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.
easYGet comes with easYPipe.
easYGet makes it possible to download all at once the mx 'PROCESSED_DATA' from a synchrotron for a given beamline (several dates possible) and a given acronym.
Download processed datasets are organized in order to launch easypipe.
Login information can be provided either in command line or in interactive mode in a terminal.
For the moment only works for data from ESRF synchrotron, but open to new implementation ...
easYPipe works with Python >= 3.6.
Some software are required:
Download easypipe package.
Unzip the archive:
$ tar xvzf easypipe-1.4.5.tar.gz
Modify (open with a text editor) config.py file (in easypipe-1.4.5 folder), in particular 'Software used by modules' part since nothing will work without links to software.
Warning
config.py file modifications have to be done before installation !! If you want to modify it afterwards, just launch installation again.
The easiest way to install easypipe is going in easypipe folder and doing:
$ python setup.py install or $ python3 setup.py install
This will install easypipe as a package in your python path.
Note
See full documentation for more details.
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 with 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 files |
| 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 |
Examples:
$ easypipe.py PROCESSED_DATA prep $ easypipe.py PROCESSED_DATA auto my_ref_folder
easyget.py [-h] [-s {ESRF}] [-l LOGIN] [[-m MX] [-b BEAMLINE] [-d DATES [DATES ...]] [-p PROTEIN] [-g GROUP]
| optional arguments | description |
|---|---|
| -h, --help | show this help message and exit |
| -s {ESRF}, --synchrotron {ESRF} | which synchrotron? (default = ERSF) |
| -l LOGIN, --login LOGIN | synchrotron login (your personal SMIS login) |
| -m MX, --mx MX | name of mx proposalsynchrotron login (Example: 'mx----') |
| -b BEAMLINE, --beamline BEAMLINE | name of the beamline |
| -d DATES [DATES ...], --dates DATES [DATES ...] | date of the run (format AAAAMMJJ) or list of dates for the same run (format AAAAMMJJ AAAAMMJJ) |
| -p PROTEIN, --protein PROTEIN | protein acronym or space if no acronym (manual collections) |
| -g GROUP, --group GROUP | group added via MxCube3 as a supplementary folder level before acronym |
Information can be provided either in command line or in interactive mode in a terminal, or mix.
For example, you can simply run:
$ easyget.py
or:
$ easyget.py --login anna2502 --mx mx1000
or:
$ easyget.py --login anna2502 --mx mx1000 --protein myprot --beamline id30a1 --dates 20210131 20210201
other commands are possible ...
Note
See full documentation for more details.
Simple semantic versioning according to https://semver.org