ihm

library2.11pypypi✓ verified 90d ago

A Python library for handling mmCIF and BinaryCIF files used in integrative/hybrid modeling, as defined by the wwPDB IHM extension. Version 2.10 is current. It supports reading, writing, and validating IHM mmCIF/BinaryCIF files, with features such as restraint representation, ensemble modeling, and reference sequence handling. The library is maintained by the IHM Working Group.

serialization data

pip install ihm

github ↗package ↗

INSTALL

IMPORT

SIG · IHM

ihm

serializationpythonv2.11

Install

3.4s avg

Import

93ms

Disk

19MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.11 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.094s · 20.5MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 3.4s · import 0.092s · 21MB

19MB installed

● package 19MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

System

✓ from ihm import System

Assembly

✓ from ihm import Assembly

Model

✓ from ihm.model import Model

Restraint

✓ from ihm.restraint import Restraint

mmCIF writer

✓ from ihm.format import CifWriter

Minimal example: create a system with one protein entity, an asym unit, and an assembly, then write a mmCIF file.

import ihm import ihm.location import ihm.model import ihm.restraint # Create a minimal IHM system system = ihm.System() # Add a protein entity entity = ihm.Entity() entity.description = "My protein" entity.sequence = "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHG" system.entities.append(entity) # Add an asym unit asym = ihm.AsymUnit(entity=entity, details="Chain A") system.asym_units.append(asym) # Create an assembly assembly = ihm.Assembly() assembly.append(asym) # Write a mmCIF string from io import StringIO from ihm.format import CifWriter out = StringIO() writer = CifWriter(out) writer.write(system) print(out.getvalue()[:500])

Debug

Known issues

gotchaThe 'ihm' library only supports Python 3.6+; Python 2 is not supported.

fix

Use Python 3.6 or later.

affects: >=2.0

deprecatedThe 'ihm.format.CifWriter' class replaced the older writer pattern. Use 'from ihm.format import CifWriter' instead of deprecated 'ihm.io' or 'ihm.cif'.

fix

Update imports to use 'from ihm.format import CifWriter'.

affects: >=2.0

gotchaWhen using BinaryCIF, the msgpack package is required but not installed by default; install with 'pip install ihm[bcif]' or manually.

fix

Run 'pip install msgpack' or 'pip install ihm[bcif]'.

affects: all

breakingIn version 2.0, the 'SeqDif' class was moved from 'ihm.reference' to 'ihm.reference.SeqDif' – old imports may break.

fix

Use 'from ihm.reference import SeqDif'.

affects: >=2.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'ihm'

Library not installed.

fix

Run 'pip install ihm'.

ModuleNotFoundError: No module named 'msgpack'

msgpack not installed, required for BinaryCIF support.

fix

Run 'pip install msgpack' or 'pip install ihm[bcif]'.

AttributeError: module 'ihm' has no attribute 'CifWriter'

Incorrect import path; CifWriter is in ihm.format.

fix

Use 'from ihm.format import CifWriter'.

ValueError: invalid character in entity sequence

Entity sequence contains invalid characters (only standard amino acid codes allowed).

fix

Check sequence for non-standard characters; use 'X' or 'O' for non-standard as needed.

Upgrade

Version history

2.11latest on PyPI · released Jun 5, 2026

Audit

Dependencies

msgpackoptionalUsed for BinaryCIF encoding/decoding.

Agent activity

15 hits · last 30 days

node

Anthropic

Resources

githubhttps://github.com/ihmwg/python-ihm ↗

packagehttps://pypi.org/project/ihm/ ↗