https://github.com/multimeric/mmcifix

Fixes mmCIF protein structure files
https://github.com/multimeric/mmcifix

bioinformatics crystallography mmcif pdb-database structural-biology

Last synced: 19 days ago
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Fixes mmCIF protein structure files

• Host: GitHub
• URL: https://github.com/multimeric/mmcifix
• Owner: multimeric
• Created: 2022-03-25T10:26:28.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2023-03-24T11:59:19.000Z (almost 2 years ago)
• Last Synced: 2024-10-28T04:59:27.979Z (2 months ago)
• Topics: bioinformatics, crystallography, mmcif, pdb-database, structural-biology
• Language: Python
• Homepage:
• Size: 253 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# 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

```python

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