Macs in Chemistry

Insanely great science

 

A comparison of six chemical drawing packages A chemical drawing package is an essential part of any chemist’s software collection and there are now an increasing number of alternatives ranging from free to very expensive. Chemists become very attached to a particular package and in an ideal world would prefer to use the same package for creating publication quality structures for manuscripts, as the front-end to query databases and as a front-end to chemoinformatics tools. Unfortunately it seems that every database uses a different drawing package and learning the quirks and limitations of each package is tedious. Interestingly ChemSpider structure searching (http://www.chemspider.com/StructureSearch.aspx) now offers a range of six different chemical drawing packages to allow the user to choose their favoured package. It also provides the ideal opportunity to compare the different chemical drawing packages side be side. If you go to the ChemSpider structure search page, and then click on the chemical structure a new window opens, there is the option to enter a text identifier such as a SMILES string or CAS Number however if you click on the “Draw Structure” tab you will be taken to the chemical drawing page.

inout_structure ACD Labs/SDA The default seems to be ACD/Labs SDA (Structure Drawing Applet) which is shown below, this is a Java app and for security reasons you will be required to give approval depending on your download speed the application may take a few 10s of seconds to appear. The alternative drawing packages can be accessed using the radio buttons at the bottom of the page.

acdlabs ACD Labs/SDA is a well established application and to be honest the interface now looks rather old-fashioned, and it is sometimes difficult to see which of the buttons is chosen (which can lead to drawing a structure based on bromine atoms!). To draw structures simply click on a particular atom type and then simply click and drag to create atoms and the joining bonds. To change an atom type you choose a different atom from the left hand column and then click on an atom in the structure, unfortunately ACD Labs/SDA does not support keyboard entry to change atom types which I find very useful, you also can’t select multiple atoms and change all to the same atom type (eg when drawing CF3). There is also a periodic table to choose less often used atom types. The Radical Table (highlighted in red) gives access to a wide range of functional groups, you then simply click to add these to the structure. This works fine for most groups but I’d not be happy with the way nitro groups are displayed. nitro In theory templates should be available from the “Templates” button but I found it only opened an empty window. Reading the manual it does seem that creating fused structures involves a rather convoluted process. A couple of things I found slightly irritating 1) when you open the periodic table or radicals window you can’t edit anything in the main window until you close the other windows and 2) I find colour coding heteroatoms very useful. 3) The “Clean Molecule” function expands the structures to fill the window, so if you use it to clean a structure halfway through drawing it becomes difficult to see further additions to the structure.

Symyx JDraw This is another Java application but the interface looks cleaner and more modern, although the letters on the atom type buttons at the bottom of the drawing panel and on the templates in the upper bar are rather small.

jdraw

To start drawing in JDraw you select a bond type and then click and drag to construct the skeleton (all in carbons) and then change the atom type subsequently. A limited number of ring templates and functional groups are are available from the top menu bar, and depending on whether you click on an atom or a bond the rings are added or fused as appropriate, and nitro groups are drawn as expected. The “Clean Molecule” function returns a structure with the same scaling as the original. The left hand menus give access options for changing bond or atom types and a right-click on an atom or bond gives further options. It is possible to change atom types via the keyboard but it works via a popup text box which seems rather cumbersome.

Elemental Elemental is written in javascript and so there is no java security dialog, it also loads very quickly. The interface is clean and uncluttered with all the regularly used functions visible.

elemental To draw structures simply choose an atom type and then click and drag to construct the molecule. To change atom types use the buttons on the left, select from the periodic table (highlighted in red) or point to an atom and use the keyboard using atomic labels (C=Carbon, Cu = Copper). Atoms are coloured using conventional coding and the valency is modified automatically. Construction of complex structures is aided by a large selection of templates available from the top menu button (highlighted in green), this includes monocyclic and bicyclic rings and users can add their own templates. Templates are added to existing structures by clicking on atoms or bonds. The built-in templates are stored in an SD file on the server. This contains tags that supply a name for each template and the template group that they belong to (e.g. 5-membered rings).The user defined templates are stored as molfiles in cookies on the user's machine.

rings A right-click on an atom or bond gives further options, in particular advanced query options. The “Clean Molecule” function returns a structure with the same scaling as the original. If you select the whole structure then right-click there is the option under “Template” to “Save Fragment” this adds it to the user defined templates. The “Clean Molecule” function returns a structure with the same scaling as the original

Ketcher Ketcher is also written in javascript and again loads rapidly, the interface is clean with all the most useful functionality readily available.

ketcher To draw structures simply choose an atom type and then click and drag to construct the molecule. To change atom types use the buttons on the right, the same atoms can be added using the keyboard with the exception of Cl (use Shift C) and Br (use Shift B). To add any other atom types you need to double click on an atom and enter data in the dialog box. Despite the atoms being colour coded in the side bar the atoms in the structure are not colour coded. There are only a few rings available, there is an option to load SMILES but that appears to require linking to a server.

JME Many people will be familiar with the JME java applet from Peter Ertl, it seems to have been around for a long while now and whilst it looks rather dated it is simple to use and has a couple of useful features.

jme To draw structures simply choose an atom type and then click and drag to construct the molecule. To change atom types use the buttons on the left. To add any other atom types you need to click on the “X” button and enter data in the dialog box. The atoms are colour coded automatically. There are only a few rings available and no option to add additional templates. One nice feature is the one click access to SMILES strings, simply click on the “SMILEY” and a text box opens containing the SMILES string.

smiles_conv The “Clean Molecule” function returns a structure with the same scaling as the original.

JChemPaint JChemPaint is the editor and viewer for 2D chemical structures developed in java using CDK. The interface has improved considerably recently.

jchempaint To draw structures simply choose an atom type and then click and drag to construct the molecule. To change atom types use the buttons on the bottom, or select from the periodic table (highlighted in red) or change to keyboard input, this works via a dialog box which is a little cumbersome. Atoms are coloured using conventional coding and the valency is modified automatically. Construction of complex structures is aided by a very large selection of templates available from the top menu item. There are also menu items to modify atoms and bonds, or to copy as SMILES in the “Edit” menu. The structure can also be saved locally in SMILES, MDL Mol or CML format and then opened later.

The choice of chemical drawing package is a very personal choice but I tend to favour the non-Java applications simply because they can be used on mobile devices such as an iPad. At the moment Elemental appears to be a much more fully featured than Ketcher.

More Reviews and Tutorials