Free chemical software for linux

kfile_chemical is a set of kfile plugins for chemistry documents. It has support for XYZ, PDB, MDL mol/sd, Mol2, CML, ShelX, SMILES and CIF files.
kfile_chemical is currently in alpha stage: 1.0 will be alpha too; it will be feature complete, i.e. proving plugins kfile plugins for all files mentioned at the official chemical mime page (and a few more).
Version 2.0 will be beta, and feature a more organized set of extracted pieces of information.
Version 3.0 will be beta too, and mime magic, which is a method to detect the mime type not from the file extension, but from the content.
Verion 4.0 will be the first stable release and is aimed to be ready with Kubuntu 6.04 and KDE 4.0.
Enhancements:
- This release adds support for chemical-mime-data, thus synchronizing with the main MIME type library for chemical data.
- It also fixes QChar / QString conversion, the FSF address, and the contact email address.

GChemPaint is a 2D chemical structures editor for the Gnome desktop.

GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.

Chemtool project is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Chemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. XDrawChem is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.

BKchem is a free chemical drawing program. BKchem was concieved and written by Beda Kosata.
BKchem is written in Python, an interpreted and very nice programming language.
Main features:
Drawing
- bond-by-bond drawing
- bond lenght and angle restrictions to assist with the drawing
- ready to use templates of common rings
- ability to expand common groups from abbreviated to structural form
- radicals, charges...
- arrows
- rich text
- color support
- simple vector graphics (rectangles, circles, polygons etc.)
Editing
- unlimited undo and redo capabilities
- aligning
- scaling
- rotation (2D, 3D)
- aligning of molecules so that particular bond is horizontal/vertical
- rotation of molecular fragments around bonds (conformation changes)
- definition of personal preferred drawing style (bond lenghts, widths, colors...)
Export
- full export to SVG (native data are transparently embedded into SVG file)
- full export to OpenOffice Draw format
- full export to Encapsulated PostScript
- basic support for both CML1 and CML2
- Molfiles
- generation of SMILES
Import
- basic support for both CML1 and CML2
- Molfiles
- SMILES (subset)
- INChI (subset)
Other features
- localization support (currently English, French, Czech and Polish translations are available)
- native format is XML based
- validity checking of drawn structures
Whats New in 0.11.6 Stable Release:
- In this release, two major bugs were fixed: one in the German translation (causing a crash when a file was saved) and one in the OpenOffice export plugin.
- A few other minor bugs were also fixed.
Whats New in 0.12.0_02 Development Release:
- This release fixes several bugs, most importantly incompatibility with Python 2.5.

Kemistry is a collection of chemical applications for the K Desktop Environment (release 3.x).

Originally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are

* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel

KMol calculates the elemental compositon and molecular weight of compounds from their chemical formula. KMol supports user defined groups and elements, unlimited nesting of subgroups, multicomponent compounds, global and per-user symbol definitions.
KMol is designed to be able to parse any chemical formula that can be
unambiguously interpreted if written as a simple character sequence (i.e.,
without subscript and superscript formating). If you can understand a chemical
formula, chances are KMol will understand it in exactly the same way.
Enhancements:
- Fixed KDE3 compilation problem. Fixed saving of user-defined weights.

KryoMol project is a KDE based program for visualization and analysis of several chemistry related files. Currently KryoMol can cope with:
- Quantum Chemical Computation logs from Gaussian98/03, GAMESS, ACESII (german version), and NwChem
- Molecular Mechanis Logs: Tinker, Macromodel
- Other formats as xyz or mol
- 1D NMR spectra and JCAMP-DX spectra
Installation:
KryoMol is a autoconf/automake based program and installs itself with the common configure/make/make install procedure.
Installation as root
$ ./configure
$ make
$su
$make install
and now log out and log in ( I strongly recommend this to properly load all new libraries and services).
Installation as user
If you dont have root privileges and want to try KryoMol you must install it in a directory with write permissions, therefore you must use the prefix switch in configure. For instance if you want to install under your personal kde tree $./configure --prefix=/home/user/.kde
$make
$make install
log out and log in
Installation as user in a new kde tree
If you want to install in a compleptly new KDE tree, for instance /home/user/mykde you must follow the above procedure:
$./configure --prefix=/home/armando/mykde && make && make install
and now add this to your .bash_profile:
MYKDE=/home/armando/mykde
export KDEDIRS=$MYKDE:$KDEDIRS
export LD_LIBRARY_PATH=$MYKDE/lib64:$LD_LIBRARY_PATH
export PATH=$MYKDE/bin:$PATH
Enhancements:
- ECD/VCD/UV spectra are properly represented
- Scale is draw in UV/ECD spectra
- Solved problem with capitalized extensions
- Solved problems in xyz parser
- Solved problem when closing window and animation is active
- Solved a bug in the varian nmr parser
- Opening of nmr spectra over remote protocols
- Solved bug in format when exporting hessian
- Replaced some old QFileDialog and QPrinter stuff by KDE widgets
- Solved problem when loading printer icon on QIRWidget