| Name | ihm JSON |
| Version |
2.2
JSON |
| download |
| home_page | https://github.com/ihmwg/python-ihm |
| Summary | Package for handling IHM mmCIF and BinaryCIF files |
| upload_time | 2025-02-14 04:39:51 |
| maintainer | None |
| docs_url | None |
| author | Ben Webb |
| requires_python | None |
| license | None |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://doi.org/10.5281/zenodo.2603378)
[](https://python-ihm.readthedocs.org/)
[](https://anaconda.org/conda-forge/ihm)
[](https://badge.fury.io/py/ihm)
[](https://github.com/ihmwg/python-ihm/actions?query=workflow%3Abuild)
[](https://ci.appveyor.com/project/benmwebb/python-ihm)
[](https://codecov.io/gh/ihmwg/python-ihm)
This is a Python package to assist in handling [mmCIF](https://mmcif.wwpdb.org/)
and [BinaryCIF](https://github.com/molstar/BinaryCIF) files compliant with the
[integrative/hybrid modeling (IHM)](https://mmcif.wwpdb.org/dictionaries/mmcif_ihm_ext.dic/Index/)
extension. It works with Python 3.6 or later.
To handle non-integrative theoretical models (for example, homology models),
see the [python-modelcif](https://github.com/ihmwg/python-modelcif) package
which supports files compliant with the
[ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/)
extension.
Please [see the documentation](https://python-ihm.readthedocs.org/)
or some
[worked examples](https://github.com/ihmwg/python-ihm/tree/main/examples)
for more details.
# Installation with conda, Homebrew or pip
If you are using [Anaconda Python](https://www.anaconda.com/), install with
```
conda install -c conda-forge ihm
```
On a Mac with [Homebrew](https://brew.sh/), install with
```
brew tap salilab/salilab; brew install ihm
```
On a Fedora or RedHat Enterprise Linux box, install with
```
dnf copr enable salilab/salilab; dnf install python3-ihm
```
On an Ubuntu LTS box, install from
[our PPA](https://launchpad.net/~salilab/+archive/ubuntu/ppa) with
```
apt install software-properties-common; add-apt-repository ppa:salilab/ppa;
apt install python3-ihm
```
Alternatively, install with pip:
```
pip install ihm
```
(Note that pip builds a C extension module for faster reading of mmCIF and
BinaryCIF files. This requires that your system has a C compiler. If you
don't want to build the C extension module, install with
`pip install ihm --install-option="--without-ext"`, and then the library
will read files using pure Python instead.)
# Installation from source code
To build and install from a clone of the GitHub repository, run
```
python setup.py build
python setup.py install
```
Note that a C extension module is built for faster reading of mmCIF and
BinaryCIF files. This requires that your system has a C compiler and
[SWIG](https://www.swig.org/). If either of these components are missing, you
can choose to build without the extension by adding `--without-ext` to both
`setup.py` command lines above, and then the library will read files using
pure Python instead.
If you want to write [BinaryCIF](https://github.com/molstar/BinaryCIF)
files (or to read them without the C extension module), you will also need the
Python [msgpack](https://github.com/msgpack/msgpack-python) package.
# Testing
There are a number of testcases in the `test` directory. Each one can be run
like a normal Python script to test the library. They can also be all run at
once using [nose](https://nose.readthedocs.io/en/latest/)
or [pytest](https://docs.pytest.org/en/latest/). They will also test
the C extension module if it is first built with
`python setup.py build_ext --inplace`.
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