NAOMI

1 Overview

NAOMI is a command-line tool for the consistent conversion of common chemical file formats (SDF, SMILES, MOL2). It is based on a robust chemical model which is designed to appropriately describe organic molecules relevant in the context of drug discovery. NAOMI also checks the chemical validity of molecules and calculates hydrogen coordinates.

To cite NAOMI and for details please refer to the following publication: S. Urbaczek, A. Kolodzik, J. R. Fischer, T. Lippert, S. Heuser, I. Groth, T. Schulz-Gasch, and M. Rarey, NAOMI - On the almost trivial task of reading molecules from different file formats, J. Chem. Inf. Model., 51(12): 3199-3207, 2011,  DOI: 10.1021/ci200324e

NAOMI is also able to read small molecules from PDB files as described in the following publication: Urbaczek, S., Kolodzik, A., Groth, I., Heuser, S., Rarey, M. (2012). Reading PDB: Perception of Molecules from 3D Atomic Coordinates. Journal of Chemical Information and Modeling, 53(1): 76-87, 2012. DOI: 10.1021/ci300358c

2 Download

The NAOMI converter was replaced by UNICON.

3 Usage

You can execute NAOMI with the following options.

-h
[ -help ]
Prints this help message
-v arg
[ -verbosity ]
Set verbosity level (0 = Quiet, 1 = Errors, 2 =Warnings, 3 = Info)
-i arg
[ -input ]
Input file(s) with suffix. Several input files can be given separated by spaces, e.g. -i a.mol2 b.sdf
-o arg      
[ -output ]
Output file, suffix is required
 Example: ./naomi_converter -i inputFile.mol2 -o outputFile.sdf -v 0 (Conversion from mol2 to sdf without any output to the console)

4 Limitations

• NAOMI does not generate three-dimensional coordinates for molecules
• NAOMI does not handle metals with covalent bonds
• NAOMI only uses the largest component for disconnected entries

5 People and references

NAOMI has been developed in a joint effort by Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, Tobias Lippert in the research group of Prof. Matthias Rarey at the Center for Bioinformatics of the University of Hamburg. 

We are grateful to our partners Inken Groth at Beiersdorf AG, Stefan Heuser at Georg Simon Ohm University, Tanja Schulz-Gasch at F. Hoffmann-La Roche Ltd, Uta Lessel at Boehringer Ingelheim Pharma GmbH & Co. KG and Holger Claußen at BioSolveIT GmbH.