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@greglandrum greglandrum released this 02 Nov 09:20
· 5303 commits to master since this release
Release_2013_09_1
b60b260

****** Release_2013.09.1 *******
(Changes relative to Release_2013.06.1)

Acknowledgements:
James Davidson, JP Ebejer, Nikolas Fechner, Grégori Gerebtzoff, Michal Nowotka, Sereina Riniker, Roger
Sayle, Gianluca Sforna, Matthew Szymkiewicz, Paolo Tosco, Dan Warner,

!!!!!! IMPORTANT !!!!!!

  • Due to a bug fix in the parameter set, the MolLogP and MolMR
    descriptor calculators now return different values for molecules
    with pyrrole (or pyrrole-like) Ns.

Bug Fixes:

  • The pymol ShowMol method can now handle molecules with more than
    999 atoms (they are sent via PDB)
  • Various stability improvements to the Pandas integration.
    (github issues 129 and 51)
  • Some RDKit methods require python lists and don't allow passing
    numpy arrays or pandas series directly
    (github issue 119)
  • mol2 parser not setting E/Z flags on double bonds
    (github issue 114)
  • Incorrect angle terms in UFF
    (github issue 105)
  • Problems with stereochemistry flags and PathToSubmol()
    (github issue 103)
  • Bad Crippen atom type for pyrrole H
    (github issue 92)
  • PandasTools tests fail with Pandas v0.12
    (github issue 91)
  • Isotope information not affecting chirality
    (github issue 90)
  • properties are not read from SDF files with V3000 mol blocks.
    (github issue 88)
  • assignStereochemistry does not remove bond wedging that shouldn't be there.
    (github issue 87)
  • Drawing code modifies wedge bonds in reactions
    (github issue 86)
  • Stereochemistry not perceived when parsing CTABs unless sanitization is done.
    (github issue 82)
  • 2D rendering issue for epoxide ( CAS 70951-83-6)
    (github issue 78)
  • PandasTools doctests should be failing, but are not
    (github issue 75)
  • Better handling of radicals to/from mol files
    (github issue 73)
  • Benzothiazolium structure can be parsed from ctab, but the SMILES generated cannot be processed.
    (github issue 72)
  • Chem.MolFromInch hangs on CID 23691477 and CID 23691480
    (github issue 68)
  • Chem.MolFromInchi on CHEMBL104337 leads to segmentation fault
    (github issue 67)
  • "Could not embed molecule." (The Anthony Conundrum)
    (github issue 55)

New Features:

  • Add fragmentOnBonds() to python wrapper
    (github issue 142)
  • Allow renumbering atoms in a molecule.
    (github issue 140)
  • MMFF94 and MMFF94S support
  • implementation of the Open3DAlign rigid alignment algorithm
  • Support for reading and writing PDB files
  • The python function AllChem.AssignBondOrdersFromTemplate() can be
    used to assign bond orders from a reference molecule to the bonds
    in another molecule. This is helpful for getting bond orders
    correct for PDB ligands.
    (github issue 135)
  • Bond lengths, angles, and torsions can now be queries and adjusted.
    (github issue 132)
  • Implementation of similarity maps
    (github issue 94)
  • Python implementation of the Fraggle similarity algorithm.
    See Jameed Hussain's presentation from the 2013 UGM for details:
    https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
  • SparseIntVects now support -=, +=, /=, and *= with ints from C++
    and Python
  • support \ in SMILES
    (github issue 136)
  • Support a similarity threshold in DbCLI
    (github issue 134)
  • Support construction molecules from other molecules in the python wrapper
    (github issue 133)
  • support tversky similarity in DbCLI
    (github issue 130)
  • support tversky similarity in cartridge
    (github issue 121)
  • support reading and writing reactionComponentType and reactionComponentNumber from ctabs
    (github issue 118)
  • Add in-place forms of addHs(), removeHs(), and mergeQueryHs()
    (github issue 117)
  • modify MolOps::cleanUp() to support this azide formulation: C-N=N#N
    (github issue 116)
  • Dihedral rotation exposed in python
    (github issue 113)
  • Support for cairocffi (cairo drop-in replacement that plays nicely with virtualenv)
    (github issue 80)
  • Grey color for Hydrogens
    (github issue 97)
  • Improvements to the Dict interface in C++
    (github issue 74)
  • customizable drawing options
    (github issue 71)
  • Add method for setting the chiral flag in mol blocks
    (github issue 64)
  • New descriptors added (Python only for now):
    MaxPartialCharge(),MinPartialCharge(),MaxAbsPartialCharge(),MinAbsPartialCharge(),
    MaxEStateIndex(),MinEStateIndex(),MaxAbsEStateIndex(),MinAbsEStateIndex()

New Database Cartridge Features:

New Java Wrapper Features:

  • MMFF support
  • PDB reading and writing
  • Open3DAlign support

Deprecated modules (to be removed in next release):

Removed modules:

Contrib updates:

Other:

Assets 2