mmcifix

A collection of "fixer" functions for mmCIF files that can fix common issues with files in that format

CLI

Usage: mmcifix [OPTIONS] STRUCTURE

  Fixes one or more issues with an mmCIF file

Options:
  --fixer [auth_seq_id|label_seq_id|database_id]
                                  Apply a fixer
  --help                          Show this message and exit.

Python API

from mmcifix import fix_file

with open("some_input.cif") as in_fp, open("some_output.cif") as out_fp:
    fix_file(in_file=in_fp, out_file=out_fp, fixers=["auth_seq_id"])

Changes

0.4.0

• Added FixAltId, which replaces ? with . in the label_alt_id, e.g. for compatibility with arpeggio

0.3.0

• Added FixAsymIdForPdb, which replaces chain IDs that are invalid for PDB format

0.2.1

• Fix bug in database_id fixer

0.2.0

• Convert all fixers into classes
• Add database_id fixer