Instruction for the command 'pkcombu' in the "KCOMBU" program

Jan 6, 2014
Takeshi Kawabata
Laboratory of Protein Informatics
Institute for Protein Research, Osaka University

[Reference for KCOMBU]
Kawabata T. Build-up algorithm for atomic correspondence between chemical structure. J.Chem.Info.Model., 2011, 51, 1775-1787.

The program 'pkcombu' is for pairwise chemical structure comparison.


The source code of the kcombu is mainly written in C, and developed and executed the linux environment. Some additional programs for 2D graphics and statistical analyses are written in python. For the installation, you need the gcc compiler. If you want to use another compipler, please change the "Makefile" in the "src" directory. The standard installation procedures are as follows:

  1. download the file "kcombu-src-[date].tar.gz" file.
  2. tar zxvf kcombu-src-[date].tar.gz
  3. cd src
  4. make -f Makefile.pkcombu

If the sources is successfully compiled, an execution file "pkcombu" will appear in the "../src" directory.

For 2D molecular graphics, we prepare python scripts in the directory "src/moldraw". The script "moldraw.cgi" is for making image/PDF file of 2D molecules, it requires python and Python Imaging Library (PIL) ( ).

visualizing pairwise atom matching using the moldraw program

When you calculate a pairwise atom matching by typing a following command,
   $pkcombu -A molA.pdb -B molB.pdb -oam 

an atom-matching file "" is generated. The python script "moldraw.cgi" is stored in '[kcombu_directory]/src/molimg/' A following command generates a PNG-format image file "out.png"
  $moldraw.cgi -iam

The image file "out.png" can be visualized by standard photo-retouching programs, such as "display" or "eog".
   $display out.png
   $eog out.png
The program "moldraw.cgi" can also generating PDF file by a following command:
  $moldraw.cgi -iam -G P -of out.pdf

Format of the file generated by pkcombu program