Sunday, September 13, 2009

3 Tools For Chemistry Students Using Ubuntu

BKChem is a chemical drawing Ubuntu chemistry software that’s packed with 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
Support for linear formulas (such as -CH2CH(COOCH3)2)
radicals, charges...
arrows (several types - normal, retro, equilibrium, etc.)
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 ODF (OpenOffice 2.0) format
full export to Encapsulated PostScript
full export to PDF
full export to PNG (if pycairo is installed, available in Windows binary build)
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, Polish, German and Traditional Chinese translations are available)
native format is XML based
validity checking of drawn structures
support for user written plugins
support for user written batch scripts
searching for BKChem files containing specified molecules or molecule fragment
Screenshot20090908at10.38.37

Chemical Calculator or GChemCalc is another Ubuntu chemistry software app that’s a simple chemical calculator for determining molecular weights of a formula and their respective percentages, all really fast and easy. There’s not much to be said about it, except I use it all the time – simple is almost always better.

Screenshot20090908at10.41.43
Kalzium provides you with all kinds of information about elements in the Periodic Table of the Elements. You can lookup information about the elements and also use visualizations to show them. It is free and licensed under the GNU Public License.
You can visualize the Periodic Table of the Elements by groups, blocks, and families. You can plot data for a range of elements for properties like the boiling point or the atomic mass and can go back in time and see what elements were known at a given data.
Screenshot20090908at10.41.30
Kalzium is divided in a navigation panel on the left and the table view which shows the elements of the periodic table. The standard menu bar allows you to choose what you want to display and the status bar reports facts. You can hide the navigation panel by using the View->Show Sidebar menu.
Screenshot20090908at11.52.52
When you move the mouse cursor on an element of the table, an overview of the current element in the Overview tab of the navigation panel will be displayed. You can choose  several views for the table: display the elements per families, per groups, per crystal structure, depending on their acidic behavior, etc. You can change all that in the menu bar in the View->Scheme menu. If you want to know facts about a precise element, click on it in the table and the information dialog will be displayed.You can also calculate the molecular mass of molecules with the tool in its sidebar. You can enter linear formulas to calculate their weight.

Screenshot20090908at11.57.03
You can install any of the Ubuntu chemistry software applications discussed in this article by searching for their name in the Synaptic Package Manager, checking the box on the left of its name and clicking ”Apply Changes”. To launch Synaptic, choose System > Administration > Synaptic Package Manager.

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