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MacroMolecular DataFrames (mmdf)

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MacroMolecular DataFrames (mmdf) is a small package for reading macromolecular structure files (.pdb/.mmCIF) into pandas dataframes.

The heavy lifting of reading structure files is performed by gemmi.

Usage

import mmdf

df = mmdf.read('4v6x.cif')
df.head()
Out[3]: 
  model chain residue  residue_id  ...       z charge occupancy  b_isotropic
0     1    Az     ASN           3  ... -54.829      0       1.0         10.0
1     1    Az     ASN           3  ... -54.691      0       1.0         10.0
2     1    Az     ASN           3  ... -53.642      0       1.0         10.0
3     1    Az     ASN           3  ... -53.007      0       1.0         10.0
4     1    Az     ASN           3  ... -54.239      0       1.0         10.0
[5 rows x 13 columns]

Changelog

v0.0.2 (20/01/24)

  • added atomic properties to dataframe output
  • added support for Path arguments in mmdf.read()
  • moved to pyproject.toml based packaging

v0.0.1

  • first release