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THESEUS: Maximum likelihood superpositioning of multiple 
         macromolecular structures

-/_|:|_|_\- 
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA  02454 

dtheobald@brandeis.edu
dtheobald@gmail.com

Copyright (c) 2004-2007 Douglas L. Theobald

  THESEUS 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.

  THESEUS is distributed in the hope that it will be useful, but
  WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with THESEUS in the file 'COPYING'; if not, write to the:

  Free Software Foundation, Inc.,
  59 Temple Place, Suite 330,
  Boston, MA  02111-1307  USA

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INSTALLATION INSTRUCTIONS:

Preliminaries:

THESEUS should compile with any C compiler that supports C99 (most).
However, I recommend the open source GNU gcc compiler, as that is
what I use for development, and in my experience it optimizes
THESEUS better than other compilers (including Intel's icc, which
also has other problems).

THESEUS requires LAPACK (and BLAS) libraries. Before compiling, you
must verify that you have these installed on your machine. Often,
your vendor will supply optimized versions of these libraries to you
upon request. For example, mac users have it very easy, as it's
built into OS X in the VecLib Framework. If you are using THESEUS
for non- commercial purposes on a Linux Intel machine, you can
obtain highly optimized LAPACK and BLAS libraries from Intel for
free in the Intel Math Kernel Library (MKL). 

http://www.intel.com/cd/software/products/asmo-na/eng/perflib/mkl/219771.htm

Otherwise, the source code (and precompiled binaries for the most
popular platforms) are freely available:

Source code:
http://www.netlib.org/lapack/
http://www.netlib.org/blas/
http://math-atlas.sourceforge.net/

Precompiled binaries:
http://www.netlib.org/lapack/archives/
http://www.netlib.org/blas/faq.html#5
http://www.netlib.org/blas/archives/
http://math-atlas.sourceforge.net/faq.html#binary
https://sourceforge.net/project/showfiles.php?group_id=23725
(make sure to look under older releases, as precompiled ATLAS
binaries are not always the latest)

Note, the best way to get BLAS is through the highly optimized ATLAS
package. ATLAS is also very easy to install on any platform (though
it takes a while). If you need to compile LAPACK and/or BLAS, note
that THESEUS only requires the double precision functions, so you
don't need to compile the others (no need for single, complex, or
complex16). Also, be aware that LAPACK uses BLAS, so you should
compile or obtain BLAS/ATLAS first, and then be prepared to tell
LAPACK in which directory it resides on your machine.

Compilation:

1) Edit the make.inc by uncommenting the appropriate sections
   for your system. The main hurdle to overcome in compiling
   THESEUS is in making sure that the compiler can find your LAPACK
   and BLAS libraries. This will involve changing BLASLIB,
   BLASLIBDIR, LAPACKLIB, and LAPACKLIBDIR. You may also need to
   include the g2c library in LIBS and tell the compiler where to
   find it in LIBDIR. 

2) Edit the makefile install directory to your directory of choice.

3) Issue the following command:

    make && make install

If you have problems, please verify that you are telling the
compiler where to find your LAPACK and BLAS libraries. If so, and 
you still have problems, I will be happy to help out with compiling
issues:

Douglas Theobald
dtheobald@brandeis.edu
dtheobald@gmail.com

Once you have a binary, for help with the program simply type
'theseus' or 'theseus -h'.


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