Re: [Rdkit-devel] Beta of Q2 2011 Release Available

[Robert D. <rkd...@gm...>]

It works here on CentOS 5.6.  Testing with my code goes fine, but the test
step (ctest from the build directory) results in 72/76 tests failed.
Problem with the test DB?





On Fri, Jul 1, 2011 at 5:40 AM, Greg Landrum <gre...@gm...> wrote:

> 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())
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>