Re: [Rdkit-discuss] [Rdkit-announce] Q2 2010 Release
Congratulations on the release, Greg!
I am really a very recent adopter of RDKit, but even in the short time I have
been using it I have been amazed at the quality and depth of functionality!
Please keep up the good work, and I hope I can continue to help a tiny amount
in the only way I know how - by selfishly requesting new features :)
Kind regards
James
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Wed 30/06/2010 21:16
To: RDKit Discuss; RDKit Developers List; rdkit-annou...@lists.sourceforge.net
Subject: [Rdkit-announce] Q2 2010 Release
Dear all,
I'm very happy to announce that the next version of the RDKit --
Q22010_1 -- is released.
The release notes are below.
The source release and windows binaries (python 2.6 only this time,
please let me know if anyone needs a python 2.5 release) will be on
the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I have also updated the online documentation.
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.
-greg
** Release_Q22010_1 ***
(Changes relative to Release_Q12010_1)
!! IMPORTANT !!
- There are a couple of refactoring changes that affect people using
the RDKit from C++. Please look in the Other section below for a list.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. Please look in the Other section below for more
information.
Acknowledgements:
- Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
Greg Magoon, Noel O'Boyle, Nik Stiefl,
Bug Fixes:
- The depictor no longer generates NaNs for some molecules on
windows (issue 2995724)
- [X] query features work correctly with chiral atoms. (issue
3000399)
- mols will no longer be deleted by python when atoms/bonds returned
from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
- a problem with force-field construction for five-coordinate atoms
was fixed. (issue 3009337)
- double bonds to terminal atoms are no longer marked as "any" bonds
when writing mol blocks. (issue 3009756)
- a problem with stereochemistry of double bonds linking rings was
fixed. (issue 3009836)
- a problem with R/S assignment was fixed. (issue 3009911)
- error and warning messages are now properly displayed when cmake
builds are used on windows.
- a canonicalization problem with double bonds incident onto aromatic
rings was fixed. (issue 3018558)
- a problem with embedding fused small ring systems was fixed.
(issue 3019283)
New Features:
- RXN files can now be written. (issue 3011399)
- reaction smarts can now be written.
- v3000 RXN files can now be read. (issue 3009807)
- better support for query information in mol blocks is present.
(issue 2942501)
- Depictions of reactions can now be generated.
- Morgan fingerprints can now be calculated as bit vectors (as
opposed to count vectors.
- the method GetFeatureDefs() has been added to
MolChemicalFeatureFactory
- repeated recursive SMARTS queries in a single SMARTS will now be
recognized and matched much faster.
- the SMILES and SMARTS parsers can now be run safely in
multi-threaded code.
Deprecated modules (to be removed in next release):
- rdkit/qtGui
- Projects/SDView
Removed modules:
- SVD code: External/svdlibc External/svdpackc rdkit/PySVD
- rdkit/Chem/CDXMLWriter.py
Other:
- The large scale changes in the handling of stereochemistry were
made for this release. These should make the code more robust.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. This is likely to be a problem on Redhat, and
redhat-derived systems. Specifically: if your version of flex is
something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
etc.), you will need to get a newer version from
http://flex.sourceforge.net in order to build the RDKit.
- Changes only affecting C++ programmers:
- The code for calculating topological-torsion and atom-pair
fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
to $RDBASE/Code/GraphMol/Fingerprints.
- The naming convention for methods of ExplicitBitVect and
SparseBitVect have been changed to make it more consistent with
the rest of the RDKit.
- the bjam-based build system should be considered
deprecated. This is the last release it will be actively
maintained.
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sp
Re: [Rdkit-discuss] Q2 2010 Release
Am 30.06.2010 22:16, schrieb Greg Landrum: > Dear all, > > I'm very happy to announce that the next version of the RDKit -- > Q22010_1 -- is released. > > The release notes are below. > > The source release and windows binaries (python 2.6 only this time, > please let me know if anyone needs a python 2.5 release) will be on > the sourceforge downloads page: If it isn't too much work for you I would very much appreciate a python 2.5 windows binary. -- Thanks, Thomas -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q2 2010 Release
Great! Good job Greg!
Will try to build for C++ tomorrow
On 30 June 2010 21:16, Greg Landrum wrote:
> Dear all,
>
> I'm very happy to announce that the next version of the RDKit --
> Q22010_1 -- is released.
>
> The release notes are below.
>
> The source release and windows binaries (python 2.6 only this time,
> please let me know if anyone needs a python 2.5 release) will be on
> the sourceforge downloads page:
> http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
> The files can also be downloaded from the google project page:
> http://code.google.com/p/rdkit/downloads/list
>
> I have also updated the online documentation.
>
> 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.
>
> -greg
>
> ** Release_Q22010_1 ***
> (Changes relative to Release_Q12010_1)
>
> !! IMPORTANT !!
> - There are a couple of refactoring changes that affect people using
> the RDKit from C++. Please look in the Other section below for a list.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. Please look in the Other section below for more
> information.
>
> Acknowledgements:
> - Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
> Greg Magoon, Noel O'Boyle, Nik Stiefl,
>
> Bug Fixes:
> - The depictor no longer generates NaNs for some molecules on
> windows (issue 2995724)
> - [X] query features work correctly with chiral atoms. (issue
> 3000399)
> - mols will no longer be deleted by python when atoms/bonds returned
> from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
> - a problem with force-field construction for five-coordinate atoms
> was fixed. (issue 3009337)
> - double bonds to terminal atoms are no longer marked as "any" bonds
> when writing mol blocks. (issue 3009756)
> - a problem with stereochemistry of double bonds linking rings was
> fixed. (issue 3009836)
> - a problem with R/S assignment was fixed. (issue 3009911)
> - error and warning messages are now properly displayed when cmake
> builds are used on windows.
> - a canonicalization problem with double bonds incident onto aromatic
> rings was fixed. (issue 3018558)
> - a problem with embedding fused small ring systems was fixed.
> (issue 3019283)
>
> New Features:
> - RXN files can now be written. (issue 3011399)
> - reaction smarts can now be written.
> - v3000 RXN files can now be read. (issue 3009807)
> - better support for query information in mol blocks is present.
> (issue 2942501)
> - Depictions of reactions can now be generated.
> - Morgan fingerprints can now be calculated as bit vectors (as
> opposed to count vectors.
> - the method GetFeatureDefs() has been added to
> MolChemicalFeatureFactory
> - repeated recursive SMARTS queries in a single SMARTS will now be
> recognized and matched much faster.
> - the SMILES and SMARTS parsers can now be run safely in
> multi-threaded code.
>
> Deprecated modules (to be removed in next release):
> - rdkit/qtGui
> - Projects/SDView
>
> Removed modules:
> - SVD code: External/svdlibc External/svdpackc rdkit/PySVD
> - rdkit/Chem/CDXMLWriter.py
>
> Other:
> - The large scale changes in the handling of stereochemistry were
> made for this release. These should make the code more robust.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. This is likely to be a problem on Redhat, and
> redhat-derived systems. Specifically: if your version of flex is
> something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
> etc.), you will need to get a newer version from
> http://flex.sourceforge.net in order to build the RDKit.
>
> - Changes only affecting C++ programmers:
> - The code for calculating topological-torsion and atom-pair
> fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
> to $RDBASE/Code/GraphMol/Fingerprints.
> - The naming convention for methods of ExplicitBitVect and
> SparseBitVect have been changed to make it more consistent with
> the rest of the RDKit.
> - the bjam-based build system should be considered
> deprecated. This is the last release it will be actively
> maintained.
>
>
> --
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Scientific Software Solutions Ltd
[Rdkit-discuss] Q2 2010 Release
Dear all,
I'm very happy to announce that the next version of the RDKit --
Q22010_1 -- is released.
The release notes are below.
The source release and windows binaries (python 2.6 only this time,
please let me know if anyone needs a python 2.5 release) will be on
the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I have also updated the online documentation.
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.
-greg
** Release_Q22010_1 ***
(Changes relative to Release_Q12010_1)
!! IMPORTANT !!
- There are a couple of refactoring changes that affect people using
the RDKit from C++. Please look in the Other section below for a list.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. Please look in the Other section below for more
information.
Acknowledgements:
- Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
Greg Magoon, Noel O'Boyle, Nik Stiefl,
Bug Fixes:
- The depictor no longer generates NaNs for some molecules on
windows (issue 2995724)
- [X] query features work correctly with chiral atoms. (issue
3000399)
- mols will no longer be deleted by python when atoms/bonds returned
from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
- a problem with force-field construction for five-coordinate atoms
was fixed. (issue 3009337)
- double bonds to terminal atoms are no longer marked as "any" bonds
when writing mol blocks. (issue 3009756)
- a problem with stereochemistry of double bonds linking rings was
fixed. (issue 3009836)
- a problem with R/S assignment was fixed. (issue 3009911)
- error and warning messages are now properly displayed when cmake
builds are used on windows.
- a canonicalization problem with double bonds incident onto aromatic
rings was fixed. (issue 3018558)
- a problem with embedding fused small ring systems was fixed.
(issue 3019283)
New Features:
- RXN files can now be written. (issue 3011399)
- reaction smarts can now be written.
- v3000 RXN files can now be read. (issue 3009807)
- better support for query information in mol blocks is present.
(issue 2942501)
- Depictions of reactions can now be generated.
- Morgan fingerprints can now be calculated as bit vectors (as
opposed to count vectors.
- the method GetFeatureDefs() has been added to
MolChemicalFeatureFactory
- repeated recursive SMARTS queries in a single SMARTS will now be
recognized and matched much faster.
- the SMILES and SMARTS parsers can now be run safely in
multi-threaded code.
Deprecated modules (to be removed in next release):
- rdkit/qtGui
- Projects/SDView
Removed modules:
- SVD code: External/svdlibc External/svdpackc rdkit/PySVD
- rdkit/Chem/CDXMLWriter.py
Other:
- The large scale changes in the handling of stereochemistry were
made for this release. These should make the code more robust.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. This is likely to be a problem on Redhat, and
redhat-derived systems. Specifically: if your version of flex is
something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
etc.), you will need to get a newer version from
http://flex.sourceforge.net in order to build the RDKit.
- Changes only affecting C++ programmers:
- The code for calculating topological-torsion and atom-pair
fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
to $RDBASE/Code/GraphMol/Fingerprints.
- The naming convention for methods of ExplicitBitVect and
SparseBitVect have been changed to make it more consistent with
the rest of the RDKit.
- the bjam-based build system should be considered
deprecated. This is the last release it will be actively
maintained.
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
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Re: [Rdkit-discuss] a boolean function
Dear Christian,
Please send RDKit questions to the mailing list, not directly to me.
2010/6/30 Christian de Bouillé :
>
> From our web server with 11 million chemicals
> basically unique, I would like to have
> the 3D to compute some descriptors
>
> I do not need to compute each structure
>
> You recommand to use Chem.CanonSmiles
> but it would be fine to include a boolean function
> as for Chem.MolFromSmiles to raise the error
I think what you are asking is how to find out if processing a
molecule failed. Is that correct?
The answer to that question is that Chem.MolFromSmiles() return None,
so you can test like this:
In [2]: from rdkit import Chem
In [3]: m = Chem.MolFromSmiles('c1c1')
In [4]: m is None
Out[4]: False
In [5]: m = Chem.MolFromSmiles('c11')
[20:58:28] Can't kekulize mol
In [6]: m is None
Out[6]: True
If you are using Supplier (either an SDMolSupplier or a
SmilesMolSupplier), you can just do:
for mol in supplier:
if mol is None: continue
# do whatever else you want to do with the molecule here.
Best Regards,
-greg
--
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