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These three command-line, unix-based pieces of software may prove useful to you. A README file to explain program usage is packaged with each download file; essentially the same instructions are available by typing program_name -h at the command line.

To download: click the program file name for the appropriate table-row. Depending upon your browser set-up you may need to “option-click” or “right-click” and “save-as”

Cluster image


Cluster is a simple unix C++ program that builds collections of interacting items from records containing interacting pairs or larger fragments. It is part of the algorithm used in Reduce to find H-bond "cliques", and it is called by the clashlistcluster script.

Platform Version Release date Download size Program
(click to download)
Linux 1.1 24-Oct-01 13 (Kb) download arrow cluster.1.1.011024.linuxi386.tgz
Mac OSX 1.2 17-Dec-02 110 (Kb) download arrow cluster.1.2.021217.macosx.tgz
SGI-irix 1.2 17-Dec-02 18 (Kb) download arrow cluster.1.2.021217.irix65.tgz
Sun SPARC 1.1 03-Jul-01 101 (Kb) download arrow cluster.1.1.010703.sun.tgz
Source code 1.3 31-Dec-08 8 (Kb) download arrow cluster.1.3.081231.src.tgz


AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume.

Platform Version Release date Download size Program
(click to download)
Linux 1.2 12-Apr-99 32 (Kb) download arrow atvol.1.2.990412.linuxi386.tgz
Mac OSX 1.2 12-Apr-99 31 (Kb) download arrow atvol.1.2.990412.macosx.tgz
SGI-irix 1.2 12-Apr-99 46 (Kb) download arrow atvol.1.2.990412.irix65.tgz
Source code 1.2 12-Apr-99 78 (Kb) download arrow atvol.1.2.990412.src.tgz


Bndlst reads a PDB format file and for each atom prints a list of covalent and H-bonded neighboring atoms, along with several atomic properties. It is useful in building scripts which process atomic structures.

Platform Version Release date Download size Program
(click to download)
Linux 1.6 27-Nov-00 37 (Kb) download arrow bndlst.1.6.001127.linuxi386.tgz
Mac OSX 1.6 27-Nov-00 34 (Kb) download arrow bndlst.1.6.001127.macosx.tgz
SGI-irix 1.6 27-Nov-00 53 (Kb) download arrow bndlst.1.6.001127.irix65.tgz
Sun-SPARC 1.6 27-Nov-00 41 (Kb) download arrow bndlst.1.6.001127.sun.tgz
Source code 1.6 27-Nov-00 37 (Kb) download arrow bndlst.1.6.001127.src.tgz