Commit 62f4d095 authored by jdurrant's avatar jdurrant

Updates, including to the README.md file.

parent 6921d638
CONTRIBUTORS
============
Patrick Ropp
Jacob Durrant
Jacob Spiegel
Jesse Kaminsky
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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\ No newline at end of file
Protonation
===========
Protonation 1.0
===============
The Protonation Module takes smiles as either input line stings or from a .smi
file and returns the protonated smiles, given a specific pH range.
What is it?
-----------
Default pH range is 6.4 to 8.4, considered biologically relevant pH.
Protonation 1.0 adds hydrogen atoms to molecular representations, as
appropriate for a user-specified pH range.
Example Run:
```bash
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: protonate.py [-h] [--min_ph MIN] [--max_ph MAX] [--st_dev STD]
[--smiles SMILES] [--smiles_file SMILES_FILE]
[--output_file OUTPUT_FILE]
Protonates small moleucles.
optional arguments:
-h, --help show this help message and exit
--min_ph MIN Minimum pH to consider.
--max_ph MAX Maximum pH to consider.
--st_dev STD Standard devation range (number of standard devs).
--smiles SMILES SMILE string to protonate.
--smiles_file SMILES_FILE
File which contains SMILES strings to protonate.
--output_file OUTPUT_FILE
File to write protonated SMILES. (Optional)
```
The default pH range is 6.4 to 8.4, considered biologically relevant pH.
Examples
--------
```
python protonate.py --smiles_file sample_molecules.smi
```
\ No newline at end of file
```
```
python protonate.py --smiles "CCC(=O)O" --min_ph -3 --max_ph -2
```
```
python protonate.py --smiles "CCCN" --min_ph -3 --max_ph -2 --output_file output.smi
```
Authors and Contacts
--------------------
See the `CONTRIBUTORS.md` file for a full list of contributors. Please contact
Jacob Durrant (durrantj@pitt.edu) with any questions.
\ No newline at end of file
......@@ -28,8 +28,7 @@ if __name__ == "__main__":
if 'output_file' in args:
with open(args['output_file'], 'w') as file:
for out in output:
file.write("\t".join(out))
file.write("\n".join(output))
else:
for out in output:
print(out)
......@@ -500,11 +500,9 @@ def convert_smiles_str_to_mol(smiles_str):
None. Then try to convert it to an RDKit Mol Object.
:param string smiles_str: The SMILES string.
:return: A rdkit.Chem.rdchem.Mol object, or None if the SMILES is invalid.
:return: A rdkit.Chem.rdchem.Mol object, or None if it is the wrong type or
if it fails to convert to a Mol Obj
"""
Return None if it is the wrong type or if it fails to convert to a Mol Obj
Return the mol object if it converts.
if smiles_str is None or type(smiles_str) is not str:
return None
......
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