[Rdkit-devel] Beta of Q2 2011 Release Available

[Greg L. <gre...@gm...>]

Dear all,

This morning I tagged the beta for the Q2 2011 (2011.06 in the new
numbering) release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2011_06_1beta1/

and uploaded a source distribution to the google code site:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_06_1beta1.tgz
If there's demand for it, I will also put up a windows binary.

As usual: if no show-stopper bugs appear, I will do the release itself
in about a week.

Excerpts from the release notes are below.

One highlight I will call your attention to is that, thanks to some
nice work from Eddie Cao, it is now possible to generate InChI codes
from within the RDKit :

In [2]: inchi = Chem.MolToInchi(Chem.MolFromSmiles('c1ccccc1C(=O)O'))
In [3]: print inchi
InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)

and then convert the InChIs to InChI keys:

In [4]: print Chem.InchiToInchiKey(inchi)
WPYMKLBDIGXBTP-UHFFFAOYSA-N

There is also experimental and partial support for converting InChI
back into a molecule:

In [5]: m2 = Chem.MolFromInchi(inchi)
In [6]: print Chem.MolToSmiles(m2)
O=C(O)c1ccccc1

Note that this last bit is not something InChI is actually designed
for, so it's probably not a good idea to rely on it.



Best Regards,
-greg


******  Release_2011.06.1 *******
(Changes relative to Release_2011.03.2)

Acknowledgements:
 - Eddie Cao, Andrew Dalke, James Davidson, JP Ebejer, Bernd Wiswedel

Bug Fixes:
 - A problem with similarity values between SparseIntVects that
   contain negative values was fixed. (Issue 3295215)
 - An edge case in SmilesMolSupplier.GetItemText() was fixed. (Issue
   3299878)
 - The drawing code now uses dashed lines for aromatic bonds without
   kekulization. (Issue 3305420)
 - AllChem.ConstrainedEmbed works again. (Issue 3305420)
 - atomic RGP values from mol files are accessible from python (Issue
   3313539)
 - M RGP blocks are now written to mol files. (Issue 3313540)
 - Atom.GetSymbol() for R atoms read from mol files is now
   correct. (Issue 3316600)
 - The handling of isotope specifications is more robust.
 - A thread-safety problem in SmilesWrite::GetAtomSmiles() was fixed.
 - some of the MACCS keys definitions have been corrected

New Features:
 - The smiles, smarts, and reaction smarts parsers all now take an additional
   argument, "replacements", that carries out string substitutions pre-parsing.
 - There is now optional support for generating InChI codes and keys
   for molecules.
 - the atom pair and topological torsion fingerprint generators now
   take an optional "ignoreAtoms" argument
 - a function to calculate exact molecular weight was added.
 - new java wrappers are now available in $RDBASE/Code/JavaWrappers
 - the methods getMostCommonIsotope() and getMostCommonIsotopeMass()
   have been added to the PeriodicTable class.

New Database Cartridge Features:

Deprecated modules (to be removed in next release):
 - The original SWIG wrappers in $RDBASE/Code/Demos/SWIG are deprecated

Removed modules:

Other:
 - The quality of the drawings produced by both the python molecule drawing
   code and $RDBASE/Code/Demos/RDKit/Draw is better.
 - the python molecule drawing code will now use superscripts and
   subscripts appropriately when using the aggdraw or cairo canvases
   (cairo canvas requires pango for this to work).
 - $RDBASE/Code/Demos/RDKit/Draw now includes an example using cairo
 - A lot of compiler warnings were cleaned up.
 - The error reporting in the SMILES, SMARTS, and SLN parsers was improved.
 - the code for calculating molecular formula is now in C++
   (Descriptors::calcMolFormula())