Indigo 1.1.11 and beautiful documentation

[Mikhail Rybalkin]

Hello Indigo Users,

We are proud to present the next version of Indigo library. It passed more then a 1.5 months since the previous release and we working hard to include your suggestions there. You may noticed that we were changing our official documentation on the GGA website quite rarely. The reason is that we not too convenient to do that on the website. But since this version we want to show a preview of our *beautiful* documentation based on Sphinx documentation system. The most boring thing in maintaining the documentation were images: one should create a molecule file, convert it into an image, upload on a website, and include a link to it. But we wrote several extensions to Sphinx and now we can include images that will be rendered into several formats directly from SMILES, Molfile, or even an arbitrary code. And the documentation system includes even the output of that code automatically!

Here is a link to the Release Notes: http://ggasoftware.com/up/indigo-doc/indigo/release-notes/1.1.11/indigo-1.1.11.html

Documentation main page is the following: http://ggasoftware.com/up/indigo-doc

Also we included a tutorial on a new atom coloring feature: http://ggasoftware.com/up/indigo-doc/indigo/examples/atom-coloring.html

and we are going to include more examples how to use Indigo efficiently.

There are quite a few pages there yet, and we going to translate our previous documentation into this new format, and include all that changes that were not reflected there.

Summary of changes in Indigo 1.1.11

Follow the Release Notes link above to get more details with examples on new features and links to the original requests or bug reports.

New features and improvements:

• Fingerprints computation is 2-4 times faster
  
• Restored source compatibility with MinGW compiler
  
• New IndigoObject methods for stereocenters: stereocenterGroup, setStereocenterGroup, markStereobonds
  
• New option to specify atom colors individually via s-groups: render-atom-color-property
  
• New rendering option for bond width: render-bond-line-width
  
• New chirality validation method: validateChirality
  
• Indigo Java API uses Maven instead of Ant for building
  
• Maven repository for Indigo Java API packages
  
• New method that releases memory for the Indigo Object: dispose
  
• Indigo Java doesn’t remove dll-modules in the temporary directory that results in a faster loading
  
• CDXML file format export
  
• New methods to read data from buffers: loadBuffer, loadString, iterateSDF, iterateSmiles, iterateCML
  
• Indigo Python API binding works for Python 3 as well as for Python 2
  
• New SGroup-related methods: getGenericSGroup, getMultipleGroup, getRepeatingUnit, data
  
• New method to remove a set of bonds: removeBonds
  

Bugfixes:

• Memory leak in the grossFormula API method in case of exceptions during computation
  
• Molfile substitution flag value was set to 4 instead of 6
  
• render-bond-length option was ignored if render-image-size were set. Now render-bond-length parameter specifies maximum bond length even if image size is specified
  
• Either cis-trans flag was ignored in Molfile V3000 loader
  
• Indigo options may be used from a previous Indigo instance when new Indigo instance is allocated
  
• Transform throws an exception when called on a molecule from SDF file
  
• .NET bindings interprocess race condition that could happen on the first run. Thanks to dimitry42 for the pull request
  
• Molecule with up/down bond is saved as chiral
  

We would be glad to get your feedback regarding new documentation format, missing features, suggestions, and bug reports! You can develop great software with our tools!

With best regards,

Mikhail Rybalkin

GGA Software Services LLC