Python package to analyse and prepare libraries of chemical compounds for molecular simulations.
- Python 3.7
- Rdkit 2019.03.4
- Schrodinger 2019 (Optional)
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.
Example of usage:
python convert_sdfs2pdb.py library.sdf --out_folder library_in_pdb --chain L --resname LIG --resnum 1
For more information:
python convert_sdfs2pdb.py -h
Program to prepare FragPELE instruction's from PDB libraries.
Exaple of usage:
python FragmentTools/prepare_to_frag.py /path/to/library /path/to/complex.pdb C1 -m first-occurrence -o /out/path/instructions.conf
For more information:
python FragmentTools/prepare_to_frag.py -h