mmdf 0.0.5

macromolecular structures (.pdb/.mmCIF) as pandas dataframes

MacroMolecular DataFrames (mmdf)

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

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

Usage

import mmdf

# Read a PDBx/mmCIF file into a dataframe
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]

# Other dataframe manipulation...

# Write dataframe to a PDBx/mmCIF file
mmdf.write('4v6x_new.cif', df)

You can also fetch structures by their PDB ID, they will be cached in your home directory.

import mmdf

df = mmdf.read("pdb:1crn")

Changelog

v0.0.4 (05/12/25)

• add pdb download functionality

v0.0.3 (12/12/24)

• added basic write functionality
• resolved gemmi 0.7.0 incompatibility issues

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