| Name | molscrub JSON |
| Version |
0.1.1
JSON |
| download |
| home_page | https://github.com/forlilab/molscrub |
| Summary | Enumerate states of small organic molecules: 3D coordinates, tautomers, pH-based adjustments |
| upload_time | 2025-01-24 02:22:35 |
| maintainer | None |
| docs_url | None |
| author | Forli Lab |
| requires_python | >=3.8 |
| license | GPL-v3 |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Scrubber
Process large numbers of small molecules for docking with AutoDock.
May be useful for structure-based modeling in general.
What happens:
- generate 3D coordinates using RDKit's ETKDGv3 and UFF minimization
- enumerate tautomers (aiming at low energy states only)
- enumerate pH corrections
- convert boats to chairs (6-member rings) and enumerate both chair states
- enumerate chiral centers (not implemented right now)
# Installation
```sh
conda activate <desired-environment> # if you are using conda environments
git clone git@github.com:forlilab/scrubber.git
cd scrubber
pip install -e .
```
Depends on the RDKit, which can be installed from conda-forge in the desired environment:
```sh
conda activate <desired-environment>
conda install rdkit -c conda-forge
```
## Python scripting
```python
from rdkit import Chem
from scrubber import Scrub
scrub = Scrub(
ph_low=7.4,
ph_high=7.4,
)
mol = Chem.MolFromSmiles("Clc1c(OCCC3)c3ccc1C(=O)Nc2nc[nH]c2")
# each state (e.g. tautomer) an rdkit mol and may have multiple conformers
for mol_state in scrub(mol):
print(Chem.MolToSmiles(mol_state), "nr conformers: %d" % mol_state.GetNumConformers())
```
## Command line tool examples
```sh
scrub.py "c1cc[nH]c(=O)c1" -o scrubbed.sdf --pH 5 --skip_gen3d
scrub.py input_mols.sdf -o scrubbed.sdf
scrub.py input_mols.smi -o scrubbed.sdf
```
Other options described in the help message:
```sh
scrub.py -h
```
Where "input\_mols.smi" can look like this:
```
CC(=O)O aceticacid
CN(C)C trimethylamine
Clc1cc(O)ccc1C(=O)Nc2nc[nH]c2 hello_mol
c1cccc1 rdkit_will_cry
CCC good4bbq
CCO alsogood4bbq
c1cccnc1CC(=O)C a_ketone
```
Raw data
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