Dear all, This morning I tagged the beta for the 2011.12 (Q4 2011 in the old numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2011_12_1beta1/
and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_12_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. Best Regards, -greg ****** Release_2011.12.1 ******* (Changes relative to Release_2011.09.1) !!!!!! IMPORTANT !!!!!! - The functions for creating bit vector fingerprints using atom pairs and topological torsions have been changed. The new default behavior will return different fingerprints than previous RDKit versions. This affects usage from c++, python, and within the postgresql cartridge. See the "Other" section below for more details. - Due to a bug fix in the parameter set, the MolLogP and MolMR descriptor calculators now return different values for some molecules. See the "Bug Fixes" section below for more details. Acknowledgements: Andrew Dalke, JP Ebejer, Roger Sayle, Adrian Schreyer, Gianluca Sforna, Riccardo Vianello, Toby Wright Bug Fixes: - molecules with polymeric S group information are now rejected by the Mol file parser. (Issue 3432136) - A bad atom type definition and a bad smarts definition were fixed in $RDBASE/Data/Crippen.txt. This affects the values returned by the logp and MR calculators. (Issue 3433771) - Unused atom-map numbers in reaction products now produce warnings instead of errors. (Issue 3434271) - rdMolDescriptors.GetHashedAtomPairFingerprint() now works. (Issue 3441641) - ReplaceSubstructs() now copies input molecule conformations to the output molecule. (Issue 3453144) - three-coordinate S and Se are now stereogenic (i.e. the stereochemistry of O=[S@](C)F is no longer ignored). (Issue 3453172) New Features: - Integration with the new IPython graphical canvas has been added. For details see this wiki page: http://code.google.com/p/rdkit/wiki/IPythonIntegration - Input and output from Andrew Dalke's FPS format (http://code.google.com/p/chem-fingerprints/wiki/FPS) for fingerprints. - The descriptor CalcNumAmideBonds() was added. New Database Cartridge Features: - Support for PostgreSQL v9.1 - Integration with PostgreSQL's KNN-GIST functionality. (Thanks to Adrian Schreyer) - the functions all_values_gt(sfp,N) and all_values_lt(sfp,N) were added. New Java Wrapper Features: - A function for doing diversity picking using fingerprint similarity. - support for the Avalon Toolkit (see below) Deprecated modules (to be removed in next release): - rdkit.Excel - rdkit.ML.Descriptors.DescriptorsCOM - rdkit.ML.Composite.CompositeCOM Removed modules: - rdkit.WebUtils - rdkit.Reports - rdkit.mixins Other: - Improvements to the SMARTS parser (Roger Sayle) - The atom-pair and topological-torsion fingerprinting functions that return bit vectors now simulate counts by setting multiple bits in the fingerprint per atom-pair/torsion. The number of bits used is controlled by the nBitsPerEntry argument, which now defaults to 4. The new default behavior does a much better job of reproducing the similarities calculated using count-based fingerprints: 95% of calculated similarities are within 0.09 of the count-based value compared with 0.22 or 0.17 for torsions and atom-pairs previously. To get the old behavior, set nBitsPerEntry to 1. - Optional support has been added for the Avalon Toolkit (https://sourceforge.net/projects/avalontoolkit/) to provide an alternate smiles canonicalization, fingerprint, and 2D coordination generation algorithm. - The SLN support can now be switched off using the cmake variable RDK_BUILD_SLN_SUPPORT. - There are now instructions for building the RDKit and the SWIG wrappers in 64bit mode on windows. ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
