biopandas

biopandas copied to clipboard

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

1

Hi all, stumbled upon this paper describing the mapping of PDB residue id's to the ones in the sequence deposited in Uniprot: - Choudhary, P.; Anyango, S.; Berrisford, J.; Varadi,...

mrauha

Stream support for exporting pdbs

6

#### Describe the workflow you want to enable I'd like to be able to export a pdb to a stream instead of to disk. In particular the reason why I'd...

djberenberg

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

6

#### Describe the workflow you want to enable Currently, the pure-python of PDB parsing in BioPandas is quite slow - certainly too slow for highthroughput structural bioinformatics or ML. ####...

a-r-j

### Code of Conduct ### Description Drop non standard columsn from ATOM and HETATM dataframes when exporting to a PDB file. cc @amorehead ### Related issues or pull requests #124...

a-r-j

#### Describe the bug The problem is that after fetching PDB and saving it to a file, it shifts one space due to the b-factor value due to 3 digits....

zehraacarsarica

#### Describe the bug When reading in PDB content via `read_pdb_from_list(),` the text itself does not contain newlines where they should be, thus making any future commands like `pdb_lines =...

uros-sipetic

These tests raise a warning with the latest version of Pandas: https://github.com/BioPandas/biopandas/blob/11362ec459d9c9c265d2f2416223569e9cf4fc93/biopandas/pdb/tests/test_multiple_models.py The specific warning is SettingWithCopyWarning: A value is trying to be set on a copy of a slice...

tommycarstensen

Currently, PDB export breaks when model_id columns are added to the dataframe. This should be an easy fix by copying the dataframe and dropping any extraneous (i.e. non standard PDB...

a-r-j

0.5.0dev Release

1

Hey @rasbt, can we get a dev release? I think we're good to go with the recent PRs. FWIW, it might be worth setting up a GitHub actions workflow to...

a-r-j

Now that we support quite a few different formats we've ended with a significant amount of code duplication in the library. This should be refactored out into an abstract base...

a-r-j