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2014_09_1 (Q3 2014) Release
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@greglandrum greglandrum released this 30 Oct 03:25
· 4681 commits to master since this release
Release_2014_09_1
6bb14c6

****** Release_2014.09.1 *******
(Changes relative to Release_2014.03.1)

Acknowledgements:
Andrew Dalke, James Davidson, Jan Domanski, Patrick Fuller, Seiji
Matsuoka, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger
Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello,
Richard West

Bug Fixes:

  • Bond query information not written to CTAB
    (github issue #266)
  • Bond topology queries not written to CTABs
    (github issue #268)
  • Combined bond query + topology query not correctly parsed from CTAB
    (github issue #269)
  • SWIG wrapped suppliers leak memory on .next()
    (github issue #270)
  • SWIG wrappers don't build with SWIG 3.0.x
    (github issue #277)
  • core leak from DataStructs.ConvertToNumpyArray
    (github issue #281)
  • MolTransforms not exposed to Java wrapper
    (github issue #285)
  • Seg fault in ReactionFromRxnBlock
    (github issue #290)
  • BitInfo from GetHashedMorganFingerprint() has non-folded values
    (github issue #295)
  • bad inchi for chiral S when the molecule is sanitized
    (github issue #296)
  • Cannot generate smiles for ChEBI 50252
    (github issue #298)
  • Either molecule-molecule substruct matching is wrong OR the docs for Atom::Match incorrect
    (github issue #304)
  • fluorine F-F gives segmentation fault with MMFF forcefield
    (github issue #308)
  • cartridge: MACCS similarity wrong when using the builtin popcount and the index
    (github issue #311)
  • Substructure Search via SMARTS implicit hydrogens
    (github issue #313)
  • SMARTS output for [x] is wrong
    (github issue #314)
  • Bonds not being set up properly in renumberAtoms
    (github issue #317)
  • Python 2 code in python 3 branch
    (github issue #326)
  • Linking error with ICC 15.0 on Linux
    (github issue #327)
  • Using explicit hydrogens in the SMILES lead to the same AP FP for two different molecules
    (github issue #334)
  • memory leaks when smiles/smarts parsers fail
    (github issue #335)
  • No double bond stereo perception from CTABs when sanitization is turned off
    (github issue #337)
  • missing MACCS key 44 might be found
    (github issue #352)
  • Hydrogens in mol blocks have a valence value set
    (github issue #357)
  • Computed props on non-sanitized molecule interfering with substructure matching
    (github issue #360)
  • Fixed a weakness in the angular restraint code
    (github pull #261 from ptosco)
  • A few fixes to improve MMFF/UFF robustness
    (github pull #274 from ptosco)
  • Static webGL rendering fix
    (github pull #287 from patrickfuller)
  • Revert #include ordering in SmilesMolSupplier.cpp
    (github pull #297 from mcs07)
  • Add missing include for RDDepict::compute2DCoords
    (github pull #301 from baoilleach)
  • Herschbach-Laurie fallback implemented to fix GitHub 308
    (github pull #312 from ptosco)
  • Issue #320 Making GetBestRMS more idiot-proof
    (github pull #322 from jandom)
  • Update URLs to InChI API after inchi-trust.org website redesign.
    (github pull #341 from rwest)

New Features:

  • Should be able to do intramolecular bond breaking in reactions.
    (github issue #58)
  • Support reactions in cartridge
    (github issue #223)
  • Documentation of Inchi methods
    (github issue #240)
  • add DescribeQuery() to Bond python wrapper
    (github issue #267)
  • support avalon fingerprint in cartridge
    (github issue #286)
  • support partial fragmentation with fragmentOnSomeBonds
    (github issue #288)
  • Add calcNumHeterocycles() descriptor
    (github issue #351)
  • C++ implementation of FMCS algorithm
  • Reordering feature for Butina clustering
    (github pull #302 from sriniker)
  • Changes and new functions for the calculation of RMS values between conformers of a molecule
    (github pull #306 from sriniker)
  • Extended chemical reaction functionality and add chemical reactions to cartridge
    (github pull #315 from NadineSchneider)
  • Custom color to highlight atoms in Mol2Image
    (github pull #316 from jandom)
  • Several different fingerprint algorithms for chemical reactions are now available
  • add Chem.Draw.MolToQPixmap
    (github pull #355 from mojaie)

New Database Cartridge Features:

  • NOTE: the configuration variable rdkit.ss_fp_size has been renamed to rdkit.sss_fp_size
  • Chemical reactions and several operations on them are now supported
  • Avalon fingerprints now supported (when support has been compiled in)

New Java Wrapper Features:

  • FMCS implementation exposed
  • Fingerprints for chemical reactions
  • Possible core leak in some of the MolSuppliers was fixed

Deprecated modules (to be removed in next release):

  • Projects/SDView4
  • rdkit/utils/
    • GUIDs.py
    • GenLicense.py
    • Licensing.py
    • PiddleTools.py
    • PilTools.py
    • REFile.py
    • SliceTools.py
  • rdkit/Logger

Removed modules:

Contrib updates:

Other:

  • The RDKit now supports both python3 and python2.
  • There is now conda integration for the RDKit.
  • SMILES generation is substantially faster
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