To run these examples your PATH needs to include tools/da_builder/ and your PYTHONPATH needs to include tools/src/. See configure-tools

Selected tools-tests

These examples are closely related to regression tests in the tools-tests repo. Each of the selections below is available as an IPython notebook, so you may explore these examples further. After clicking on the example, there is a download link. Click on the download and drag the desired file to a location on your computer. The IPython web interface for a notebook can be started from the command line by e.g.

ipython notebook example_test.ipynb

Molecular generation and replication

These examples create molecular structures files, and input files for Gaussian , GROMACS and LAMMPS by reading in reference structures from the BuildingBlocks repository and reference force-field parameters from conj.itp. The BuildingBlocks repository can be cloned manually:

git clone

(this will create a directory streamm-BuildingBlocks so if you clone manually you will need to alter the directory name/path in the examples below.) To avoid this, one can instead use


which will also check that the PATH and PYTHONPATH enviromental variables were set correctly by the configure-tools script.