easYPipe is a pipeline for the automatization of ligand and fragment X-Ray crystallographic screening.

easYPipe sequentially runs phenix.ligand_pipeline [1] on several datasets of a protein that has been screened with different ligands.

When ligand smiles are given, ligand can be placed automatically in each corresponding structure.

Results are gathered and organized in a ‘RESULTS’ directory, which facilitates future visualization, refinement and deposition. Corresponding relevant information is summarized in a csv file.

easYPipe is specially adapted for ligand or fragment screening in structure-based drug design projects.

See also

easYGet that comes with easYPipe, for an automated download of processed data from synchrotron.

easYPipe usage

easypipe.py [-h] data {prep,reindex,ligands,launch,pandda} …

arguments description
data folder with datasets in subfolders (mandatory)
-h, –help show this help message and exit


$ easypipe.py PROCESSED_DATA -h
subcommands description
prep prepare data: listing of mtz to treat with information
reindex try to reindex mtz according to the space group of reference file
ligands generate ligands files before launching with ligand search
launch launch all the “phenix.ligand-pipeline” (after the preparation steps)
summary compile the results of all the ‘launch’ execution in a single csv file
auto run main easYPipe steps (prep, reindex, launch, summary) in automatic mode, but without ligand search
pandda copy results from easypipe to a ‘PANDDA’ folder, as data ready to launch PanDDA


$ easypipe.py PROCESSED_DATA prep

You can have a look to the quickstart guide.

For a better experience, also read instructions for each subcommands.