Dear all, This morning I tagged the beta for the Q4 2010 (2010.12 in the new numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2010_12_1beta1/
and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2010_12_1beta1.tg 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_2010.12.1 ******* (Changes relative to Release_2010.09.1) !!!!!! IMPORTANT !!!!!! - Due to changes made to the fingerprinting code, RDKit and layered fingerprints generated with this release are not compatible with those from previous releases. For users of the database cartridge: you will need to re-generate RDKit fingerprint columns and any indices on molecule tables. Acknowledgements: - Eddie Cao, Andrew Dalke, James Davidson, Kirk DeLisle, Peter Gedeck, Gianluca Sforna, Nik Stiefl, Riccardo Vianello Bug Fixes: - The depiction code no longer crashes with single-atom templates (issue 3122141) - Aromatic bonds in the beginning of a SMILES branch are now correctly parsed (issue 3127883) - A crash when generating 2d constrained coordinates was fixed (issue 3135833) - Stereochemistry no longer removed from double bonds in large rings. (issue 3139534) - Atom mapping information no longer in reaction products (issue 3140490) - Smiles parse failure with repeated ring labels and dot disconnects fixed (issue 3145697) - a bug causing the molecule drawing code to not use the cairo canvas when it's installed was fixed New Features: - All molecular descriptor calculators are now pulled in by the rdkit.Chem.Descriptors module. So you can do things like: Descriptors.MolLogP(mol) or Descriptors.fr_amide(mol) - Atom-map numbers in SMILES are now supported. They can be accessed as the atomic "molAtomMapNumber" property. (issue 3140494) - It's now possible to tell the RDKit to generate non-canonical SMILES via an optional argument to MolToSmiles. This is faster than generating canonical SMILES, but is primarity intended for debugging/testing. (issue 3140495) - The function GenerateDepictionMatching2DStructure() has been added to the rdkit.Chem.AllChem module to make generating template-aligned depictions easier. - Generating FCFP-like fingerprints is now more straightforward via the useFeatures optional argument to GetMorganFingerprint() - Extensive changes were made to the layere fingerprinting code to allow better coverage of queries. - Functionality for stripping common salts from molecules has been added in rdkit.Chem.SaltRemover. The salts themselves are defined in $RDBASE/Data/Salts.txt - Functionality for recognizing common functional groups has been added in rdkit.Chem.FunctionalGroups. The functional groups themselves are defined in $RDBASE/Data/Functional_Group_Hierarchy.txt New Database Cartridge Features: - The cartridge now supports SMARTS queries. - The functions is_valid_{smiles,smarts}() are now available (issue 3097359). - The operator @= is now supported for testing molecule equality. (issue 3120707) - The functions featmorgan_fp() and featmorganbv_fp() are now available for generating FCFP-like fingerprints. Deprecated modules (to be removed in next release): - rdkit.Chem.AvailDescriptors : the same functionality is now available in a more useable manner from rdkit.Chem.Descriptors (see above). Removed modules: Other: - RDKit support has been added to the Knime data mining and reporting tool. More information is available from the knime.org community site: http://tech.knime.org/community/rdkit Thanks to Thorsten, Bernd, Michael, and the rest of the crew at knime.com for making this possible. - RPMs to allow easy installation of the RDKit on Fedora/CentOS/RHEL and similar systems are now available. Thanks to Gianluca Sforna for doing this work. ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
