Dear all, I'm very happy to announce that the next version of the RDKit -- 2010.12 (a.k.a Q4 2010) -- is released.
The release notes are below. The source release and windows binaries (python 2.6 only, again please let me know if anyone needs a python 2.5 release) are on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q4_2010/ The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list Thanks to the everyone who submitted bug reports and suggestions for this release! Please let me know if you find any problems with the release or have suggestions for the next one. -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, TJ O'Donnell, 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 - the SMILES generated for charged, aromatic Se or Te has been fixed (issue 3152751) - PropertyMols constructed from pickles and then written to SD files will now include the properties in the SD file. - SMILES can now be generated correctly for very large molecules where more than 50 rings are open at once. (issue 3154028) 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 layered 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. - The database cartridge now statically links the RDKit libraries. This should make installation easier. - The RDKit fingerprinter now by default sets 2 bits per hashed subgraph instead of 4. The old behavior can be regained by setting nBitsPerHash to 4. ------------------------------------------------------------------------------ Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. 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