NeedleHaystack software

by Dr. Andreas Hoppe


The computer program NeedleHaystack computes molecular superpositions. A possible large molecule (target=haystack) is scanned for the occurence of a given molecular motif (model=needle) within tolerances. The advance over other methods is that it can handle very large atom sets, e.g. targets of up to 100000 atoms and has not necessarily to include any chemical information and connectivity between atoms: chemical constraints to restrict the solution space are not used to pertain nonobvious superpositions based on geometric fit.

The specialization to the needle-haystack-problem allows a very fast algorithm. Trade-offs between runtime and tolerance levels are possible. The program is fast enough to screen large databases in an acceptable time.

Please cite the following reference when using NeedleHaystack:
Andreas Hoppe and Cornelius Frömmel. NeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates. J. Appl. Cryst. (2003). 36, 1090-1097. [pdf, ps]

Online version (version 1.1, since 20.03.03), currently out of service

Planned to move to
simple interface
tutorial for the simple interface
complex interface
paramter files interface

Offline version

NeedleHaystack is distributed free of charge as an executable for Pentium compatible computers with the operating system LINUX. It is run from the command line and can easily embedded in scripts.


last update: 9th Feb 2009