Published October 30, 2014
| Version Release_2014_09_1
Software
Open
rdkit: 2014_09_1 (Q3 2014) Release
Creators
- 1. Department of Drug Science and Technology, University of Turin
- 2. NuMat Technologies
- 3. EMBL-EBI
- 4. BioMed X GmbH
- 5. InhibOx
- 6. Northeastern University
Description
****** 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
Files
rdkit-Release_2014_09_1.zip
Files
(24.9 MB)
Name | Size | Download all |
---|---|---|
md5:08fbe74567519fc23b66e0abfffea6c3
|
24.9 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/rdkit/rdkit/tree/Release_2014_09_1 (URL)