 years ago
#302 - ImportError: cannot import name 'AdaptiveFancyArrow'
Issue -
State: closed - Opened by rowenaliv over 3 years ago
- 11 comments
Labels: bug
#214 - Switching setup to Poetry
Issue -
State: closed - Opened by padix-key over 4 years ago
- 1 comment
#131 - Support writing multiple `AtomArray` to structure file
Issue -
State: open - Opened by dnlbauer about 5 years ago
- 5 comments
Labels: enhancement