Dimorphite-DL 1.0.0

What is it?

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

Users can provide SMILES strings from the command line or via an .smi file.

Licensing

Protonation is released under the Apache 2.0 license. See LICENCE.txt for details.

Usage

usage: dimorphite_dl.py [-h] [--min_ph MIN] [--max_ph MAX]
                        [--pka_precision PRE] [--smiles SMI]
                        [--smiles_file FILE] [--output_file FILE]
                        [--label_states] [--test]

Protonates small moleucles.

optional arguments:
  -h, --help           show this help message and exit
  --min_ph MIN         minimum pH to consider (default: 6.4)
  --max_ph MAX         maximum pH to consider (default: 8.4)
  --pka_precision PRE  pKa precision factor (number of standard devations,
                       default: 1.0)
  --smiles SMI         SMILES string to protonate
  --smiles_file FILE   file that contains SMILES strings to protonate
  --output_file FILE   output file to write protonated SMILES (optional)
  --label_states       label protonated SMILES with target state (i.e.,
                       "DEPROTONATED", "PROTONATED", or "BOTH").
  --test               run unit tests (for debugging)

The default pH range is 6.4 to 8.4, considered biologically relevant pH.

Examples

python dimorphite_dl.py --smiles_file sample_molecules.smi
python dimorphite_dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
python dimorphite_dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
python dimorphite_dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
python dimorphite_dl.py --test

Authors and Contacts

See the CONTRIBUTORS.md file for a full list of contributors. Please contact Jacob Durrant ([email protected]) with any questions.