This file describes the unofficial complete topsuite installation
After following the instructions in this file, please read through the readme
files for the individual TopSuite methods if you have any problems with the installation

THE SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND,
INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS,
MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK
AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE.
SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT
LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. NO USE OF THE
PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER.

TopSuite and its constituents are available only for academic non-for-profit
research purposes.

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How to Install TopSuite:

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TopScore requires a crapload (~3TB) of harddrive space, please make sure that you have
enough space available before attempting to install TopSuite. To install
TopSuite please follow these steps:

1. Make sure that you have all the pre-requisite libraries installed on your
   linux machine. This Installer has been tested on OpenSuse, CentOS and
   Ubuntu distributions, but unless your computer is completely clean, many
   of these libraries should be already installed. 

   We have done a lot to include everything nessesary in this package but
   some primary predictors look for libraries in specific system paths which
   is why these needs to be installed. The libraries required for TopSuite are:

   libboost_python.so.1.54.0 should be located in /usr/lib64
   fftw3   and fftw3-devel   should be located in /usr/lib
   libqt4  and libqt4-devel  should be located in /usr/lib
   libxml2 and libxml2-devel should be located in /usr/lib
   libtiff and libtiff-devel should be located in /usr/lib
   libpng  and libpng-devel  should be located in /usr/lib
   libstdc++.so.5            should be located in /usr/lib
   libg2c.so.0               should be located in /usr/lib
   cmake                     should be located in /usr/bin

2. Install TopSuite. Run the automated installer using the command:
   ./topsuite_installer.py

   You can follow the installation in the logfile topmodel_installation.log.
   This can also help you find errors during installation (if you neglected to
   install the pre-requisite libraries for instance).

   This will take a while, as it installs all of the primary methods and their
   dependencies to the respective folders in /path/to/topsuite_standalone/external
   including all required R, python, Java and perl requirements and libraries in the
   proper versions. TopSuite also includes some bugfixes to the individual programs.

2. Initialize TopSuite by running:
   cd topsuite_standalone
   ./top_installer.py setpython

3. Copy the obtained ProSa2003 License file to the correct location using:
   cp LicenseDB /path/to/topsuite/external/prosa/ProSaData/.

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How to test TopScore:

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To test TopScore run:

cd tests/topscore_test
./test_topscore.py

The output files in scores should be the same (within system-specific
rounding errors) as in comparison_scores. The output .global file should
be the same as comparison.global