BioPandas/biopandas issues and pull requests

#143 - Collection of structures & TMAlign

Pull Request - State: open - Opened by gezmi about 2 months ago

#142 - Adding possibility for a collection of structures

Issue - State: open - Opened by gezmi 2 months ago - 1 comment

#141 - Stream support for exporting pdbs not working with OTHERS record

Issue - State: open - Opened by gate-tec 4 months ago

#140 - empty lines in mol2

Pull Request - State: closed - Opened by Ruibin-Liu 9 months ago - 4 comments

#139 - [RFC] Enabling Cython-based PDB parser backend for speed improvements

Issue - State: open - Opened by a-r-j 10 months ago - 4 comments

#138 - add autopublish

Pull Request - State: closed - Opened by a-r-j 10 months ago

#137 - minor change to force release

Pull Request - State: closed - Opened by a-r-j 10 months ago

#136 - read_mol2 fails on normal-looking file

Issue - State: closed - Opened by RafiBrent 11 months ago - 2 comments

#135 - Add automated tests and release v0.5.0-dev

Pull Request - State: closed - Opened by AH-Merii 11 months ago - 2 comments

#134 - b_factor one white space format fix

Pull Request - State: closed - Opened by zehraacarsarica 12 months ago - 3 comments

#133 - Fetching PDB and saving it to a PDB file shifts one space element type due to b-factor 3 digits

Issue - State: open - Opened by zehraacarsarica 12 months ago

#132 - Saving new pdb from dataframe

Issue - State: closed - Opened by SkwisgaarSkwigelf 12 months ago - 2 comments

#131 - explicit copy dataframe in pandas_pdb.py to avoid warnings

Pull Request - State: closed - Opened by nunziati 12 months ago - 1 comment

#130 - read_pdb_from_list() not containing newlines

Issue - State: open - Opened by uros-sipetic almost 1 year ago

#129 - Implement `add_remark` for `PandasPdb`

Pull Request - State: closed - Opened by anton-bushuiev about 1 year ago

#128 - Add support for pathlib

Pull Request - State: closed - Opened by anton-bushuiev about 1 year ago - 1 comment

#127 - SettingWithCopyWarning

Issue - State: open - Opened by tommycarstensen about 1 year ago

#126 - Mmtf gzip

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#125 - Drop unexpected columsn when writing PDB dataframes #124

Pull Request - State: open - Opened by a-r-j about 1 year ago

#124 - Unable to export PDB DFs with model_id columns

Issue - State: open - Opened by a-r-j about 1 year ago

#123 - Add MMTF gzip reading support

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#122 - Add GH action for autorelease on tag #120

Pull Request - State: closed - Opened by a-r-j about 1 year ago - 2 comments

#121 - update af2 versions to latest

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#120 - 0.5.0dev Release

Issue - State: closed - Opened by a-r-j about 1 year ago - 1 comment

#119 - feature: MMTF Parser Improvements + MMTF Export

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#118 - Add PandasPdb.gyradius

Pull Request - State: closed - Opened by goniochromatic over 1 year ago

#117 - [Refactor] Reduce code duplication by using abstract base classes

Issue - State: open - Opened by a-r-j over 1 year ago
Labels: enhancement, help wanted

#116 - Fix to pdb stream

Pull Request - State: closed - Opened by goniochromatic over 1 year ago - 2 comments

#115 - update url

Pull Request - State: closed - Opened by rasbt over 1 year ago

#114 - Esmfold

Pull Request - State: open - Opened by a-r-j over 1 year ago - 8 comments

#111 - Mmtf

Pull Request - State: closed - Opened by a-r-j almost 2 years ago - 5 comments

#110 - Using SIFTS data for renumbering residues to match the Uniprot sequence resids

Issue - State: open - Opened by mrauha almost 2 years ago - 1 comment

#109 - Biopandas PDB output formatting leads to a ton of segments when reading with MDAnalysis: reason and my quick fix

Issue - State: open - Opened by mrauha almost 2 years ago - 1 comment
Labels: bug, help wanted

#108 - Stream support for exporting pdbs

Issue - State: open - Opened by djberenberg almost 2 years ago - 6 comments

#107 - Add mmCIF -> PDB conversion

Pull Request - State: closed - Opened by a-r-j almost 2 years ago - 12 comments

#106 - Docs tutorials & API reference out of date

Issue - State: closed - Opened by a-r-j almost 2 years ago - 1 comment

#105 - Adding 200m structures to biopandas

Pull Request - State: closed - Opened by a-r-j almost 2 years ago - 6 comments

#104 - update for 3.7 compat

Pull Request - State: closed - Opened by a-r-j about 2 years ago - 1 comment

#103 - Remove walrus operator for py3.7 support

Issue - State: closed - Opened by a-r-j about 2 years ago

#102 - Add support for reading PDBs from AF2 database

Pull Request - State: closed - Opened by a-r-j about 2 years ago - 8 comments

#101 - Add support for handling PDBs with multiple models

Pull Request - State: closed - Opened by a-r-j about 2 years ago - 12 comments

#99 - Adjust README in gh dark mode to ensure readability of pngs

Pull Request - State: closed - Opened by braniii about 2 years ago - 1 comment

#98 - v0.3.0

Pull Request - State: closed - Opened by rasbt about 2 years ago

#97 - mmCIF -> PDB conversion method

Issue - State: closed - Opened by rasbt about 2 years ago - 3 comments
Labels: enhancement

#96 - Get carbon bugfix

Pull Request - State: closed - Opened by a-r-j over 2 years ago - 1 comment

#95 - Get Carbon Method in PandasPDB

Issue - State: closed - Opened by a-r-j over 2 years ago - 1 comment

#94 - [WIP] Very rough initial draft of mmcif parser

Pull Request - State: closed - Opened by a-r-j over 2 years ago - 15 comments

#93 - Implement CIF and mmCIF format support for large biological assemblies

Issue - State: closed - Opened by rasbt over 2 years ago - 2 comments
Labels: enhancement

#90 - fix bug reg long coordinates

Pull Request - State: closed - Opened by rasbt almost 3 years ago

#89 - PandasPdb.to_pdb() will add one more blank for coordinate larger than 1000

Issue - State: closed - Opened by chrischen1 almost 3 years ago - 2 comments
Labels: bug

#88 - 0.2.9 version release

Pull Request - State: closed - Opened by rasbt almost 3 years ago

#87 - Update setup.py with recent Python versions

Pull Request - State: closed - Opened by rasbt almost 3 years ago

#86 - Latest conda-forge release 0.2.7 instead of 0.2.8?

Issue - State: closed - Opened by dominiquesydow almost 3 years ago - 3 comments

#85 - fix typos in documentation

Pull Request - State: closed - Opened by rasbt almost 3 years ago

#84 - Update Working_with_PDB_Structures_in_DataFrames.md

Pull Request - State: closed - Opened by tugceoruc almost 3 years ago - 1 comment

#83 - Unnecessary source code in a tutorial

Issue - State: closed - Opened by igordub almost 3 years ago - 1 comment

#82 - allow .ent & .ent.gz file extensions

Pull Request - State: closed - Opened by rasbt about 3 years ago

#81 - Biopandas cannot open ent.gz

Issue - State: closed - Opened by gezmi about 3 years ago - 3 comments

#80 - support mmCIF files

Issue - State: closed - Opened by jaydeepsb over 3 years ago - 3 comments
Labels: enhancement

#79 - Website

Pull Request - State: closed - Opened by rasbt over 3 years ago - 1 comment

#78 - Version 0.2.8

Pull Request - State: closed - Opened by rasbt over 3 years ago

#77 - Update documentation files

Pull Request - State: closed - Opened by rasbt over 3 years ago - 1 comment

#75 - 2021 update

Pull Request - State: closed - Opened by rasbt over 3 years ago

#74 - Improve "Examples" parsing in make_api.py documentation builder

Pull Request - State: closed - Opened by rasbt over 3 years ago - 1 comment

#73 - Raise error if file format is incorrect

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 7 comments

#72 - Add PandasPdb.read_pdb_from_list method + unit test

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 3 comments

#71 - Error handling when reading wrong file formats

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 3 comments

#70 - Read pdb from list of strings (instead of from file)

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 3 comments

#69 - RMSD calculation for whole PDBs

Issue - State: open - Opened by LivC193 over 3 years ago - 3 comments
Labels: enhancement

#68 - fix manifest file

Pull Request - State: closed - Opened by rasbt almost 4 years ago

#67 - V0.2.6

Pull Request - State: closed - Opened by rasbt almost 4 years ago - 1 comment

#66 - PDB link on rcsb has changed

Issue - State: closed - Opened by luc-j-bourhis almost 4 years ago - 2 comments

#65 - Covid struct analysis example file commit

Pull Request - State: closed - Opened by SowmyaLR about 4 years ago - 1 comment

#64 - column 'line_idx' gets 'object' d_type for empty frames.

Issue - State: open - Opened by ZivBA about 4 years ago

#63 - Missing files in the PyPi tarball

Issue - State: open - Opened by moorepants about 4 years ago - 2 comments

#62 - Fix doc links

Pull Request - State: closed - Opened by rasbt over 4 years ago

#61 - Documentation links are 404 missing

Issue - State: closed - Opened by chendaniely over 4 years ago - 2 comments

#60 - Don't import biopandas during install

Pull Request - State: closed - Opened by ecederstrand over 4 years ago - 7 comments

#59 - v0.2.5

Pull Request - State: closed - Opened by rasbt almost 5 years ago - 2 comments

#58 - ppdb.amino3to1()

Issue - State: closed - Opened by tbc01 almost 5 years ago - 10 comments

#57 - [fyi] Dask for dataframes bigger than memory

Issue - State: closed - Opened by floer32 over 5 years ago

#56 - v0.2.4

Pull Request - State: closed - Opened by rasbt over 5 years ago - 1 comment

#55 - Sort when Saving PDB

Issue - State: closed - Opened by RMeli over 5 years ago - 3 comments

#54 - Mol2 files bonds

Issue - State: open - Opened by btyukodi almost 6 years ago - 8 comments
Labels: enhancement

#53 - Merging HETATM and ATOM entries into one DataFrame

Issue - State: open - Opened by rasbt about 6 years ago
Labels: bug, enhancement

#52 - fix typo in a tutorial

Pull Request - State: closed - Opened by wojdyr about 6 years ago - 3 comments

#51 - Renumbering residues

Issue - State: open - Opened by ajasja about 6 years ago - 9 comments
Labels: enhancement

#50 - Handling multi-PDB files

Issue - State: open - Opened by rasbt about 6 years ago
Labels: bug, enhancement

#49 - version 0.2.3

Pull Request - State: closed - Opened by rasbt about 6 years ago - 1 comment

#48 - BioPandas 0.2.3 release in 2018?

Issue - State: closed - Opened by auvipy over 6 years ago - 2 comments

#47 - update to 2018

Pull Request - State: closed - Opened by rasbt over 6 years ago - 1 comment

#46 - add static distance methods

Pull Request - State: closed - Opened by rasbt almost 7 years ago - 4 comments

GitHub / BioPandas/biopandas issues and pull requests