Datasets

Data Sources & Download Links

Data Source	Download Link
mcule	https://mcule.s3.amazonaws.com/database/mcule_purchasable_full_230323.smi.gz
Pubchem	https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/
ChEMBL	https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_32_chemreps.txt.gz
Zinc (Clean, Drug-like)	http://zinc12.docking.org/db/bysubset/13/usual.sdf.csh

Required Major Dependencies

1. gcc and g++
2. cmake
3. boost
4. RDKit
5. Datamol

Running The Code (Python)

Run python process_molecules --in-fname path_to_input_file.txt --out-fname path_to_output_file.txt.

Running the Code (C++)

To build and run the proc_chembl.cpp program, do the following:

mkdir build
cd build

cmake ..
make

You can now run the program on the ChEMBL dataset. The accepted command line usage is shown below.

./proc_chembl --help
Usage: ./proc_chembl
  -i/--input <path to input .tsv file>
  -o/--output <path to output .tsv file>
  -m/--max-mol-weight <max mol weight to process> (default: 1000 dA)
  -f/--max-frag-weight <max frag weight to process> (default: 300 dA)