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 greg.land...@gmail.com
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
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