easYPipe ‘auto’

This mode allows to launch main easYPipe steps (prep, reindex, launch, summary) without any intervention. Ligand search is not possible for the moment.

Usage

easypipe.py data auto [-h] [-m {fast,full,allsg}] ref

arguments description
ref folder with fasta file and pdb file for replacement, and cif(s) if ligand(s) in the model

Warning

reference pdb files should include the row starting with ‘CRYST1’ containing information on space group

optional arguments description
-h, –help show this help message and exit
-m {fast,full,allsg}, –mode {fast,full,allsg} running mode: fast, full, or allsg (default = fast)
-b NUMBER, –best NUMBER launch only for mtz with best completeness, NUMBER indicates how many mtz to treat (default 1), ex: –best 2
-a, –autoproc launch only for mtz from autoPROC, or if none launch for mtz with best completeness
-w, –whole launch for the whole mtz processes
-t TEMPLATE, –template TEMPLATE optional template name for log files and result folders, in case re-launching with different reference pdb of the same space group (else will overwrite).

Example:

$ easypipe.py PROCESSED_DATA auto my_ref_folder --best 2 --mode full
equivalent to:
$ easypipe.py PROCESSED_DATA auto my_ref_folder -b 2 -m full

How the data should be organized ?

Processed data should be in datasets folders, all grouped in a folder. More information on how to organize your data here.

What does it do ?

Executes successively, without any intervention, the following steps:

The options are the same as for launch, except for the options concerning the search for ligands which is not enabled at the moment. In the same way, the option “simulate” is not possible because it would imply an intervention. A new ‘launch csv’ file is therefore generated each time.