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Riccardo Vianello
Riccardo Vianello's posts

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Trying out py3DMol
I first saw 3DMol.js from Dave Koes' group at the ACS meeting in San Diego. It looked great, but I haven't had time to get back to it. This morning Dave Tweeted about Jupyter integration for 3DMol.js and I just had to try it. This is the small experiment to...

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Registration for the 2016 RDKit UGM, being held from 26-28 October in Basel, is now open.

For more information:

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Non mancate l'appuntamento con Release Party per Fedora 19, in collaborazione con +Associazione GNU/Linux User Group Perugia.

In occasione della consueta Linux Night parleremo del progetto, delle feature contenute in  questa nuova versione e saranno disponibili i DVD live della nuova release. Sarà inoltre possibile vedere in azione OpenShift con una piccola applicazione demo.

A fine serata premi ad estrazione, ovviamente a marchio Fedora!

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VTK 6.0.0 was released - this is the first major release of VTK since 2005, and it includes considerable refactoring of the pipeline and build system. To learn more about VTK 6 and to see what other new features and enhancements have been made, please see Dave's blog post.

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Do you speak italian and wish to join Europython in Florence, July 1-5th, for free, with room and lunch included? Join us as a volunteer!

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I'm pleased to announce that the next version of the RDKit --
2013.03 (a.k.a Q1 2013) -- is released.

The release notes are below.

The source release is on the sourceforge downloads page:
The files can also be downloaded from the google project page:
I will be uploading 32-bit and 64-bit Windows binaries for Python 2.7
later today.

The online version of the documentation at has been updated.

Thanks to the everyone who submitted 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.

****  Release_2013.03.1 *****
(Changes relative to Release_2012.12.1)

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

 - The algorithm for hashing subgraphs used in the RDKit fingerprinter
   has changed. The new default behavior will return different
   fingerprints than previous RDKit versions. This affects usage from
   c++, python, and within the postgresql cartridge. See the "Other"
   section below for more details.

Paul Czodrowski, Andrew Dalke, Jan Domanski, Jean-Paul Ebejer, Nikolas
Fechner, Jameed Hussain, Stephan Reiling, Sereina Riniker, Roger
Sayle, Riccardo Vianello 

Bug Fixes: 
 - removeBond now updates bond indices ( issue 284)
 - dummy labels are no longer lost when atoms are copied ( issue
 - more specific BRICS queries now match before less specific ones
   ( issue 287, github issue 1) 
 - molAtomMapNumber can now be set from Python ( issue 288)
 - the legend centering for molecular image grids has been improved
   ( issue 289) 
 - make install now includes all headers (github issue 2)
 - InChIs generaged after clearing computed properties are now correct
   (github issue 3)
 - Reacting atoms that don't change connectivity no longer lose
   stereochemistry (github issue 4)  
 - Aromatic Si is now accepted (github issue 5)  
 - removeAtom (and deleteSubstructs) now correctly updates stereoAtoms
   (github issue 8)  
 - [cartridge] pg_dump no longer fails when molecules cannot be
    converted to SMILES (github issue 9)  
 - a canonicalization bug in MolFragmentToSmiles was fixed (github issue 12)  
 - atom labels at the edge of the drawing are no longer cut off (github issue 13)  
 - a bug in query-atom -- query-atom matching was fixed (github issue 15)  
 - calling ChemicalReaction.RunReactants from Python with None
   molecules no longer leads to a seg fault. (github issue 16)  
 - AllChem.ReactionFromSmarts now generates an error message when called
   with an empty string.
 - Writing CTABs now includes information about atom aliases.
 - An error in the example fdef file
   has been fixed. (github issue 17)
 - Quantize.FindVarMultQuantBounds() no longer generates a seg fault
   when called with bad arguments. (github issue 18)
 - The length of SDMolSuppliers constructed from empty files is no
   longer reported as 1. (github issue 19)
 - Partial charge calculations now work for B, Si, Be, Mg, and Al.
   (github issue 20)
 - Two logging problems were fixed (github issues 21 and 24)
 - Molecules that have had kappa descriptors generated can now be
   written to SD files (github issue 23)

New Features:
 - The handling of chirality in reactions has been reworked and
   improved. Please see the RDKit Book for an explanation.
 - Atom-pair and topological-torsion fingerprints now support the
   inclusion of chirality in the atom invariants.
 - A number of new compositional descriptors have been added:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
 - An implementation of the molecular quantum number (MQN) descriptors
   has been added.
 - RDKFingerprintMol now takes an optional atomBits argument which is
   used to return information about which bits atoms are involved in.
 - LayeredFingerprintMol no longer takes the arguments tgtDensity and
   minSize. They were not being used.
 - LayeredFingerprintMol2 has been renamed to PatternFingerprintMol
 - The substructure matcher can now properly take stereochemistry into
   account if the useChirality flag is provided.
 - The module rdkit.Chem.Draw.mplCanvas has been added back to svn.
 - A new module integrating the RDKit with Pandas (rdkit.Chem.PandasTools)
   has been added.

New Database Cartridge Features: 
 - The new compositional descriptors are available:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
 - MACCS fingerprints are available
 - the substruct_count function is now available
 - substructure indexing has improved. NOTE: indexes on molecule
    columns will need to be rebuilt.

New Java Wrapper Features:
 - The new compositional descriptors are available:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
 - The molecular quantum number (MQN) descriptors are available
 - MACCS fingerprints are available
 - BRICS decomposition is available.

Deprecated modules (to be removed in next release):

Removed modules:

 - RDKit fingerprint generation is now faster. The hashing algorithm
   used in the RDKit fingerprinter has changed.
 - Force-field calculations are substantially faster ( issue 290)
 - The core of the BRICS implementation has been moved into C++.
 - The MACCS fingerprint implementation has been moved into
   C++. (contribution from Roger Sayle)
 - New documentation has been added: Cartridge.rst, Overview.rst,

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I'm very happy to announce the 2nd RDKit User Group Meeting. The
meeting, which is being hosted by George Papadatos at the European
Bioinformatics Institute (EBI), will take place October 2nd-4th at the
Genome Campus in Hinxton, UK.

We're using a different format this year:

Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, and
something new: talktorials. Talktorials are somewhere between a
talk and a tutorial, they cover something interesting done with the
RDKit and include the code used to do the work. During the
presentation you'll give an overview of what you did and also show the
pieces of the code that are central to the work. The idea is to mix
the science up with the tutorial aspects.

Day 3 will be the first ever RDKit sprint: those who choose to stay
will spend an intense day working in small groups to produce useful
artifacts: new bits of code, knime nodes, knime workflows, tutorials,
documentation, IPython notebooks, etc. We'll see who's there and what
folks are interested in contributing and go from there.

There will also be, of course, social activities.

Registration is free at the following link:

We are looking now for people who are willing to do presentations or
talktorials on the first two days. If you're interested in
contributing, please send George and I an email. Lighting talks don't
need to be arranged too far in advance; I will start collecting the
list of people interested in doing those shortly before the event.

Many thanks to George for volunteering to host this event!

I'm really looking forward to the chance to see a bunch of you again,
to meet some new people, and to hear some more cool stories about what
people do with the RDKit.
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