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New version of GRO supporting more proteins

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README

This version of GRO was developed at the AI-UDP lab atop the original version, created by Eric Klavins at University of Washington.

What is this repository for?

  • This repository holds the latest developer's version of GRO at AI-UDP. There is an executable version for Windows, and the source code can be compiled on MacOS, Linux or Windows.
  • The current version is 1.0

How do I get set up?

  • Setup -
  1. Download and decompress or clone the repository.
  2. If you want to use the Windows executable version, work from the WIN-Executable subfolder and follow the instructions in the Readme in that folder.
  3. To compile in any OS, make sure the directory structure is created and available. This is done by running the script located in the main project folder, which creates this directory structure. (create_dirs.sh on MacOS and Linux. In case of compiling on Windows, it should be renamed to create_dirs.bat)
  • Dependencies -
  1. For every OS, you should install the latest version of QT Creator (https://www.qt.io/ide/).
  2. Flex (https://github.com/westes/flex) and Bison (https://www.gnu.org/software/bison/) should also be installed. Windows versions may be found at https://sourceforge.net/projects/winflexbison/.
  3. A C/C++ compiler needs to be installed. This version has been tested with clang/clang++ in MacOS, gcc/g++ in Linux (CentOS 7.0) and MinGW in Windows.
  4. Go to https://github.com/calccrypto/uint256_t, download and decompress or clone the repository, and put the ‘uint256_t-master’ folder in the main project directory.
  5. If you are in linux, make sure the format in your system is set to United States(settings/region & language)
  • Instructions for compiling -
  1. Open a terminal and run create_dirs.sh (from the project directory)
  2. From the same project directory run the script for compiling all modules: modules.sh <mode> (MacOS and Linux) or modules-win.bat <mode> (Windows). <mode> is either debug or release.
  3. Open QT Creator and load both projects, ccl-master and gro-master. Set the correct output of the projects to ccl_Debug, ccl_Release, gro_Debug and gro_Release respectively when setting up the projects in QT Creator.
  4. Build ccl-master on QT Creator.
  5. Build gro-master on QT Creator.
  6. To run gro, just press the green arrow on the bottom left of QT Creator.
  7. Upon execution of gro, look up the bottom line of the window to check the Working Directory (a guide is shown in the Readme in the WIN-Executable folder). Copy standard.gro and gro.gro from the gro-master/include folder to the Working Directory on your computer.

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