Re: [Rdkit-discuss] Beta of the 2019.03 release available

2019-04-06 Thread Paolo Tosco 

Dear Markus,

in case you ran into the Float8GetDatum undefined symbol issue (it just 
happened to me), please make sure that you are actually building the 
cartridge against the PostgreSQL 11 headers.


You may check this in the CMake output; for example, in my case it has 
to be:


postgres: /usr/pgsql-11/include;/usr/pgsql-11/include/server

and to obtain this I had to define in my cmake command line:

  -DPostgreSQL_ROOT=/usr/pgsql-11 \
  -DPostgreSQL_INCLUDE_DIR=/usr/pgsql-11/include \
-DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-11/include/server \
  -DPostgreSQL_LIBRARY_DIR=/usr/pgsql-11/lib \

in addition to the usual

  -DRDK_BUILD_PGSQL=ON \
  -DRDK_PGSQL_STATIC=ON \

to avoid that FindPostgreSQL.cmake finds the headers of the system 
CentOS 7 PostgreSQL in /usr/include rather than the PostgreSQL headers 
in /usr/pgsql-11/include.


HTH, cheers,
p.

On 05/04/2019 17:42, Markus Sitzmann wrote:

Hi Greg,

my Chembience RDKit image build with version 2019.03-b1b went fine 
(well, I just pull it with conda; in case someone is interested it is 
available with tag 0.2.10-beta-1 at Dockerhub).


For the Postgres extension (which I still compile myself during the 
Docker build against Postgress), your python 3 enforcement uncovered 
some dark corners of my build process, but that is fixed. However, 
compiling 2019.03-b1b against Postgres 11 fails during compilation (am 
I too cheeky?).


Markus

On Wed, Apr 3, 2019 at 11:38 AM Greg Landrum > wrote:


Dear all,

The beta of the 2019.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1

There are a couple more bug fixes and maybe one more feature
expected before the actual release, but I wanted to go ahead and
get the beta out there.

I've done conda builds for Python 3.6 and 3.7 for Windows, Mac,
and Linux. These all use the beta label so that they do not
install by default; you'll need to run "conda install" as follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you
are prompted (if there's no build available, it will pick the
current production release instead).

The relevant section of the release notes is below, or you can see
a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual
release early next week.

Best,
-greg

# Release_2019.03.1
(Changes relative to Release_2018.09.1)

## REALLY IMPORTANT ANNOUNCEMENT
- As of this realease (2019.03.1) the RDKit no longer supports Python 2. 
Please read this rdkit-discuss post to learn what your options are if you need 
to keep using Python 2:
   
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html

## Backwards incompatible changes
- The fix for github #2245 means that the default behavior of the 
MaxMinPicker
   is now truly random. If you would like to reproduce the previous 
behavior,
   provide a seed value of 42.
- The uncharging method in the MolStandardizer now attempts to generate
   canonical results for a given molecule. This may result in different 
output
   for some molecules.
   
## Highlights:

- There's now a Japanese translation of large parts of the RDKit 
documentation
- SGroup data can now be read from and written to Mol/SDF files
- The enhanced stereo handling has been improved: the information is now
   accessible from Python, EnumerateStereoisomers takes advantage of it, 
and it
   can be read from and written to CXSmiles

## Acknowledgements:
Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
Bakary N'tji Diallo, Guillaume Godin, Jan Holst Jensen, Sunhwan Jo, Brian
Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer, 
Dan
Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca
Sforna, Ricardo Rodriguez Schmidt, Matt Swain, Paolo Tosco, Ricardo 
Vianello,
'John-Videogames', 'magattaca', 'msteijaert', 'paconius', 'sirbiscuit'

## Bug Fixes:
   - PgSQL: fix boolean definitions for Postgresql 11
  (github pull #2129 from pkubatrh)
   - update fingerprint tutorial notebook
  (github pull #2130 from greglandrum)
   - Fix typo in RecapHierarchyNode destructor
  (github pull #2137 from iwatobipen)
   - SMARTS roundtrip failure
  (github issue #2142 from mcs07)
   - Error thrown in rdMolStandardize.ChargeParent
  (github issue #2144 from paconius)
   - SMILES parsing inconsistency based on input order
  (github issue #2148 from coleb)
   - MolDraw2D: line width not in python wrapper
  (github issue #2149 from greglandrum)
   - Missing Python API

Re: [Rdkit-discuss] Beta of the 2019.03 release available

2019-04-05 Thread Markus Sitzmann 
Hi Greg,

my Chembience RDKit image build with version 2019.03-b1b went fine (well, I
just pull it with conda; in case someone is interested it is available with
tag 0.2.10-beta-1 at Dockerhub).

For the Postgres extension (which I still compile myself during the Docker
build against Postgress), your python 3 enforcement uncovered some dark
corners of my build process, but that is fixed. However, compiling
2019.03-b1b against Postgres 11 fails during compilation (am I too cheeky?).

Markus

On Wed, Apr 3, 2019 at 11:38 AM Greg Landrum  wrote:

> Dear all,
>
> The beta of the 2019.03 RDKit release has been tagged in github:
> https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1
>
> There are a couple more bug fixes and maybe one more feature expected
> before the actual release, but I wanted to go ahead and get the beta out
> there.
>
> I've done conda builds for Python 3.6 and 3.7 for Windows, Mac, and Linux.
> These all use the beta label so that they do not install by default; you'll
> need to run "conda install" as follows:
>
> conda install -c rdkit/label/beta rdkit
>
> Be sure to confirm that it's installing the right version when you are
> prompted (if there's no build available, it will pick the current
> production release instead).
>
> The relevant section of the release notes is below, or you can see a
> nicely formatted version here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1
>
> As usual, if you have time to try out the new release I would love
> feedback. If nothing major comes up, I plan to do the actual release early
> next week.
>
> Best,
> -greg
>
> # Release_2019.03.1
> (Changes relative to Release_2018.09.1)
>
> ## REALLY IMPORTANT ANNOUNCEMENT
> - As of this realease (2019.03.1) the RDKit no longer supports Python 2. 
> Please read this rdkit-discuss post to learn what your options are if you 
> need to keep using Python 2:
>   
> https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html
>
> ## Backwards incompatible changes
> - The fix for github #2245 means that the default behavior of the MaxMinPicker
>   is now truly random. If you would like to reproduce the previous behavior,
>   provide a seed value of 42.
> - The uncharging method in the MolStandardizer now attempts to generate
>   canonical results for a given molecule. This may result in different output
>   for some molecules.
>
> ## Highlights:
> - There's now a Japanese translation of large parts of the RDKit documentation
> - SGroup data can now be read from and written to Mol/SDF files
> - The enhanced stereo handling has been improved: the information is now
>   accessible from Python, EnumerateStereoisomers takes advantage of it, and it
>   can be read from and written to CXSmiles
>
> ## Acknowledgements:
> Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
> Bakary N'tji Diallo, Guillaume Godin, Jan Holst Jensen, Sunhwan Jo, Brian
> Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer, Dan
> Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca
> Sforna, Ricardo Rodriguez Schmidt, Matt Swain, Paolo Tosco, Ricardo Vianello,
> 'John-Videogames', 'magattaca', 'msteijaert', 'paconius', 'sirbiscuit'
>
> ## Bug Fixes:
>   - PgSQL: fix boolean definitions for Postgresql 11
>  (github pull #2129 from pkubatrh)
>   - update fingerprint tutorial notebook
>  (github pull #2130 from greglandrum)
>   - Fix typo in RecapHierarchyNode destructor
>  (github pull #2137 from iwatobipen)
>   - SMARTS roundtrip failure
>  (github issue #2142 from mcs07)
>   - Error thrown in rdMolStandardize.ChargeParent
>  (github issue #2144 from paconius)
>   - SMILES parsing inconsistency based on input order
>  (github issue #2148 from coleb)
>   - MolDraw2D: line width not in python wrapper
>  (github issue #2149 from greglandrum)
>   - Missing Python API Documentation
>  (github issue #2158 from greglandrum)
>   - PgSQL: mol_to_svg() changes input molecule.
>  (github issue #2174 from janholstjensen)
>   - Remove Unicode From AcidBasePair Name
>  (github pull #2185 from lilleswing)
>   - Inconsistent treatment of `[as]` in SMILES and SMARTS
>  (github issue #2197 from greglandrum)
>   - RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups
>  (github pull #2202 from bp-kelley)
>   - Fix TautomerTransform in operator=
>  (github pull #2203 from bp-kelley)
>   - testEnumeration hangs/takes where long on 32bit architectures
>  (github issue #2209 from mbanck)
>   - Silencing some Python 3 warning messages
>  (github pull #2223 from coleb)
>   - removeHs shouldn't remove atom lists
>  (github issue #2224 from rvianello)
>   - failure round-tripping mol block with Q atom
>  (github issue #2225 from rvianello)
>   - problem round-tripping mol files that include bond topology info
>  (github issue #2229 from rvianello)
>   - aromatic main-group atoms written to SMARTS incorrectly
>  (github issue #2237 from gregland

[Rdkit-discuss] Beta of the 2019.03 release available

2019-04-03 Thread Greg Landrum 
Dear all,

The beta of the 2019.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1

There are a couple more bug fixes and maybe one more feature expected
before the actual release, but I wanted to go ahead and get the beta out
there.

I've done conda builds for Python 3.6 and 3.7 for Windows, Mac, and Linux.
These all use the beta label so that they do not install by default; you'll
need to run "conda install" as follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

The relevant section of the release notes is below, or you can see a nicely
formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release early
next week.

Best,
-greg

# Release_2019.03.1
(Changes relative to Release_2018.09.1)

## REALLY IMPORTANT ANNOUNCEMENT
- As of this realease (2019.03.1) the RDKit no longer supports Python
2. Please read this rdkit-discuss post to learn what your options are
if you need to keep using Python 2:
  https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html

## Backwards incompatible changes
- The fix for github #2245 means that the default behavior of the MaxMinPicker
  is now truly random. If you would like to reproduce the previous behavior,
  provide a seed value of 42.
- The uncharging method in the MolStandardizer now attempts to generate
  canonical results for a given molecule. This may result in different output
  for some molecules.

## Highlights:
- There's now a Japanese translation of large parts of the RDKit documentation
- SGroup data can now be read from and written to Mol/SDF files
- The enhanced stereo handling has been improved: the information is now
  accessible from Python, EnumerateStereoisomers takes advantage of it, and it
  can be read from and written to CXSmiles

## Acknowledgements:
Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
Bakary N'tji Diallo, Guillaume Godin, Jan Holst Jensen, Sunhwan Jo, Brian
Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer, Dan
Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca
Sforna, Ricardo Rodriguez Schmidt, Matt Swain, Paolo Tosco, Ricardo Vianello,
'John-Videogames', 'magattaca', 'msteijaert', 'paconius', 'sirbiscuit'

## Bug Fixes:
  - PgSQL: fix boolean definitions for Postgresql 11
 (github pull #2129 from pkubatrh)
  - update fingerprint tutorial notebook
 (github pull #2130 from greglandrum)
  - Fix typo in RecapHierarchyNode destructor
 (github pull #2137 from iwatobipen)
  - SMARTS roundtrip failure
 (github issue #2142 from mcs07)
  - Error thrown in rdMolStandardize.ChargeParent
 (github issue #2144 from paconius)
  - SMILES parsing inconsistency based on input order
 (github issue #2148 from coleb)
  - MolDraw2D: line width not in python wrapper
 (github issue #2149 from greglandrum)
  - Missing Python API Documentation
 (github issue #2158 from greglandrum)
  - PgSQL: mol_to_svg() changes input molecule.
 (github issue #2174 from janholstjensen)
  - Remove Unicode From AcidBasePair Name
 (github pull #2185 from lilleswing)
  - Inconsistent treatment of `[as]` in SMILES and SMARTS
 (github issue #2197 from greglandrum)
  - RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups
 (github pull #2202 from bp-kelley)
  - Fix TautomerTransform in operator=
 (github pull #2203 from bp-kelley)
  - testEnumeration hangs/takes where long on 32bit architectures
 (github issue #2209 from mbanck)
  - Silencing some Python 3 warning messages
 (github pull #2223 from coleb)
  - removeHs shouldn't remove atom lists
 (github issue #2224 from rvianello)
  - failure round-tripping mol block with Q atom
 (github issue #2225 from rvianello)
  - problem round-tripping mol files that include bond topology info
 (github issue #2229 from rvianello)
  - aromatic main-group atoms written to SMARTS incorrectly
 (github issue #2237 from greglandrum)
  - findPotentialStereoBonds() stopping too early
 (github issue #2244 from greglandrum)
  - MinMax Diversity picker seeding shows deterministic / non-random behaviour
 (github issue #2245 from sroughley)
  - Fix to serialize binary strings
 (github pull #2264 from bp-kelley)
  - Recognize N in three-membered rings as potentially chiral
 (github issue #2268 from greglandrum)
  - Failure when parsing mol block with M  PXA
 (github issue #2277 from greglandrum)
  - query-query matching failing for atoms constructed from SMARTS
 (github issue #2299 from greglandrum)
  - SMILES parsing fails for dative ring closures
 (github issue #2303 from greglandrum)
  - Missing Dict.h overload: std::string Dict::getVal
 (github issue #2308 from