Biopandas PDB Format Cannot Handle Atomic Charges

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Introduction

Biopandas is a powerful library for reading and writing various molecular file formats, including the Protein Data Bank (PDB) format. However, a critical issue has been identified in the PDB format handling of Biopandas, specifically with regards to atomic charges. This article will delve into the problem, provide a step-by-step guide to reproduce the issue, and propose a fix to resolve the issue.

Describe the Bug

The PDB format specifies the notation for atomic charges explicitly via columns 79-80, which indicate any charge on the atom. However, the current implementation in Biopandas uses a float type for the charge column, which fails to parse strings like 2+ and results in the entire charge column being filled with NaN values. Furthermore, the formatter for writing charge values is specified as +2.1f, which does not match the PDB format.

Steps/Code to Reproduce

The following is a minimal working example (MWE) for reading a PDB with charged atoms:

from biopandas.pdb import PandasPdb

atom_df = PandasPdb().fetch_pdb("2mjz").get_model(1).df["ATOM"]

print(len(atom_df.loc[atom_df["charge"].notnull(), "charge"]))

Expected Results

Detection of charged atoms in PDB data (first model of 2MJZ should have 350 charged atoms).

Actual Results

The output is 0 (since only NaN values are present).

Proposed Fix

To resolve this issue, we suggest changing the definition in the pdb_atomdict and pdb_anisoudict to type charges as str and change the string formatter accordingly. A setup that seems to be working is:

{
    "id": "charge",
    "line": [78, 80],
    "type": str,
    "strf": lambda x: (
        str(int(re.sub(r"[+-]", "", x)))[-1] + ("-" if "-" in x else "+") if len(x.strip()) > 0 else ""
    ),
}

Versions

  • biopandas: 0.5.1
  • Linux: 5.4.0-91-generic-x86_64-with-glibc2.31
  • Python: 3.10.15 (main, Oct 3 2024, 07:27:34) [GCC 11.2.0]
  • NumPy: 1.23.5

Conclusion

Q: What is the issue with the Biopandas PDB format handling of atomic charges?

A: The issue lies in the type and formatter used for the charge column. The current implementation uses a float type, which fails to parse strings like 2+ and results in the entire charge column being filled with NaN values. Additionally, the formatter for writing charge values is specified as +2.1f, which does not match the PDB format.

Q: What is the expected behavior for reading and writing PDB data with atomic charges?

A: When reading PDB data, Biopandas should be able to detect charged atoms and store their charges correctly. When writing PDB data, Biopandas should be able to write the charge values in the correct format, as specified in the PDB format.

Q: What is the proposed fix for this issue?

A: The proposed fix involves changing the definition in the pdb_atomdict and pdb_anisoudict to type charges as str and modifying the string formatter accordingly. This will allow Biopandas to correctly handle atomic charges in the PDB format.

Q: What is the impact of this issue on users of Biopandas?

A: This issue affects users who work with PDB data and need to accurately handle atomic charges. Without a fix, users may experience errors or incorrect results when working with PDB data that contains charged atoms.

Q: How can users of Biopandas contribute to resolving this issue?

A: Users can contribute to resolving this issue by:

  • Reporting the issue and providing a minimal working example (MWE) to reproduce the issue.
  • Providing feedback on the proposed fix and suggesting alternative solutions.
  • Contributing to the development of Biopandas by implementing the proposed fix or suggesting alternative solutions.

Q: What are the next steps for resolving this issue?

A: The next steps involve:

  • Implementing the proposed fix in Biopandas.
  • Testing the fix to ensure it resolves the issue.
  • Releasing the updated version of Biopandas with the fix.

Q: How can users stay up-to-date with the latest developments on this issue?

A: Users can stay up-to-date with the latest developments on this issue by:

  • Following the Biopandas GitHub repository.
  • Subscribing to the Biopandas mailing list.
  • Checking the Biopandas documentation for updates on the issue.

Conclusion

The Biopandas PDB format cannot handle atomic charges due to a mismatch in the type and formatter used for the charge column. By changing the type of the charge column to str and modifying the string formatter, we can resolve this issue and ensure accurate handling of atomic charges in the PDB format. Users can contribute to resolving this issue by reporting the issue, providing feedback on the proposed fix, and contributing to the development of Biopandas.