****** 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.
