[Rdkit-discuss] Beta of Q1 2011 Release Available
Dear all, This morning I tagged the beta for the Q1 2011 (2011.03 in the new numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2011_03_1beta1/ and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_03_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_2011.03.1 *** (Changes relative to Release_2010.12.1) Acknowledgements: - Eddie Cao, James Davidson, Kirk DeLisle, Peter Gedeck, George Magoon, TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Bernd Wiswedel Bug Fixes: - The performance of SSSR finding for molecules with multiple highly-fused ring systems has been improved. (Issue 3185548) - Isotope information is now correctly saved when molecules are serialized (pickled). (Issue 3205280) - Generating SMILES for a molecule no longer changes the molecule. This fixes a round-trip bug with certain highly symmetric molecules read from SD files. (Issue 3228150) - Another bounds-matrix generation bug for highly (con)strained systems was fixed. (Issue 3238580) - Conformation information is now better handled by deleteSubstructs(), replaceSubstructs(), and replaceCore(). New Features: - the rdkit.Chem.Draw package has been significantly refactored. - Code for doing Murcko decomposition of molecules has been added. From Python this is in the module: rdkit.Chem.Scaffolds.MurckoScaffold It's available in C++ in the GraphMol/ChemTransforms area. - rdkit.Chem.AllChem.TransformMol() now takes optional arguments allowing the conformation to be transformed to be specified and other existing conformations to be preserved. - Calculations for most of the descriptors in rdkit.Chem.Lipinski and rdkit.Chem.MolSurf have been moved into C++. The python API is the same, but the calculations should be somewhat faster. - Extensive feature additions to the SWIG-based java wrapper. - The Chem.ReplaceCore() function is now better suited for use in R-group decomposition. - The Morgan fingerprinting code can now return information about which atoms set particular bits. - The function pathToSubmol() now copies coordinate information from conformations (if present). The function is also now available from Python - The path and subgraph finding code now takes an optional rootedAtAtom argument to allow only paths/subgraphs that start at a particular atom to be generated. - The function findAtomEnvironmentOfRadiusN has been added to allow circular atom environments to be located in molecules. - MolOps::assignStereochemistry now can also flag potential stereocenters that are not specified. New Database Cartridge Features: - the descriptor-calculation functions mol_numrotatablebonds(), mol_numheteroatoms(), mol_numrings(), and mol_tpsa() have been added. Deprecated modules (to be removed in next release): Removed modules: Other: - In C++, the functions CalcCrippenDescriptors and CalcAMW have been renamed calcCrippenDescriptors and calcAMW to make them consistent with the other descriptor calculators. - The molecule serialization (pickling) format has been changed. The new format is more compact. -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q1 2011 Release Available
Hi Greg - great news about the beta / new functionality! > Greg wrote: > This morning I tagged the beta for the Q1 2011 (2011.03 in the new > numbering) release in svn: > http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_201 > 1_03_1beta1/ > > and uploaded a source distribution to the google code site: > http://code.google.com/p/rdkit/downloads/detail?name=RDKit_201 > 1_03_1beta1.tgz > If there's demand for it, I will also put up a windows binary. As usual, "yes, please" for a python 2.6 windows binary if possible : ) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q1 2011 Release Available
On Mon, Apr 4, 2011 at 3:29 PM, James Davidson wrote: >> >> and uploaded a source distribution to the google code site: >> http://code.google.com/p/rdkit/downloads/detail?name=RDKit_201 >> 1_03_1beta1.tgz >> If there's demand for it, I will also put up a windows binary. > > As usual, "yes, please" for a python 2.6 windows binary if possible : ) It's up now: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_03_1beta1.win32.ziip Best, -greg -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q1 2011 Release Available
Kirk, On Tue, Apr 5, 2011 at 7:20 PM, Robert DeLisle wrote: > Greg, > > I built and tested the new beta release on CentOS 5.5 and it seemed to build > fine as per the instructions I have on the wiki. It did fail, however, in > two tests: > > 71:pythonTestDirML > 76:pythonTestDirChem > > I've attached the LastTest.log file, for your perusal. Please let me know > if I've done something wrong here. The error messages make it look like something is wrong with the test database. Can you please check that $RDBASE/Data/RDTests.sqlt is not modified? Thanks, -greg -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q1 2011 Release Available
I failed to include rdkit-discuss on that last message - sorry about that. See below... That did the trick. I re-copied the RDTests.sqlt and RDData.sqlt databases as instructed on the wiki, re-ran the tests, and 100% pass. I will bet that when I did the database copy the first time around, my environment variables ($RDBASE in particular weren't up to date and I got the databases from the previous version. Regardless, it all seems A-OK now. Thank you! I'll update the CentOS wiki to show that these instructions should work on the latest release. I hope all is well with you. -Kirk On Tue, Apr 5, 2011 at 12:49 PM, Greg Landrum wrote: > Kirk, > > On Tue, Apr 5, 2011 at 7:20 PM, Robert DeLisle > wrote: > > Greg, > > > > I built and tested the new beta release on CentOS 5.5 and it seemed to > build > > fine as per the instructions I have on the wiki. It did fail, however, > in > > two tests: > > > > 71:pythonTestDirML > > 76:pythonTestDirChem > > > > I've attached the LastTest.log file, for your perusal. Please let me > know > > if I've done something wrong here. > > The error messages make it look like something is wrong with the test > database. Can you please check that $RDBASE/Data/RDTests.sqlt is not > modified? > > Thanks, > -greg > -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
