Hi researchers,
I have downloaded 20,000 compounds from databases in .sdf format in a single file (size: 108 GB).
Could someone guide me on splitting the enormous single ligand file into separate files? In the past, I've used open babel to convert the file from .sdf into .pdb. But, I wish to split this vast database ligand file into separate ligand files for molecular docking. Can I use the Open babel, command prompt for this work? Kindly do give suggestions on this issue.
thanks in advance
You can use openbabel and this command:
obabel -isdf database.sdf -osdf -O *.sdf -m
Nikolaos Kourkoumelis Thank you for the reply, what if I use the open babel window version? I'm using the window version. I'm not sure where I can input the command.
I think this page should help as it refers to the command line interface:
https://openbabel.org/wiki/Tutorial:Basic_Usage
You can use Galaxy server. Use the tool "split file".
https://cheminformatics.usegalaxy.eu/
the best option to split the single ligand file into separate ligand files is to use open babel software; by selecting the split option prior converting the compounds
If Open Babel is installed on your computer, In the command prompt, use the following Open Babel command to split the large ligand file into separate files:
babel input.sdf output_{}.sdf --split all
Replace "input.sdf" with the name of your input file, and "output_{}.sdf" with the desired naming pattern for the output files. The {} placeholder will be replaced with sequential numbers for each output file.
You can use this split_SDF.py python package to spilt your SDF files into smaller chunks
https://github.com/CreedxAsif/Split-SDF/blob/a28f7f6063317ad96491ae3c3009b369b38d7036/split_SDF.py
How to use: