I just noticed that the latest update to iBabel has now been downloaded over 500 times.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates, but gradually became unsupportable. So rather than try to patch the AppleScript Studio/ApplescriptObjC application I decided on a starting afresh with a complete rewrite using Cocoa/Swift to take advantage of new technologies, this has meant some features have been lost, some new ones added but hopefully the core features are still there.

Instructions for download and installing are on the main iBabel page, remember you need to install OpenBabel first.

 

I just noticed there have been 250 downloads of iBabel4, I can count these like citations right ? 😁 x You can download iBabel here.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel

I'm starting to compile a list of updates/additions, if you have any suggestions let me know.

 

I just noticed there have been 150 downloads of iBabel4, I can count these like citations right ? 😁

You can download iBabel here.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel

 

A minor update to iBabel Currently when you use the Viewer tab to display molecules only a 2D display is available as shown below.

However, now there are a couple of radio buttons below the image that can be used to choose either a 2D viewer or 3D viewer, this should be particularly useful when looking at the conformation of docked ligands. It should be noted that this does not actually generate a 3D structure it merely displays the input file using a 3D viewer 3Dmol.js if the file only contains 2D coordinates a 2D structure will be displayed.

You can read more and download iBabel here.

 

The current COVID-19 pandemic has resulted in many groups sharing chemical structure files, however it is useful to understand the file format definition to do so accurately. There are many chemistry file formats, iBabel using the OpenBabel toolkit supports around 100 different file formats. One of the most popular is the sdf file format.

When handling, searching, combining sdf files it is often very useful to have a unique identifier to act as a key for each molecule, many software packages expect this to be the first line or title, unfortunately this line is often left blank and the unique identifier is held in a data field that might be called "ID", "IDNUMBER", "MOL", "molNAME"……..

iBabel can be used to generate the title in these cases, there is a detailed description of how to do this here.

You can download iBabel here.

 

A number of times recently I've come across interesting publications regarding molecules that might be of interest for treating COVID-19.

An example being and this review by The Centre for Evidence-Based Medicine provides an excellent summary of the trials that are taking place. Unfortunately, it does not include the structures of the drugs named.

You can use molSeeker to get an individual molecule but what if you want to get a list of molecules?

Fortunately, you can use iBabel to get all the structures from PubChem.

Here is a 2 minute video showing how it is done.

You can download iBabel here.

 

At the start of 2020 I decided that I'd try learning to program in Swift using Xcode, my first project was molSeeker a tool for searching online resources using chemical identifiers. This was really just a vehicle for me to learn Swift and now I'm delighted to be able to release a more substantial effort, a complete rewrite of iBabel.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates. However, recent changes have made this unsupportable so I decided on a complete Cocoa/Swift rewrite.

You can read all about the new version of iBabel here including the links to the download. I've attached a couple of screenshots to give you an idea of what functionality is available.

File Conversion Tools

Viewing Molecule Files

Extension of molSeeker

iBabel 4.0 is freely available for download.

Many thanks to Peter Ertl and Bruno Bienfait for the JSME editor and David Koes for 3Dmol.js the 3D viewer and all the OpenBabel team.

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 70,000 unique visitors with 25% visiting the site on multiple occasions. The US provided 30% of the visitors and the UK 7% with Germany, India and France around 5%. As you might expect the majority were Mac users (56%), but there were also Windows (25%), iOS (12%), and Android (2.5%) users.

Of the Mac users, 51% are now using 10.14 (Mojave), 27% 10.13 with all older versions each well below 10%.

Chrome and Safari were the preferred browsers with both around 40%.

The most popular web pages were (other than the main page)

• Fortran on a Mac
• Cheminformatics on a Mac
• Data Analysis Application on a Mac
• iBabel
• ChemDraw 17 review
• LaTeX and MathML support in Pages

The popularity of the Fortran on a Mac page has continued for several years now and it has been updated several times with user provided information.

The most viewed blog pages in 2018 were

• Xcode 9.0 is available for download
• Scientific Applications under Mojave
• Mac OSX installer for Coot
• Scientific keyboards for iOS
• Tools for Mac Fortran Programmers

The update to Mojave seems to have been another daily smooth transition, with most software developers reporting no major issues.

A couple of recent additions have generated significant interest.

• Cheminformatics toolkits - A listing of Cheminformatics toolkits

• Data Science Libraries - A list of useful python libraries for data science

As has an article I wrote on my thoughts on scientific software

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 60,000 unique visitors with 25% visiting the site on multiple occasions. The US provided 30% of the visitors and the UK 10% with Germany, Canada and Japan around 5%. As might be expected 60% of the visitors were using a Mac, but 25% of the visitors were Windows users and 10% iOS. Looking at the last month's Mac visitors, 53% were using Mac OS X 10.13, 25% 10.12 and 12% 10.11.

Safari and Chrome (each 41%) were the most used web browsers with the once dominant Internet Explorer down at 2%.

The most viewed blog pages in 2017 were

• Installing Molden
• ChemBioDraw and Word 15
• Mac OSX installer for Coot
• Scientific keyboards for iOS
• Tools for Mac Fortran Programmers

The most popular web pages were (other than the main page)

• Fortran on a Mac
• Cheminformatics on a Mac
• Data Analysis Application on a Mac
• Hints and Tutorials
• Spectroscopy
• Reference Management

The continued popularity of the Fortran on a Mac web page is interesting, I'm not a big Fortran user but if anyone knows of items that could be added to the page I'd be delighted to hear about them. I've done a couple of updates to the Cheminformatics on a Mac page and I think I'll need to add a section on Bioconda in the future.

Interestingly the Scientific Applications under High Sierra page was of only transient popularity. It seem this update to Mac OSX was relatively benign with very few issues.

2017 also saw the 2000th download of iBabel, iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a molecule viewer. I'm planning to do an update to iBabel to take advantage of some of the updates to OpenBabel but if you have any suggestions I'd happy to see if I can include them.

2017 also saw the migration of the website from http to https, a change that went pretty seamlessly with only a couple of minor glitches.

The Twitter feed is increasing in popularity with 390 followers. The most popular tweets were

Creating a Bioconda recipe
RSC meeting on AI in Chemistry

The RSS feed still has around 100 followers

 

I just noticed that the latest version of iBabel has been downloaded over 1000 times, this is fantastic news and it certainly allows me to justify the effort put into creating the application.

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 javascript viewers via an embedded web view.

I’m occasionally asked about the best way to install OpenBabel and I usually refer people to the page I wrote on installing cheminformatics tools on a Mac, this gives instructions on how to install a wide variety of cheminformatics toolkits and applications.

If you only want to install Openbabel then the best way is to use Homebrew.

Homebrew is a package manager for Mac OSX that installs packages in it’s own directory then symlinks the files to /usr/local. To install Homebrew you first need to have access to the command line tools for Xcode, the easiest way to do this is to download Xcode from the Mac Appstore

1. Start Xcode on the Mac.
2. Choose Preferences from the Xcode menu.
3. In the General panel, click Downloads.
4. On the Downloads window, choose the Components tab.
5. Click the Install button next to Command Line Tools. You are asked for your Apple Developer login during the install process.

Or You can download the Xcode command line tools directly from the developer portal as a .dmg file. https://developer.apple.com/downloads/index.action. On the "Downloads for Apple Developers" list, select the Command Line Tools entry that you want.

To install Homebrew type this command in the Terminal

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

Then type

brew doctor

The 'brew doctor' command checks everything is fine. e.g. it will warn if the developer tools are missing, and if there are unexpected items in /usr/local/bin and /usr/local/lib that may clash and might need to be deleted.

It is a good idea to first update the package list

brew update

To install a range of cheminformatics packages we can use a custom “tap” created by Matt

brew tap mcs07/cheminformatics

Then to specifically install Openbabel use

brew install mcs07/cheminformatics/open-babel

To check OpenBabel is working type this in a Terminal window:

obabel -:'C1=CC=CC=C1F' -ocan 
Fc1ccccc1   
1 molecule converted

 

I just noticed that the latest version of iBabel has now been downloaded over 700 times since it was released at the start of the year.

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.

 

I just noticed that iBabel has now been downloaded over 500 times since the start of the year. I'm surprised and delighted that it has proved so popular.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a variety of molecule viewers.

 

The latest version of iBabel has now been downloaded over 400 times since it was released in January.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and molecule viewers

 

I thought I'd have a look at the number of downloads of iBabel there have been since I announced the latest release last month. So far there have been over 250 downloads and there seems to be a steady stream of downloads as shown in the plot below.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a selection of molecule viewers

 

A couple of readers have asked if they need to install OpenBabel in order to use iBabel. The answer is YES, iBabel is a graphical user interface that means you don't have to remember all the command line instructions in order to use OpenBabel.

More details here…

 

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.

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 calls to remote web servers to provide javascript viewers also cause security issues. 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. Security updates, Sandboxing and changes within El Capitan also meant I had to update a number of features.

Now things have settled down a bit I've restarted work on iBabel and an update is now available.

I've transitioned most of the calls to babel over 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.

Updating the viewers however has taken more time than I expected with new security features in Mac OSX updates causing unexpected issues. Whilst not yet complete, I have removed all the java or plugin-based molecular viewers and replaced them with javascript versions.

Full details are here.

I’ve been slowly updating iBabel.

As you might have imagined the issues with Java security have made it impossible to support the use of Java Applets as the molecule viewer so I’ve been busy trying out various options. I’ve decided to abandon the use of Java applets and the use of plugins; sorting out which version of a plugin works with which version of browser and/or operating system version was becoming a nightmare. So I’m moving to a variety of Javascript based molecule viewers.

There are now separate versions for Mac OS X 10.7.x and 10.8.x

More details on the iBabel3 page.