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regiosqm
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README.md

README.md

RegioSQM

Avaliable on regioqm.org.

Predict Regioselectivity of electrophilic aromatic substitution reactions in heteroaromatic systems. RegioSQM finds the aromatic CH group with the highest proton affinity estimated by the PM3/COSMO method using the MOPAC program. More information is available at the RegioSQM paper.

Installation

- MOPAC (http://openmopac.net/)
- RDKit (http://www.rdkit.org/docs/Install.html)
- obabel (https://openbabel.org/docs/dev/Installation/install.html)

RegioSQM depends on MOPAC for quantum calculations, OpenBabel for some formation convertion and RDkit in the python enviroment for everything else.

Usage

The workflow is as following

cd example

# generate conformations from SMILES
python ../regiosqm/regiosqm.py -g example.csv > example.csv

# Run all .mop files with mopac
# or submit them to a cluster
ls *mop | parallel -j4 "mopac {}"

# use the generated csv file to analyse all the 
python ../regiosqm/regiosqm.py -a example.csv example.csv > example_results.csv

The results are now parseable from the results file, or viewable by 2D structures with regioselective indicators (in svg format).