easYPipe¶
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 |
Example:
$ 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 |
Example:
$ easypipe.py PROCESSED_DATA prep
You can have a look to the quickstart guide.
For a better experience, also read instructions for each subcommands.
