I'm pleased to announce that the next version of the RDKit - 2018.03 - is
released. The release notes are below.
The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1
Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 2.7, 3.5, 3.6
Mac OS 64bit: python 2.7, 3.5, 3.6
Windows 64bit: python 3.5, 3.6
The missing binary for python 2.7 on windows is explained here:
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07850.html
Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version and
new conda builds will be available in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit).
- The homebrew script
- The online version of the documentation at rdkit.org (I'm traveling this
week, so this is unlikely to be done before next weekend).
Thanks to everyone who submitted code, bug reports, and suggestions for
this release!
Please let me know if you find any problems with the release or have
suggestions for the next one, which is scheduled for Octobera 2018.
Best Regards,
-greg
# Release_2018.03.1
(Changes relative to Release_2017.09.1)
## C++11 notes
Starting with this release, the RDKit core C++ code is written in modern
C++;
for this release that means C++11. This means that the compilers used to
build
it cannot be completely ancient. Here are the minimum tested versions:
- g++ v4.8: though note that the SLN parser code cannot be built with v4.8.
It
will automatically be disabled when this older compiler is used.
- clang v3.9: it may be that older versions of the compiler also work, but
we
haven't tested them.
- Visual Studio 2015: it may be that older versions of the compiler also
work,
but we haven't tested them.
## Backwards incompatible changes
This release includes a set of changes to make the default arguments to
common
functions less error prone (github #1679).
- MolToSmiles() now generates isomeric SMILES by default.
- The embedding code now uses the ETKDG method by default.
- MolToMolBlock() will now by default generate a set of 2D coordinates for
molecules when the includeStereo option is set to True. The changes are
made
to a copy of the molecule; the molecule itself will not be modified.
- The Mol file (and SDF) parser now determines atomic stereochemisty based
on
the 3D coordinates provided (if 3D coordinates are provided).
- The SMILES parser now supports CXSMILES by default (assuming that
additional
text that looks like CXSMILES extensions is there).
In every case the old behavior can be obtained by providing an optional
argument
to the function(s) mentioned.
## Acknowledgements:
Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall,
Thomas
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris,
Dan
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker,
Jeff
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb,
Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',
## Highlights:
- An initial version of an integration with Schrodinger's coordgen
library is
included. This produces much better 2D coordinates for complex
molecules.
- Thanks to the move to modern C++ the RDKit is now faster and uses less
memory
- A number of improvements were made to the PDB reader
- v2 of the ETKDG torsions and potentials is now available
## Contrib updates:
- Implementation of Peter Ertl's IFG method for identifying functional
groups
from Guillaume Godin and Richard Hall
(github pull #1813 from thegodone)
## New Features and Enhancements:
- Support InChi 1.05
(github issue #1533 from greglandrum)
- Update CPack to create .deb files correctly
(github pull #1580 from psavery)
- Initial commit of EnumerateHeterocycles
(github pull #1588 from coleb)
- Version 2 of ETKDG
(github pull #1597 from sriniker)
- GetMolFrags now optionally returns atom indices along with mols
(github pull #1602 from ptosco)
- NP Likeness with confidence value
(github pull #1608 from apahl)
- Adding an option to EnumerateStereoisomers to only return unique isomers
(github pull #1612 from coleb)
- Add function wedgeBond()
(github issue #1615 from greglandrum)
- Dev/substructlibrary docs
(github pull #1620 from bp-kelley)
- Turns off exception throwing for certain classes Rlabel sanitization.
(github pull #1621 from bp-kelley)
- Add an "MDL" aromaticity model
(github issue #1622 from hjuinj)
- Add support for %(NNN) notation for ring closures
(github pull #1624 from baoilleach)
- Enable windows build that uses cairo
(github pull #1628 from greglandrum)
- [MRG] Fix PDB reader + add argument to toggle proximity bonding
(github pull #1629 from
