Macs in Chemistry

Insanely Great Science

Strings in Swift 2

 

The latest entry on the Swift Blog discusses a change in the way Strings are handled in Swift.

Read more here

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SeeSAR version 3.2 released

 

SeeSAR 3.2 can now be used in cases where there is no protein. For example if for the analysis of a ligand-based virtual screen

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Release Notes version 3.2 2015-07-24

Utilizing SeeSAR without a protein

  • SeeSAR has grown from a single purpose affinity assessment tool to a multi purpose 3D structural viewer for compound design and prioritization. With this update it is now also possible to use all these nice features for 3D ligand-based projects. You may, for example, visually inspect small molecules alignments. You may filter a hit list by means of calculated and external properties...
  • Big data booster, With version 3.0 we first equipped SeeSAR with database functionality. Version 3.2 comes with a load of performance enhancements that speed up the calculation by up to a factor of 5, now utilizing all available CPUs in your computer even more efficiently.
  • 3D graphics enhancement, In this version we updated the graphics support and SeeSAR is now compatible with more graphics cards than ever before. Especially the compatibility with integrated graphics cards (the type most frequently found in laptop computers) - which used to be the major trouble makers - has been greatly improved.

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ChEMBL python update.

 

Excellent blog post on the ChEMBL python update.

http://chembl.blogspot.co.uk/2015/07/chembl-python-client-update.html




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So what's happening with iBabel?

 

A couple of people have asked me what is happening with iBabel recently so I thought I'd give a bit of background.

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of java applets and plugins via an embedded web view.

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This all worked perfectly for a while but various security issues mean that java applets and plugins via an embedded web view no longer function. In addition OpenBabel has been substantially rewritten so that many of the small programs built on OpenBabel are no longer supported. This functionality has not been lost however, they have now been incorporated into the main OpenBabel program.

Now things have settled down a bit I've restarted work on iBabel, I've transitioned all the calls to babel to obabel the differences are highlighted here and replaced the calls to the tools based built on OpenBabel with the new corresponding calls to obabel.

I'm in the process of replacing the java and plugin based molecule viewers with javascript-based alternatives.

All being well I hope to have a new version for next month.

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Accessing Open Source Malaria Data using an iPython Notebook

 

The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.

I've recently published a Vortex script to access the information, I've now published an iPython notebook that also shows how to import the data. Why not give it a try and then contribute your findings and suggestions to the Open Source Malaria project.

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