[Rdkit-discuss] Beta of Q4 2010 release up
Dear all,
This morning I tagged the beta for the Q4 2010 (2010.12 in the new
numbering) release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2010_12_1beta1/
and uploaded a source distribution to the google code site:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2010_12_1beta1.tg
If there's demand for it, I will also put up a windows binary.
As usual: if no show-stopper bugs appear, I will do the release itself
in about a week.
Excerpts from the release notes are below.
Best Regards,
-greg
** Release_2010.12.1 ***
(Changes relative to Release_2010.09.1)
!! IMPORTANT !!
- Due to changes made to the fingerprinting code, RDKit and layered
fingerprints generated with this release are not compatible with
those from previous releases. For users of the database cartridge:
you will need to re-generate RDKit fingerprint columns and any
indices on molecule tables.
Acknowledgements:
- Eddie Cao, Andrew Dalke, James Davidson, Kirk DeLisle, Peter Gedeck,
Gianluca Sforna, Nik Stiefl, Riccardo Vianello
Bug Fixes:
- The depiction code no longer crashes with single-atom templates
(issue 3122141)
- Aromatic bonds in the beginning of a SMILES branch are now
correctly parsed (issue 3127883)
- A crash when generating 2d constrained coordinates was fixed (issue
3135833)
- Stereochemistry no longer removed from double bonds in large
rings. (issue 3139534)
- Atom mapping information no longer in reaction products (issue
3140490)
- Smiles parse failure with repeated ring labels and dot disconnects
fixed (issue 3145697)
- a bug causing the molecule drawing code to not use the cairo canvas
when it's installed was fixed
New Features:
- All molecular descriptor calculators are now pulled in by the
rdkit.Chem.Descriptors module. So you can do things like:
Descriptors.MolLogP(mol) or Descriptors.fr_amide(mol)
- Atom-map numbers in SMILES are now supported. They can be accessed
as the atomic "molAtomMapNumber" property. (issue 3140494)
- It's now possible to tell the RDKit to generate non-canonical
SMILES via an optional argument to MolToSmiles. This is faster than
generating canonical SMILES, but is primarity intended for
debugging/testing. (issue 3140495)
- The function GenerateDepictionMatching2DStructure() has been added
to the rdkit.Chem.AllChem module to make generating
template-aligned depictions easier.
- Generating FCFP-like fingerprints is now more straightforward via
the useFeatures optional argument to GetMorganFingerprint()
- Extensive changes were made to the layere fingerprinting code to
allow better coverage of queries.
- Functionality for stripping common salts from molecules has been
added in rdkit.Chem.SaltRemover. The salts themselves are defined
in $RDBASE/Data/Salts.txt
- Functionality for recognizing common functional groups has been
added in rdkit.Chem.FunctionalGroups. The functional groups
themselves are defined in
$RDBASE/Data/Functional_Group_Hierarchy.txt
New Database Cartridge Features:
- The cartridge now supports SMARTS queries.
- The functions is_valid_{smiles,smarts}() are now available
(issue 3097359).
- The operator @= is now supported for testing molecule equality.
(issue 3120707)
- The functions featmorgan_fp() and featmorganbv_fp() are now
available for generating FCFP-like fingerprints.
Deprecated modules (to be removed in next release):
- rdkit.Chem.AvailDescriptors : the same functionality is now available
in a more useable manner from rdkit.Chem.Descriptors (see above).
Removed modules:
Other:
- RDKit support has been added to the Knime data mining and reporting
tool. More information is available from the knime.org community
site: http://tech.knime.org/community/rdkit
Thanks to Thorsten, Bernd, Michael, and the rest of the crew at
knime.com for making this possible.
- RPMs to allow easy installation of the RDKit on Fedora/CentOS/RHEL
and similar systems are now available. Thanks to Gianluca Sforna
for doing this work.
--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
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[Rdkit-discuss] Beta of Q4 2010 release up
Hi Greg, > Greg wrote: > If there's demand for it, I will also put up a windows binary. > > As usual: if no show-stopper bugs appear, I will do the release itself > in about a week. I would appreciate a Windows binary to check out the beta release - but if it is just me, I can obviously wait for the full release (presuming a windows binary would be available at that point?) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q4 2010 release up
Hi James, On Wed, Jan 5, 2011 at 11:43 AM, James Davidson wrote: > Hi Greg, > >> Greg wrote: >> If there's demand for it, I will also put up a windows binary. >> >> As usual: if no show-stopper bugs appear, I will do the release itself >> in about a week. > > I would appreciate a Windows binary to check out the beta release - but > if it is just me, I can obviously wait for the full release (presuming a > windows binary would be available at that point?) No problem, I will put up a windows binary for python2.6 tonight. -greg -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q4 2010 release up
On Wed, Jan 5, 2011 at 11:49 AM, Greg Landrum wrote: > Hi James, > > On Wed, Jan 5, 2011 at 11:43 AM, James Davidson > wrote: >> Hi Greg, >> >>> Greg wrote: >>> If there's demand for it, I will also put up a windows binary. >>> >>> As usual: if no show-stopper bugs appear, I will do the release itself >>> in about a week. >> >> I would appreciate a Windows binary to check out the beta release - but >> if it is just me, I can obviously wait for the full release (presuming a >> windows binary would be available at that point?) > > No problem, I will put up a windows binary for python2.6 tonight. Ok, getting the python2.6 builds working on my new machine took longer than I thought it would. I just uploaded a python2.6 build to the google code site: http://rdkit.googlecode.com/files/RDKit_2010_12_1beta2.win32.zip Note: this corresponds to the current svn state of the code, so it includes a couple changes relative to the source archive that's up. -greg -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q4 2010 release up
Dear all, On Thu, Jan 6, 2011 at 7:39 AM, Greg Landrum wrote: > > Ok, getting the python2.6 builds working on my new machine took longer > than I thought it would. I just uploaded a python2.6 build to the > google code site: > http://rdkit.googlecode.com/files/RDKit_2010_12_1beta2.win32.zip > > Note: this corresponds to the current svn state of the code, so it > includes a couple changes relative to the source archive that's up. I made a mistake with this zip file and forgot a couple of critical DLLs. I just deleted the (broken) version and will upload a new version later tonight. Best, -greg -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q4 2010 release up
On Thu, Jan 6, 2011 at 5:28 PM, Greg Landrum wrote: > > I made a mistake with this zip file and forgot a couple of critical > DLLs. I just deleted the (broken) version and will upload a new > version later tonight. New version up now: http://rdkit.googlecode.com/files/RDKit_2010_12_1beta2.win32.zip hopefully this one works better than the last one. -greg -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
