Installing StoneHinge

Downloading StoneHinge is only necessary if you wish to run predictions locally. If you want to make a hinge prediction using the StoneHinge server, please head to the submission page.

To run StoneHinge locally, four programs are required: StoneHinge, ProFlex, DomDecomp, and Gromacs. StoneHinge, Proflex, and DomDecomp can be downloaded from the download page. On many Linux distributions, Gromacs may be installed through the repositories. When this is not possible, Gromacs may be obtained at http://www.gromacs.org/.

StoneHinge can be run on Linux or Unix machines. StoneHinge may also be run on Windows by using Cygwin. However, DomDecomp frequently fails when run under Cygwin, so running StoneHinge under Cygwin is not recommended.

Below, we assume that StoneHinge, ProFlex, and DomDecomp are being installed to /opt/stonehinge, /opt/proflexv5.0, and /opt/domdecomp respectively. The instructions also assume that are using the GNU C, C++, and Fortran compilers and have already installed them (gcc, g++, and g77). StoneHinge also requires Perl version 5.8 or greater, which should already be installed on most modern systems.

Note that ProFlex will compile under GCC version 4.x but will NOT run properly. If you are using GCC, ProFlex MUST be compiled using version 3.x. Click here for instructions on how to do this (or if you don't know what version of GCC you are running).

DomDecomp

1. First, extract the DomDecomp tarball
   tar -xzf domdecomp.tgz
2. Go into the DomDecomp source directory
   cd domdecomp/source
3. Compile DomDecomp
   g77 -O gnm-domdecomp.f -o gnm-domdecomp.e
4. Create a link to the DomDecomp executable in /usr/local/bin
   sudo ln -s /opt/domdecomp/source/gnm-domdecomp.e /usr/local/bin/domdecomp

ProFlex

1. Extract the ProFlex tarball
   tar -xzf proflexv5.0.tgz
2. Go into the ProFlex directory
   cd proflexv5.0
3. See instructions here if you have GCC version 4 (or if you don't know what version of GCC you are running).
4. Compile ProFlex
   make all
5. Create links to the ProFlex executables in /usr/local/bin
   sudo make links

StoneHinge

1. Install Gromacs. On many Linux distributions, Gromacs may be installed through the repositories. When this is not possible, Gromacs may be obtained at http://www.gromacs.org/.
2. Extract the StoneHinge tarball
   tar -xzf stonehinge.tgz
3. If desired, create a link to StoneHinge in /usr/local/bin
   sudo ln -s /opt/stonehinge/stonehinge.pl /usr/local/bin/stonehinge

Instructions for running StoneHinge may be found online or by running stonehinge -h.