SADIC: Simple Atom Depth Index Calculator

Copyright © 2004-2006 by Daniele Varrazzo

University of Siena
Dept. of Molecular Biology
Via Fiorentina, 1
53100 Siena - Italy

What is SADIC?

SADIC samples the space around each atom of a given molecule evaluating the portion of volume that is external to any protein atom. The program can return absolute volume and surfaces exposition as well as the depth index.

SADIC input is a PDB file. Calculations can be performed on local files as well as remote files using http and ftp protocols.

SADIC is implemented as a Python package, with the core loop implemented in C language. It can be run on POSIX and Windows platforms.

What is the Depth Index?

The depth index is a novel way to measure how an atom in a molecule is exposed to a probe of given size. The atom depth takes into account the three dimensional shape of the molecule, thus resulting more expressive than measures based on the distance from the closest surface point or the closest solvent molecule.

The article Three-dimensional Computation of Atom Depth in Complex Molecular Structures, with the motivations an the results of SADIC algorithm, has been published on Bioinformatics journal and is available for download.

HEWL molecule

Hen egg white lysozyme: alpha-carbon 47 (red) and 58 (green) are both on the molecule surface, but accessibility of the former is quite greater


SADIC current stable version is 1.0, released on 2005-03-12.

SADIC current testing version is 1.1b1, released on 2006-07-17.

Before installing the program, you need the following software installed on your system:

  • Python (at least Python 2.3 is required);
  • The Python Numarray package.


Documentation is included in the package. It is also available online:


SADIC is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.


SADIC was developed at the University of Siena, with the help of the SienaBioGrafiX crew.

Many thanks to...

  • Prof. Neri Niccolai (for the original idea);
  • Andrea Bernini (for everything in between an idea and something useful);
  • Ottavia Spiga and Vincenzo Venditti (for testing and usage).


SADIC is hosted on SourceForge. You can access to: Logo