BioPandas/biopandas

View on GitHub

Working with molecular structures in pandas DataFrames

Stars: 756
Forks: 119
Open beginner issues: 0
Indexed issues: 21
Avg merge: 23h 8m
Merged PRs (30d): 2

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 13, 2026
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Open All

21 open issues indexed

Add function for structural alignments via least-squares fit Open

enhancement

BioPandas/biopandas#5 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Adding a SDF submodule and DataFrames Open

enhancement

BioPandas/biopandas#7 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Adding a function for Q-Score computation Open

enhancement

BioPandas/biopandas#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Adding a function to compute the lengths and angles of the bonds in the (PDB) molecule Open

enhancement

BioPandas/biopandas#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improve RMSD function to take molecular symmetry into consideration? Open

enhancement

BioPandas/biopandas#13 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add/Parse Information about Secondary Structure Elements Open

enhancement

BioPandas/biopandas#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Handling multi-PDB files Open

bug enhancement

BioPandas/biopandas#50 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Renumbering residues Open

enhancement

BioPandas/biopandas#51 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Merging HETATM and ATOM entries into one DataFrame Open

bug enhancement

BioPandas/biopandas#53 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Mol2 files bonds Open

enhancement

BioPandas/biopandas#54 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Missing files in the PyPi tarball Open

BioPandas/biopandas#63 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
column 'line_idx' gets 'object' d_type for empty frames. Open

BioPandas/biopandas#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
RMSD calculation for whole PDBs Open

enhancement

BioPandas/biopandas#69 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Biopandas PDB output formatting leads to a ton of segments when reading with MDAnalysis: reason and my quick fix Open

bug help wanted

BioPandas/biopandas#109 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Using SIFTS data for renumbering residues to match the Uniprot sequence resids Open

BioPandas/biopandas#110 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[Refactor] Reduce code duplication by using abstract base classes Open

enhancement help wanted

BioPandas/biopandas#117 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Unable to export PDB DFs with model_id columns Open

BioPandas/biopandas#124 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
SettingWithCopyWarning Open

BioPandas/biopandas#127 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
read_pdb_from_list() not containing newlines Open

BioPandas/biopandas#130 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[RFC] Enabling Cython-based PDB parser backend for speed improvements Open

BioPandas/biopandas#139 · 6 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Adding possibility for a collection of structures Open

BioPandas/biopandas#142 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

BioPandas/biopandas

Get new issues in your inbox