Macs in Chemistry

Insanely Great Science

Over 1000 downloads of iBabel

 

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.

3dviewers

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

Comments

Over 700 iBabel 3.6 Downloads

 

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.

viewersss


Comments

iBabel over 500 downloads

 

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.

3dviewers

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.


Comments

Over 400 iBabel downloads

 

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

3dviewers

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


Comments

iBabel Downloads

 

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.

ibabeldownloads

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


Comments

iBabel and Openbabel

 

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.

3dviewers

More details here…

Comments

iBabel 3.6 is released

 

Bable

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.

Comments

iBabel3

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.



Comments

Cheminformatics on a Mac

I gave a talk at the Cambridge Cheminformatics meeting last week, I’ve put the slides here. It was more of a demonstration than a talk but the slides give an overview and links to the various tools.

Slide01

Updated

A couple of people have asked for a pdf version of the slides for download.



Comments

iBabel update

I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.

The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle and Chris Morley in particular the ability to colour a substructure within a molecule. This requires installation of the development version of OpenBabel at present.

I’ve added a movie to show it in action.

Comments

iBabel 3.0 beta

As I mentioned a little while ago I’m in the process of rewriting iBabel using AppleScriptObjC, and thanks to the invaluable help of AppleScriptObjC Explored by Shane Stanley and the contributors to the MacScripter website I now have the first beta available.
It can be downloaded from
here (24MB), this version requires Mac OS X 10.6 or higher and OpenBabel 2.3
Much will seem familiar to previous users of iBabel and the
screenshots of the old version give a good overview of the capabilities, whilst the images below highlight a few of the new features.
The “Add title and index” option appends a title (default is Mol, but you can edit this in the adjacent text box) and an index number to multi-molecular files, e.g. Mol 1, Mol 2, Mol 3 etc. This is essential if you want to search files displayed in the “Viewer” since you need a unique identifier for each structure. In many cases the molecules will already have a molecule id.


Another new feature with OpenBabel 2.3 is the ability to generate 2D and 3D coordinates.
Perhaps the biggest changes have come with the “Viewer”, by storing the table data in an array we can use some of the cool ObjC functions such as the continuously updating selection count and the live searching of the “Name” text field. To import records identify the input file using the input button and then click the “Import” button.



The buttons highlighted in green allow the user to delete the highlighted row, delete all the “Selected” rows or clear all records completely. The selection can be modified using the buttons highlighted in pale blue.
There are a selection of supported viewers chosen using the iBabel Preferences. ChemDoodle is an included lightweight javascript library that works very well for most file formats but does not at present support SMILES (you can of course use iBabel to convert SMILES to sdf using the generate 2D option). I’m looking at doing this on the fly but I need to see what the performance hit will be.
For the other viewers, JMOL/JChemPaint are in the application bundle. ChemBioDraw needs to be in the Application folder but only works on some machines (something to do with only supporting 32-bit which I think we will have to wait for CambridgeSoft to address). Because of Java security issues Marvin has to be in the same file structure as the htm page, I think you only need to put an alias to Marvin in the Macintosh HD:Public folder or User:Public folder. the 2D and 3D radio buttons allow you to choose an appropriate display.

It also support JME as the editor but you need to get a copy from Peter Ertl directly and put it in the Public folder.

The PChem button pulls structures from PubChem, this can either be a single structure of a list (here is an example
caslist.txt you can download to try).
As you can see the list contains a mixture of systematic names, trivial names, drug names and CAS numbers but the smart people at PubChem sort all that out nicely.

64318-79-2
iodobenzene
trinitrotoluene
anisaldehyde
170729-80-3
nonsense
Clomipramine
Loratidine
108-86-1
63-75-2
Promethazine
Chlorpromazine

The result is two files on your output.smi which contains the successful searches and NoStructure.txt which contains cases where no structure was found. You can then import the file to view the structures.

I’d be delighted to hear of any bugs (honest) any suggestions for how iBabel might be improved.
Comments

Latest iBabel Update

I’ve just released the latest version of iBabel (2.6) Read More...
Comments

iBabel 2.6 beta1

I’ve just uploaded the first beta version of the updated iBabel.

You can read about it
here.

All input welcome.
Comments

iBabel rated excellent

iBabel rated excellent Read More...
Comments

New version of iBabel

Updated iBabel to version 2.5.2. Read More...
Comments

New version of iBabel

Updated version of iBabel Read More...
Comments

Comparing version number in applescript

Using the applescript command "considering numeric strings" Read More...
Comments