General purpose helper classes around the RDKit and Openeye toolkits for handling molecular input files. This packages tries to abstract the toolkits away and thus provides a toolkit independent interface to dealing with molecular files and, to some extend, with molecule objects.
The underlying toolkit can be set with cdd_chem.toolkit.set_toolkit. If it's not
set then the underlying toolkit is taken from the CDDLIB_TOOLKIT environment
variable. If this environment variable is not set then the default toolkit will be
oechem provided that oechem can be imported. Otherwise the toolkit will be set
to rdkit.
The package is still under development but here is an example on how to get started:
#!/usr/bin/env python3
import argparse
import sys
from cdd_chem.io import get_mol_input_stream, get_mol_output_stream
def main() -> int:
"""Console script"""
args = parse_options()
with get_mol_input_stream(args.input) as in_file, get_mol_output_stream(args.output) as out_file:
for mol in in_file:
# set SD tag data (that has to be a string)
mol['num_atoms'] = str(mol.num_atoms)
out_file.write_mol(mol)
return 0
def parse_options() -> argparse.Namespace:
"""Parse main options."""
parser = argparse.ArgumentParser(description="Command line arguments:")
parser.add_argument('--input', type=str, metavar='molfile', required=True, help='input molecule file')
parser.add_argument('--output', type=str, metavar='molfile', required=True, help='output molecule file')
return parser.parse_args()
if __name__ == "__main__":
sys.exit(main())
Toolkit-agnostic features for:
- Reading and writing molecules to SD files
- Converting between molecules and SMILES
- Setting and retrieving properties of molecules
- Reading and writing pandas dataframes containing representations of molecules with properties
This Python package was created with