Getting Started

The general workflow of the preparation of a fragment’s library follows the next schema:

_images/schema.png

Input Files

Therefore, the required input file is:

  • SDF file: Must contain fragments or ligands in 3D, optimized, and protonated. We recommend to use previously LigPrep onto the library to do the preparation.

Pipeline

The whole pipeline consist of two main steps: prepare and scan. The first one would be performed by the script convert2pdb.py, and the second by FragmentTools/prepare2frag.py

Convert2PDB

Program to transform 3D SDF files with large amount of molecular compounds to several PDBs, renaming also chains, resnames, and resnums to the desired ones.

i.e:

python convert_sdfs2pdb.py library.sdf --out_folder library_in_pdb --chain L --resname LIG --resnum 1

Prepare to Frag

Program to prepare FragPELE instruction’s from PDB libraries.

i.e:

python FragmentTools/prepare_to_frag.py /path/to/library /path/to/complex.pdb C1 -m first-occurrence -o /out/path/instructions.conf