1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
[](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 have a C compiler available, 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 this will attempt to build a C extension module 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,
the library will fall back to reading 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`.
|
