ThumbFish Release 1.0 is out

Check out the new release on ThumbFish Project Page or GitHub repository.

A new version of ThumbFish is now available with some cool new features, bug fixes and component updates. I have added three new features viz Molecule Browser, Generate and QuickFix. I also updated the Indigo Chemistry Toolkit (the chemistry brain of ThumbFish) to the latest version and updated the Cairo graphics engine. Apart from the technical stuff, a new funnymols.sdf file has been added to the sample files. It contains molecules with funny names and interesting description and can be viewed using the Browse feature.

I am particularly proud of the “Molecule Browser” feature that works on multi-molecule files SDF, RDF, CML and SMI. It displays the molecule structure and related properties in a list and can handle files with large number of molecules (I tested with files having 10K+ records) by loading them in the background on a separate thread so a user can continue browsing while records are being loaded.

The other new features are Generate and QuickFix.

Generate can create a new molecule from SMILES or InChi string. The structure is rendered as user types the string and can be saved to file in a variety of formats.

QuickFix allows a user to apply some quick options such as fold/unfold hydrogens, Normalize, Aromatize etc to a structure. The modified structure can then be saved.

This new version contains an updated Indigo Toolkit. Previous versions of ThumbFish were using 1.11 which was released in mid-2013 so it was quite old. This new version uses the Indigo library built from latest code (April-2015) from Indigo’s GitHub repository so this will have a lot of bug fixes and improvements.

The graphics engine used by Indigo (Cairo) has also been updated to or I can say had to be updated due to a bug in the engine itself. The bug would crash the application if “render-hdc-offset” option is used in Indigo. This option allows us to draw at any point on a device and was required for the Browse feature to work because the Browse dialog needs to draw molecules at different places on the list. Cairo has been updated to version 1.14.2. The bug is here and the fix is here.

INCHIKEY is now enabled in both Copy menu and molecule properties in Preview window. In previous versions, INCHIKEY was disabled because it caused a crash but the problem was in the calling code. I was re-using the string returned by Indigo API which is not a good thing to do. So all good now with INCHIKEY.

Detailed warning messages has been DISABLED in this build because it is no longer a beta. Only WARNING, ERROR and CRITICAL messages will be logged to the log file. Please see the ThumbFish project page for log file location.

And finally I moved the project to Visual Studio 2013 Community Edition. Though I am not very impressed with this new version of VS because of broken Intellisense and unwanted (un-removable I say) plugins. I always prefer using the latest products so there it is. Hopefully MS will fix the problems in some future updates.

I haven’t checked-in the new static libraries for Indigo yet into GitHub. Sorry about that. I plan to do it soon along with other third-party include files.

I haven’t decided yet about the next version features but it will surely have the Search feature along with some improvements to the Browse feature. If you have any suggestions or comments or bugs then please do send them across to “abhimanyusirohi@gmail.com”. You can look at the product backlog.

See you soon with a new version…