IHM (Integrative/Hybrid Modeling) Python Library

2.10 verified Fri May 01 auth: no python

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.

pip install ihm

Common errors

error ModuleNotFoundError: No module named 'ihm' ↓

cause Library not installed.

fix

Run 'pip install ihm'.

error ModuleNotFoundError: No module named 'msgpack' ↓

cause msgpack not installed, required for BinaryCIF support.

fix

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

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

cause Incorrect import path; CifWriter is in ihm.format.

fix

Use 'from ihm.format import CifWriter'.

error ValueError: invalid character in entity sequence ↓

cause 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.

Warnings

gotcha The 'ihm' library only supports Python 3.6+; Python 2 is not supported. ↓

fix Use Python 3.6 or later.

deprecated The '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'.

gotcha When 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]'.

breaking In 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'.

Imports

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
```

Quickstart

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])