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

#420 - Support stack-wise iteration over trajectory files

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

#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