PROFASI comes with two kinds of application programs. One kind, such as, SimTempRun, ParTempRun etc., are meant to run elaborate simulations of a protein system using a certain Monte Carlo method. The other kind of applications, such as "mimiqa", are utilities performing very useful short tasks that can be created using the PROFASI libraries. These two types of applications will be documented in the following.
PROFASI should be thought of as a library. Most serious users of the program write their own main programs suited to their specific projects which they link with the PROFASI library. Still , we provide many application programs with the distribution, which we have used in our research. These can sometimes be used directly. But it is more probable that the user, after learning how these programs work, and how they are structured, modifies them to suit his/her own research project. There are currently 4 programs in this category: BasicMCRun, SimAnnealRun, SimTempRun and ParTempRun. They can be found in the "app" directory.
These programs are not "simulation programs". They are often useful in connection with analysis of data generated by PROFASI simulation programs. Some of them, such as "mimiqa", might be useful in contexts unrelated to simulations with the model represented by PROFASI.
The basic syntax for a lot of these utility programs is similar. If you forget, simply type the name of the program without any arguments, and you will get some usage information. Normally they take some arguments, and some options. An option in PROFASI is an adjustible parameter or switch that changes the behaviour of the program in a well defined way. They are passed to the program as command line arguments with a hyphen ("-") in front of their names. They are almost always "optional". An option might take additional arguments. Arguments to the options could be numbers or filenames or some other switch depending on the program. Options must be followed by the corresponding arguments; for instance, if you want to write output to a particular file, you will typically specify with " -o filename". The filename must be the word following the option "-o".
If there are multiple options, they could be specified in arbitrary order.
-extract_snapshot Extracting snapshot conformations from finished runs
The top level bin directory in PROFASI also contains a few scripts we have found very useful.
-extract_props Calculating properties, retrieving snapshots for a range
-Merging histogram data from different runs Merging histogram data from different compute nodes
-Merging binary data from His2D objects Merging binary His2D data for 3D plots
-MimiqA : A swiss army knife for RMSD calculations A command line RMSD tool
-Extracting parts of a PDB file Retrieve portions of a pdb file.
-Calculating energies of a PROFASI generated PDB file PROFASI energy terms for a pdb file
-Converting binary conf files to gzipped text and back Transferring PROFASI binary configuration files to a different machine.
- find_avg.pl : This is a PERL script to process the averages files produced by the PROFASI simulation programs. There are no arguments to this script. Simply type the name of the program (with PATH) in the run directory. It looks for files called "n0/averages", "n1/averages", ... and combines the information from all such files into global averages. But then it also splits the global averages data into many files, one for each measurement, convenient for plotting. So, after running the script, it will produce "Etot.avg", "Bias.avg" ,... Each file contains a comment line at the top describing what is written in that file.
- build_grouplib.py (Warning: advanced users only!!): This is a PYTHON script that may be useful for some advanced users. It is used to create the class files GroupLib.hh and GroupLib.cc, from a simple description of the amino acids and other groups which are parts of PROFASI. If, for instance, you want your version of PROFASI to handle Hydroxy-proline, you will start the implementation of the class by adding a few lines for Hydroxy-proline in the "residue_info.dat" file in the model directory, and then running build_grouplib.py. This will generate a new GroupLib class, and you copy the ".hh" and ".cc" files into PROFASI/model/Elements . Most of the book keeping about atom orders, writing PDB files etc, is then already done! You will only need to add a small hydroxyproline class definition, by following what is done for proline and making small modifications. If your new addition has special properties with respect to particular energy terms, you would need to make changes in the energy classes. Take a look, in particular, in PROFASI/model/Energy/Hydrophobicity.cc.
PROFASI: Protein Folding and Aggregation Simulator, Version 1.1
© (2005-2008) Anders Irbäck
and Sandipan Mohanty
Documentation generated on 10 Oct 2008 using Doxygen version 1.5.0