Package: dimorphite-ojmb
Dimorphite-DLThis repository is a modified version ofDurrant Lab's originalDimorphite-DLimplementation (original article).Changes were brought to facilitate its installation and integration in bigger cheminformatics projects (seeCHANGES.md).What is it?As stated on Durrant's Lab original GitLab page: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.CitationIf you use Dimorphite-DL in your research, please cite: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.LicensingDimorphite-DL is released under the Apache 2.0 license. See LICENCE.txt for
details.InstallationThis modified version of Dimorphite-DL can be installed usingpip:pipinstalldimorphite-ojmbIf the above does not work, you can run the installation like so:python-mpipinstalldimorphite-ojmbUsageusage: dimorphite [-h] [--min_ph MIN] [--max_ph MAX] [--pka_precision PRE]
                  [--smiles SMI] [--smiles_file FILE] [--output_file FILE]
                  [--max_variants MXV] [--label_states] [--silent] [--test]

Dimorphite 1.2.4: Creates models of appropriately protonated small moleucles.
Apache 2.0 License. Copyright 2020 Jacob D. Durrant.

Options:
  -h, --help           Show this 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 NOTE: This argument is
                       mutually exclusive with smiles_file.  [required]
  --smiles_file FILE   file that contains SMILES strings to protonate NOTE:
                       This argument is mutually exclusive with smiles.
                       [required]
  --output_file FILE   output file to write protonated SMILES (optional)
  --max_variants MXV   limit number of variants per input compound (default:
                       128)
  --label_states       label protonated SMILES with target state (i.e.,
                       "DEPROTONATED", "PROTONATED", or "BOTH").
  --silent             do not print any messages to the screen
  --test               run unit tests (for debugging)The default pH range is 6.4 to 8.4, considered biologically relevant pH.CLI usage examplesdimorphite --smiles_file sample_molecules.smi
  dimorphite --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
  dimorphite --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
  dimorphite --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
  dimorphite --testAdvanced UsageIt is also possible to access Dimorphite-DL from another Python script, rather
than from the command line. Here's an example:fromrdkitimportChemimportdimorphite_dl# Using the dimorphite_dl.run() function, you can run Dimorphite-DL exactly as# you would from the command line. Here's an example:dimorphite_dl.run(smiles="CCCN",min_ph=-3.0,max_ph=-2.0)# One can also provide multiple SMILES at once.dimorphite_dl.run(["C[C@](F)(Br)CC(O)=O","CCCCCN"],min_ph=5.0,max_ph=9.0,silent=True)CaveatsDimorphite-DL deprotonates indoles and pyrroles around pH 14.5. But these
substructures can also be protonated around pH -3.5. Dimorphite does not
perform the protonation.Authors and ContactsSee theCONTRIBUTORS.mdfile for a full list of contributors. Please contact
Jacob Durrant (durrantj@pitt.edu) with any questions.