easYPipe ‘ligands’

This step is mandatory if you want Phenix to search ligand, else it is optional.

‘ligands’ subcommand generates pdb and cif from smiles with eLBOW [2] .


First, template csv file generated with ‘prep’ subcommand’ have to be completed with ligands names and smiles.


easypipe.py data ligands [-h] ligands_csv

arguments description
-h, –help show this help message and exit
ligands_csv ligands_for_datasets.csv file from ‘prep’ with ligands names and smiles completed (mandatory)


$ easypipe.py PROCESSED_DATA ligands easYPipe/1c_ligands/ligands_for_datasets_OK.csv

What does it do ?

  • First, you have to fill in the fields ‘ligand name’ and ‘ligand smiles’ of /1c_ligands/ligands_for_datasets.csv csv file, then save the csv file somewhere else or with another name if you don’t want to overwrite it in case you run ‘prep’ subcommand again …
  • ‘ligands’ subcommand generates pdb and cif of ligands and copies them in corresponding processed dataset folders, in a ‘ligand’ folder. It first creates a smiles file accordingly to the ligands_csv input, canonizes it thanks to Open Babel [1] and converts it with eLBOW [2] to pdb and cif.


If eLBOW [2] fails to generate pdb and cif from smiles, you can copy your own cif in ligand sub-folder of the corresponding dataset, eLBOW [2] will generate pdb from this cif.