# The &kembabel; Handbook

Francesco
Bresciani

    fbresciani@users.sourceforge.net

2000-2002
Francesco Bresciani
&FDLNotice;
01/21/2002
0.1.10

This handbook documents &kembabel; version 0.1.1

&kembabel; is a program distributed with &kemistry; designed to interconvert between several chemical file formats.

KDE
Kemistry
Chemistry
KemBabel
File conversion

## Introduction

&kembabel; is a program designed to convert between several chemical formats. Actually &kembabel; is simply a graphical version of &openbabel; since it is linked to the &openbabel; library. &openbabel; is the open source version of a well known program: Babel

### &kembabel; features

Here is a brief list of &kembabel; features:

- &kembabel; can read and write all the file types supported by the &openbabel; library.

- &kembabel; can apply some transformations before writing the converted file

## Using &kembabel;

Using &kembabel; is really simple. Simply enter the input and output file name and format (or choose Autodetect from file extension).

If you want to apply some transformations select the trasformations to apply in the Common options tab.

To write the converted file click on the Convert

## Command reference

### &kembabel; window

The following image shows the &kembabel; main window

Input file

  The input file name should be entered here

Input file format

  Select the format of the input file from this list or choose Autodetect from file extension to detetct automatically the file format from the input file extension

Output file

  The output file name should be entered here

Output file format

  Select the format of the output file from this list or choose Autodetect from file extension to detetct automatically the file format from the output file extension

Convert

  Clicking this button the conversion will be performed (after applying the requested transformations)

Help

  This button shows the standard &kde; help menu

Close

  Clicking this button will exit &kembabel;

#### Transformation options

Delete hydrogens

  Checking this item, hydrogen atoms will be removed before writing the converted file. This option is equivalent to the &openbabel; ``-d`` option.

Add hydrogens

  Checking this item, implicit hydrogen atoms will be added before writing the converted file. This option is equivalent to the &openbabel; ``-h`` option.

Add hydrogens appropriate for pH

  Checking this item, implicit hydrogen atoms appropriate for pH will be added before writing the converted file. This option is similar to the above one, but uses a group of trasnformations defined in the file `phmodel.txt`. This option is equivalent to the &openbabel; ``-hpH`` option.

## Credits and License

&kembabel;

Program copyright 2002 Francesco Bresciani fbresciani@users.sourceforge.net

Contributors:

Documentation copyright 2002 Francesco Bresciani fbresciani@users.sourceforge.net

&underFDL;

&underGPL;

## Installation

### How to obtain &kembabel;

&kembabel; is part of &kemistry;, a collection of chemistry application for &kde;. See the &kemistry; Homepage or the &kemistry; project page on SourceForge for information on obtaining &kemistry;.

### Requirements

In order to succesfully compile &kembabel; you need &kde; 3.0

All required libraries can be found on ftp://ftp.kde.org/pub/kde/

### Compilation and Installation

In order to compile and install &kembabel; extract the &kemistry; package and type the following commands in the base directory of the &kemistry; distribution:

    %./configure
    %make
    %make install

See the &kemistry; Homepage for further informations on compiling and installing &kemistry;.

Since &kemistry; uses autoconf and automake you should have no trouble compiling it.

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