pyFoXS

Python version of the FoXS software

This is a python port of the open source program FoXS (https://github.com/salilab/imp/tree/develop/modules/foxs) in the Integrated Modelling Platform (https://integrativemodeling.org/). It is used to determine theoretical small angle x-ray scattering (SAXS) profiles from atomic models.

The python version is still in development, so use with caution!

Install and run

Depends on:

• numpy
• scipy
• numba

Once you install dependencies you can run the foxs.py file like a normal python file:

python foxs.py examples/nup133/3KFO.pdb examples/nup133/23922_merge.dat

IMP Code and build

This is not needed, it is only if you want to access the C++ code.

First, you need to download the IMP library. Two possibilities:

• Download the source code tarball from our download page, then extract it with something like: tar -xvzf ../imp-<version>.tar.gz
• Alternatively you can use git to get the code directly from our GitHub repository with something like:

git clone -b main https://github.com/salilab/imp.git
(cd imp && git submodule update --init && ./setup_git.py)

Then, you need to build/install it for python:

To build IMP source found in path/to/imp-source and install it in path_to_install do:

1. mkdir build && cd build
2. cmake path/to/imp-source -DCMAKE_INSTALL_PREFIX=path_to_install
3. make -j4
4. make install

Everything about IMP and how to download/compile it is here: https://integrativemodeling.org/nightly/doc/manual/installation.html.

Then you can run pyFoXS/foxs.py like a normal python file.