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

July 23, 2015
Takeshi Kawabata
(kawabata@protein.osaka-u.ac.jp)
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 ckcombu is developed for converting the file format of chemical structure. Especially, the program ckcombu can input and output SMILES string, it can generate a 2D structure of chemical comound.

Installation

The source code of the kcombu is mainly written in C, and developed and executed the linux environment (actually on the Fedora Core). 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:

download the file "kcombu-src-[date].tar.gz" file.
```
tar zxvf kcombu-src-[date].tar.gz
```
```
cd src
```
```
make -f Makefile.ckcombu
```

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

Simple Usage of 'ckcombu' program

for converting into SDF format.

$ckcombu -A [molecule_file] -osdf [output SDF file]

for converting into SMILES format.

$ckcombu -A [molecule_file] -osmi [output SMILES file]

for making 2D-coordinates and writing in SDF format.

$ckcombu -A [molecule_file] -gen2d T -osdf [output SDF file]

for assigning 'DAMRL' atomic classification as the ChainID of output PDB file.
```
$ckcombu -A [molecule_file] -opdbdamrl [output PDB file]
```
for showing options in detail
```
$ckcombu -h
```

Reference

Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf.Comput. Sci. 28, 31-36 (1988).
Weininger, D., Weininger, A. & Weininger, J. L. SMILES. 2. a lgorithms for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci. 29, 97-101 (1989).