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                      PDEN - Protein Density Tools

PDEN is offering tools and a C library to work on density files (typically pro- teins). The entier library is using an object oriented approach, hiding al lot of optimizations. While optimizing DireX(http://www.schroderlab.org) density processing, it became helpful to extract the density handling from the original program and offer all functions in another module. The first approach was SplitFFT which just extracted functions operating on densities, today the entire datamanagment has been ex- tracted.

INSTALL:

Installing PDEN is pretty straightforward on Unix or Unix-like (Linux, Mac OS X, BSD) systems with a C compiler, Make and GNU Build Tools (using GIT) installed. Installing on other platforms is not tested but should be possible on Windows using MinGW.

PDEN depends on FFTW3 (see Dependencies).

Default Installation:

If you start from GIT, please run:

$ sh autogen.sh

It will setup the buildscripts and directly call configure with the given arguments and make.

If you downloaded a package (tar.gz ...) please run:

$ sh configure

You can get information about available configuration options by running:

$ sh configure --help

If everything went okay, type

$ make

to build the library and all tools.

Finally to install to a system-wide location you might need to become root or:

$ sudo make install

Important configuration options are: --enable-openmp/--disable-openmp to build lib with openMP support (default is yes) (in development)

--enable-single/--disable-single       to build as single precision library
                                       this can be usefull if you plan to 
				   handle sets of densities to reduce 
				   memory footprint (default is double) 

TOOLS:

The tested tools of PDEN. Especially if you start building from GIT there may be additional tools available.

pdnormalize      normalize a density map to mu=0.0 and sigma=1.0

pdcalcsf         calculate the structur factor of a density (radial 
                 structure factor)

pdapplysf        apply a structure factor correcting function (today only
                 Babinet's principal is supported

pdrefinesf       refine coefficients for structure factor correction that 
                 can be used in 'pdapplysf'

LIBRARY:

A documentation of the library can be created using Doxygen.

$ sh autogen.sh doxygen

All exported/pulic functions are listed in pden.h (double precision) and pdenf.h (single prcision

DEPENDENCIES:

Right now PDEN only depends on FFTW3 for Fourier transforms. The library is available at http://www.fftw.org.

On Linux most distributions offer the FFTW3 as a prebuild package. Use:

apt-get install fftw3

on Debian, Ubuntu etc. or

yum install fftw3

on Fedora, Suse, Redhead ...

If you have to install FFTW3 it is suggested to install single and double precision libraries. Therefor you have to build fftw3 twice.

Change to FFTW3 source directory and run:

$ sh configure $ sh make

and as root or sudo:

$ make install

Now you have to build the single precision library:

$ make clean $ configure --enable-float $ make and again as root/sudo:

$ make install

On newer Macs with OS X ( >= 10.7 ? ) there is a known problem with the library path, so if this problem appears please run:

$ echo "PATH=/usr/local/bin:$PATH export PATH" >> ~/.bash_profile

KNOWN BUGS:

• compiling on linux with gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) could causes problems during sfrefinement: "Armijo rule line search not converged" SOLUTION: could be removed because of some changes in the code seems to be connected to type qualifiers nd optimization

• compiling with "-ffast-math" causes several functions to produce very large values SOLUTION: do not use "-ffast-math"