Re: [Rdkit-discuss] beta of Q2 release available
On Sun, Jun 21, 2009 at 10:24 AM, Evgueni Kolossov wrote: > > Can you please explain the usage of atom labels Q, A, and *. I know that * > used in fragments. Where you using Q and A? > My interpretation of these is: * : a query matching any atom A : a query matching anything but H Q : a query matching anything but C or H Note that molecules processed by the RDKit don't normally contain Hs, so the "H" bits of the queries above don't really do anything and a '*' doesn't match where it ought to. For example, a Mol file query with a C connected to a * should match methane. Using the RDKit it normally will not (since the Hs are not present in the graph and molecules normally have had Hs removed). This is something that ought to be fixed at some point in the future. -greg
Re: [Rdkit-discuss] beta of Q2 release available
Dear Greg, Can you please explain the usage of atom labels Q, A, and *. I know that * used in fragments. Where you using Q and A? Regards, Evgueni 2009/6/21 Greg Landrum > Dear all, > > It's getting to be time for the next RDKit release. Yesterday I tagged > the Q2 2009 release: > http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q22009_1beta1/ > > and put a source tar ball up on the google code site: > http://code.google.com/p/rdkit/downloads/list > > I'm going to continue to work on the code, particularly on the > documentation, but if no substantial problems are found, I will do the > release towards the end of the month. > > Release notes (more complete than usual) are below. > > -greg > > ** Release_Q22009_1 *** > (Changes relative to Release_Q12009_2) > > Acknowledgements > - Uwe Hoffmann, Marshall Levesque, Armin Widmer > > Bug Fixes > - handling of crossed bonds in mol files fixed (issue 2804599) > - serialization bug fixed (issue 2788233) > - pi systems with 2 electrons now flagged as aromatic (issue 2787221) > - Chirality swap on AddHs (issue 2762917) > - core leak in UFFOptimizeMolecule fixed (issue 2757824) > > New Features > - cairo support in the mol drawing code (from Uwe Hoffmann) (issue > 2720611) > - Tversky and Tanimoto similarities now supported for SparseIntVects > - AllProbeBitsMatch supported for BitVect-BitVect comparisons > - ChemicalReactions support serialization (pickling) (issue 2799770) > - GetAtomPairFingerprint() supports minLength and maxLength arguments > - GetHashedTopologicalTorsionFingerprint() added > - preliminary support added for v3K mol files > - ForwardSDMolSupplier added > - CompressedSDMolSupplier added (not supported on windows) > - UFFHasAllMoleculeParams() added > - substructure searching code now uses an RDKit implementation of >the vf2 algorithm. It's much faster. > - Atom.GetPropNames() and Bond.GetPropNames() now available from >python > - BRICS code now supports FindBRICSBonds() and BreakBRICSBonds() > - atom labels Q, A, and * in CTABs are more correctly supported >(issue 2797708) > - rdkit.Chem.PropertyMol added (issue 2742959) > - support has been added for enabling and disabling logs >(issue 2738020) > > Other > - A demo has been added for using MPI with the RDKit >($RDBASE/Code/Demos/RDKit/MPI). > - Embedding code is now better at handling chiral structures and >should produce results for molecules with atoms that don't have >UFF parameters. > - the UFF code is more robust w.r.t. missing parameters > - GetHashedAtomPairFingerprint() returns SparseIntVect instead of >ExplicitBitVect > - the CTAB parser (used for mol files and SD files) is faster > - extensive changes to the layered fingerprinting code; >fingerprinting queries is now possible > - molecule discriminator code moved into $RDBASE/Code/GraphMol/Subgraphs > - the SDView4 prototype has been expanded > - $RDBASE/Regress has been added to contain regression and >benchmarking data and scripts. > - support for sqlalchemy has been added to $RDBASE/rdkit/Chem/MolDb > - the BRICS code has been refactored > > > -- > Are you an open source citizen? Join us for the Open Source Bridge > conference! > Portland, OR, June 17-19. Two days of sessions, one day of unconference: > $250. > Need another reason to go? 24-hour hacker lounge. Register today! > > http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
[Rdkit-discuss] beta of Q2 release available
Dear all, It's getting to be time for the next RDKit release. Yesterday I tagged the Q2 2009 release: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q22009_1beta1/ and put a source tar ball up on the google code site: http://code.google.com/p/rdkit/downloads/list I'm going to continue to work on the code, particularly on the documentation, but if no substantial problems are found, I will do the release towards the end of the month. Release notes (more complete than usual) are below. -greg ** Release_Q22009_1 *** (Changes relative to Release_Q12009_2) Acknowledgements - Uwe Hoffmann, Marshall Levesque, Armin Widmer Bug Fixes - handling of crossed bonds in mol files fixed (issue 2804599) - serialization bug fixed (issue 2788233) - pi systems with 2 electrons now flagged as aromatic (issue 2787221) - Chirality swap on AddHs (issue 2762917) - core leak in UFFOptimizeMolecule fixed (issue 2757824) New Features - cairo support in the mol drawing code (from Uwe Hoffmann) (issue 2720611) - Tversky and Tanimoto similarities now supported for SparseIntVects - AllProbeBitsMatch supported for BitVect-BitVect comparisons - ChemicalReactions support serialization (pickling) (issue 2799770) - GetAtomPairFingerprint() supports minLength and maxLength arguments - GetHashedTopologicalTorsionFingerprint() added - preliminary support added for v3K mol files - ForwardSDMolSupplier added - CompressedSDMolSupplier added (not supported on windows) - UFFHasAllMoleculeParams() added - substructure searching code now uses an RDKit implementation of the vf2 algorithm. It's much faster. - Atom.GetPropNames() and Bond.GetPropNames() now available from python - BRICS code now supports FindBRICSBonds() and BreakBRICSBonds() - atom labels Q, A, and * in CTABs are more correctly supported (issue 2797708) - rdkit.Chem.PropertyMol added (issue 2742959) - support has been added for enabling and disabling logs (issue 2738020) Other - A demo has been added for using MPI with the RDKit ($RDBASE/Code/Demos/RDKit/MPI). - Embedding code is now better at handling chiral structures and should produce results for molecules with atoms that don't have UFF parameters. - the UFF code is more robust w.r.t. missing parameters - GetHashedAtomPairFingerprint() returns SparseIntVect instead of ExplicitBitVect - the CTAB parser (used for mol files and SD files) is faster - extensive changes to the layered fingerprinting code; fingerprinting queries is now possible - molecule discriminator code moved into $RDBASE/Code/GraphMol/Subgraphs - the SDView4 prototype has been expanded - $RDBASE/Regress has been added to contain regression and benchmarking data and scripts. - support for sqlalchemy has been added to $RDBASE/rdkit/Chem/MolDb - the BRICS code has been refactored
