Macs in Chemistry

Insanely Great Science

Scaffold Hunter update


Scaffold Hunter is a chemical data organization and analysis tool and that has been continuously enhanced since the start of its development in 2007. The platform-independent open-source tool was first released in 2009 and provided an interactive visualisation of the so-called scaffold tree, which is a hierarchical classification scheme for molecules based on their common scaffolds. A recent publication describes recent extensions that significantly increase the applicability for a variety of tasks DOI.

When I first opened the application I did not find it particularly intuitive, fortunately there is a online tutorial and sample datasets available.


Java Applet Technology: The Past and Future and The End


An interesting article from ChemAxon on the history and demise of Java Applets.


A review of cApp


One of the most common tasks for those involved in cheminformatics is handling files containing molecular information, these files can be in a variety of file types and usually the task involved is relatively minor. cApp is Java application that provides a simple interface to a variety of everyday activities.

cApp requires JRE7 and uses the Chemistry Development Kit (CDK), an open-source Java library for chem- and bioinformatics, and associated software, JChemPaint as chemical editor, and routines developed within the Program Collection for Structural Biology and Biophysical Chemistry by the Hofmann group. Full details of cApp are described in a J Cheminformatics paper DOI.

You can read the review here.


Java security update

Oracle Security Alert for CVE-2012-4681

Description This Security Alert addresses security issues CVE-2012-4681 (US-CERT Alert TA12-240A and Vulnerability Note VU#636312) and two other vulnerabilities affecting Java running in web browsers on desktops. These vulnerabilities are not applicable to Java running on servers or standalone Java desktop applications. They also do not affect Oracle server-based software. These vulnerabilities may be remotely exploitable without authentication, i.e., they may be exploited over a network without the need for a username and password. To be successfully exploited, an unsuspecting user running an affected release in a browser will need to visit a malicious web page that leverages this vulnerability. Successful exploits can impact the availability, integrity, and confidentiality of the user's system. In addition, this Security Alert includes a security-in-depth fix in the AWT subcomponent of the Java Runtime Environment. Due to the severity of these vulnerabilities, the public disclosure of technical details and the reported exploitation of CVE-2012-4681 "in the wild," Oracle strongly recommends that customers apply the updates provided by this Security Alert as soon as possible.

Download for the update is here


Chocolat Mac text editor

I’m a long time BBEdit user but I do keep an eye out for Mac text editors. Chocolat is a new text editor for the Mac that might be worth looking at, it supports split-window editing, code folding, and code completion. It can be used for a wide range of programming and scripting languages.


SMARTCyp Updated

SMARTCyp 2.2 has been released including the following updates:   One new energy rule for sulfur atoms double bonded to sp2 carbon atoms. Update protonated amine SMARTS matching due to analysis of larger 2D6 data set. Faster predictions by rewriting the SMARTS matching code for the pharmacophores in the 2D6 and 2C9 models. Web site update with links to the 2C9 model paper, and prediction accuracy results on nine different isoforms.


SMARTcyp Updated

SMARTCyp has been updated to version 2.1.1. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450 a major contributor to oxidative metabolism.

The latest update now includes models for prediction of CYP2D6 and CYP2C9 specific metabolism


Added ChemDoodle

New java-based chemical drawing package added to list of applications. Read More...

Marvin and JChem

Marvin and JChem have been updated

Marvin Update

Marvin 5.0.1 has been released.

ChemAxon's 2008 European User Group Meeting

ChemAxon's 2008 European User Group Meeting will be held on Wednesday and Thursday, May 7-8 at the Thermal Hotel, in Visegrad, Hungary Read More...

Instant JChem Review

A review of Instant JChem an easy to use chemical structure database. Read More...

Marvin Updated

Marvin has just been updated, I've made a few additions to my review. Read More...

Mavin Review

I've written a review of Marvin from Chemaxon.


I just heard about this offering from ChemAxon LibraryMCS clusters a set of chemical structures on a structural basis. Read More...


I had a message from ChemAxon saying they had updated some of their products and I thought it might be worth a summary of their wares. Whilst Java based everything works fine on a Mac and note:-
  1. Instant JChem Personal (an new OS independent desktop application for working with chemical and non chemical data) and Marvin, a chemical editor and viewer suite are free for all users
  2. All products are free for academic teachers and researchers - including the enterprise edition of Instant JChem
  3. Most products are free for freely accessible, non commercial websites