README.md 1.92 KB
Newer Older
jdurrant's avatar
jdurrant committed
1 2
Dimorphite-DL 1.0
=================
pjropp's avatar
pjropp committed
3

4 5
What is it?
-----------
pjropp's avatar
pjropp committed
6

jdurrant's avatar
jdurrant committed
7
Dimorphite-DL 1.0 adds hydrogen atoms to molecular representations, as
8
appropriate for a user-specified pH range.
pjropp's avatar
pjropp committed
9

10 11 12 13 14
Users can provide SMILES strings from the command line or via an .smi file.

Licensing
---------

jdurrant's avatar
jdurrant committed
15
Protonation is released under the Apache 2.0 license. See LICENCE.txt for
16 17 18 19 20 21
details.

Usage
-----

```
jdurrant's avatar
jdurrant committed
22 23 24 25
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]
26

jdurrant's avatar
jdurrant committed
27
Protonates small moleucles.
28 29

optional arguments:
jdurrant's avatar
jdurrant committed
30 31 32 33 34 35 36 37 38 39 40
  -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)
41 42 43 44 45 46 47 48
```

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

Examples
--------

```
jdurrant's avatar
jdurrant committed
49 50 51 52 53
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
54 55
```

56 57 58 59
Authors and Contacts
--------------------

See the `CONTRIBUTORS.md` file for a full list of contributors. Please contact
jdurrant's avatar
jdurrant committed
60
Jacob Durrant (durrantj@pitt.edu) with any questions.