Download

Our most up to date code available on GitHub: [LINK]


How to install

Note: Code intended for Unix based machines only.
  1. Download the code: [LINK]
  2. Extract the code:
    tar -xzvf staar.tgz
  3. Dowload and install OpenBabel: [LINK]
  4. Make sure you set the following environment variable to indicate the location of OpenBabel's library:
    In bash: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/data/AQ/openbabel-2.3.0/build/lib/
  5. Edit the following lines in the Makefile:
    # Edit these!
    BABEL_LIBDIR := /data/AQ/openbabel-2.3.0/build/lib/
    BABEL_INCDIR := /data/AQ/openbabel-2.3.0/include /data/AQ/openbabel-2.3.0/build/include
  6. Compile the code:
    make

How to run

Note: We are assuming you already have GAMESS installed, but our C++ program can be run without GAMESS. You just won't be able to get the energy calculations.
  1. To get a list of commands, type:
    ./staar -h
    and you should see somthing like:

    command line arguments
  2. The following is a list of required arguments:
    • -p
    • -o
    • -r

    Some notes about the '-r' flag: The argument that follows can be kinda complicated. Take the example from the screenshot, -r "PHE;GLU,ASP". What the program does is it will look for the PHE-GLU pairs and PHE-ASP pairs. So the residues before the ';' are matched with each of the ones following the ';'. There must be residues before and after the semicolon, otherwise you will get an error. The '-l' is used in combination with the '-r' flag. Using it tells the program to look for pairs that include the residues to the left of the ';' and the ones specified by the '-l' flag. So if you had something like -r "PHE;GLU,ASP" -l "PO4", the program would look for PHE-GLU, PHE-ASP, and PHE-PO4 pairs.

  3. An example run: Look for PHE-GLU, PHE-ASP, and PHE-PO4 pairs in 1JUY, 1NV2, 1NV6, 2OKN, 3ETJ (these are in the lists/Example.txt included with the code) within chains, with a generous threshold of 15 Angstroms, outputting GAMESS input files of results
    ./staar -r "PHE;GLU,ASP" -l "PO4" -s -t 15 -o STAAR.out -p PDB -L lists/PDBList.txt -g inp

Some special notes

If you have any problems/questions, email: staarutk [at] gmail [dot] com