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1.2.4

  • Dimorphite-DL now better protonates compounds with polyphosphate chains (e.g., ATP). See site_substructures.smarts for the rationale behind the added pKa values.
  • Added test cases for ATP and NAD.
  • site_substructures.smarts now allows comments (lines that start with #).
  • Fixed a bug that affected how Dimorphite-DL deals with new protonation states that yield invalid SMILES strings.
    • Previously, it simply returned the original input SMILES in these rare cases (better than nothing). Now, it instead returns the last valid SMILES produced, not necessarily the original SMILES.
    • Consider O=C(O)N1C=CC=C1 at pH 3.5 as an example.
      • Dimorphite-DL first deprotonates the carboxyl group, producing O=C([O-])n1cccc1 (a valid SMILES).
      • It then attempts to protonate the aromatic nitrogen, producing O=C([O-])[n+]1cccc1, an invalid SMILES.
      • Previously, it would output the original SMILES, O=C(O)N1C=CC=C1. Now it outputs the last valid SMILES, O=C([O-])n1cccc1.
  • Improved suport for the --silent option.
  • Reformatted code per the Black Python code formatter.

1.2.3

  • Updated protonation of nitrogen, oxygen, and sulfur atoms to be compatible with the latest version of RDKit, which broke backwards compatibility.
  • Added "silent" option to suppress all output.
  • Added code to suppress unnecessary RDKit warnings.
  • Updated copyright to 2020.

1.2.2

  • Added a new parameter to limit the number of variants per compound (--max_variants). The default is 128.

1.2.1

  • Corrected a bug that rarely misprotonated/deprotonated compounds with multiple ionization sites (e.g., producing a carbanion).

1.2

  • Corrected a bug that led Dimorphite-DL to sometimes produce output molecules that are non-physical.
  • Corrected a bug that gave incorrect protonation states for rare molecules (aromatic rings with nitrogens that are protonated when electrically neutral, e.g. pyridin-4(1H)-one).
  • run_with_mol_list() now preserves non-string properties.
  • run_with_mol_list() throws a warning if it cannot process a molecule, rather than terminating the program with an error.

1.1

  • Dimorphite-DL now distinguishes between indoles/pyrroles and Aromatic_nitrogen_protonated.
  • It is now possible to call Dimorphite-DL from another Python script, in addition to the command line. See the README.md file for instructions.

1.0

The original version described in:

Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.