rdkit-devel — Developers information and discussion.

Re: [Rdkit-devel] [Rdkit-announce] 2015.09 (Q3 2015) RDKit Release

[Greg L. <gre...@gm...>]

And I have now pushed the python 2.7 and python 3.4 builds for the Mac to
the rdkit channel at anaconda.org.

-greg

On Mon, Nov 23, 2015 at 11:04 PM, Riccardo Vianello <
ric...@gm...> wrote:

>
> ​Dear all,
>
> RDKit 2015.09.2 conda packages for linux and win-64 are now available for
> download from the rdkit channel on anaconda.org. This build includes
> python3 packages for windows too (thanks Paolo Tosco for help building
> boost). I'll send an update when win-32 pkgs are also online.
>
> Best,
> Riccardo
>

Re: [Rdkit-devel] [Rdkit-announce] 2015.09 (Q3 2015) RDKit Release

[Riccardo V. <ric...@gm...>]

​Dear all,

RDKit 2015.09.2 conda packages for linux and win-64 are now available for
download from the rdkit channel on anaconda.org. This build includes
python3 packages for windows too (thanks Paolo Tosco for help building
boost). I'll send an update when win-32 pkgs are also online.

Best,
Riccardo

[Rdkit-devel] CentOS 6 build failure

[Gianluca S. <gi...@gm...>]

The CentOS 6 build for the latest RDKit is failing with this error:

In file included from /usr/include/boost/python/to_python_indirect.hpp:11,
                 from /usr/include/boost/python/converter/arg_to_python.hpp:11,
                 from /usr/include/boost/python/call.hpp:16,
                 from /usr/include/boost/python/object_core.hpp:13,
                 from /usr/include/boost/python/args.hpp:26,
                 from /usr/include/boost/python.hpp:12,
                 from
/builddir/build/BUILD/rdkit-Release_2015_09_2/python2/Code/RDBoost/Wrap.h:18,
                 from
/builddir/build/BUILD/rdkit-Release_2015_09_2/python2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:32:
/usr/include/boost/python/object/pointer_holder.hpp: In member
function 'void* boost::python::objects::pointer_holder<Pointer,
Value>::holds
(boost::python::type_info, bool) [with Pointer =
boost::shared_ptr<const RDKit::FilterCatalogEntry>, Value = const
RDKit::FilterCatalogEntry
]':
/builddir/build/BUILD/rdkit-Release_2015_09_2/python2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:492:
  instantiated from here
/usr/include/boost/python/object/pointer_holder.hpp:145: error:
invalid conversion from 'const void*' to 'void*'
/usr/include/boost/python/object/pointer_holder.hpp:145: error:
initializing argument 1 of 'void*
boost::python::objects::find_dynamic_typ
e(void*, boost::python::type_info, boost::python::type_info)'
/usr/include/boost/python/object/pointer_holder.hpp:145: error:
invalid conversion from 'const void*' to 'void*'

I need to note CentOS 6 has an older boost version (1.41) so if that
is the culprit and we can't fix that code to work with it, I will
probably keep the package at the last know working release (2015.03)

Regards

G.

-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

Re: [Rdkit-devel] PDF Book

[Gianluca S. <gi...@gm...>]

On Sat, Nov 7, 2015 at 4:58 AM, Greg Landrum <gre...@gm...> wrote:
> hmmm, I replied too quickly: that's already fixed in git.
>
> The PDF book is no longer checked in (it needs to be built with the rest of
> the docs). It was in git up until June, but I removed it after Michael Banck
> pointed out the old version (https://github.com/rdkit/rdkit/issues/516)
>
> Maybe the copy you have in the directory is from an old pull?

Possibly. In fact, I just tried the build from the tarball of the
latest release and it's not there.

I managed to build the Book on Fedora after fighting a bit with tex
dependencies. RHEL/CentOS seems to be harder, I'm asking people with
more knowledge on the topic so I hope to have it fixed soon


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

Re: [Rdkit-devel] [Rdkit-discuss] 2015.09 (Q3 2015) RDKit Release

[Gianluca S. <gi...@gm...>]

On Wed, Nov 18, 2015 at 3:24 AM, Greg Landrum <gre...@gm...> wrote:
>
> Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 will be
> available from
> this repository:
> https://copr.fedoraproject.org/coprs/giallu/rdkit/

2015_09_1 is already there for Fedora 21, 22 and 23, I'm rebuilding
now for 2015_09_2. In this release, i added a python3 subpackage that
seems to work correctly (but tests need some patch to work, so they
are currently disabled).

RHEL/CentOS packages will come later, as I am investigating how to
build the documentation there.

[Rdkit-devel] 2015.09 (Q3 2015) RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the next version of the RDKit -- 2015.09
(a.k.a. Q3 2015) -- is released. The new RDKit release theme is: Better
late than never. :-)

Note that this is a patch release (the version number ends in _2). We
discovered a couple of problems in the original release before I actually
announced it and decided we should fix those before announcing the release.

The release notes are below.

The release and binary files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_09_2
Unless there's serious demand for it, I do not plan to duplicate these on
the sourceforge download page.

I will be uploading 32-bit and 64-bit Windows binaries for Python 2.7 and,
in response to a couple of requests, 32-bit and 64-bit Windows binaries for
Java.

Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 will be
available from
this repository:
https://copr.fedoraproject.org/coprs/giallu/rdkit/

Conda builds will start to appear in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit) over the next few days.

We have updated the homebrew recipe and will update the conda build script
to reflect the new version.

The online version of the documentation at rdkit.org 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, which is scheduled for March 2016.

Best Regards,
-greg

# Release_2015.09.2
(Changes relative to Release_2015.09.1)

## Acknowledgements:
Brian Kelley, Paolo Tosco, Riccardo Vianello

## Bug Fixes:
  - Fixed a post-decrement which causes a crash when compiling under
Windows with MSVC 9
  (from ptosco)
  - Fixes a memory leak in fragmentMol
  (github #669 from bp-kelley)
  - MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
  (github #655 from rvianello)

# Release_2015.09.1
(Changes relative to Release_2015.03.1)

## Acknowledgements:

Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
Maciek Wojcikowski

## Highlights:

  - Addition of parsers/writers for sequence notation, FASTA, and basic HELM
  - Improved conformation generation based on experimental torsional
parameters
  - Much better filtering of generated conformations to ensure they
    match the chirality of the input structure
  - New method for enumerating molecular resonance structures
  - Addition of a molecular FilterCatalog data structure

## Bug Fixes:
  - Draw.MolToImage(mol) does not work for Python 3, because cairo for
Python 3 has not yet implemented Surface.create_for_data
 (github issue #460 from apahl)
  - SDWriter.close() fails when the underlying stream has an error
 (github issue #498 from greglandrum)
  - Hexafluorophosphate cannot be handled
 (github issue #510 from greglandrum)
  - Labels of highlighted atoms are invisible
 (github issue #519 from NadineSchneider)
  - MolDraw2D: Fix in highlighting atoms
 (github pull #521 from NadineSchneider)
  - Cartridge: index failing for molecular equality in some circumstances
 (github issue #525 from greglandrum)
  - Bad ring finding in a complex fused ring
 (github issue #526 from greglandrum)
  - Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for
use with SDWriter under Python3
 (github pull #531 from ptosco)
  - Regression: _smilesAtomOutputOrder incorrect for dot disconnected
molecules
 (github issue #532 from baoilleach)
  - Fix #532 - smilesAtomOutputOrder incorrect
 (github pull #535 from baoilleach)
  - Fix Python3 encoding for FilterCatalog/Entry serialization
 (github pull #537 from bp-kelley)
  - Catalog::setCatalogParams needs to be virtual now
 (github pull #538 from bp-kelley)
  - Bonds in allyl cation are not conjugated
 (github issue #539 from greglandrum)
  - Fixes GitHub issue 539
 (github pull #540 from ptosco)
  - SaltBuilder._initPatterns incorrectly handles SMARTS errors
 (github issue #541 from adalke)
  - merging query Hs failing on recursive SMARTS
 (github issue #544 from greglandrum)
  - Crash in O3A alignment when running multi-threaded
 (github issue #546 from greglandrum)
  - PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - fix MMPA bugs for some tests
 (github pull #548 from AlexanderSavelyev)
  - TFD fix for single bonds adjacent to triple bonds
 (github pull #550 from sriniker)
  - Canonicalization paper Aug2015
 (github pull #552 from NadineSchneider)
  - Chirality not affected by atom-map index
 (github issue #553 from adalke)
  - Implicit Hs should not appear in depictions for query atoms.
 (github issue #556 from greglandrum)
  - Fix issue with invalid reactions throwing NameError
 (github pull #559 from bp-kelley)
  - InChI radicals not properly converted
 (github issue #562 from pierrelb)
  - MMPA code not python3 compatible
 (github issue #564 from greglandrum)
  - mmpa: fix bug with num_of_cuts > 2 case
 (github pull #566 from AlexanderSavelyev)
  - Incorrect stereochemistry after embedding
 (github issue #568 from greglandrum)
  - changed FrameToGridImage() so that the dataframe index can be used as
legend
 (github pull #570 from apahl)
  - MolDraw2DCairo.GetDrawingText() doesn't work with Python3
 (github issue #571 from greglandrum)
  - addBond return value
 (github issue #572 from JLVarjo)
  - Process aborts during ForwardSDMolSupplier gc when the file object is
closed
 (github issue #579 from adalke)
  - Fix/update pains filter catalog
 (github pull #581 from bp-kelley)
  - Importing PandasTools on Windows fails due to Salts.txt
 (github issue #583 from baoilleach)
  - renumberAtoms() not setting conformer dimensionality properly
 (github issue #584 from greglandrum)
  - stereo atoms property on double bonds not being updated properly with
insertMol
 (github issue #608 from greglandrum)
  - UFF Atom type not properly assigned to lanthanides
 (github issue #613 from greglandrum)
  - segfault from MolToInchi when bad bond stereochem info is present
 (github issue #614 from greglandrum)
  - MQN12 (heavy atom count) seems to be always 0.
 (github issue #623 from kienerj)
  - fmcs: fix issue with initial seed for PR 580
 (github pull #624 from AlexanderSavelyev)
  - fmcs: fixes #631 with chiralirty
 (github pull #634 from AlexanderSavelyev)
  - Fixes sprintf not found on some gcc compiles
 (github pull #635 from bp-kelley)
  - Fix AppVeyor and Travis UnitTests
 (github pull #636 from bp-kelley)
  - Fixes #629 - python GetSubstructureMatch thread safety
 (github pull #637 from bp-kelley)
  - Fix regressions occurring when building with msvc9
 (github pull #638 from rvianello)
  - Fix/python gil release on rdkit threadsafe sss only
 (github pull #639 from bp-kelley)
  - ctest not running some of the python tests.
 (github issue #643 from greglandrum)
  - Issue643
 (github pull #646 from greglandrum)
  - Fix/various bug fixes filtercatalog and bad operator
 (github pull #648 from bp-kelley)
  - unlocking or destroying a locked mutex in the substructure matcher
 (github issue #653 from greglandrum)
  - MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
 (github issue #655 from rvianello)
  - new canon: fix in special symmetry invariant
 (github pull #663 from NadineSchneider)

## New Features and Enhancements:
  - enable popcount by default for cartridge
 (github issue #428 from greglandrum)
  - Added the RSMD calculation over N molecules in the cookbook.
 (github pull #495 from malteseunderdog)
  - Modified force field constraint tests to be more robust
 (github pull #503 from ptosco)
  - Fix mol drawing on Python3 (issue #460)
 (github pull #504 from apahl)
  - mmpa first version was added
 (github pull #505 from AlexanderSavelyev)
  - Forcefield tests now use RDKit::feq() instead of RDKit::round()
 (github pull #506 from ptosco)
  - SDMolSupplier(), setData() and strictParsing
 (github pull #507 from ptosco)
  - Improvements to LoadSDF and WriteSDF
 (github pull #513 from samoturk)
  - updates to mmpa. reduce number of smiles parsing
 (github pull #515 from AlexanderSavelyev)
  - Some enhancements for the new canonicalization
 (github pull #520 from NadineSchneider)
  - mmpa: remove boost_regex dependency at all. Add new test references
 (github pull #527 from AlexanderSavelyev)
  - Support getting atoms involved in Pharm2D bits
 (github issue #530 from greglandrum)
  - Optimized MMFF::MMFFOptimizeMoleculeConfs()
 (github pull #534 from ptosco)
  - RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
 (github pull #536 from bp-kelley)
  - Expose Conformer's copy constructor to Python
 (github issue #545 from greglandrum)
  - PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - Update PAINS smarts to validated set.  Always use mergeQueryHs when
reading Smarts
 (github pull #549 from bp-kelley)
  - Add a curated set of PAINS filters to the RDKit
 (github issue #555 from greglandrum)
  - Update pains from wehi_pains.csv
 (github pull #560 from bp-kelley)
  - Change MMPA to use CanonicalRankAtoms instead of _CIPRank
 (github issue #561 from adalke)
  - Add adjustQuery() function to make substructure queries more specific.
 (github issue #567 from greglandrum)
  - changed sascorer.py to enable import from different location
 (github pull #569 from apahl)
  - add export_values() to enums in the python wrapper where it's sensible
to do so
 (github issue #573 from greglandrum)
  - Support Sheridan's BT and BP fingerprints
 (github issue #574 from greglandrum)
  - Locale dependent float for _GasteigerCharge
 (github issue #577 from adalke)
  - fmcs: implement adding an initial seed structure
 (github pull #580 from AlexanderSavelyev)
  - Where possible convert docs from RST to MD
 (github issue #585 from greglandrum)
  - [UGM2015] Autodetection of numThreads
 (github issue #586 from mwojcikowski)
  - Generating SVG Images with Transparent Background
 (github issue #587 from gungorbudak)
  - updates to PandasTools.LoadSDF
 (github pull #599 from adalke)
  - Can control mol depiction size with PandasTools.molSize = (200,200).
 (github pull #600 from samoturk)
  - pandas performance and functionality improvements
 (github pull #601 from adalke)
  - Adding documentation for installation with conda.
 (github pull #602 from strets123)
  - Automatic atom reordering in TorsionFingerprints
 (github pull #603 from sriniker)
  - remove bare excepts
 (github pull #606 from adalke)
  - Added option to use SVG rendering in pandas data frames
 (github pull #609 from samoturk)
  - Handle inserting molecules with conformers into molecules without
conformers
 (github issue #610 from greglandrum)
  - If wedged bonds are already present, write them to mol blocks
 (github issue #611 from greglandrum)
  - Dev/filter catalog java wrapper
 (github pull #612 from bp-kelley)
  - Support extended reduced graphs
 (github issue #615 from greglandrum)
  - port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
 (github issue #617 from greglandrum)
  - Add parser/writer for peptide sequences
 (github issue #620 from greglandrum)
  - Add parser/writer for FASTA
 (github issue #621 from greglandrum)
  - Add parser/writer for HELM
 (github issue #622 from greglandrum)
  - Migrate std::string APIs to const std::string &
 (github pull #627 from bp-kelley)
  - Chirality tests
 (github pull #628 from sriniker)
  - Improvements of TFD
 (github pull #630 from sriniker)
  - Added ResonanceMolSupplier
 (github pull #632 from ptosco)
  - Image tostring/fromstring methods replaced by tobytes/frombytes
 (github pull #644 from rvianello)
  - ET(K)DG implementation
 (github pull #647 from sriniker)
  - Build multithreading support by default when boost::threads is present
 (github issue #649 from greglandrum)
  - Minimal SWIG Java wrappers for ResonanceMolSupplier
 (github pull #657 from ptosco)

## New Database Cartridge Features:
  - Support for PostgreSQL v8.x has been removed
  - NumSpiroCenters and NumBridgeheadAtoms added

## New Java Wrapper Features:
  - Support for FilterCatalogs
  - Support for ResonanceMolSuppliers

## Deprecated code (to be removed in next release):

## Removed code:
  - rdkit/DataStructs/BitVect.py : a C++ version is used, this was only
present for historical reasons
  - rdkit/DataStructs/SparseIntVect.py : a C++ version is used, this was
only present for historical reasons

## Contrib updates:
  - Addition of Peter Ertl's Natural Product Likeness score.

## Other:
  - Much of the documentation has been translated from RST to MD

Re: [Rdkit-devel] PDF Book

[Greg L. <gre...@gm...>]

hmmm, I replied too quickly: that's already fixed in git.

The PDF book is no longer checked in (it needs to be built with the rest of
the docs). It was in git up until June, but I removed it after Michael
Banck pointed out the old version (https://github.com/rdkit/rdkit/issues/516
)

Maybe the copy you have in the directory is from an old pull?

-greg


On Sat, Nov 7, 2015 at 4:47 AM, Greg Landrum <gre...@gm...> wrote:

> Thanks for pointing that out. I'll fix it.
>
> -greg
>
>
> On Fri, Nov 6, 2015 at 8:42 PM, Gianluca Sforna <gi...@gm...> wrote:
>
>> I noticed the RDKit Book I find in Docs/Book after the build claims to
>> be from the 2013.09 release.
>>
>> Is it correct? Maybe it's just in need of a rebuild?
>>
>> Regards
>>
>> G.
>>
>> --
>> Gianluca Sforna
>>
>> http://morefedora.blogspot.com
>> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>
>

Re: [Rdkit-devel] PDF Book

[Greg L. <gre...@gm...>]

Thanks for pointing that out. I'll fix it.

-greg


On Fri, Nov 6, 2015 at 8:42 PM, Gianluca Sforna <gi...@gm...> wrote:

> I noticed the RDKit Book I find in Docs/Book after the build claims to
> be from the 2013.09 release.
>
> Is it correct? Maybe it's just in need of a rebuild?
>
> Regards
>
> G.
>
> --
> Gianluca Sforna
>
> http://morefedora.blogspot.com
> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] PDF Book

[Gianluca S. <gi...@gm...>]

I noticed the RDKit Book I find in Docs/Book after the build claims to
be from the 2013.09 release.

Is it correct? Maybe it's just in need of a rebuild?

Regards

G.

-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

[Rdkit-devel] Beta of Q3 2015 release now up

[Greg L. <gre...@gm...>]

Dear all,

I have tagged a beta of the next RDKit release here:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_09_1beta1

The relevant section of the release notes is below. Note that the list of
people in the acknowledgement section was mostly created automatically from
github. If you feel like I missed you, please let me know so that I can
update the release notes before the actual release.

I will try to get windows binaries up in the next few days, but I'm not
sure this is going to happen.

Unless major problems are found, I plan to do the actual release in the
next week or so. Between now and then I hope to get a few more bugs
crushed, but there shouldn't be any additional feature additions.

Best,
-greg


# Release_2015.09.1
(Changes relative to Release_2015.03.1)

## Acknowledgements:

Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
Maciek Wojcikowski

## Highlights:

  - Addition of parsers/writers for sequence notation, FASTA, and basic HELM
  - Improved conformation generation based on experimental torsional
parameters
  - New method for enumerating molecular resonance structures
  - Addition of a molecular FilterCatalog data structure

## Bug Fixes:
  - Draw.MolToImage(mol) does not work for Python 3, because cairo for
Python 3 has not yet implemented Surface.create_for_data
 (github issue #460 from apahl)
  - SDWriter.close() fails when the underlying stream has an error
 (github issue #498 from greglandrum)
  - Hexafluorophosphate cannot be handled
 (github issue #510 from greglandrum)
  - Labels of highlighted atoms are invisible
 (github issue #519 from NadineSchneider)
  - MolDraw2D: Fix in highlighting atoms
 (github pull #521 from NadineSchneider)
  - Bad ring finding in a complex fused ring
 (github issue #526 from greglandrum)
  - Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for
use with SDWriter under Python3
 (github pull #531 from ptosco)
  - Regression: _smilesAtomOutputOrder incorrect for dot disconnected
molecules
 (github issue #532 from baoilleach)
  - Fix #532 - smilesAtomOutputOrder incorrect
 (github pull #535 from baoilleach)
  - Fix Python3 encoding for FilterCatalog/Entry serialization
 (github pull #537 from bp-kelley)
  - Catalog::setCatalogParams needs to be virtual now
 (github pull #538 from bp-kelley)
  - Bonds in allyl cation are not conjugated
 (github issue #539 from greglandrum)
  - Fixes GitHub issue 539
 (github pull #540 from ptosco)
  - SaltBuilder._initPatterns incorrectly handles SMARTS errors
 (github issue #541 from adalke)
  - merging query Hs failing on recursive SMARTS
 (github issue #544 from greglandrum)
  - Crash in O3A alignment when running multi-threaded
 (github issue #546 from greglandrum)
  - PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - fix MMPA bugs for some tests
 (github pull #548 from AlexanderSavelyev)
  - TFD fix for single bonds adjacent to triple bonds
 (github pull #550 from sriniker)
  - Canonicalization paper Aug2015
 (github pull #552 from NadineSchneider)
  - Chirality not affected by atom-map index
 (github issue #553 from adalke)
  - Implicit Hs should not appear in depictions for query atoms.
 (github issue #556 from greglandrum)
  - Fix issue with invalid reactions throwing NameError
 (github pull #559 from bp-kelley)
  - InChI radicals not properly converted
 (github issue #562 from pierrelb)
  - MMPA code not python3 compatible
 (github issue #564 from greglandrum)
  - mmpa: fix bug with num_of_cuts > 2 case
 (github pull #566 from AlexanderSavelyev)
  - Incorrect stereochemistry after embedding
 (github issue #568 from greglandrum)
  - changed FrameToGridImage() so that the dataframe index can be used as
legend
 (github pull #570 from apahl)
  - MolDraw2DCairo.GetDrawingText() doesn't work with Python3
 (github issue #571 from greglandrum)
  - addBond return value
 (github issue #572 from JLVarjo)
  - Process aborts during ForwardSDMolSupplier gc when the file object is
closed
 (github issue #579 from adalke)
  - Fix/update pains filter catalog
 (github pull #581 from bp-kelley)
  - Importing PandasTools on Windows fails due to Salts.txt
 (github issue #583 from baoilleach)
  - renumberAtoms() not setting conformer dimensionality properly
 (github issue #584 from greglandrum)
  - stereo atoms property on double bonds not being updated properly with
insertMol
 (github issue #608 from greglandrum)
  - UFF Atom type not properly assigned to lanthanides
 (github issue #613 from greglandrum)
  - segfault from MolToInchi when bad bond stereochem info is present
 (github issue #614 from greglandrum)
  - MQN12 (heavy atom count) seems to be always 0.
 (github issue #623 from kienerj)
  - fmcs: fix issue with initial seed for PR 580
 (github pull #624 from AlexanderSavelyev)
  - fmcs: fixes #631 with chiralirty
 (github pull #634 from AlexanderSavelyev)
  - Fixes sprintf not found on some gcc compiles
 (github pull #635 from bp-kelley)
  - Fix AppVeyor and Travis UnitTests
 (github pull #636 from bp-kelley)
  - Fixes #629 - python GetSubstructureMatch thread safety
 (github pull #637 from bp-kelley)
  - Fix regressions occurring when building with msvc9
 (github pull #638 from rvianello)
  - Fix/python gil release on rdkit threadsafe sss only
 (github pull #639 from bp-kelley)
  - ctest not running some of the python tests.
 (github issue #643 from greglandrum)
  - Issue643
 (github pull #646 from greglandrum)
  - Fix/various bug fixes filtercatalog and bad operator
 (github pull #648 from bp-kelley)

## New Features and Enhancements:
  - Added the RSMD calculation over N molecules in the cookbook.
 (github pull #495 from malteseunderdog)
  - Modified force field constraint tests to be more robust
 (github pull #503 from ptosco)
  - Fix mol drawing on Python3 (issue #460)
 (github pull #504 from apahl)
  - Forcefield tests now use RDKit::feq() instead of RDKit::round()
 (github pull #506 from ptosco)
  - SDMolSupplier(), setData() and strictParsing
 (github pull #507 from ptosco)
  - Improvements to LoadSDF and WriteSDF
 (github pull #513 from samoturk)
  - updates to mmpa. reduce number of smiles parsing
 (github pull #515 from AlexanderSavelyev)
  - Some enhancements for the new canonicalization
 (github pull #520 from NadineSchneider)
  - mmpa: remove boost_regex dependency at all. Add new test references
 (github pull #527 from AlexanderSavelyev)
  - Support getting atoms involved in Pharm2D bits
 (github issue #530 from greglandrum)
  - Optimized MMFF::MMFFOptimizeMoleculeConfs()
 (github pull #534 from ptosco)
  - RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
 (github pull #536 from bp-kelley)
  - Expose Conformer's copy constructor to Python
 (github issue #545 from greglandrum)
  - PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - Update PAINS smarts to validated set.  Always use mergeQueryHs when
reading Smarts
 (github pull #549 from bp-kelley)
  - Add a curated set of PAINS filters to the RDKit
 (github issue #555 from greglandrum)
  - Update pains from wehi_pains.csv
 (github pull #560 from bp-kelley)
  - Change MMPA to use CanonicalRankAtoms instead of _CIPRank
 (github issue #561 from adalke)
  - Add adjustQuery() function to make substructure queries more specific.
 (github issue #567 from greglandrum)
  - changed sascorer.py to enable import from different location
 (github pull #569 from apahl)
  - add export_values() to enums in the python wrapper where it's sensible
to do so
 (github issue #573 from greglandrum)
  - Support Sheridan's BT and BP fingerprints
 (github issue #574 from greglandrum)
  - Locale dependent float for _GasteigerCharge
 (github issue #577 from adalke)
  - fmcs: implement adding an initial seed structure
 (github pull #580 from AlexanderSavelyev)
  - Where possible convert docs from RST to MD
 (github issue #585 from greglandrum)
  - [UGM2015] Autodetection of numThreads
 (github issue #586 from mwojcikowski)
  - Generating SVG Images with Transparent Background
 (github issue #587 from gungorbudak)
  - updates to PandasTools.LoadSDF
 (github pull #599 from adalke)
  - Can control mol depiction size with PandasTools.molSize = (200,200).
 (github pull #600 from samoturk)
  - pandas performance and functionality improvements
 (github pull #601 from adalke)
  - Adding documentation for installation with conda.
 (github pull #602 from strets123)
  - Automatic atom reordering in TorsionFingerprints
 (github pull #603 from sriniker)
  - Added option to use SVG rendering in pandas data frames
 (github pull #609 from samoturk)
  - Handle inserting molecules with conformers into molecules without
conformers
 (github issue #610 from greglandrum)
  - If wedged bonds are already present, write them to mol blocks
 (github issue #611 from greglandrum)
  - Dev/filter catalog java wrapper
 (github pull #612 from bp-kelley)
  - Support extended reduced graphs
 (github issue #615 from greglandrum)
  - port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
 (github issue #617 from greglandrum)
  - Add parser/writer for peptide sequences
 (github issue #620 from greglandrum)
  - Add parser/writer for FASTA
 (github issue #621 from greglandrum)
  - Add parser/writer for HELM
 (github issue #622 from greglandrum)
  - Migrate std::string APIs to const std::string &
 (github pull #627 from bp-kelley)
  - Chirality tests
 (github pull #628 from sriniker)
  - Improvements of TFD
 (github pull #630 from sriniker)
  - Added ResonanceMolSupplier
 (github pull #632 from ptosco)
  - Image tostring/fromstring methods replaced by tobytes/frombytes
 (github pull #644 from rvianello)
  - ET(K)DG implementation
 (github pull #647 from sriniker)
  - Build multithreading support by default when boost::threads is present
 (github issue #649 from greglandrum)

## New Database Cartridge Features:
  - Support for PostgreSQL v8.x has been removed
  - NumSpiroCenters and NumBridgeheadAtoms added

## New Java Wrapper Features:
  - Support for FilterCatalogs

## Deprecated code (to be removed in next release):

## Removed code:
  - rdkit/DataStructs/BitVect.py : a C++ version is used, this was only
present for historical reasons
  - rdkit/DataStructs/SparseIntVect.py : a C++ version is used, this was
only present for historical reasons

## Contrib updates:
  - Addition of Peter Ertl's Natural Product Likeness score.

## Other:
  - Much of the documentation has been translated from RST to MD

[Rdkit-devel] Keeping coordinates of explicit hydrogen atoms

[JW F. <fe...@dn...>]

Hi,

I am using "suppl = Chem.SDMolSupplier(infile)" to read a SD file
containing molecules with 3D coordinates for explicit hydrogen atoms. Upon
retrieving a mol from suppl, the explicit hydrogen atoms are suppressed and
3D coordinates were lost. Is there a way to keep explicit hydrogen atoms
and their coordinates when using Chem.SDMolSupplier()?

Thanks,

JW
___________________
JW Feng, Ph.D.
Denali Therapeutics Inc.
201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628

Re: [Rdkit-devel] Keeping coordinates of explicit hydrogen atoms

[JW F. <fe...@dn...>]

Found the solution:
    suppl = Chem.SDMolSupplier(infile, removeHs=False)

JW

___________________
JW Feng, Ph.D.
Denali Therapeutics Inc.
201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628

On Thu, Oct 8, 2015 at 10:30 PM, JW Feng <fe...@dn...> wrote:

> Hi,
>
> I am using "suppl = Chem.SDMolSupplier(infile)" to read a SD file
> containing molecules with 3D coordinates for explicit hydrogen atoms. Upon
> retrieving a mol from suppl, the explicit hydrogen atoms are suppressed and
> 3D coordinates were lost. Is there a way to keep explicit hydrogen atoms
> and their coordinates when using Chem.SDMolSupplier()?
>
> Thanks,
>
> JW
> ___________________
> JW Feng, Ph.D.
> Denali Therapeutics Inc.
> 201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628
>

Re: [Rdkit-devel] SVG font size problem

[Greg L. <gre...@gm...>]

Cyrus,

When you generate a PDF with the RDKit drawing code, it attempts to find
installed versions of cairo and aggdraw. If these both fail, then it uses
an old (and buggy) cross-platform drawing library called sping (which is
included with the RDKit). It looks like the problem you are having is due
to the use of sping.

The best (though certainly not painless) solution is to get cairo and a
python wrapper for it installed on your Mac. I would suggest getting cairo
with homebrew and then using pip to install cairocffi. From a bit of
googling, that seems to be an approach that works.

-greg


On Sat, May 16, 2015 at 7:58 PM, Cyrus Harmon <cyr...@gm...> wrote:

> So (now that I've gotten the basics working on MacOS) I have a little
> python program that generates an image from a SMILES string:
>
> #!/usr/bin/env python
> import argparse, sys
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> from rdkit.Chem import Draw
> from rdkit.Chem.Draw.MolDrawing import MolDrawing
> from rdkit.Chem.Draw.MolDrawing import DrawingOptions
>
> parser = argparse.ArgumentParser()
> parser.add_argument('-s', "--smiles", nargs='?', help="input smiles")
> parser.add_argument('-o', "--output", type=str, default=sys.stdout)
>
> args = parser.parse_args()
> smiles = args.smiles
> mol = AllChem.MolFromSmiles(smiles)
>
> options = DrawingOptions()
> options.atomLabelFontSize = 18
> options.atomLabelFontFace = "sans"
>
> Draw.MolToFile(mol,args.output,size=(300,300),options=options)
>
>
>
> Everything works as expected for PDF and PNG files:
>
> e.g.
>
> ./draw-test.py -s "N[C@@H](C(C)C)C(O)=O" -o ~/tmp/valine.pdf
>
> looks fine. But if I try that as a PDF, I get a big mess where the font
> size is enormous (>100 pt) and the glyph isn't placed right.
>
> This sounds similar to the problem described here:
> http://sourceforge.net/p/rdkit/mailman/message/26208338/
>
> although that seems to be some sort of Adobe problem.
>
> I've tried a similar example (a couple of weeks, on a slightly earlier
> version of Rdkit) on a different computer (running linux) and things look
> good. Perhaps this is once again some library installation/configuration
> issue, but I'm not sure what would be causing the problem.
>
> Any ideas?
>
> thanks,
>
> Cyrus
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

Re: [Rdkit-devel] seg faults running tests on a mac

[Greg L. <gre...@gm...>]

Hi Cyrus,

I'm glad you were able to find something that works. If I had to guess, I
would say that the root cause of all of this was the homebrew version of
python confusing things.

-greg

On Sat, May 16, 2015 at 7:27 PM, Cyrus Harmon <cyr...@gm...> wrote:

> Ok, I think I've solved (or at least worked around) my python woes. The
> following seems to do the trick:
>
> export RDBASE=/Users/sly/projects/rdkit
> export PYTHONPATH=/usr/local/:${RDBASE}:
> export
> DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:${RDBASE}/lib:/usr/local/lib:
>
> # running cmake:
> cmake \
>   -D PYTHON_EXECUTABLE=/usr/local/bin/python \
>   -D
> PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Headers
> \
>   -D
> PYTHON_LIBRARY=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
> \
>   ..
>
> # build it
> make -j4
>
> # install
> make install
>
> # test
> ctest
>
>
>
> Now onto the next problem...
>
>
> On Sat, May 16, 2015 at 3:20 PM, Cyrus Harmon <cyr...@gm...>
> wrote:
>
>> Following up on my own message...
>>
>> I noticed that the python executable and python libraries found by cmake
>> don't match. cmake finds the homebrew installed python binary, but the
>> system installed libraries.
>>
>> If I remove the homebrew python I can at least get the tests to pass (but
>> run into problems with various other missing python packages).  A step in
>> the right direction.
>>
>> On Sat, May 16, 2015 at 10:11 AM, Cyrus Harmon <cyr...@gm...>
>> wrote:
>>
>>> Hi Greg,
>>>
>>> Sorry it's been a while since I first reported my troubles on a Mac. I
>>> continue to have problems on my MacBook Pro, but things seem to work fine
>>> on linux for me.
>>>
>>> The problem is that many of the tests fail with a segfault and there
>>> doesn't seem to much information in any of the log files about the problem.
>>> In an effort to figure out what's going on here, I've been trying to run
>>> things under gdb.
>>>
>>> If I run the testBV.py test under gdb I see the following:
>>>
>>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>>> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
>>> 0x00000001029e7cb9 in PyInt_FromLong ()
>>> (gdb) bt
>>> #0  0x00000001029e7cb9 in PyInt_FromLong ()
>>> #1  0x0000000102844908 in
>>> boost::python::detail::keywords<1ul>::operator=<int> ()
>>> #2  0x000000010284277a in init_module_rdBase ()
>>> #3  0x0000000102b2f391 in boost::python::handle_exception_impl ()
>>> #4  0x0000000102b303b9 in boost::python::detail::init_module ()
>>> #5  0x00000001000a04ea in _PyImport_LoadDynamicModule ()
>>> #6  0x00000001000a01d2 in import_submodule ()
>>> #7  0x000000010009fd9c in load_next ()
>>> #8  0x000000010009df99 in PyImport_ImportModuleLevel ()
>>> #9  0x0000000100083459 in builtin___import__ ()
>>> #10 0x000000010000e3b6 in PyObject_Call ()
>>> #11 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
>>> #12 0x000000010008a0b7 in PyEval_EvalFrameEx ()
>>> #13 0x0000000100087df9 in PyEval_EvalCodeEx ()
>>> #14 0x000000010008786f in PyEval_EvalCode ()
>>> #15 0x000000010009ca46 in PyImport_ExecCodeModuleEx ()
>>> #16 0x000000010009f731 in load_source_module ()
>>> #17 0x000000010009f9f2 in load_package ()
>>> #18 0x00000001000a01d2 in import_submodule ()
>>> #19 0x000000010009fd9c in load_next ()
>>> #20 0x000000010009df99 in PyImport_ImportModuleLevel ()
>>> #21 0x0000000100083459 in builtin___import__ ()
>>> #22 0x000000010000e3b6 in PyObject_Call ()
>>> #23 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
>>> #24 0x000000010008a0b7 in PyEval_EvalFrameEx ()
>>> #25 0x0000000100087df9 in PyEval_EvalCodeEx ()
>>> #26 0x000000010008786f in PyEval_EvalCode ()
>>> #27 0x00000001000a7a2a in run_mod ()
>>> #28 0x00000001000a7acd in PyRun_FileExFlags ()
>>> #29 0x00000001000a766a in PyRun_SimpleFileExFlags ()
>>> #30 0x00000001000b8d6f in Py_Main ()
>>> #31 0x00007fff947ec5c9 in start ()
>>>
>>> So it looks to me like things are sort of working for a while, but that
>>> somewhere along the line I'm getting a segfault, which may in turn be
>>> triggered by a problem loading a dylib.
>>>
>>> I'm guessing that part of the problem is that there are a lot of moving
>>> parts here:
>>>
>>> 1. RDKIT -- I'm using the latest git head as of today
>>> 2. Python
>>>  a. version 2 or version 3?
>>>    - I'm trying to get things working with python2, but python3 would be
>>> nice at some point
>>>  b. system installed, hombrew, or self-installed?
>>>    - I'm trying to use the homebrew-installed python2. Perhaps this is a
>>> mistake.
>>> 3. Python libraries (installed via pip)
>>> 4. Homebrew libraries
>>> 5. System libraries
>>> 6. Environment variables
>>> 7. etc...
>>>
>>> What a mess...
>>>
>>> speaking of environment variables, one thing that might be problematic
>>> for me is that I am trying to use the following environment variables:
>>>
>>> export PYTHONPATH=/Users/sly/projects/rdkit/
>>> export RDBASE=/Users/sly/projects/rdkit/
>>> export
>>> DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:/Users/sly/projects/rdkit/lib:/usr/local/lib:
>>>
>>> If I don't add the system ImageIO path, cmake fails with:
>>>
>>> dyld: Symbol not found: __cg_png_create_info_struct
>>>   Referenced from:
>>> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>>>   Expected in: /usr/local/lib/libPng.dylib
>>>  in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>>>
>>> Adding that to DYLD_LIBRARY_PATH at least gets things to build and has
>>> some tests running.
>>>
>>> Happy to provide more info if that will help figure out what's going on
>>> here.
>>>
>>> thanks,
>>>
>>> Cyrus
>>>
>>> p.s. sorry about the duplicate subscription and sending this from
>>> not-my-normal-email account, but I'm having travel-based connectivity
>>> issues.
>>>
>>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

[Rdkit-devel] SVG font size problem

[Cyrus H. <cyr...@gm...>]

So (now that I've gotten the basics working on MacOS) I have a little
python program that generates an image from a SMILES string:

#!/usr/bin/env python
import argparse, sys

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw.MolDrawing import MolDrawing
from rdkit.Chem.Draw.MolDrawing import DrawingOptions

parser = argparse.ArgumentParser()
parser.add_argument('-s', "--smiles", nargs='?', help="input smiles")
parser.add_argument('-o', "--output", type=str, default=sys.stdout)

args = parser.parse_args()
smiles = args.smiles
mol = AllChem.MolFromSmiles(smiles)

options = DrawingOptions()
options.atomLabelFontSize = 18
options.atomLabelFontFace = "sans"

Draw.MolToFile(mol,args.output,size=(300,300),options=options)



Everything works as expected for PDF and PNG files:

e.g.

./draw-test.py -s "N[C@@H](C(C)C)C(O)=O" -o ~/tmp/valine.pdf

looks fine. But if I try that as a PDF, I get a big mess where the font
size is enormous (>100 pt) and the glyph isn't placed right.

This sounds similar to the problem described here:
http://sourceforge.net/p/rdkit/mailman/message/26208338/

although that seems to be some sort of Adobe problem.

I've tried a similar example (a couple of weeks, on a slightly earlier
version of Rdkit) on a different computer (running linux) and things look
good. Perhaps this is once again some library installation/configuration
issue, but I'm not sure what would be causing the problem.

Any ideas?

thanks,

Cyrus

Re: [Rdkit-devel] seg faults running tests on a mac

[Cyrus H. <cyr...@gm...>]

Ok, I think I've solved (or at least worked around) my python woes. The
following seems to do the trick:

export RDBASE=/Users/sly/projects/rdkit
export PYTHONPATH=/usr/local/:${RDBASE}:
export
DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:${RDBASE}/lib:/usr/local/lib:

# running cmake:
cmake \
  -D PYTHON_EXECUTABLE=/usr/local/bin/python \
  -D
PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Headers
\
  -D
PYTHON_LIBRARY=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
\
  ..

# build it
make -j4

# install
make install

# test
ctest



Now onto the next problem...


On Sat, May 16, 2015 at 3:20 PM, Cyrus Harmon <cyr...@gm...> wrote:

> Following up on my own message...
>
> I noticed that the python executable and python libraries found by cmake
> don't match. cmake finds the homebrew installed python binary, but the
> system installed libraries.
>
> If I remove the homebrew python I can at least get the tests to pass (but
> run into problems with various other missing python packages).  A step in
> the right direction.
>
> On Sat, May 16, 2015 at 10:11 AM, Cyrus Harmon <cyr...@gm...>
> wrote:
>
>> Hi Greg,
>>
>> Sorry it's been a while since I first reported my troubles on a Mac. I
>> continue to have problems on my MacBook Pro, but things seem to work fine
>> on linux for me.
>>
>> The problem is that many of the tests fail with a segfault and there
>> doesn't seem to much information in any of the log files about the problem.
>> In an effort to figure out what's going on here, I've been trying to run
>> things under gdb.
>>
>> If I run the testBV.py test under gdb I see the following:
>>
>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
>> 0x00000001029e7cb9 in PyInt_FromLong ()
>> (gdb) bt
>> #0  0x00000001029e7cb9 in PyInt_FromLong ()
>> #1  0x0000000102844908 in
>> boost::python::detail::keywords<1ul>::operator=<int> ()
>> #2  0x000000010284277a in init_module_rdBase ()
>> #3  0x0000000102b2f391 in boost::python::handle_exception_impl ()
>> #4  0x0000000102b303b9 in boost::python::detail::init_module ()
>> #5  0x00000001000a04ea in _PyImport_LoadDynamicModule ()
>> #6  0x00000001000a01d2 in import_submodule ()
>> #7  0x000000010009fd9c in load_next ()
>> #8  0x000000010009df99 in PyImport_ImportModuleLevel ()
>> #9  0x0000000100083459 in builtin___import__ ()
>> #10 0x000000010000e3b6 in PyObject_Call ()
>> #11 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
>> #12 0x000000010008a0b7 in PyEval_EvalFrameEx ()
>> #13 0x0000000100087df9 in PyEval_EvalCodeEx ()
>> #14 0x000000010008786f in PyEval_EvalCode ()
>> #15 0x000000010009ca46 in PyImport_ExecCodeModuleEx ()
>> #16 0x000000010009f731 in load_source_module ()
>> #17 0x000000010009f9f2 in load_package ()
>> #18 0x00000001000a01d2 in import_submodule ()
>> #19 0x000000010009fd9c in load_next ()
>> #20 0x000000010009df99 in PyImport_ImportModuleLevel ()
>> #21 0x0000000100083459 in builtin___import__ ()
>> #22 0x000000010000e3b6 in PyObject_Call ()
>> #23 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
>> #24 0x000000010008a0b7 in PyEval_EvalFrameEx ()
>> #25 0x0000000100087df9 in PyEval_EvalCodeEx ()
>> #26 0x000000010008786f in PyEval_EvalCode ()
>> #27 0x00000001000a7a2a in run_mod ()
>> #28 0x00000001000a7acd in PyRun_FileExFlags ()
>> #29 0x00000001000a766a in PyRun_SimpleFileExFlags ()
>> #30 0x00000001000b8d6f in Py_Main ()
>> #31 0x00007fff947ec5c9 in start ()
>>
>> So it looks to me like things are sort of working for a while, but that
>> somewhere along the line I'm getting a segfault, which may in turn be
>> triggered by a problem loading a dylib.
>>
>> I'm guessing that part of the problem is that there are a lot of moving
>> parts here:
>>
>> 1. RDKIT -- I'm using the latest git head as of today
>> 2. Python
>>  a. version 2 or version 3?
>>    - I'm trying to get things working with python2, but python3 would be
>> nice at some point
>>  b. system installed, hombrew, or self-installed?
>>    - I'm trying to use the homebrew-installed python2. Perhaps this is a
>> mistake.
>> 3. Python libraries (installed via pip)
>> 4. Homebrew libraries
>> 5. System libraries
>> 6. Environment variables
>> 7. etc...
>>
>> What a mess...
>>
>> speaking of environment variables, one thing that might be problematic
>> for me is that I am trying to use the following environment variables:
>>
>> export PYTHONPATH=/Users/sly/projects/rdkit/
>> export RDBASE=/Users/sly/projects/rdkit/
>> export
>> DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:/Users/sly/projects/rdkit/lib:/usr/local/lib:
>>
>> If I don't add the system ImageIO path, cmake fails with:
>>
>> dyld: Symbol not found: __cg_png_create_info_struct
>>   Referenced from:
>> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>>   Expected in: /usr/local/lib/libPng.dylib
>>  in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>>
>> Adding that to DYLD_LIBRARY_PATH at least gets things to build and has
>> some tests running.
>>
>> Happy to provide more info if that will help figure out what's going on
>> here.
>>
>> thanks,
>>
>> Cyrus
>>
>> p.s. sorry about the duplicate subscription and sending this from
>> not-my-normal-email account, but I'm having travel-based connectivity
>> issues.
>>
>>
>
>

Re: [Rdkit-devel] seg faults running tests on a mac

[Cyrus H. <cyr...@gm...>]

Following up on my own message...

I noticed that the python executable and python libraries found by cmake
don't match. cmake finds the homebrew installed python binary, but the
system installed libraries.

If I remove the homebrew python I can at least get the tests to pass (but
run into problems with various other missing python packages).  A step in
the right direction.

On Sat, May 16, 2015 at 10:11 AM, Cyrus Harmon <cyr...@gm...>
wrote:

> Hi Greg,
>
> Sorry it's been a while since I first reported my troubles on a Mac. I
> continue to have problems on my MacBook Pro, but things seem to work fine
> on linux for me.
>
> The problem is that many of the tests fail with a segfault and there
> doesn't seem to much information in any of the log files about the problem.
> In an effort to figure out what's going on here, I've been trying to run
> things under gdb.
>
> If I run the testBV.py test under gdb I see the following:
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
> 0x00000001029e7cb9 in PyInt_FromLong ()
> (gdb) bt
> #0  0x00000001029e7cb9 in PyInt_FromLong ()
> #1  0x0000000102844908 in
> boost::python::detail::keywords<1ul>::operator=<int> ()
> #2  0x000000010284277a in init_module_rdBase ()
> #3  0x0000000102b2f391 in boost::python::handle_exception_impl ()
> #4  0x0000000102b303b9 in boost::python::detail::init_module ()
> #5  0x00000001000a04ea in _PyImport_LoadDynamicModule ()
> #6  0x00000001000a01d2 in import_submodule ()
> #7  0x000000010009fd9c in load_next ()
> #8  0x000000010009df99 in PyImport_ImportModuleLevel ()
> #9  0x0000000100083459 in builtin___import__ ()
> #10 0x000000010000e3b6 in PyObject_Call ()
> #11 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
> #12 0x000000010008a0b7 in PyEval_EvalFrameEx ()
> #13 0x0000000100087df9 in PyEval_EvalCodeEx ()
> #14 0x000000010008786f in PyEval_EvalCode ()
> #15 0x000000010009ca46 in PyImport_ExecCodeModuleEx ()
> #16 0x000000010009f731 in load_source_module ()
> #17 0x000000010009f9f2 in load_package ()
> #18 0x00000001000a01d2 in import_submodule ()
> #19 0x000000010009fd9c in load_next ()
> #20 0x000000010009df99 in PyImport_ImportModuleLevel ()
> #21 0x0000000100083459 in builtin___import__ ()
> #22 0x000000010000e3b6 in PyObject_Call ()
> #23 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
> #24 0x000000010008a0b7 in PyEval_EvalFrameEx ()
> #25 0x0000000100087df9 in PyEval_EvalCodeEx ()
> #26 0x000000010008786f in PyEval_EvalCode ()
> #27 0x00000001000a7a2a in run_mod ()
> #28 0x00000001000a7acd in PyRun_FileExFlags ()
> #29 0x00000001000a766a in PyRun_SimpleFileExFlags ()
> #30 0x00000001000b8d6f in Py_Main ()
> #31 0x00007fff947ec5c9 in start ()
>
> So it looks to me like things are sort of working for a while, but that
> somewhere along the line I'm getting a segfault, which may in turn be
> triggered by a problem loading a dylib.
>
> I'm guessing that part of the problem is that there are a lot of moving
> parts here:
>
> 1. RDKIT -- I'm using the latest git head as of today
> 2. Python
>  a. version 2 or version 3?
>    - I'm trying to get things working with python2, but python3 would be
> nice at some point
>  b. system installed, hombrew, or self-installed?
>    - I'm trying to use the homebrew-installed python2. Perhaps this is a
> mistake.
> 3. Python libraries (installed via pip)
> 4. Homebrew libraries
> 5. System libraries
> 6. Environment variables
> 7. etc...
>
> What a mess...
>
> speaking of environment variables, one thing that might be problematic for
> me is that I am trying to use the following environment variables:
>
> export PYTHONPATH=/Users/sly/projects/rdkit/
> export RDBASE=/Users/sly/projects/rdkit/
> export
> DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:/Users/sly/projects/rdkit/lib:/usr/local/lib:
>
> If I don't add the system ImageIO path, cmake fails with:
>
> dyld: Symbol not found: __cg_png_create_info_struct
>   Referenced from:
> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>   Expected in: /usr/local/lib/libPng.dylib
>  in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
>
> Adding that to DYLD_LIBRARY_PATH at least gets things to build and has
> some tests running.
>
> Happy to provide more info if that will help figure out what's going on
> here.
>
> thanks,
>
> Cyrus
>
> p.s. sorry about the duplicate subscription and sending this from
> not-my-normal-email account, but I'm having travel-based connectivity
> issues.
>
>

[Rdkit-devel] seg faults running tests on a mac

[Cyrus H. <cyr...@gm...>]

Hi Greg,

Sorry it's been a while since I first reported my troubles on a Mac. I
continue to have problems on my MacBook Pro, but things seem to work fine
on linux for me.

The problem is that many of the tests fail with a segfault and there
doesn't seem to much information in any of the log files about the problem.
In an effort to figure out what's going on here, I've been trying to run
things under gdb.

If I run the testBV.py test under gdb I see the following:

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
0x00000001029e7cb9 in PyInt_FromLong ()
(gdb) bt
#0  0x00000001029e7cb9 in PyInt_FromLong ()
#1  0x0000000102844908 in
boost::python::detail::keywords<1ul>::operator=<int> ()
#2  0x000000010284277a in init_module_rdBase ()
#3  0x0000000102b2f391 in boost::python::handle_exception_impl ()
#4  0x0000000102b303b9 in boost::python::detail::init_module ()
#5  0x00000001000a04ea in _PyImport_LoadDynamicModule ()
#6  0x00000001000a01d2 in import_submodule ()
#7  0x000000010009fd9c in load_next ()
#8  0x000000010009df99 in PyImport_ImportModuleLevel ()
#9  0x0000000100083459 in builtin___import__ ()
#10 0x000000010000e3b6 in PyObject_Call ()
#11 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
#12 0x000000010008a0b7 in PyEval_EvalFrameEx ()
#13 0x0000000100087df9 in PyEval_EvalCodeEx ()
#14 0x000000010008786f in PyEval_EvalCode ()
#15 0x000000010009ca46 in PyImport_ExecCodeModuleEx ()
#16 0x000000010009f731 in load_source_module ()
#17 0x000000010009f9f2 in load_package ()
#18 0x00000001000a01d2 in import_submodule ()
#19 0x000000010009fd9c in load_next ()
#20 0x000000010009df99 in PyImport_ImportModuleLevel ()
#21 0x0000000100083459 in builtin___import__ ()
#22 0x000000010000e3b6 in PyObject_Call ()
#23 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
#24 0x000000010008a0b7 in PyEval_EvalFrameEx ()
#25 0x0000000100087df9 in PyEval_EvalCodeEx ()
#26 0x000000010008786f in PyEval_EvalCode ()
#27 0x00000001000a7a2a in run_mod ()
#28 0x00000001000a7acd in PyRun_FileExFlags ()
#29 0x00000001000a766a in PyRun_SimpleFileExFlags ()
#30 0x00000001000b8d6f in Py_Main ()
#31 0x00007fff947ec5c9 in start ()

So it looks to me like things are sort of working for a while, but that
somewhere along the line I'm getting a segfault, which may in turn be
triggered by a problem loading a dylib.

I'm guessing that part of the problem is that there are a lot of moving
parts here:

1. RDKIT -- I'm using the latest git head as of today
2. Python
 a. version 2 or version 3?
   - I'm trying to get things working with python2, but python3 would be
nice at some point
 b. system installed, hombrew, or self-installed?
   - I'm trying to use the homebrew-installed python2. Perhaps this is a
mistake.
3. Python libraries (installed via pip)
4. Homebrew libraries
5. System libraries
6. Environment variables
7. etc...

What a mess...

speaking of environment variables, one thing that might be problematic for
me is that I am trying to use the following environment variables:

export PYTHONPATH=/Users/sly/projects/rdkit/
export RDBASE=/Users/sly/projects/rdkit/
export
DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:/Users/sly/projects/rdkit/lib:/usr/local/lib:

If I don't add the system ImageIO path, cmake fails with:

dyld: Symbol not found: __cg_png_create_info_struct
  Referenced from:
/System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
  Expected in: /usr/local/lib/libPng.dylib
 in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO

Adding that to DYLD_LIBRARY_PATH at least gets things to build and has some
tests running.

Happy to provide more info if that will help figure out what's going on
here.

thanks,

Cyrus

p.s. sorry about the duplicate subscription and sending this from
not-my-normal-email account, but I'm having travel-based connectivity
issues.

Re: [Rdkit-devel] The RDKit and modern C++

[Gianluca S. <gi...@gm...>]

On Tue, May 12, 2015 at 1:40 PM, David Cosgrove
<dav...@gm...> wrote:
> Hi Greg et al,
>
> You can increment by one the number of large organisations still not fully
> converted to RH6!  It's a real pain for me as a developer. I have been
> unable to build the latest few releases of Qt 5 on a RH6 machine with the
> system g++4.4, for example.

Weird, given qt5 is packages in EPEL:
http://dl.fedoraproject.org/pub/epel/6/x86_64/repoview/letter_q.group.html

maybe they have some not-yet-upstreamed patch.



> However, my experience developing code for a
> large organisation with hardware dispersed over a number of sites each with
> its own peculiarities of linux support is that it's essential that the final
> production version is built with the default system compiler for the target
> OS. Otherwise you get compatibility issues with missing libraries, wrong
> version of glib etc.

What you wrote above is basically the reason you are looking for below :)

> I don't know why RedHat is so behind with its compiler
> support,

However, Red Hat is quite proactive in either backporting bug fixes
(for instance, they fixed this way a compiler issue I found compiling
RDKit for RHEL5), or even backward compatible new features. I think we
could start to add new stuff and see if the g++ 4.4 shipped in RHEL6
is able to cope with it; if not, try to report bugs on RH Bugzilla and
see if the compiler team would be able to backport the missing
feature. I can assist with this process if needed.



-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

Re: [Rdkit-devel] The RDKit and modern C++

[David C. <dav...@gm...>]

Hi Greg et al,

You can increment by one the number of large organisations still not fully
converted to RH6!  It's a real pain for me as a developer. I have been
unable to build the latest few releases of Qt 5 on a RH6 machine with the
system g++4.4, for example.  However, my experience developing code for a
large organisation with hardware dispersed over a number of sites each with
its own peculiarities of linux support is that it's essential that the
final production version is built with the default system compiler for the
target OS. Otherwise you get compatibility issues with missing libraries,
wrong version of glib etc.  This means that I am still having to compile
some code with g++4.1 on RH5. I don't know why RedHat is so behind with its
compiler support, but whilst it is I would need to continue to be able to
build code with g++4.4.  Your idea of a compatibility branch is a good
stopgap. Having said that I wonder if, in practice, it's much different
from just saying if you have an old compiler you need to use an older
version of RDKit that works with it. You might maybe promise to fix, or
help affected people to fix, the most egregious(*) of bugs in the last
version supported by the older compiler, but no more than that.  I think
this would be an acceptable stance to take - the fact that the compiler I
use can't support a standard that's nearly 4 years old is surely my problem
and shouldn't be an excuse to hold everyone else up.

Cheers,
Dave

(*) And from what I see, the quality of the testing is such that that is an
exceptionally rare thing.


On Tue, May 12, 2015 at 5:32 AM, Greg Landrum <gre...@gm...>
wrote:

> Dear all,
>
> I would like to start "allowing" the use of modern C++ (by which I mean C
> ++11/14) in the RDKit. I think this is an important step both for code
> quality in the toolkit itself and for allowing us (the developers) to
> continue to learn and use modern tools. Who knows, it may even help with
> performance. :-)
>
> This move would, of course, break compatibility with some older compilers.
> Here's one view of compiler support for C++11 and some of C++14:
> http://en.cppreference.com/w/cpp/compiler_support
>
> It looks like g++ 4.8+ and VC++ 2013 are both fine with most/all C++11 features.
> VC++ 2015 does even better and g++5 is very solid. Clang, which is the
> default on the Mac and available for both windows and linux, has great
> support.
>
> The thing I am most concerned about is that RHEL6 only includes g++ 4.4.
> RHEL7 is fine, but I would guess that most large organizations aren't that
> up-to-date yet. I know of at least one (ahem) that is hasn't even finished
> the move to RHEL6. It looks like an "enterprise" alternative here is to use
> the RedHat Developer Toolset, but I don't have personal experience with
> that yet. Clang is always an option, but it something people will have to
> install on their own.
>
> Here's how I would propose that we proceed:
>  - If no fundamental objections come up here, we'll create a document
> listing the C++ features that should not be used (yet) due to compiler
> compatibility. We'll also agree on a new baseline version of Boost that can
> be assumed to be present.
>  - I will create a compatibility branch based on the current master. Bug
> fixes will be ported back onto this branch for the next release or two, but
> new features will not be added.
>  - We can start using modern C++ on master.
>
> Best,
> -greg
>
>
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>

[Rdkit-devel] The RDKit and modern C++

[Greg L. <gre...@gm...>]

Dear all,

I would like to start "allowing" the use of modern C++ (by which I mean C++
11/14) in the RDKit. I think this is an important step both for code
quality in the toolkit itself and for allowing us (the developers) to
continue to learn and use modern tools. Who knows, it may even help with
performance. :-)

This move would, of course, break compatibility with some older compilers.
Here's one view of compiler support for C++11 and some of C++14:
http://en.cppreference.com/w/cpp/compiler_support

It looks like g++ 4.8+ and VC++ 2013 are both fine with most/all C++11
features.
VC++ 2015 does even better and g++5 is very solid. Clang, which is the
default on the Mac and available for both windows and linux, has great
support.

The thing I am most concerned about is that RHEL6 only includes g++ 4.4.
RHEL7 is fine, but I would guess that most large organizations aren't that
up-to-date yet. I know of at least one (ahem) that is hasn't even finished
the move to RHEL6. It looks like an "enterprise" alternative here is to use
the RedHat Developer Toolset, but I don't have personal experience with
that yet. Clang is always an option, but it something people will have to
install on their own.

Here's how I would propose that we proceed:
 - If no fundamental objections come up here, we'll create a document
listing the C++ features that should not be used (yet) due to compiler
compatibility. We'll also agree on a new baseline version of Boost that can
be assumed to be present.
 - I will create a compatibility branch based on the current master. Bug
fixes will be ported back onto this branch for the next release or two, but
new features will not be added.
 - We can start using modern C++ on master.

Best,
-greg

[Rdkit-devel] 2015.03 (Q1 2015) RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the next version of the RDKit -- 2015.03
(a.k.a. Q1 2015) -- is released. Better late than never. :-)

The release notes are below.

The release and binary files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1
and will be uploaded to the sourceforge downloads page in the next few days:
http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2015/

I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in
response to a couple of requests, 32-bit and 64-bit Windows binaries for
Java.

Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 are available
from
this repository:
https://copr.fedoraproject.org/coprs/giallu/rdkit/

We have updated the homebrew recipe and conda build script (thanks
Riccardo!) to reflect the new version.

The online version of the documentation at rdkit.org will be updated in the
next week.

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, which is scheduled for September 2015.

Best Regards,
-greg


******  Release_2015.03.1 *******
(Changes relative to Release_2014.09.2)

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

 - This release has a new algorithm for canonical atom ordering. This
   means that canonical SMILES generated with the new version will be
   different from those generated with previous versions.

Acknowledgements:
David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
Kelley, Rich Lewis, John May, Michael Reutlinger, Sereina Riniker,
Alexander Savelyev, Roger Sayle, Nadine Schneider, Gianluca Sforna,
Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vianello

Highlights:

  - A new algorithm for generating canonical atom orders. The new
    algorithm is faster and more robust than the old one.
  - C++-based molecule drawing code, allows consistent molecule
    renderings from C++, Java, and Python. This will become the
    default renderer in the next release.
  - General performance improvements and reduction of memory usage.
  - Torsion Fingerprints for comparing 3D conformations to each other
  - MCS code now available from the PostgreSQL cartridge

Bug Fixes:

  - fmcs: use the zero bond type instead of other
    (github issue #368 from AlexanderSavelyev)
  - bug fixed in TorsionFingerprints.GetTFDMatrix
    (github issue #376 from sriniker)
  - rdkit.Chem.MolDb.Loader_sa does not work with python3.4
    (github issue #390)
  - ChemReactions: Bugfix/Memleak-fix in runReactants
    (github issue #394 from NadineSchneider)
  - TorsionConstraint bug fix
    (github issue #395 from ptosco)
  - Fixed LoadSDF to keep 3D info
    (github pull #401 from samoturk)
  - Incorrect expected absolute stereochemistries in a test
    (github issue #407)
  - GetSubstructMatches() consumes all available memory
    (github issue #409)
  - Bugfix in the chirality handling of chemical reactions
    (github pull #410 from NadineSchneider)
  - fixed two minor bugs in MMFF code
    (github issue #416 from ptosco)
  - Varied sanitise rejection with hydrogen representation
    (github issue #418)
  - Fixed two trivial bugs
    (github issue #419 from ptosco)
  - RDKit learns how to roundtrip MOLFile values.
    (github issue #420 from bp-kelley)
  - cairoCanvas.py python3 compatibility
    (github issue #426 from bach-hardie)
  - Chem.FragmentOnSomeBonds() should update implicit H count on aromatic
heteroatoms when  addDummies is False
    (github issue #429)
  - Chem.FragmentOnSomeBonds() crashes if the bond list is empty
    (github issue #430)
  - Increase limit for smallest ring size
    (github issue #431 from cowsandmilk)
  - Problems caused by heteroatoms with radicals in aromatic rings.
    (github issue #432)
  - Conversion from mol to InChI getting ring stereo wrong
    (github issue #437)
  - Metals in mol2 blocks handled incorrectly
    (github issue #438)
  - Fixed a few tests failing when the Windows git client is used
    (github pull #439 from ptosco)
  - Fixed tests failing on Windows when retrieving sources through the
 Windows git client
    (github pull #440 from ptosco)
  - Conformers not copied correctly in renumberAtoms
    (github issue #441)
  - Radicals are not correctly assigned when reading from SMILES
    (github issue #447)
  - moving RDBoost/Exceptions.h to RDGeneral
    (github pull #458 from rvianello)
  - Add code to accept blank SMILES input.
    (github issue #468 from janholstjensen)
  - Accept empty SMILES and SMARTS
    (github issue #470)
  - Fix MolFile Atom Line List Writer
    (github issue #471 from bp-kelley)
  - Moved 3D ipython renderer to dependency
    (github pull #472 from patrickfuller)
  - Windows build/test failure fixes
    (github issue #473 from ptosco)
  - install missing FMCS/Graph.h header file
    (github pull #478 from rvianello)
  - added const qualifiers to some methods of Atom/Bond iterator classes
    (github pull #479 from rvianello)
  - Bugfix in SmilesWrite and some additional tests for getMolFrags function
    (github issue #482 from NadineSchneider)
  - Removed a while(1) {} in BFGSOpt.h which might result in an infinite
loop
    (github issue #484 from ptosco)
  - Gasteiger charge calculation fails with hexavalent sulfur #485
    (github issue #485)
  - SmilesWriter not creating automatic name values for molecules read from
CTABs
    (github issue #488)
  - Fix StringType access, remove unused imports
    (github issue #494 from bp-kelley)

New Features:

  - Isomeric fix in PandasTools
    (github issue #369 from samoturk)
  - added SaveXlsxFromFrame - first version
    (github issue #371 from samoturk)
  - New feature: Torsion fingerprints
    (github issue #372 from sriniker)
  - Add function to extract a molecule with a single (particular) conformer
from a multiconf mol
    (github issue #384)
  - Added C++ and Python helpers to retrieve force-field parameters
    (github issue #387 from ptosco)
  - Support providing all options to SWIG-wrapped FMCS
    (github issue #397)
  - Add function to request if calling UpdatePropertyCache is necessary
    (github issue #399)
  - Add function to test if UpdatePropertyCache is necessary
    (github issue #400 from NadineSchneider)
  - Substructure highlighting in pandas dataframe (fixes #362)
    (github issue #403 from nhfechner)
  - Added SDF Export to PandasTools and adjusted SDF Import
    (github issue #404 from nhfechner)
  - support count-based avalon fingerprint
    (github issue #408)
  - New C++ drawing code
    (github issue #412 from greglandrum)
  - RDKit learns how to compute code coverage for tests
    (github issue #413 from bp-kelley)
  - Dictionary access is saniztized and optimized.
    (github issue #414 from bp-kelley)
  - expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
    (github issue #421)
  - Dev/expose rank atoms to python
    (github issue #422 from bp-kelley)
  - rdkit learns how to wrap a proper RWMol in python
    (github issue #423 from bp-kelley)
  - Docs: document "magic" property values that are used throughout the code
    (github issue #425)
  - MolDraw2D: expose class to Python
    (github issue #433)
  - RDKit learns how to query properties on Atoms
    (github issue #442 from bp-kelley)
  - Issue445: provide helper functions for multithreaded evaluation of some
expensive functions
    (github issue #448 from greglandrum)
  - RDKit learns how to release the GIL in python
    (github pull #449 from bp-kelley)
  - Dev/property queries
    (github pull #450 from bp-kelley)
  - Support a confId argument to the atom pair fingerprinting code
    (github issue #453)
  - Save the atom bookmarks so we can deconvolute reaction products.
    (github pull #454 from bp-kelley)
  - Cartridge: Support converting no structs to InChI
    (github issue #455)
  - RDKit learns how to expose ChemicalReaction copy constructor to python
    (github pull #456 from bp-kelley)
  - chirality flag was implemented for fmcs() function
    (github pull #466 from AlexanderSavelyev)
  - Support copy and deepcopy properly for at least Mol and RWMol
    (github issue #467)
  - Cartridge: add qmol_from_smiles() and qmol_from_ctab()
    (github issue #469)
  - restore java and python wrappers. New parameter (matchChiralTag)
    (github issue #477 from AlexanderSavelyev)
  - Added a Python wrapper for getShortestPath()
    (github issue #487 from ptosco)
  - Dev/merge query hs no unmapped atoms
    (github issue #490 from bp-kelley)

New Database Cartridge Features:

  - The MCS code is now available within the cartridge
  - The functions qmol_from_smiles() and qmol_from_ctab()

New Java Wrapper Features:

  - The new molecule rendering code is accessible from the SWIG wrappers.

Deprecated code (to be removed in next release):

  - C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
    superseded by the new drawing code in $RDBASE/Code/GraphMol and will
    be removed in the next release.
  - Python:
     - rdkit/Dbase/Pubmed
     - rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
  - Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
    supported by the PostgreSQL project team as of July 2014)

Removed code:

  - the method Atom::setMass() has been removed. Please use setIsotope()
    instead.
  - the methods involving an atom's dativeFlag have been removed.

Contrib updates:

Other:
  - Python 2.6 support is deprecated. Starting with the next RDKit
release, we will only support python 2.7 and python 3.4 and
higher. Python 2.6 has not been supported since October 2013. If you
believe that you are stuck with python 2.6 because of the version of
RHEL you are running, please read this post to learn about your
options:
http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
  - The RDKit molecule objects (ROMol and RWMol) now require about 15%
less memory to store

Re: [Rdkit-devel] Beta of Q1 2015 release now up

[Greg L. <gre...@gm...>]

The URL in the email below is incorrect (copy-paste bug!), it should be:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1beta1

Apologies for the mistake.
-greg

On Fri, Apr 17, 2015 at 4:32 AM, Greg Landrum <gre...@gm...>
wrote:

> Dear all,
>
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/2014_09_1beta1
>
> The relevant section of the release notes is below.
>
> I will try to get windows binaries up in the next few days.
>
> Unless major problems are found, I plan to do the actual release in about
> two weeks.
>
> Best,
> -greg
>
> ******  Release_2015.03.1 *******
> (Changes relative to Release_2014.09.2)
>
> !!!!!! IMPORTANT !!!!!!
>
>  - This release has a new algorithm for canonical atom ordering. This
>    means that canonical SMILES generated with the new version will be
>    different from those generated with previous versions.
>
> Acknowledgements:
> David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
> Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
> Kelley, Rich Lewis, John May, Sereina Riniker, Alexander Savelyev,
> Roger Sayle, Nadine Schneider, Paolo Tosco, Samo Turk, JL Varjo,
> Riccardo Vianello
>
> Highlights:
>
>   - A new algorithm for generating canonical atom orders. The new
>     algorithm is faster and more robust than the old one.
>   - C++-based molecule drawing code, allows consistent molecule
>     renderings from C++, Java, and Python. This will become the
>     default renderer in the next release.
>   - General performance improvements and reduction of memory usage.
>   - Torsion Fingerprints for comparing 3D conformations to each other
>   - MCS code now available from the PostgreSQL cartridge
>
> Bug Fixes:
>
>   - fmcs: use the zero bond type instead of other
>     (github issue #368 from AlexanderSavelyev)
>   - bug fixed in TorsionFingerprints.GetTFDMatrix
>     (github issue #376 from sriniker)
>   - rdkit.Chem.MolDb.Loader_sa does not work with python3.4
>     (github issue #390)
>   - ChemReactions: Bugfix/Memleak-fix in runReactants
>     (github issue #394 from NadineSchneider)
>   - TorsionConstraint bug fix
>     (github issue #395 from ptosco)
>   - Fixed LoadSDF to keep 3D info
>     (github pull #401 from samoturk)
>   - Incorrect expected absolute stereochemistries in a test
>     (github issue #407)
>   - GetSubstructMatches() consumes all available memory
>     (github issue #409)
>   - Bugfix in the chirality handling of chemical reactions
>     (github pull #410 from NadineSchneider)
>   - fixed two minor bugs in MMFF code
>     (github issue #416 from ptosco)
>   - Varied sanitise rejection with hydrogen representation
>     (github issue #418)
>   - Fixed two trivial bugs
>     (github issue #419 from ptosco)
>   - RDKit learns how to roundtrip MOLFile values.
>     (github issue #420 from bp-kelley)
>   - cairoCanvas.py python3 compatibility
>     (github issue #426 from bach-hardie)
>   - Chem.FragmentOnSomeBonds() should update implicit H count on aromatic
> heteroatoms when  addDummies is False
>     (github issue #429)
>   - Chem.FragmentOnSomeBonds() crashes if the bond list is empty
>     (github issue #430)
>   - Increase limit for smallest ring size
>     (github issue #431 from cowsandmilk)
>   - Problems caused by heteroatoms with radicals in aromatic rings.
>     (github issue #432)
>   - Metals in mol2 blocks handled incorrectly
>     (github issue #438)
>   - Fixed a few tests failing when the Windows git client is used
>     (github pull #439 from ptosco)
>   - Fixed tests failing on Windows when retrieving sources through the
>  Windows git client
>     (github pull #440 from ptosco)
>   - Conformers not copied correctly in renumberAtoms
>     (github issue #441)
>   - Radicals are not correctly assigned when reading from SMILES
>     (github issue #447)
>   - moving RDBoost/Exceptions.h to RDGeneral
>     (github pull #458 from rvianello)
>   - Add code to accept blank SMILES input.
>     (github issue #468 from janholstjensen)
>   - Accept empty SMILES and SMARTS
>     (github issue #470)
>   - Fix MolFile Atom Line List Writer
>     (github issue #471 from bp-kelley)
>   - Moved 3D ipython renderer to dependency
>     (github pull #472 from patrickfuller)
>   - Windows build/test failure fixes
>     (github issue #473 from ptosco)
>
> New Features:
>
>   - Isomeric fix in PandasTools
>     (github issue #369 from samoturk)
>   - added SaveXlsxFromFrame - first version
>     (github issue #371 from samoturk)
>   - New feature: Torsion fingerprints
>     (github issue #372 from sriniker)
>   - Add function to extract a molecule with a single (particular)
> conformer from a multiconf mol
>     (github issue #384)
>   - Added C++ and Python helpers to retrieve force-field parameters
>     (github issue #387 from ptosco)
>   - Support providing all options to SWIG-wrapped FMCS
>     (github issue #397)
>   - Add function to request if calling UpdatePropertyCache is necessary
>     (github issue #399)
>   - Add function to test if UpdatePropertyCache is necessary
>     (github issue #400 from NadineSchneider)
>   - Substructure highlighting in pandas dataframe (fixes #362)
>     (github issue #403 from nhfechner)
>   - Added SDF Export to PandasTools and adjusted SDF Import
>     (github issue #404 from nhfechner)
>   - support count-based avalon fingerprint
>     (github issue #408)
>   - New C++ drawing code
>     (github issue #412 from greglandrum)
>   - RDKit learns how to compute code coverage for tests
>     (github issue #413 from bp-kelley)
>   - Dictionary access is saniztized and optimized.
>     (github issue #414 from bp-kelley)
>   - expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
>     (github issue #421)
>   - Dev/expose rank atoms to python
>     (github issue #422 from bp-kelley)
>   - rdkit learns how to wrap a proper RWMol in python
>     (github issue #423 from bp-kelley)
>   - Docs: document "magic" property values that are used throughout the
> code
>     (github issue #425)
>   - MolDraw2D: expose class to Python
>     (github issue #433)
>   - RDKit learns how to query properties on Atoms
>     (github issue #442 from bp-kelley)
>   - Issue445: provide helper functions for multithreaded evaluation of
> some expensive functions
>     (github issue #448 from greglandrum)
>   - RDKit learns how to release the GIL in python
>     (github pull #449 from bp-kelley)
>   - Dev/property queries
>     (github pull #450 from bp-kelley)
>   - Support a confId argument to the atom pair fingerprinting code
>     (github issue #453)
>   - Save the atom bookmarks so we can deconvolute reaction products.
>     (github pull #454 from bp-kelley)
>   - Cartridge: Support converting no structs to InChI
>     (github issue #455)
>   - RDKit learns how to expose ChemicalReaction copy constructor to python
>     (github pull #456 from bp-kelley)
>   - chirality flag was implemented for fmcs() function. NOTE: as of the
> beta release,
>     there is a known order-dependency bug in this functionality.
>     (github pull #466 from AlexanderSavelyev)
>   - Support copy and deepcopy properly for at least Mol and RWMol
>     (github issue #467)
>   - Cartridge: add qmol_from_smiles() and qmol_from_ctab()
>     (github issue #469)
>   - restore java and python wrappers. New parameter (matchChiralTag)
>     (github issue #477 from AlexanderSavelyev)
>
> New Database Cartridge Features:
>
>   - The MCS code is now available within the cartridge
>   - The functions qmol_from_smiles() and qmol_from_ctab()
>
> New Java Wrapper Features:
>
>   - The new molecule rendering code is accessible from the SWIG wrappers.
>
> Deprecated code (to be removed in next release):
>
>   - C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
>     superseded by the new drawing code in $RDBASE/Code/GraphMol and will
>     be removed in the next release.
>   - Python:
>      - rdkit/Dbase/Pubmed
>      - rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
>   - Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
>     supported by the PostgreSQL project team as of July 2014)
>
> Removed code:
>
>   - the method Atom::setMass() has been removed. Please use setIsotope()
>     instead.
>   - the methods involving an atom's dativeFlag have been removed.
>
> Contrib updates:
>
> Other:
>   - Python 2.6 support is deprecated. Starting with the next RDKit
> release, we will only support python 2.7 and python 3.4 and
> higher. Python 2.6 has not been supported since October 2013. If you
> believe that you are stuck with python 2.6 because of the version of
> RHEL you are running, please read this post to learn about your
> options:
>
> http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
>   - The RDKit molecule objects (ROMol and RWMol) now require about 15%
> less memory to store
>
>

[Rdkit-devel] Beta of Q1 2015 release now up

[Greg L. <gre...@gm...>]

Dear all,

I have tagged a beta of the next RDKit release here:
https://github.com/rdkit/rdkit/releases/tag/2014_09_1beta1

The relevant section of the release notes is below.

I will try to get windows binaries up in the next few days.

Unless major problems are found, I plan to do the actual release in about
two weeks.

Best,
-greg

******  Release_2015.03.1 *******
(Changes relative to Release_2014.09.2)

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

 - This release has a new algorithm for canonical atom ordering. This
   means that canonical SMILES generated with the new version will be
   different from those generated with previous versions.

Acknowledgements:
David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
Kelley, Rich Lewis, John May, Sereina Riniker, Alexander Savelyev,
Roger Sayle, Nadine Schneider, Paolo Tosco, Samo Turk, JL Varjo,
Riccardo Vianello

Highlights:

  - A new algorithm for generating canonical atom orders. The new
    algorithm is faster and more robust than the old one.
  - C++-based molecule drawing code, allows consistent molecule
    renderings from C++, Java, and Python. This will become the
    default renderer in the next release.
  - General performance improvements and reduction of memory usage.
  - Torsion Fingerprints for comparing 3D conformations to each other
  - MCS code now available from the PostgreSQL cartridge

Bug Fixes:

  - fmcs: use the zero bond type instead of other
    (github issue #368 from AlexanderSavelyev)
  - bug fixed in TorsionFingerprints.GetTFDMatrix
    (github issue #376 from sriniker)
  - rdkit.Chem.MolDb.Loader_sa does not work with python3.4
    (github issue #390)
  - ChemReactions: Bugfix/Memleak-fix in runReactants
    (github issue #394 from NadineSchneider)
  - TorsionConstraint bug fix
    (github issue #395 from ptosco)
  - Fixed LoadSDF to keep 3D info
    (github pull #401 from samoturk)
  - Incorrect expected absolute stereochemistries in a test
    (github issue #407)
  - GetSubstructMatches() consumes all available memory
    (github issue #409)
  - Bugfix in the chirality handling of chemical reactions
    (github pull #410 from NadineSchneider)
  - fixed two minor bugs in MMFF code
    (github issue #416 from ptosco)
  - Varied sanitise rejection with hydrogen representation
    (github issue #418)
  - Fixed two trivial bugs
    (github issue #419 from ptosco)
  - RDKit learns how to roundtrip MOLFile values.
    (github issue #420 from bp-kelley)
  - cairoCanvas.py python3 compatibility
    (github issue #426 from bach-hardie)
  - Chem.FragmentOnSomeBonds() should update implicit H count on aromatic
heteroatoms when  addDummies is False
    (github issue #429)
  - Chem.FragmentOnSomeBonds() crashes if the bond list is empty
    (github issue #430)
  - Increase limit for smallest ring size
    (github issue #431 from cowsandmilk)
  - Problems caused by heteroatoms with radicals in aromatic rings.
    (github issue #432)
  - Metals in mol2 blocks handled incorrectly
    (github issue #438)
  - Fixed a few tests failing when the Windows git client is used
    (github pull #439 from ptosco)
  - Fixed tests failing on Windows when retrieving sources through the
 Windows git client
    (github pull #440 from ptosco)
  - Conformers not copied correctly in renumberAtoms
    (github issue #441)
  - Radicals are not correctly assigned when reading from SMILES
    (github issue #447)
  - moving RDBoost/Exceptions.h to RDGeneral
    (github pull #458 from rvianello)
  - Add code to accept blank SMILES input.
    (github issue #468 from janholstjensen)
  - Accept empty SMILES and SMARTS
    (github issue #470)
  - Fix MolFile Atom Line List Writer
    (github issue #471 from bp-kelley)
  - Moved 3D ipython renderer to dependency
    (github pull #472 from patrickfuller)
  - Windows build/test failure fixes
    (github issue #473 from ptosco)

New Features:

  - Isomeric fix in PandasTools
    (github issue #369 from samoturk)
  - added SaveXlsxFromFrame - first version
    (github issue #371 from samoturk)
  - New feature: Torsion fingerprints
    (github issue #372 from sriniker)
  - Add function to extract a molecule with a single (particular) conformer
from a multiconf mol
    (github issue #384)
  - Added C++ and Python helpers to retrieve force-field parameters
    (github issue #387 from ptosco)
  - Support providing all options to SWIG-wrapped FMCS
    (github issue #397)
  - Add function to request if calling UpdatePropertyCache is necessary
    (github issue #399)
  - Add function to test if UpdatePropertyCache is necessary
    (github issue #400 from NadineSchneider)
  - Substructure highlighting in pandas dataframe (fixes #362)
    (github issue #403 from nhfechner)
  - Added SDF Export to PandasTools and adjusted SDF Import
    (github issue #404 from nhfechner)
  - support count-based avalon fingerprint
    (github issue #408)
  - New C++ drawing code
    (github issue #412 from greglandrum)
  - RDKit learns how to compute code coverage for tests
    (github issue #413 from bp-kelley)
  - Dictionary access is saniztized and optimized.
    (github issue #414 from bp-kelley)
  - expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
    (github issue #421)
  - Dev/expose rank atoms to python
    (github issue #422 from bp-kelley)
  - rdkit learns how to wrap a proper RWMol in python
    (github issue #423 from bp-kelley)
  - Docs: document "magic" property values that are used throughout the code
    (github issue #425)
  - MolDraw2D: expose class to Python
    (github issue #433)
  - RDKit learns how to query properties on Atoms
    (github issue #442 from bp-kelley)
  - Issue445: provide helper functions for multithreaded evaluation of some
expensive functions
    (github issue #448 from greglandrum)
  - RDKit learns how to release the GIL in python
    (github pull #449 from bp-kelley)
  - Dev/property queries
    (github pull #450 from bp-kelley)
  - Support a confId argument to the atom pair fingerprinting code
    (github issue #453)
  - Save the atom bookmarks so we can deconvolute reaction products.
    (github pull #454 from bp-kelley)
  - Cartridge: Support converting no structs to InChI
    (github issue #455)
  - RDKit learns how to expose ChemicalReaction copy constructor to python
    (github pull #456 from bp-kelley)
  - chirality flag was implemented for fmcs() function. NOTE: as of the
beta release,
    there is a known order-dependency bug in this functionality.
    (github pull #466 from AlexanderSavelyev)
  - Support copy and deepcopy properly for at least Mol and RWMol
    (github issue #467)
  - Cartridge: add qmol_from_smiles() and qmol_from_ctab()
    (github issue #469)
  - restore java and python wrappers. New parameter (matchChiralTag)
    (github issue #477 from AlexanderSavelyev)

New Database Cartridge Features:

  - The MCS code is now available within the cartridge
  - The functions qmol_from_smiles() and qmol_from_ctab()

New Java Wrapper Features:

  - The new molecule rendering code is accessible from the SWIG wrappers.

Deprecated code (to be removed in next release):

  - C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
    superseded by the new drawing code in $RDBASE/Code/GraphMol and will
    be removed in the next release.
  - Python:
     - rdkit/Dbase/Pubmed
     - rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
  - Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
    supported by the PostgreSQL project team as of July 2014)

Removed code:

  - the method Atom::setMass() has been removed. Please use setIsotope()
    instead.
  - the methods involving an atom's dativeFlag have been removed.

Contrib updates:

Other:
  - Python 2.6 support is deprecated. Starting with the next RDKit
release, we will only support python 2.7 and python 3.4 and
higher. Python 2.6 has not been supported since October 2013. If you
believe that you are stuck with python 2.6 because of the version of
RHEL you are running, please read this post to learn about your
options:
http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
  - The RDKit molecule objects (ROMol and RWMol) now require about 15%
less memory to store

Re: [Rdkit-devel] ImportError: No module named 'pidSVG'

[Greg L. <gre...@gm...>]

Hi Cyrus,

I regularly build and test on the Mac, so assuming you're following the
build instructions in the documentation, I wouldn't expect any tests to
fail.

I would suggest ensuring that you ran "make install" before running ctest
and then exporting those variables so that they are set in the shell and
not just for that one command (I'm not sure if that makes a difference or
not) and then re-running the tests.
If that doesn't work, please send me, not the full list, the contents of
build/Testing/Temporary/LastTest.log as an attachment and I will try to
figure out what's going on.

-greg


On Sat, Apr 4, 2015 at 1:30 AM, Cyrus Harmon <cy...@bo...> wrote:

> Ok, continuing to try debug my own silly problems… I forgot about RDBASE,
> PYTHONPATH, etc...
>
> When I run the tests with:
>
> PYTHONPATH=/home/sly/projects/rdkit/ RDBASE=/home/sly/projects/rdkit/
> LD_LIBRARY_PATH=/home/sly/projects/rdkit/lib ctest
>
> I get 64% of the tests passing. An improvement, but still not 100%. Is
> this to be expected?
>
> thanks,
>
> Cyrus
>
> On Apr 3, 2015, at 3:51 PM, Cyrus Harmon <cy...@bo...> wrote:
>
> Hi Greg,
>
> Thanks for looking into this. Some time has gone by and I’m not sure if
> the changes you were referring to have been checked in yet, but I’m back to
> trying to get things running on both macos and linux.
>
> Unfortunately, things seem to be getting worse. While everything seems to
> build OK, when I run “make test” on macos, I get only 46% of tests passing.
> About half of the failures are seg faults, the other half are failures. Is
> this to be expected? On my linux box, it’s actually even worse, 38% of
> tests passing.
>
> I’m happy to send the list of failing tests, but I figured I’m probably
> doing something wrong and that I should get the basics working first before
> I try to figure out which specific tests are failing (much less solve my
> SVG problem). It’s quite possible that the twisty maze of multiple versions
> of python (not to mention python libraries), boost, etc… are rearing the
> ugly head and I’m not quite sure where to begin trying to fix things.
> Suggestions?
>
> thanks,
>
> Cyrus
>
> On Mar 9, 2015, at 10:37 PM, Greg Landrum <gre...@gm...> wrote:
>
> Hi Cyrus,
>
> That's something we missed when we did the Python3 port of the RDKit.
> It turns out that there are a few of these problems in the rdkit.sping
> package that need to be brought up to date.
>
> I will get those fixed and checked in the next day or so.
>
> Thanks for reporting the problem,
> -greg
>
>
> On Tue, Mar 10, 2015 at 2:37 AM, Cyrus Harmon <cy...@bo...> wrote:
>
>> I’m trying to get a python program that uses rdkit running on macos and I
>> keep getting the following error:
>>
>>   File "./rdkit-2d-draw.py", line 31, in <module>
>>     Draw.MolToFile(mol,args.output,size=(500,500))
>>   File
>> "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py", line
>> 167, in MolToFile
>>     canvas = Canvas(size=size,name=fileName,imageType=imageType)
>>   File
>> "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py",
>> line 33, in __init__
>>     from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
>>   File
>> "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py", line
>> 3, in <module>
>>     from pidSVG import *
>> ImportError: No module named 'pidSVG'
>>
>> It works for me on my unix box that uses the debian packaged rdkit, but
>> fails for me on MacOS. Surely I’m doing something wrong in configuring my
>> various python libraries, but I’m at a loss as to how to fix this.
>>
>> Any suggestions on how to make my program find the pidSVG stuff?
>>
>> thanks,
>>
>> Cyrus
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now.
> http://goparallel.sourceforge.net/_______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>