Indigo-1.1 Release Candidate

[Mikhail Rybalkin]

Hello!

We have just uploaded Indigo 1.1 Release Candidate and we are in a
week of releasing stable version of Indigo toolkit. Before releasing
stable version we are going to update the published documentation.
There was not special announcement for beta-11 version as in that
version we added new API for molecule decomposition. This announcement
includes the latest changes since beta-10 version.

As usual you can download it from our site:
http://ggasoftware.com/download/indigo_next

Highlights:

1. InChI stereochemistry layer is supported both for loading and saving
molecules. The only difference with the standard utility occurs when
stereochemistry is defined not in a proper way. Allenes and cumulenes
are not supported yet.

2. new RGroup-Decomposition API was added: createDecomposer(),
addDecomposition(), decomposeMolecule(), iterateDecompositions().
See more details at
http://groups.google.com/group/indigo-general/browse_thread/thread/75281df2f70ec1a
Thanks to Gerhard:
http://groups.google.com/group/indigo-general/browse_thread/thread/c1dbc67ece5f78b0
,
Mederich:
http://groups.google.com/group/indigo-general/browse_thread/thread/6d77029359364dd8
, and
Simon: http://tech.knime.org/forum/indigo/r-group-decomposer

3. We completely switched to CMake project configurations.

Changes:

1. AAM new algorithm heuristic was implemented for disconnected
reactant and product molecules.

2. correctReactingCenters() method was added for reactions. It
highlights bond reacting centers according to AAM.
Thanks to James:
http://tech.knime.org/forum/indigo/reaction-automapper-bond-highlighting

3. "timeout" option is used for MCS computation.

Fixes:

1. The bug with aam for query reactions was fixed

2. The bug with aam timeout was fixed.
Thanks to Daniel:
http://groups.google.com/group/indigo-bugs/browse_thread/thread/1cc5b9dffd740240

3. clearStereocenters() method now resets bond directions. After
calling this method molecule is saved into Molfile format without
tetrahedral bond directions.

4. Exception during saving Molfile with pseudoatoms within aromatic
rings

5. Exception when loading a molecule from Molfile with 3D coordinates
with invalid valences during automatic stereocenters detection.

6. Some other issues.

ChemDiff and Legio are not built yet. You can use the binaries from the
Indigo 1.1-beta7 release for ChemDiff, and Indigo 1.0 release for Legio.

With best regards,
Mikhail Rybalkin
GGA Software Services LLC

[Daniel Lowe]

Thanks for the new release. I'll be checking out the improvements to AAM shortly. An immediate thing I noticed though is that the indigo-renderer appears to be missing from the Java packages

[Mikhail Rybalkin]

Hello Daniel,

Thank you! I just missed it due to misprint. Release Candidate 2 is uploaded with additional minor issue with s-group serialization fixed.

Best

Mikhail

[Hinnerk Rey]

Hi,
great to here, that there are only some small steps left towards a
stable release. Will the knime nodes also be updated?
Best, Hinnerk

[Mikhail Rybalkin]

Hi Hinnerk,

Yes, we plan to update Indigo Knime nodes up to stable version also just after making Indigo stable release.

Best,

Mikhail