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              uQlust ver. 2.0
Efficient Macromolecular Structure Analysis
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This file contains a brief instruction as to how to run uQlust
and get started performing clustering or ranking of macromolecular
(protein or RNA) structure. For more information, please see
the manual.

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Windows
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In order to run uQlust in GUI mode use uQlust.exe file

To run uQlust in batch mode use the following command:

uQlustTerminal.exe -f configuration_file

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Linux
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First compile libraries libRNA.so and libDSSP.so. To do it just run
the following command in the distribution directory:

make

In order to run uQlust in GUI mode use:

mono uQlust.exe

Batch mode:

mono uQlustTerminal.exe -f configuration_file

Note that uQlustTerminal.exe must be in the same directory as uQlust.exe!

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More options can be displayed by running uQlustTerminal.exe without any option.

uQlust can be run in GUI or batch mode. The former provides a number of pre-loaded workflows that can be explored using the 'easy' mode.

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For example, in order to run uQlustTerminal with a predefined workflow to rank a set of protein models (see data directory) use the following command:

uQlustTerminal.exe -f workFlows/protein/uQlust_config_file_1DJury.txt

or for RNA

uQlustTerminal.exe -f workFlows/rna/uQlust_config_file_RNA_1DJury.txt -m RNA

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The following five directories are included in the uQlust distribution:

data - contains example data sets for protein and rna
workFlows - contains configuration files for typical use cases
profiles - contains pre-defined profiles that can be used in uQlust
results - the default directory to store the results
generatedProfiles - contains intermediate profiles generated when running uQlust

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Since uQlust is written in C#, it is compiled to a bytecode (CIL) which is contained within the uQlust.exe file. Thus, the main uQlust module does not need re-compiling. However, two additional modules based on C/C++ distributions of DSSP and RNAview utilities (kindly made available by their authors - see references) do need to be compiled into libDSSP.so and libRNA.so files. In order to create these two files, just run the 'make' command in the main distribution directory (referred to as uQlustDistr). The boost library is used to compile the DSSP module and create libDSSP.so. Check if the files libDSSP.so and libRNA.so have been created in the main uQlust directory, which contains the uQlust.exe file. Similar steps, i.e. installing mono and boost libraries, and re-compiling DSSP and RNAview libraries, should work on Mac OS as well.

More information about uQlust can be found in the manual provided with the distribution and also available at http://github.com/uQlust.