I'm very happy to announce that the next version of the RDKit -- May2008_1 -- is released.
The release notes are below. There are some change that affect backwards compatibility, so please at least skim them. The source release and a windows binary are on the sourceforge downloads page: http://sourceforge.net/project/showfiles.php?group_id=160139&package_id=180003&release_id=601793 The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list If you plan to build from source, please read the new build instructions: 1) For Linux: http://code.google.com/p/rdkit/wiki/BuildingOnLinux 2) For Windows: http://code.google.com/p/rdkit/wiki/BuildingOnWindows An updated documentation distribution has been added to sourceforge: http://sourceforge.net/project/showfiles.php?group_id=160139&package_id=230191&release_id=601803 note that this PDF is also included in the source and binary downloads. I also updated the browseable documentation at rdkit.org: http://www.rdkit.org/C++_Docs http://www.rdkit.org/Python_Docs 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 any suggestions. -greg ****** Release_May2008_1 ******* (Changes relative to Release_Jan2008_1) !!!!!! IMPORTANT !!!!!! - A fix to the values of the parameters for the Crippen LogP calculator means that the values calculated with this version are not backwards compatible. Old values should be recalculated. - topological fingerprints generated with this version *may* not be compatible with those from earlier versions. Please read the note below in the "Other" section. - Please read the point about dummy atoms in the "New Features" section. It explains a change that affects backwards compatibility when dealing with dummy atoms. Acknowledgements: - Some of the bugs fixed in this release were found and reported by Adrian Schreyer, Noel O'Boyle, and Markus Kossner. Bug Fixes - A core leak in MolAlign::getAlignmentTransform was fixed (issue 1899787) - Mol suppliers now reset the EOF flag on their stream after they run off the end (issue 1904170) - A problem causing the string "Sc" to not parse correctly in recursive SMARTS was fixed (issue 1912895) - Combined recursive smarts queries are now output correctly. (issue 1914154) - A bug in the handling of chirality in reactions was fixed (issue 1920627) - Looping directly over a supplier no longer causes a crash (issue 1928819) - a core leak in the smiles parser was fixed (issue 1929199) - Se and Te are now potential aromatic atoms (per the proposed OpenSmiles standard). (issue 1932365) - isotope information (and other atomic modifiers) are now correctly propagated by chemical reactions (issue 1934052) - triple bonds no longer contribute 2 electrons to the count for aromaticity (issue 1940646) - Two bugs connected with square brackets in SMILES were fixed (issues 1942220 and 1942657) - atoms with coordination numbers higher than 4 now have tetrahedral stereochemistry removed (issue 1942656) - Bond.SetStereo() is no longer exposed to Python (issue 1944575) - A few typos in the parameter data for the Crippen logp calculator were fixed. Values calculated with this version should be assumed to not be backwards compatible with older versions (issue 1950302) - Isotope queries are now added correctly (if perhaps not optimally) to SMARTS. - some drawing-related bugs have been cleared up. - A bug in Chem.WedgeMolBonds (used in the drawing code) that was causing incorrect stereochemistry in drawn structures was fixed. (issue 1965035) - A bug causing errors or crashes on Windows with [r<n>] queries was fixed. (issue 1968930) - A bug in the calculation of TPSA values in molecules that have Hs in the graph was fixed. (issue 1969745) New Features - Support for supplying dummy atoms as "[Du]", "[X]", "[Xa]", etc. is now considered deprecated. In this release a warning will be generated for these forms and in the next release the old form will generate errors. Note that the output of dummy atoms has also changed: the default output format is now "*", this means that the canonical SMILES for molecules containing dummies are no longer compatible with the canonical SMILES from previous releases. (feature request 186217) - Atom and bond query information is now serializable; i.e. query molecules can now be pickled and not lose the query information. (feature request 1756596) - Query features from mol files are now fully supported. (feature request 1756962) - Conformations now support a dimensionality flag. Dimensionality information is now read from mol blocks and TDT files. (feature request 1906758) - Bulk Dice similarity functions have been added for IntSparseIntVect and LongSparseIntVect (feature request 1936450) - Exceptions are no longer thrown during molecule parsing. Failure in molecule parsing is indicated by returning None. Failure to *open* a file when reading a molecule throws BadFileExceptions (feature requests 1932875 and 1938303) - The various similarity functions for BitVects and SparseIntVects now take an optional returnDistance argument. If this is provided, the functions return the corresponding distance instead of similarity. - Some additional query information from Mol files is now translated when generating SMARTS. Additional queries now translated: - number of ring bonds - unsaturation queries - atom lists are handled better as well (feature request 1902466) - A new algorithm for generating the bits for topological fingerprints has been added. The new approach is a bit quicker and more robust than the old, but is not backwards compatible. Similarity trends are more or less conserved. - The molecule drawing code in Chem.Draw.MolDrawing has been modified so that it creates better drawings. A new option for drawing that uses the aggdraw graphics library has been added. - The RingInfo class supports two new methods: AtomRings() and BondRings() that return tuples of tuples with indices of the atoms or bonds that make up the molecule's rings. Other - Changes in the underlying boost random-number generator in version 1.35 of the boost library may have broken backwards compatibility of 2D fingerprints generated using the old fingerprinter. It is strongly suggested that you regenerate any stored fingerprints (and switch to the new fingerprinter if possible). There is an explicit test for this in $RDBASE/Code/GraphMol/Fingerprints/test1.cpp - The unofficial and very obsolete version of John Torjo's v1 boost::logging library that was included with the RDKit distribution is no longer used. The logging library has been replaced with the much less powerful and flexible approach of just sending things to stdout or stderr. If and when the logging library is accepted into Boost, it will be integrated. - The DbCLI tools (in $RDBASE/Projects/DbCLI) generate topological fingerprints using both the old and new algorithms (unless the --noOldFingerprints option is provided). The default search uses the newer fingerprint. - The directory $RDBASE/Data/SmartsLib contains a library of sample SMARTS contributed by Richard Lewis.
