Re: [Rdkit-discuss] RDKit C wrappers?

[Riccardo Vianello]

Hi Axel,

On Sun, Apr 26, 2020 at 6:21 PM Axel Pahl  wrote:

> is anyone aware of efforts for creating "bridging" C wrappers for the
> RDKit?
> This would make it easier to bind the toolkit to other programming
> languages, in addition to Python and Java.
>

I'm not aware of any active/existing projects, but I've been also thinking
about this possibility in a couple of occasions.

Could the existing SWIG interface be perused for this?

as far as I know, this isn't (or at least wasn't) directly possible. SWIG
includes the core functionality required to generate these wrappers, but C
is not a supported target language. Last time I checked a mostly functional
but not ready to merge GSoC branch existed, that was aimed at providing
this feature, but I am not sure it made any progress.

Best,
Riccardo
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Re: [Rdkit-discuss] Postgres query performance

[Riccardo Vianello]

Hi Rajarshi,

On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
wrote:

> Hi, I'm working on an application that is trying to do arbitrary
> substructure queries across ChEMBL 23. I pretty much followed the
> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
> RAM.
>

some 2016 releases were affected by a bug in the cartridge Makefile that
disabled any compiler optimization. If possible, I would suggest trying a
more recent version (>= 2016.09.1).

Best,
Riccardo
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Re: [Rdkit-discuss] ImportError: No module named rdkit

[Riccardo Vianello]

On Thu, Sep 14, 2017 at 9:07 PM, Dimitri Maziuk 
wrote:

>
> All great when it's one computer and that one's your own personal laptop.
>
> > # yum ls \*python27\*
> > ...
> > python27.x86_642.7.13-2.ius.el6
>   @salt-2015.8
> > [...]...
>
> Any guesses as to how many things will break in my infrastructure
> manglement setup (saltstack) if I enable Software Collections and some
> of those get updated from SCL and some: from Salt?
>

sorry, I'm not familiar with saltstack, so I am unable to comment much. as
far as I understood, the RH software collection packages are meant to be
installed in parallel to the system software without overwriting any RHEL
package (it's not just an extension repository, users need to enable the
SCL packages to make them available in the runtime environment, similarly
to how virtualenvs are activated or environment modules are added), I don't
know how the saltstack packages are designed to work, so the discussion
would quickly go further off-topic (but I seem to understand it provides
yet another alternative to the system python, or not?)
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Re: [Rdkit-discuss] ImportError: No module named rdkit

[Riccardo Vianello]

On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk 
wrote:

> Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of
> linux distros that will be officially with us until June 30, 2024.
>

True, but there shouldn't be any strong need for using the system python
for running application software. Python 2.7 (together with python 3) has
been available to RHEL6 subscribers since almost five years, as part of the
Red Hat Software Collections (also available to non-subscribers from the
upstream CentOS/Fedora repositories). A detailed discussion is available
from this post
http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html

And the anaconda python distribution of course provides another alternative.

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Re: [Rdkit-discuss] Trouble with conda build in Docker

[Riccardo Vianello]

Hi Markus,

On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann 
wrote:

> Hi (Riccardo).
>
> I have trouble with the conda build in Docker (I just updated to the most
> recent version which triggered the new build) - below is the error trace. I
> took the original Docker file and just edited out all non-Python35 builds -
> so it does only the Python35 builds and ends somewhere when
> rdkit-postgres95 is built. Does somebody have the same problem?
>

I couldn't work on this during the last few months so I didn't test any
recent builds. I might be able to have a closer look and run some tests
next week. What branch of the conda-rdkit repository are you using (master
or development)?

Best,
Riccardo


>
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/port'
> make -C ../backend submake-errcodes
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
> ./duplicate_oids
> make -C utils probes.h
> ***
> ERROR: Perl is missing on your system. It is needed unless you are building
> from an unmodified official distribution of PostgreSQL.
> ***
> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>
>
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Re: [Rdkit-discuss] RDKit patch releases in conda?

[Riccardo Vianello]

Hi James,

On Wed, Nov 2, 2016 at 3:11 PM, James Davidson 
wrote:

> I think I probably know the answer to this already, but wanted to double
> check – did any of the four 2016_03 patch releases ever get pushed to conda?
>
> I only seem to get 2016_03_1 with “conda update –c
> https://conda.anaconda.org/rdkit rdkit”
>

are you working on Windows? Pre-built conda packages targeting the 2016.03
patch releases are at this time only available for linux and osx.


> (if not available then I guess this is academic with 2016_09_1 around the
> corner?)
>

an additional patch release was tagged before the UGM, and I think it
wasn't yet pushed to the anaconda channel. if there's interest for making
this revision available, I can try to include some windows packages (for
the amd64 platform at least), otherwise it might make sense to wait for the
upcoming release?

Best regards,
Riccardo
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Re: [Rdkit-discuss] PostgreSQL in Windows 7

[Riccardo Vianello]

Hi Gonzalo,

On Thu, Jul 21, 2016 at 11:26 AM, Gonzalo Colmenarejo <
colmenarejo.gonz...@gmail.com> wrote:

> I'm trying to install PostgreSQL and the corresponding RDKit cartridge in
> a Windows 7 laptop with Anaconda with Python 2.7 by running
>
> conda install -c https://conda.binstar.org/rdkit rdkit-postgresql
>
> However, I get the following error:
>
> Package missing in current win-64 channels.
>
> Unfortunately, no conda packages are at this time available from the rdkit
channel providing the RDKit PostgreSQL cartridge for windows. Some recent
contributions by Paolo Tosco allowed integrating the cartridge into the
regular cmake build, and this should strongly improve the portability and
help extending the conda recipes to support postgres and the rdkit
cartridge on the other platforms, but this still requires some work.

I'm afraid that the easiest options could reduce to either building the
rdkit and the cartridge from source code, separately from the anaconda
installation and following the generic build workflow for the windows
platform, or alternatively install the regular linux packages into a local
virtual machine. In both cases you will still be able to query the database
from the python code that is deployed using anaconda, but some setup is
required.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

[Riccardo Vianello]

Hi Markus,

I think the problem should be fixed now. The recipes were building the
cartridge using the earlier release tag, and therefore executing tests that
were not fully up-to-date. Please try again and let me know in case the
problem persisted.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

[Riccardo Vianello]

On Tue, Jun 28, 2016 at 11:40 PM, Markus Sitzmann  wrote:

> unfortunately I have another problem - rdkit-postgres isn't building for
> me since the change to Release_2016_03_2. Is that a known problem?
>

I tested a couple of full builds and the master branch looks ok, but I
could reproduce this error with the tagged release. I will try to identify
the exact cause.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

[Riccardo Vianello]

Hi Markus,

On Tue, Jun 28, 2016 at 11:40 PM, Markus Sitzmann  wrote:

> unfortunately I have another problem - rdkit-postgres isn't building for
> me since the change to Release_2016_03_2. Is that a known problem?
>

no, I'm not aware of any similar problems, what branch of the conda recipes
repository are you using? I will test and review the recipes for the latest
rdkit tag as soon as possible.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

[Riccardo Vianello]

Hi Axel,

thanks a lot for your help, using the development branch and the
> Release_2016_03_2 git tag in rdkit/meta.yaml worked.
> I now get a strange error in anaconda when actually trying to install the
> package (Error: Invalid version spec: ==), but that seems to be unrelated
> to RDKit (there is already an issue on anaconda github).
> My understanding was that the preferred way to install the RDKit was via
> anaconda (RDKit was the reason I started using anaconda), is that still
> correct?
>

I'm not exactly sure about the commands you used, but I'm afraid I wasn't
able to reproduce the described problem using conda 4.1.4 and conda-build
1.21.2 on my fedora box. In case the error persisted, could you please
provide some additional context?

Best regards,
Riccardo
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Re: [Rdkit-discuss] Segmentation fault when creating postgres GiST index on maccs_fp fingerprint column

[Riccardo Vianello]

Hi Michał,

could you please also post (or send me) the 'conda list' output for the
environment you are using?

thanks,
riccardo
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Re: [Rdkit-discuss] Conda and Rdkit 2016-03 Pains

[Riccardo Vianello]

Hi Markus,

On Tue, May 3, 2016 at 1:41 AM, Markus Sitzmann 
wrote:
>
> thanks for your great software - unfortunately, I have some building
> pains. I recently decided to go from RDKit 2015-03 to 2015-09  (yes I
> was late) , everything still on python 2.7.
>
> As part of this migration I decided to give Conda a try and it worked
> nicely in my Docker container (which is very similar to the the
> official Conda RDKit container at
>
> https://github.com/rdkit/conda-rdkit
>
> but starts from Debian Jessie instead of Centos6 - however it still
> clones from this repository).
>
>
> Unfortunately, since you switched to RDKit 2016-03 my troubles began.
>

A set of changes have been recently merged into the conda-rdkit development
branch in order to re-sync it with the rdkit master branch. If your tests
with the development branch are earlier than just a few days, then you
might want to try that again (and I would be actually interested to know in
case the problems persisted). Please note that the current tip of the rdkit
master branch already includes a few additions/changes compared to the
latest release.

I am also preparing a PR that will fully update the conda-rdkit master
branch to the current 2016.03.1 release, I am about to run some final tests
but I think it should be hopefully ready between today and tomorrow.

Best,
Riccardo
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Re: [Rdkit-discuss] compiling error with C++ on maverick

[Riccardo Vianello]

Hi Yingfeng,

do you use cmake to build your own project? in case you did, some cmake
configuration files are usually installed together with the RDKit libraries
and may help manage these details:

rdkit-config.cmake
rdkit-config-version.cmake
rdkit-targets.cmake
rdkit-targets-release.cmake

The location of these files (matching the libraries installation path in
the current RDKit version) should be passed on the cmake command line:

$ cmake -D RDKit_DIR=/rdkit/libraries/installation/path/lib [...]

And the CMakeLists.txt script can then use the information from these files
to configure the build:

find_package(RDKit REQUIRED)
include_directories(${RDKit_INCLUDE_DIRS})
[...]
add_library(mylibrary [...])
target_link_libraries(mylibrary Descriptors Fingerprints GraphMol)

Specifying the most direct dependencies should be usually sufficient, and
cmake should be able to complement this information with the target
dependencies originally collected during the RDKit build and then tracked
in the configuration files.

Best,
Riccardo
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Re: [Rdkit-discuss] rdkit installation problem

[Riccardo Vianello]

Hi Kapil,

I was able to reproduce the problem, I'm having the impression that this
might be a regression due to changes implemented in conda 4.0+. I couldn't
find a way to use 'conda update' to upgrade the initial configuration to
the latest rdkit package, so - as a shortest term solution - I would
suggest reinstalling the environment from scratch. You should be able to
remove the existing environment with something like

> deactivate my-rdkit-env
> conda remove -n my-rdkit-env --all

and then create it again, but this time specifying the desired rdkit
version:

>conda create -n my-rdkit-env -c rdkit rdkit=2015.*

this should select rdkit 2015.09.2, numpy 1.10 and boost 1.56

I hope that helps, ​please let me know if the problems persist,

Best,
Riccardo
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Re: [Rdkit-discuss] Windows 7 ImportError: DLL load failed

[Riccardo Vianello]

Hi Nico,

On Wed, Feb 24, 2016 at 1:03 AM, Nico Cantone  wrote:

> Thanks for your reply! I did not have %PYTHONPATH% or %RDBASE% defined,
> and the qtconsole I used is installed in the same environment as rdkit.
> Until your reply, I had only tried to import Chem using qtconsole or
> jupyter notebook (being sure I was in the proper environment), without
> success. Now that you mention the command prompt, though, I tried it and it
> works! I was able to successfully import the module, read a SMILES string,
> and draw a structure. However, I still get the same error when I try to use
> PyCharm or Spyder. Can you think of any reason why this might be happening?
>

I can't at the moment think of any specific reason, but I would initially
check if a different %PATH% or a different working directory, may be
affecting the DLL resolution in the two cases.

HTH,
Riccardo
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Re: [Rdkit-discuss] Windows 7 ImportError: DLL load failed

[Riccardo Vianello]

Hi Nico,

no environment variable settings should be in general required beyond those
eventually set by the activate command (and even those should be optional).
In case you manually set the %PYTHONPATH% or the %RDBASE% I would suggest
removing them until the problem is resolved.

It is not clear from your message if the problem is specific to the
qtconsole (can you successfully import the rdkit packages when the
interpreter runs from the command prompt?). Also, it is not clear if the
qtconsole is installed in the same environment as the rdkit (myrdkit27) or
if it's the one available from the root environment (I wouldn't expect this
latter to work correctly).

Best,
Riccardo
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Re: [Rdkit-discuss] rdkit 2015.09.2 in Anaconda still version 2015.03.1

[Riccardo Vianello]

hello,

On Mon, Feb 8, 2016 at 7:57 PM, Naeem Attari  wrote:

> I am facing the same problem (in windows 7)
> Installed rdkit in miniconda by following command
>
> conda install -c https://conda.anaconda.org/rdkit rdkit
>
>
> by conda list command it is showing
> *rdkit 2015.09.2   np110py27_0rdkit*
>
> but with
> ​​  from rdkit import rdBase
>   print rdBase.rdkitVersion
> I am getting
>   2014.09.2
>
>>
>>
it is most likely that you are listing the configuration for one
environment, but executing code that belongs to another one. Regardless the
currently activated environment, this may happen because of environment
variables affecting the code execution (for example %PYTHONPATH% or
%RDBASE% - in particular, these two shouldn't be usually set), but it may
also happen if the current working directory matches a location where a
different python executable is present (e.g. the anaconda root directory).
You may want to verify that the value of rdBase.__file__ corresponds to the
expected installation path.

I hope that helps, please let me know if the problem persisted,

Best,
Riccardo
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Re: [Rdkit-discuss] Latest version

[Riccardo Vianello]

Hi Dave,

the RDKit source code repositories are now on GitHub
https://github.com/rdkit/rdkit

Please see the README.md file for pointers to documentation and other
resources.

Best,
Riccardo

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Re: [Rdkit-discuss] RDKit Linux install error

[Riccardo Vianello]

Hi Hong,

if /usr/local/src/RDKit_2015_03_1 is the top directory of the RDKit
distribution then I think you should probably move your build one directory
up and run cmake from inside /usr/local/src/RDKit_2015_03_1/build/ (instead
of /usr/local/src/RDKit_2015_03_1/rdkit/build/).

Best,
Riccardo
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Re: [Rdkit-discuss] [Rdkit-announce] 2015.09 (Q3 2015) RDKit Release

[Riccardo Vianello]

​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
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Re: [Rdkit-discuss] Conda packages bug

[Riccardo Vianello]

Hi Maciek,

the actual problem here is that some older rdkit packages predate the
availability of boost from anaconda, and rdkit 2014.09 doesn't specify its
dependency from a specific version of boost.This worked until an
incompatible boost 1.57 has been added to the anaconda distribution, so
rdkit 2015.03 has been packaged with an explicit dependency from boost=1.56

when 'conda install -c rdkit rdkit' is issued, no version constraints are
specified, neither for boost, nor for rdkit. In planning the installation
conda apparently selects the most up-to-date boost package from its own
channels and then picks the "compatible" rdkit 2014.09 package.

an alternate workaround may consist in specifying the version for the boost
package, so that the one from the anaconda channels is ignored (conda
install -c rdkit boost=1.56), but solving the problem I think will require
updating the metadata in the older packages, so that they are no longer
accidentally selected.

Thanks for the report, I will try to have this fixed during the next few
days.

Best,
Riccardo


On Wed, Nov 18, 2015 at 10:47 AM, Maciek Wójcikowski 
wrote:

> Hi,
>
> I've noticed a bug in conda packages, when you're doing a clean install
> ["conda install -c https://conda.anaconda.org/rdkit rdkit"] the old
> version 2014.09 is install by default.
>
> To force installation of 2015.03 you have to specify it's version:
> conda install -c https://conda.anaconda.org/rdkit rdkit=2015
>
> Here comes the probable bug cause: the 2015.03 package requires *older*
> version of boost (as I recall 1.56), where 2014.09 version requires newer
> version: 1.57. During the update boost is downgraded.
>
> Code to reproduce the bug:
> conda create -n test_rdkit python
> source activate test_rdkit
> conda install -c rdkit rdkit
> conda install -c rdkit rdkit=2015
>
> I hope we manage to get it fixed for 2015.09 :)
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
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Re: [Rdkit-discuss] Python 3, windows 64, rdkit builds

[Riccardo Vianello]

Hi Paolo,

That would be really great, I would be definitely interested in trying to
wrap your scripts into the conda recipe for the boost package.

Thanks,
Riccardo

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Re: [Rdkit-discuss] Python 3, windows 64, rdkit builds

[Riccardo Vianello]

Hi Clyde,

with regard to the conda packages, I built the windows packages that are
available from anaconda.org, and the reasons for excluding the python3
version have mainly been that there wasn't very much demand for it. I am
not aware of any particular problems, but (based on my own experience
alone) I can't exclude that some windows specific issues may have passed
unnoticed.

Best,
Riccardo



On Wed, Sep 23, 2015 at 2:55 PM, Clyde Fare  wrote:

> Hi,
>
> Some colleagues have been trying to get rdkit to work with a python 3
> anaconda environment running on a windows machine and have been running
> into difficulties.
>
> I notice there is no python 3 windows rdkit binary, nor is there a windows
> conda package for python 3.
>
> Is there some windows python 3 related problem?
>
> Cheers
>
> Clyde
>
>
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Re: [Rdkit-discuss] RHEL6 compilation - Python issues?

[Riccardo Vianello]

Hi Joerg,

in order to run the tests and use the local rdkit installation, I think
you'll also need to set the LD_LIBRARY_PATH environment variable to include
$RDBASE/lib and the PYTHONPATH environment variable to include $RDBASE:

export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH

(there might be additional issues, but those two env variables are a likely
cause for the failing tests).

An easier way to get the latest RDKit release (including the python
bindings, but not the Java wrappers) is provided by the conda packages that
are available from the rdkit channel on https://anaconda.org. With a
conda-based environment the whole installation process could reduce to a
single command e.g.:

$ conda create -c rdkit -n my_rdkit_env rdkit

HTH,
Riccardo

On Sat, Sep 5, 2015 at 4:08 PM, Jörg Kurt Wegner 
wrote:

> Hi all, I am trying to get RDKit to work from a source install on RHEL6.
> I already disabled Java (due to errors), but would like to get Python to
> work, though neither a Python import, nor ctest seem to work.
> So, Python-RDKit was not correctly installed. Here the toolchain I use,
> any idea why this is not working?
>
> ## dependencies
> #Boost version: 1.55.0
> #SWIG: /usr/local/bin/swig (found version "3.0.7")
>
> cd /tmp
> wget
> http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2015/RDKit_2015_03_1.tgz
> tar xzvf RDKit_2015_03_1.tgz
> export RDBASE=/tmp/rdkit-Release_2015_03_1
> cd $RDBASE
> mkdir build
> cd build
> wget -nv -O junit.jar
> http://search.maven.org/remotecontent?filepath=junit/junit/4.12/junit-4.12.jar
> mkdir ../External/java_lib
> mv junit.jar ../External/java_lib/
> export DEPENDENCY_BOOST=boost_1_55_0
> export BOOST_ROOT=/usr/local/src/$DEPENDENCY_BOOST
> export BOOST_INCLUDEDIR=/usr/local/include
> export BOOST_LIBRARYDIR=/usr/local/lib
> export PYTHONBASE=/usr/local/lib/python2.7
> export
> PYTHON_NUMPY_INCLUDE_PATH=/usr/local/lib/python2.7/site-packages/numpy/core/include
> export PYTHONPATH=$PYTHONBASE/site-packages:$PYTHONPATH
> cmake -D Boost_NO_SYSTEM_PATHS=ON -D RDK_BUILD_SWIG_WRAPPERS=ON -D
> RDK_BUILD_SWIG_JAVA_WRAPPER=OFF -D
> PYTHON_LIBRARY=$PYTHONBASE/config/libpython2.7.a -D
> PYTHON_INCLUDE_DIR=$PYTHONBASE -D
> PYTHON_EXECUTABLE=/usr/local/bin/python2.7 ..
> #cmake -D Boost_NO_SYSTEM_PATHS=ON -D RDK_BUILD_SWIG_WRAPPERS=ON -D
> PYTHON_LIBRARY=/usr/local/lib/python2.7/config/libpython2.7.a -D
> PYTHON_INCLUDE_DIR=/usr/local/include/python2.7/ -D
> PYTHON_EXECUTABLE=/usr/local/bin/python2.7 ..
> make -j8
> make install
> ctest
>
>   Start  1: testDict
>  1/90 Test  #1: testDict .   Passed0.03 sec
>   Start  2: testDataStructs
>  2/90 Test  #2: testDataStructs ..   Passed0.01 sec
>   Start  3: pyBV
>  3/90 Test  #3: pyBV .***Failed0.02 sec
>   Start  4: pyDiscreteValueVect
>  4/90 Test  #4: pyDiscreteValueVect ..***Failed0.03 sec
>   Start  5: pySparseIntVect
>  5/90 Test  #5: pySparseIntVect ..***Failed0.03 sec
>
>
> /.Joerg
>
>
>
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Re: [Rdkit-discuss] Inchi installation in postgresql database driving me mad

[Riccardo Vianello]

Hi Jean-Paul,


On Thu, Feb 12, 2015 at 3:37 PM, JP  wrote:

> cd $RDBASE/Code/PgSQL/rdkit
> make clean
> make
> sudo make install # in order to get this to work I had to change the this
> line in the Makefile PG_CONFIG  = /opt/postgresql-9.3.4/bin/pg_config
> make installcheck # before this I restart postgresql
>

just a guess, but maybe in the above you need to edit the Makefile to set
the value for the USE_INCHI variable, or pass this variable on the make
command line? (default configuration is documented at the top of the
Makefile)

Best,
Riccardo
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Re: [Rdkit-discuss] Using rdkit with Anaconda package -- ImportError

[Riccardo Vianello]

Hi Jiří,

On Thu, Jan 22, 2015 at 4:30 PM, Jiří Novotný  wrote:

> I am using 64-bit version of Windows 8.1. I have installed 32-bit version
> of Anaconda with Python 2.7. Then I have installed rdkit from binstar.org
> repository with conda:
>
> conda install -c https://conda.binstar.org/rdkit rdkit
>
> I have verified that it has installed this version of rdkit:
> https://binstar.org/rdkit/rdkit/2014.09.2/download/win-32/rdkit-2014.09.2-np19py27_0.tar.bz2
>
> When I try to run some basic stuff, I got this error:
>
> Traceback (most recent call last):
>   File "C:/_JN/Dropbox/__bakalarka/_python/__pokusy/rdkit01.py", line 2,
> in 
> from rdkit import Chem
>   File "C:\Anaconda\lib\site-packages\rdkit\Chem\__init__.py", line 18, in
> 
> from rdkit import rdBase
> ImportError: DLL load failed: The specified module could not be found.
>

I could reproduce the same error on a win32 machine, and in my case the
problem was related to the installed boost package.

In the same environment where the rdkit is installed, could you please try
executing

conda list

and verify that boost 1.56.0 is installed? Should the output list boost
1.57.0 then you can try downgrading it using the package that is also
available from the rdkit binstar channel:

conda install -c rdkit boost==1.56.0

Apparently, some boost packages have been recently added to the default
anaconda channels, and the windows version places its DLLs into a different
location.

HTH,
Riccardo
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Re: [Rdkit-discuss] conda-rdkit fails to install Win7.

[Riccardo Vianello]

Hi Steve,

On Wed, Nov 19, 2014 at 12:50 PM, Stephen O'hagan 
wrote:

>  Some tests failed, but info has since scrolled off into hyperspace… is
> there an easy method to re-run the RDKit test suite?
>

I'm afraid it is not possible to resume the recipe execution, but if the
temporary build environment wasn't yet removed (the output from conda info
-e would list an environment named _build) it may be possible to activate
it and then change directory to conda-bld\work and run 'make test' again
manually (provided that all of the required environment variables are set,
those defining the compiler environment, plus %RDBASE%, and %PYTHONPATH%).
Moreover, additional details about the tests execution might be still
available from the LastTest.log file.

Alternatively, you could try installing the build-time dependencies (see
the recipe's meta.yaml file for a list) into a regular conda environment
and use it to build the RDKit with commands similar to those used by the
recipe's bld.bat build script. Managing the whole process manually might be
convenient in case you had to first troubleshoot your build environment
before proceeding to the actual packaging.

Regards,
Riccardo


>
>
> BTW, ‘LastTestsFailed.log’ contains:
>
>
>
> 7:pyDiscreteValueVect
>
> 8:pySparseIntVect
>
> 34:testMolSupplier
>
> 50:pyPartialCharges
>
> 71:pyGraphMolWrap
>
> 77:pyRanker
>
> 79:pyFeatures
>
> 80:pythonTestDbCLI
>
> 81:pythonTestDirML
>
> 86:pythonTestDirChem
>
>
>
> Cheers,
>
> Steve.
>
>
>
> *From:* Riccardo Vianello [mailto:riccardo.viane...@gmail.com]
> *Sent:* 18 November 2014 19:46
> *To:* Stephen O'hagan
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] conda-rdkit fails to install Win7.
>
>
>
> Hi Steve,
>
>
> On Tue, Nov 18, 2014 at 2:33 PM, Stephen O'hagan 
> wrote:
>
>  Trying to install conda-rdkit on win7 64-bit as per instructions
> https://github.com/rdkit/conda-rdkit
>
>
>
> ‘conda build boost’ appears to work.
>
>
>
> Yes, the conda recipe for boost on windows currently simply performs a
> repackaging of the official boost binary distribution, so it should work in
> almost all cases.
>
>
>  ‘conda build rdkit’ appears to download and re-install boost during
> installation.
>
>
> This is probably expected, during the build process boost is installed
> together with the other build-time dependencies into a temporary
> environment which is automatically created by conda. A message saying that
> some packages are being downloaded is most likely to refer to packages that
> are not already available from the local conda cache. These packages are
> most usually downloaded from a remote distribution channel, but the list
> may also include packages that are copied from the local build directory
> (which I think was probably the case for boost).
>
>
>  It then fails with cmake unable to find boost, and subsequently ‘nmake
> error U1073’.
>
>
>
> And this is quite unexpected, but also difficult to interpret with the
> provided amount of information.. Could you please send a copy of the actual
> cmake command line that was issued, and/or the CMakeCache.txt file that
> should have been created inside the top-level RDKit source distribution
> directory at \conda-bld\work?
>
> Finally, I don't know if it may be of help, but some windows 64-bit
> packages for the latest RDKit release should now be also available from the
> binstar rdkit channel (in order to fetch them, you would just need to add
> '-c rdkit' to the conda create/install/update command line. The build for
> these packages passed all tests but the two related to the avalon tools).
>
>
>
> Best,
>
> Riccardo
>
>
>
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Re: [Rdkit-discuss] conda-rdkit fails to install Win7.

[Riccardo Vianello]

Hi Steve,

On Tue, Nov 18, 2014 at 2:33 PM, Stephen O'hagan 
wrote:

>  Trying to install conda-rdkit on win7 64-bit as per instructions
> https://github.com/rdkit/conda-rdkit
>
>
>
> ‘conda build boost’ appears to work.
>

Yes, the conda recipe for boost on windows currently simply performs a
repackaging of the official boost binary distribution, so it should work in
almost all cases.


> ‘conda build rdkit’ appears to download and re-install boost during
> installation.
>

This is probably expected, during the build process boost is installed
together with the other build-time dependencies into a temporary
environment which is automatically created by conda. A message saying that
some packages are being downloaded is most likely to refer to packages that
are not already available from the local conda cache. These packages are
most usually downloaded from a remote distribution channel, but the list
may also include packages that are copied from the local build directory
(which I think was probably the case for boost).


> It then fails with cmake unable to find boost, and subsequently ‘nmake
> error U1073’.
>

And this is quite unexpected, but also difficult to interpret with the
provided amount of information.. Could you please send a copy of the actual
cmake command line that was issued, and/or the CMakeCache.txt file that
should have been created inside the top-level RDKit source distribution
directory at \conda-bld\work?

Finally, I don't know if it may be of help, but some windows 64-bit
packages for the latest RDKit release should now be also available from the
binstar rdkit channel (in order to fetch them, you would just need to add
'-c rdkit' to the conda create/install/update command line. The build for
these packages passed all tests but the two related to the avalon tools).

Best,
Riccardo
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Re: [Rdkit-discuss] [Rdkit-devel] 2014.09 (Q3 2014) RDKit Release

[Riccardo Vianello]

Dear all,

Some updated conda packages for the 2014.09 release are also now available
from the RDKit channel on binstar: https://binstar.org/rdkit/

In particular, python 2.6, 2.7 and 3.4 versions of the RDKit toolkit, and
an updated version of the RDKit-PostgreSQL cartridge are available for
linux-64. Prebuilt python 2.7 RDKit packages are also already available for
the osx-64 and win-32 operating systems, and additional platforms should be
covered in the next future.

Conda users can download and use these packages with their own
anaconda/miniconda installations, using the create, install and update
commands. Here are a couple of example commands:

# Create a python envviroment with installed ipython and the rdkit
$ conda create -c rdkit -n myenv ipython rdkit

# Install the rdkit into the active environment
$ conda install -c rdkit rdkit

(please note that the '-c rdkit' or the more verbose '-c
https://conda.binstar.org/rdkit' options are required to inform conda that
some packages should be fetched from the RDKit distribution channel on
binstar).

Best regards,
Riccardo
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Re: [Rdkit-discuss] FYI: the RDKit is incompatible with numpy v1.9

[Riccardo Vianello]

Hi Samo,

Yes, it should have been fixed, sorry I forgot to send an update to the
list.

Best,
Riccardo


On Wed, Oct 29, 2014 at 1:11 PM, Samo Turk  wrote:

> Hi,
>
> Was this resolved? It seems to work for me with numpy v1.9.0...
>
> Samo
>
> On Mon, Sep 15, 2014 at 5:23 PM, Greg Landrum 
> wrote:
>
>> Dear all,
>>
>> Riccardo and I have "accidentally" discovered that the RDKit is
>> incompatible with the most recent version of numpy (v1.9.0). We're working
>> on getting it cleared up. In the meantime: please don't upgrade to that
>> version if you are an RDKit user.
>>
>> -greg
>>
>>
>>
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Re: [Rdkit-discuss] python3 support completed

[Riccardo Vianello]

Hi all,

I made some small changes to the development version of the RDKit conda
recipes, so that building in a python3 environment will currently use the
code from the python3-support branch on GitHub. Building from sources may
this way just require the following commands:

$ git clone https://github.com/rdkit/conda-rdkit.git
$ cd conda-rdkit/
$ git checkout development
$ CONDA_PY=34 conda build boost
$ CONDA_PY=34 conda build rdkit
$ conda create -n python3-rdkit python=3.4 rdkit --use-local
$ source activate python3-rdkit

I'll take the occasion to thank Greg for all the work he put in completing
this port.

Best regards,
Riccardo
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Re: [Rdkit-discuss] Reg:pip not installing rdkit( existing package in pypi)

[Riccardo Vianello]

On Thu, Jun 12, 2014 at 3:55 PM, janardhan swamy 
wrote:

> Hi, i need to install rdkit in heroku cloud to run my app, but i am not
> able to do it. i tried using pip install rdkit and pip install
> python-rdkit, but they are not working. can you tell me how to install
> rdkit in heroku?
>

I'm not familiar with heroku, but I could recently install the rdkit on
openshift using conda. A google search for conda and heroku returned a link
to this repository https://github.com/kennethreitz/anaconda-buildpack,
hopefully it may be of help.

As far as I know it is not possible to build and install the rdkit and it's
python bindings using pip, so the other alternatives I could think of
reduce to building form sources on a different machine and then
transferring the binaries with some suitable strategy. But depending on
what you'd like to do the dependency stack can grow fairly big, so I think
using conda is likely to be a good option (rdkit recipes for conda are
available on github https://github.com/rdkit/conda-rdkit).

Best regards,
Riccardo
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[Rdkit-discuss] conda recipes for the RDKit

[Riccardo Vianello]

Dear all,

I'm very happy to inform you that some conda recipes for the latest RDKit
release are now available on GitHub:

https://github.com/rdkit/conda-rdkit

Hopefully, these recipes will strongly simplify building RDKit packages for
the Anaconda/Miniconda python distributions.

Please note that the degree of testing performed so far differs a bit
across the supported operating systems (linux, os x and windows) so
feedback would be very appreciated. Some "getting started" documentation is
available from the README file at the repository above, but please feel
free to write here or contact me in case you had any questions.

Best regards,
Riccardo
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Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

[Riccardo Vianello]

On Wed, Feb 26, 2014 at 7:26 PM, Adrian Jasiński
wrote:

> you can try use razi:
>

Unfortunately, razi is currenly a bit old and unmaintained. Moreover it's
based on sqlalchemy and it wouldn't therefore integrate easily with the
django database api. One might consider having a look at django-chem, but
that is also quite old (iirc it targeted django 1.3), and it's based on an
implementation approach that I think is becoming in part obsolete.

As it has been also mentioned in reply to Hari's question on stackoverflow,
the upcoming version 1.7 of django will support custom lookup operators.
This is likely to help, but I also partly agree that extending the database
api is still quite a lot of work compared to the fraction of
domain-specific queries, and a single application project could just
consider using raw SQL queries in the few places where it is needed.

Of course things are much simpler if one doesn't need/want to abstract the
api from the database backend and it could be also of interest that there's
currently a kickstarter project which is aimed at contributing extended
postgresql support to django:
https://www.kickstarter.com/projects/mjtamlyn/improved-postgresql-support-in-django
.

Best regards,
Riccardo



>
> http://razi.readthedocs.org/en/latest/database_creation_tutorial.html
>
> pozdrawiam
> Adrian
>
>
> 2014-02-26 18:34 GMT+01:00 Greg Landrum :
>
> Hi Hari,
>>
>> You can use "mol_from_pkl()". Here's a quick demo:
>> In [20]: m = Chem.MolFromSmiles('c1cnccc1')
>>
>> In [21]: pkl = buffer(m.ToBinary())
>>
>> In [22]: curs.execute('select mol_from_pkl(%s)',(pkl,))
>>
>> In [23]: curs.fetchone()
>> Out[23]: ('c1ccncc1',)
>>
>> Is that enough to get you started?
>> -greg
>>
>>
>>
>> On Tue, Feb 25, 2014 at 8:28 PM, hari jayaram  wrote:
>>
>>> Hi ,
>>> I am a newbie to postgres and the rdkit postgres database cartridge.
>>>
>>> I have gotten the cartridge installed and can query sub-structure
>>> similarity and do other things as documented in the cartridge documentation
>>> page.
>>>
>>> To create a molecule from the cartridge the documentation
>>> recommends something like:
>>>
>>>
>>> >>> curs.execute('select molregno,mol_send(m) from rdk.mols where m@
>>> >%s',('c12c1nncc2',))
>>> >>> row = curs.fetchone()
>>> >>> row
>>> (9830, )
>>>
>>> Then the pickled output of mol_send will be used to create a new molecule
>>>
>>> >>> from rdkit import Chem
>>> >>> m = Chem.Mol(str(row[1]))
>>> >>> Chem.MolToSmiles(m,True)
>>> 'CC(C)Sc1ccc(CC2CCN(C3CCN(C(=O)c4cnnc5c54)CC3)CC2)cc1'
>>>
>>>
>>> My question is : how about the other way .Is the only way to use the
>>> smiles and do an sql insert with the smiles and the mol_from_smiles
>>> function as in :
>>>
>>>  insert into compounds (smiles,rdkit_mol,internal,external) VALUES
>>> ('C',mol_from_smiles('C);'ID-111','EI-222');
>>>
>>> Is there a way to insert the python rdkit mol object into the database
>>> rdkit "mol" column directly.
>>>
>>> This is in some ways connected to a question I just asked ( django
>>> related) on stack 
>>> overflow.
>>>
>>> Thanks a tonne for your help in advance
>>> Hari
>>>
>>>
>>>
>>>
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Re: [Rdkit-discuss] pythonTestDirChem test failing

[Riccardo Vianello]

On Mon, Jun 17, 2013 at 4:08 PM, Michał Nowotka  wrote:
> I'm trying to understand your advice? Should I check if I have pandas
> installed and uninstall it? Or installing pandas will help me with testing?

sorry, I was confusing. I could reproduce an error that occurs with
the current development version if pandas is not available, and I
presumed the same error could have caused the test failure you
initially reported. On the other hand, if you are building RDKit v.
2012.09.1 (as it could seem from the paths in your last message) then
I'm most probably wrong.

Best regards,
Riccardo

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Re: [Rdkit-discuss] pythonTestDirChem test failing

[Riccardo Vianello]

Hi Michał,

Is pandas available in your test environment? I could reproduce a
similar problem on my own linux box, but it's apparently due to an
oversight in the PandasTools module that can raise an exception when
pandas is not imported. The interested output could be similar to the
following:

77: Traceback (most recent call last):
77:   File "PandasTools.py", line 98, in 
77: defPandasRendering = pd.core.frame.DataFrame.to_html
77: AttributeError: 'NoneType' object has no attribute 'core'

Best regards,
Riccardo

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Re: [Rdkit-discuss] Tversky similarity

[Riccardo Vianello]

Hi Gonzalo,

I think the problem could be that the function passed with the
'metric' argument of DataStruct.FingerprintSimilarity is called with
two only parameters, but the signature of the TverskySimilarity
function is different and two additional parameters are required.

Maybe you can work around this with a small wrapper function:

In [10]: DataStructs.FingerprintSimilarity(fps[0], fps[1],
   : metric=lambda x, y: DataStructs.TverskySimilarity(x, y, 0.01, 0.99))

or call the similarity function directly, as you did in C++:

In [9]: DataStructs.TverskySimilarity(fps[0], fps[1], 0.01, 0.99)
Out[9]: 0.9933774834437088

HTH,

Best regards,
Riccardo

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[Rdkit-discuss] chemicalite

[Riccardo Vianello]

Dear all,

I recently spent some time working around the idea of an RDKit-based
chemical extension for SQLite. The project is still in an early stage
and some features are missing, but I think it has now reached a stage
in development where experimenting with it could actually start to be
interesting. As you may guess, the idea is similar in concept to the
existing postgresql cartridge, but targeting a quite different
database system, so I'm hoping it may provide distinct trade-offs and
support complementary use cases.

Some documentation is available online
(https://chemicalite.readthedocs.org/en/latest/) and code is on github
(https://github.com/rvianello/chemicalite). The current revision was
tagged 2013.03.2 and it should play well with the current RDKit
release (only tested on linux though).

If you use SQLite, and sometimes wished it could also understand some
chemistry, then I hope you will find this project interesting and I
would really love to hear from you.

Best regards,
Riccardo

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Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.

[Riccardo Vianello]

Hi Jan,

On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
 wrote:
> [...]
> ../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
> `boost::thread_resource_error::~thread_resource_error()'
> collect2: ld returned 1 exit status
> make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1
> make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2
> make: *** [all] Error 2

I encontered a similar link problem in building rdkit on an oldish
linux x86_64 machine with boost 1.39 (that, according to the cmake
build files, is the minimum required version), but I couldn't yet find
the time to investigate the details. For the time being I worked
around it with the addition of

find_package(Boost 1.39.0 COMPONENTS thread REQUIRED)

in $RDBASE/CMakeLists.txt (after the assignment of
Boost_ADDITIONAL_VERSIONS and before "if(RDK_BUILD_PYTHON_WRAPPERS)")
and with the addition of ${Boost_THREAD_LIBRARY} to the GraphMol's
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt

If I'm not wrong, a direct dependency from boost-thread is introduced
in the GraphMol library by the QueryOps module, but I can't say why
this results in a link error only in some cases.

Best regards,
Riccardo

>
>
> On the very same machine 2012_06_1 builds without a hitch. I have tried
> installing libboost-thread-dev but it makes no difference (I did
> recreate the "build" directory and re-run "cmake .." after installing
> libboost-thread-dev, just in case).
>
> I considered whether the boost version, which is 1.40.0, is too old -
> but I didn't see anything in the RDKit INSTALL file that hints that the
> boost version requirements should have changed from 2012_06_1 to
> 2012_09_1 (or did I miss it ?). boost::thread_resource_error has anyway
> been in boost since 1.34 as far as I can tell:
>
> http://www.boost.org/doc/libs/1_34_0/doc/html/boost/thread_resource_error.html
>
> So... hints ? I can get by fine with 2012_06_1 for now, so it is not urgent.
>
> Cheers
> -- Jan Holst Jensen
>
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Re: [Rdkit-discuss] how to install rdkit systemwide on Ubuntu 12.04

[Riccardo Vianello]

Hi Michał,

On Thu, Nov 8, 2012 at 6:21 PM, Michał Nowotka  wrote:
> I would like to install rdkit in such a way, I don't have to append anything
> to LD_LIBRARY_PATH.

I'm not a Ubuntu user so I don't know/remember the details, but I
think RDKit deb distribution packages for Ubuntu are periodically made
available by one of the users, you might want to search the web and/or
the mailing list archives about this possibility.

If you still want to install rdkit from sources, passing
-DRDK_INSTALL_INTREE=OFF to cmake should cause the libraries to be
installed in the standard locations under ${CMAKE_INSTALL_PREFIX}
(defaults to /usr/local on UNIX) and the python bindings to be
installed inside the system site-packages directory.

A basic recipe could be something like the following:

$ wget 
http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2012/RDKit_2012_09_1.tgz/download
$ tar zxvf RDKit_2012_09_1.tgz
$ cd RDKit_2012_09_1
$ cmake -DRDK_INSTALL_INTREE=OFF
-DCMAKE_INSTALL_PREFIX=/your/installation/prefix .
$ make
$ RDBASE=$PWD PYTHONPATH=$PWD LD_LIBRARY_PATH=$PWD/lib make test
$ make install # as root (if required by the install prefix)

please notice that running the build inside the source tree is
required if you want to execute the test before installing.

If you are building for x86_64 and need the libraries to be installed
under e.g. ${CMAKE_INSTALL_PREFIX}/lib64 instead of
${CMAKE_INSTALL_PREFIX}/lib also pass -DLIB_SUFFIX=64 (additional
build options are available, please see the wiki at
http://code.google.com/p/rdkit/wiki/BuildingWithCmake and the main
CMakeLists.txt file).

if you are fine with the default install prefix, setting it on the
cmake command line is not necessary, but  you may want to perform a
couple of installations locally to your home directory just to make
sure that everything is built and installed as desired.

Since upgrading and/or uninstalling a large library that was installed
from sources into the standard locations as described above is not
usually fun I sometimes found it more convenient to install RDKit
under /opt/rdkit and use ld.so.conf to avoid the need for
LD_LIBRARY_PATH.

HTH,

Best regards,
Riccardo

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Re: [Rdkit-discuss] runtime error with fingerprints in new release of RDKit

[Riccardo Vianello]

Hello,

On Mon, Jul 23, 2012 at 10:35 AM, Gonzalo Colmenarejo-Sanchez
 wrote:
> I’m trying to run a program that calculates a similarity matrix that worked
> in the previous RDKit release. Now I recompile with the new release:
>
> g++ -o tanird tanird.cpp -I$RDBASE/Code -I$RDBASE/Extern -L$RDBASE/lib
> -lChemReactions -lFileParsers -lSmilesParse -lDepictor -lSubstructMatch
> -lGraphMol -lDataStructs -lRDGeometryLib -lRDGeneral -lFingerprints
> -I/GWD/schem/apps/rdkit/build-env/include
>
> but when I run it I get the following error message:
>
> ../../../bin/tanird: symbol lookup error: ../../../bin/tanird: undefined
> symbol: _ZN5RDKit17RDKFingerprintMolERKNS_5ROMolEbdjbbPSt6vectorIjSaIjEE

I think one possible explanation for the error message is that you
built the executable linking against a library version which is not
the same that is used at program execution. I would check the output
from running "ldd ../../../bin/tanird" and eventually the value of
LD_LIBRARY_PATH in the same environment.

Best Regards,
Riccardo

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Re: [Rdkit-discuss] boost confused

[Riccardo Vianello]

sorry, ignore my earlier message.

On Tue, Apr 10, 2012 at 5:55 PM,   wrote:
> rdkit/Chem/__init__.py", line 18, in 
>     from rdkit import rdBase
> ImportError: libboost_python.so.1.42.0: cannot open shared object file: No
> such file or directory

I read the error message more carefully and noticed it actually refers
boost 1.42.

Riccardo

> "
>
>
> This confuses me, since - to my naive understanding - I have told RDKit to
> use the boost 1.46 version.
>
> What did I wrong?
>
>
> Cheers,
> Paul
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Re: [Rdkit-discuss] boost confused

[Riccardo Vianello]

Hi Paul,

I think you might need to set the LD_LIBRARY_PATH to include the
location of your system-wide boost 1.46 installation on pc Y too,
since it's used at runtime to locate the shared libraries that were
linked at build-time.

HTH,
Riccardo

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Re: [Rdkit-discuss] build issue with sample.cpp

[Riccardo Vianello]

Hello,

On Thu, Jan 5, 2012 at 12:29 PM, Gonzalo Colmenarejo-Sanchez
 wrote:
> Hi,
>
> I’m trying to build sample.cpp as specified in the file (g++ -o sample.exe
> sample.cpp -I$RDBASE/Code -I$RDBASE/Extern -L$RDBASE/lib -lChemReactions
> -lFileParsers -lSmilesParse -lDepictor -lSubstructMatch -lGraphMol
> -lDataStructs -lRDGeometryLib -lRDGeneral
>
> ) but get the following error message:
>
> In file included from
> /GWD/schem/apps/rdkit/default/Code/GraphMol/RDKitBase.h:22,
>
>  from sample.cpp:17:
>
> /GWD/schem/apps/rdkit/default/Code/GraphMol/Atom.h:20:29: error:
> boost/foreach.hpp: No such file or directory

It looks like the compiler can't find the boost libraries header
files. Maybe they are installed into a non-standard location and you
just need to provide the path to your boost installation with an
additional include path (-I) in the g++ command line.

HTH,
Riccardo

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Re: [Rdkit-discuss] An installation question...

[Riccardo Vianello]

Hi,

On Wed, Nov 23, 2011 at 11:08 AM, JP  wrote:
> Are CMake, Flex, Bison only used at compile/build time or are they
> required for running RDKit as well?

yes, cmake, flex and bison are only needed at build time. IIRC,
runtime dependencies are mainly represented by the python and regex
boost libraries and the numpy python package.

Cheers,
Riccardo

>
> The issue is I am building RDKit on a front end head node and making
> it available to all compute nodes (pretty much by nfs sharing
> $RDBASE).  However if these packages are needed at runtime, I have to
> install them on each compute node as well.
>
> What about other packages?
>
> -
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> Early Stage Researcher
>
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Re: [Rdkit-discuss] rdkit version (from code)

[Riccardo Vianello]

Hi Jean-Paul,

On Fri, Jul 8, 2011 at 4:56 PM, JP  wrote:
>
> Is there an RDkit method call which returns the version number of RDKit ?

In C++ the RDKit version information is available as a string pointer
defined by the RDGeneral/versions.h header file:


namespace RDKit {
  const char *rdkitVersion="2011.06.1pre";
 

>From Python the same string should be available as a constant from the
rdkit.rdBase module:

>>> from rdkit.rdBase import rdkitVersion

HTH,
Riccardo

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Re: [Rdkit-discuss] Using SQLAlchemy with the RDKit database cartridge

[Riccardo Vianello]

On Tue, Jul 5, 2011 at 5:38 AM, Greg Landrum  wrote:
> On Mon, Jul 4, 2011 at 3:15 PM, Riccardo Vianello
>  wrote:
>>
>> Useful hint, thanks. I'm still learning about SQLAlchemy and I would
>> have probably missed the proper management of the autocommit flag.
>> Btw, I actually postponed the management of the threshold values
>> because of some technical details that are unclear to me and I should
>> have asked about anyway. More specifically, I'm not sure about the
>> scope associated to these "global" parameters. The question is
>> probably for Greg, but do these values hold for the whole server, or
>> for the given database, or for the specific database connection?
>
> The setting applies to the current connection.

Thanks. I was investigating this last night and that was more or less
my conclusion (and if I'm not mistaken postgres spawns a process for
each connection so maybe I could have guessed that a bit earlier..).

Thanks again,
Riccardo

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Re: [Rdkit-discuss] Using SQLAlchemy with the RDKit database cartridge

[Riccardo Vianello]

Dear Greg,

On Tue, Jul 5, 2011 at 5:37 AM, Greg Landrum  wrote:
> I haven't had a chance to do more than just read the docs, but I
> really like the idea a lot. This is one on of those things that I'd
> probably never have the time to do but that makes using the cartridge
> a lot easier for people who don't necessarily want to learn SQL.
> Thanks for doing it! Double thanks for including good docs. :-)

Thanks, I'm glad you liked it. Wrt the docs, I copied the examples
from a good source :-) and sphinx+github+readthedocs really helped a
lot. I will hopefully add some more complete api documentation in the
next days.

> [...]
>
> I'm going to point it out to some folks at work and see what they
> think. We'll send feedback.

It would be great, thank you very much.

Regards,
Riccardo

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Re: [Rdkit-discuss] Using SQLAlchemy with the RDKit database cartridge

[Riccardo Vianello]

Hi Adrian,

On Mon, Jul 4, 2011 at 11:22 AM, Adrian Schreyer  wrote:
> Hi Riccardo,
>
> are you planning on supporting other cartridges/database dialects? If
> you only want to include RDKit/PostgreSQL then your implementation
> might be much more of what you actually need :)

yes, at present I'm focusing almost exclusively on RDKit/PostgreSQL,
but the longer term goal includes supporting additional backends. I'm
particularly interested in the RDKit's cartridge, and I plan to
implement full support for it, but you are correct, if that were the
only supported cartridge/database this kind of approach could be
considered overkill.

> If you want to change the similarity thresholds you will need
> something like session.execute(text("SET
> rdkit.tanimoto_threshold=:threshold").execution_options(autocommit=True).params(threshold=threshold)),
> probably wrapped inside a function. Important is that you use
> execution_options(autocommit=True) because SQLAlchemy won't autocommit
> SET operations (if you set it in the engine config).

Useful hint, thanks. I'm still learning about SQLAlchemy and I would
have probably missed the proper management of the autocommit flag.
Btw, I actually postponed the management of the threshold values
because of some technical details that are unclear to me and I should
have asked about anyway. More specifically, I'm not sure about the
scope associated to these "global" parameters. The question is
probably for Greg, but do these values hold for the whole server, or
for the given database, or for the specific database connection?

> I also have rdkit in my database api but I went for the hybrid
> approach in SQLAlchemy that allows you to distinguish between methods
> on the class and instance level. With an instance of an rdkit molecule
> for example, the api will use the local rdkit installation for a
> substructure pattern match. On the class level however, the same
> expression is turned into an SQL expression to query the database. I
> also use the @reconstructor decorator to turn the database rdmol
> smiles string back in to a Python RDMol but this is only useful if you
> plan on using RDKit on the client side as well.

Currently I'm making no assumptions on the toolkit available on the
client side, I had quickly read the documentation related to the
hybrid approach and I wasn't very convinced it was what I was looking
for, but from your examples I would say I should reconsider that, at
least in part.

Thanks a lot for your reply and suggestions,

Cheers,
Riccardo

>
> # instance of ChemCompRDMol
>>>>> print sti.RDMol.contains('c1c1')
> True
>
> # class itself
>>>>> print ChemCompRDMol.contains(sti.ism)
> pdbchem.chem_comp_rdmols.rdmol OPERATOR(rdkit.@>) :rdmol_1
>
> Here is an example:
>
>   @reconstructor
>   def init_on_load(self):
>       '''
>       Turns the rdmol column that is returned as a SMILES string back into an
>       RDMol object.
>       '''
>       self.rdmol = MolFromSmiles(self.rdmol)
>
>   @hybrid_method
>   def contains(self, smiles):
>       '''
>       '''
>       return self.rdmol.HasSubstructMatch(MolFromSmiles(smiles))
>
>   @contains.expression
>   def contains(self, smiles):
>       '''
>       '''
>       return self.rdmol.op('OPERATOR(rdkit.@>)')(smiles)
>
> and that's basically it. I have the cartridge installed in it's own
> schema, that's why I need the OPERATOR() syntax.
>
> Cheers,
>
> Adrian
>
> On Fri, Jul 1, 2011 at 17:22, Riccardo Vianello
>  wrote:
>> Hi all,
>>
>> I've started working on an extension of the SQLAlchemy database
>> toolkit that is aimed to support direct access from python to the
>> functions and data types exposed by the database chemical cartridge.
>> In brief this means that instead of interacting with the RDBMS using
>> raw SQL queries, it may become possible to execute the entire workflow
>> (data preprocessing and cleanup, insertion, selection and further
>> processing) without leaving the python interpreter, and at the same
>> time delegating the construction of the required SQL expressions to a
>> higher-level API. Just to make a simple example, instead of using
>>
>> select count(*) from molecules where structure @> 'O=C1OC2=CC=CC=C2C=C1';
>>
>> one might type something like the following:
>>
>>>>> constraint = Molecule.structure.contains('O=C1OC2=CC=CC=C2C=C1')
>>>>> print session.query(Molecule).filter(constraint).count()
>>
>> (ok, in this specific case th

[Rdkit-discuss] Using SQLAlchemy with the RDKit database cartridge

[Riccardo Vianello]

Hi all,

I've started working on an extension of the SQLAlchemy database
toolkit that is aimed to support direct access from python to the
functions and data types exposed by the database chemical cartridge.
In brief this means that instead of interacting with the RDBMS using
raw SQL queries, it may become possible to execute the entire workflow
(data preprocessing and cleanup, insertion, selection and further
processing) without leaving the python interpreter, and at the same
time delegating the construction of the required SQL expressions to a
higher-level API. Just to make a simple example, instead of using

select count(*) from molecules where structure @> 'O=C1OC2=CC=CC=C2C=C1';

one might type something like the following:

>>> constraint = Molecule.structure.contains('O=C1OC2=CC=CC=C2C=C1')
>>> print session.query(Molecule).filter(constraint).count()

(ok, in this specific case the python expression is a bit more
verbose, but it's a very simple SQL query :-)

The project is still in an initial phase, and the code is far from
being mature, but the development is currently strongly focused on the
RDKit postgresql extension. Structure searches and molecular
descriptors should be fully supported, and bit fingerprints and
associated similarity operators are also available (but modifying the
default threshold similarity values is not yet possible). The code is
currently hosted on github

https://github.com/rvianello/razi

and some draft documentation (at the moment mainly intended to
illustrate the idea than providing a detailed reference) is also
available:

http://razi.readthedocs.org

If you use the RDKit chemical cartridge or SQLAlchemy (or both), I
hope you will find the idea interesting and I'd love to hear from you.
Comments, ideas and suggestions would be very welcome.

Cheers,
Riccardo

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Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)

[Riccardo Vianello]

Hi James,

On Thu, Jun 9, 2011 at 8:22 PM, James Davidson  wrote:
> [...]
> File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py", line 54, in
> MolToImage
>     canvas = Canvas(img)
>   File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\cairoCanvas.py", line
> 38, in __init__
>     imgd = image.tostring("raw","BGRA")
>   File "C:\Python26\lib\site-packages\PIL\Image.py", line 516, in tostring
>     e = _getencoder(self.mode, encoder_name, args)
>   File "C:\Python26\lib\site-packages\PIL\Image.py", line 389, in
> _getencoder
>     return apply(encoder, (mode,) + args + extra)
> : unknown raw mode

I don't know exactly about the other problems, but this one should be
related to the version of the installed PIL. If I remember correctly,
BGRA raw mode requires PIL 1.1.7.

Regards,
Riccardo

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Re: [Rdkit-discuss] Access RDKit from Java

[Riccardo Vianello]

On Tue, May 10, 2011 at 11:41 AM, Riccardo Vianello
 wrote:
> I'm not sure if this may be useful, but Greg recently announced the
> availability of new SWIG-based wrappers in $RDBASE/Code/JavaWrappers.
> Do you specifically need the KNIME ones?

sorry for the double post, the information appeared on the rdkit-devel
list, so I guess those bindings are currently only available in the
svn ..

Riccardo

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Re: [Rdkit-discuss] Access RDKit from Java

[Riccardo Vianello]

Hi Noel,

On Tue, May 10, 2011 at 11:30 AM, Noel O'Boyle  wrote:
> Hi Greg,
>
> You mentioned that there is a Jar file and associated shared library
> for RDKit in the KNIME repository. Unfortunately, they don't provide
> access except on request (see http://tech.knime.org/node/20231 for
> example). Could you make these available somewhere or include them in
> a future release?

I'm not sure if this may be useful, but Greg recently announced the
availability of new SWIG-based wrappers in $RDBASE/Code/JavaWrappers.
Do you specifically need the KNIME ones?

Riccardo

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Re: [Rdkit-discuss] Fwd: Re: Re: Re: Bug in MolToFile?

[Riccardo Vianello]

Hi Greg,

On Wed, Apr 20, 2011 at 1:44 PM, Greg Landrum  wrote:
>> On my Linux box the script failed, but the issue is related to the PIL
>> version (1.1.6) provided with Fedora 12 (now a bit old). I then
>
> I guess the complaint came somewhere around line 79 of cairoCanvas.py ?
> I saw an error here this morning when using the old version of PIL in
> Scientific Linux.

in my case it's at line 38 (but I see line 79 might trigger the same problem):

/.../rdkit/Chem/Draw/cairoCanvas.pyc in __init__(self, image, size,
ctx, imageType, fileName)
 36 self.imageType=imageType
 37 if image is not None:
---> 38   imgd = image.tostring("raw","BGRA")
 39   a = array.array('B',imgd)
 40   stride=image.size[0]*4

apparently the BGRA encoder wasn't yet available in PIL 1.1.6.

In any case, also on this machine, I could quickly override the
library available from the system with an updated one installed in a
virtualenv, and this fixed the issue with the image file generation.

Riccardo

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Re: [Rdkit-discuss] Fwd: Re: Re: Re: Bug in MolToFile?

[Riccardo Vianello]

Hello,

I don't use the RDKit graphics subsytem much, but I ran a couple of
smoke tests based on the following lines from the "Getting started"
pages (in case this is not exercising the problematic code please let
me know):

from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('c1ccncc1CC(=O)O')
Draw.MolToImageFile(mol,'test.png')

On my Linux box the script failed, but the issue is related to the PIL
version (1.1.6) provided with Fedora 12 (now a bit old). I then
updated my windows7 mingw32-python26 build and it executed without
problems both with and without the cairo backend.

Regards,
Riccardo

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Re: [Rdkit-discuss] Postgres cartridge '=' operator

[Riccardo Vianello]

On Wed, Feb 2, 2011 at 6:16 AM, Greg Landrum  wrote:
> Dear Riccardo,
>
> On Tue, Feb 1, 2011 at 11:13 PM, Riccardo Vianello
>  wrote:
>> Hi Greg,
>>
>> On Mon, Dec 13, 2010 at 5:15 PM, Greg Landrum  wrote:
>>> On Mon, Dec 13, 2010 at 3:33 PM, gia...@gmail.com  wrote:
>>>> On Sat, Dec 11, 2010 at 5:23 PM, Greg Landrum  
>>>> wrote:
>>>>
>>>>> I used the operator == instead of =. It
>>>>> might even be worth considering using @=, since substructure and
>>>>> superstructure searches are @> and <@, respectively.
>>
>> just a quick question about the syntax to be used. The release notes
>> clearly report @= was finally adopted, but what about the cast to mol
>> type? It appears in the earlier examples in this thread, but in a
>> couple of tests today it was accidentally omitted and the query was
>> successfully processed. Is it now possible to pass a plain SMILES
>> string as with the other structure operator?
>
> It is possible to pass a plain string: postgres is smart enough to
> automatically convert the string to a molecule:
> chembl=# select 'c1c1'@='c1n1';
>  ?column?
> --
>  f
> (1 row)
>
> chembl=# select 'c1c1'@='c1c1';
>  ?column?
> --
>  t
> (1 row)
>
> I still think it's useful to be explicit and include the conversion in
> queries though, so I find this style to be better:
> chembl=# select 'c1c1'::mol@='c1c1'::mol;
>  ?column?
> --
>  t
> (1 row)

I see, now it's clearer. Thank you very much,

Best Regards,
Riccardo

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Re: [Rdkit-discuss] Postgres cartridge '=' operator

[Riccardo Vianello]

Hi Greg,

On Mon, Dec 13, 2010 at 5:15 PM, Greg Landrum  wrote:
> On Mon, Dec 13, 2010 at 3:33 PM, gia...@gmail.com  wrote:
>> On Sat, Dec 11, 2010 at 5:23 PM, Greg Landrum  wrote:
>>
>>> I used the operator == instead of =. It
>>> might even be worth considering using @=, since substructure and
>>> superstructure searches are @> and <@, respectively.

just a quick question about the syntax to be used. The release notes
clearly report @= was finally adopted, but what about the cast to mol
type? It appears in the earlier examples in this thread, but in a
couple of tests today it was accidentally omitted and the query was
successfully processed. Is it now possible to pass a plain SMILES
string as with the other structure operator?

Best Regards,
Riccardo

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Re: [Rdkit-discuss] Fedora RPMs for rdkit 2010.12

[Riccardo Vianello]

On Sun, Jan 9, 2011 at 11:00 PM, gia...@gmail.com  wrote:
> * rpmlint complains about "exit()" being called in two libraries
> (libSmilesParse and libSLNParse)

I briefly investigated this and I think it's not probably a problem
with the rdkit implementation, but a bug in the Flex lexer generator.
It's been already reported on sourceforge

http://sourceforge.net/tracker/index.php?func=detail&aid=2125513&group_id=97492&atid=618177

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Re: [Rdkit-discuss] pg_config

[Riccardo Vianello]

Hi Christian,

On Mon, Nov 15, 2010 at 12:26 PM, bouille  wrote:
> Dear Greg
>
> With Fedora13 using
> yum install postgresql postgresql-server postgresql-contrib
>
> [...]
> pg_config is not found ???

I think it's part of the postgresql-devel package.

Hope that helps,

Regards,
Riccardo

>
> Could you help me
>
> Best Regards
> Christian
>
>
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Re: [Rdkit-discuss] problem compiling RDKit_Q22010_1

[Riccardo Vianello]

Hi Paul,

On Wed, Aug 25, 2010 at 4:26 PM, Paul Emsley  wrote:
>
> Hi,
>
> I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64
>
> Linking CXX shared library libSLNParse.so
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a(instances.o):
> relocation R_X86_64_32 against
> `boost::object_cache,
> boost::re_detail::cpp_regex_traits_implementation
>  >::do_get(boost::re_detail::cpp_regex_traits_base const&,
> unsigned long)::s_data' can not be used when making a shared object;
> recompile with -fPIC
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a:
> could not read symbols: Bad value
> collect2: ld returned 1 exit status

I never compiled rdkit on that distribution, but it looks like you
encountered one of the "Frequently Encountered Problems" documented at
the end of this wiki page:
http://code.google.com/p/rdkit/wiki/BuildingWithCmake

The suggested fix is: "Add this to the arguments when you call cmake:
-DBoost_USE_STATIC_LIBS=OFF"

Hope that helps,
Riccardo

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Re: [Rdkit-discuss] colours in 2d depition

[Riccardo Vianello]

Hi Uwe,

thanks for your answer. Good to know that the problem is specific to
the version of the PIL library in use.

On Sat, Aug 7, 2010 at 12:11 AM, Uwe Hoffmann  wrote:
> [...].  As a temporary workaround you can try :
>
> from rdkit.Chem.AllChem import MolFromSmiles, Compute2DCoords
> from rdkit.Chem.Draw import MolToFile
> molecule = MolFromSmiles('c1c1')
> Compute2DCoords(molecule)
> MolToFile(molecule,'img.png', size=(250, 250),  #img.pdf,img.svg,img.ps
>  kekulize=True, wedgeBonds=True,
>  highlightAtoms=[])
>
>
> In this case you circumvent PIL (and agg) completely.

thanks, I will try this.

>
> The functionality of MolToFile should be folded into MolToImageFile.
> The problem with MolToImage is still open in this case.

After some reading of the PIL documentation I was wondering if
splitting the image into bands, swapping the two colors "manually" and
merging the bands back into a single image could represent a decent
workaround when the PIL version is <= 1.1.6. Do you think it would be
critically inefficient?

Regards,
Riccardo

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Re: [Rdkit-discuss] colours in 2d depition

[Riccardo Vianello]

Hello,

On Fri, Jul 30, 2010 at 6:51 AM, Greg Landrum  wrote:
> Dear all,
>
> This morning I had the chance to look at this on a machine with cairo 
> installed.
>
> There were a couple of problems that were making this happen.
>
> Uwe caught the first already: the convertColor() function was
> returning the wrong values.
>
> The second problem was with using the cairoCanvas and a PIL Image
> (this is what rdkit.Draw.ShowMol() does): there the pixel order
> expected by the PIL Image and that being provided by the cairo canvas
> were different, so the red and blue channels were being swapped. I
> just checked a fix for both of these into svn.

I was reported a problem by a friend, and I think it could be related
to these latest changes.

With the svn trunk revision 1473 (current head revision) the following snippet:

from rdkit.Chem.AllChem import MolFromSmiles, Compute2DCoords
from rdkit.Chem.Draw import MolToImage
molecule = MolFromSmiles('c1c1')
Compute2DCoords(molecule)
image = MolToImage(molecule, size=(250, 250),
   kekulize=True, wedgeBonds=True,
   highlightAtoms=[])
image.save('ciccio.png', 'PNG')

raises an exception on a couple of Linux machines (running Fedora 12 and 13):

Traceback (most recent call last):
  File "./testcase.py", line 8, in 
highlightAtoms=[])
  File "/home/ric/ric/RDKit/rdkit-trunk/rdkit/Chem/Draw/__init__.py",
line 35, in MolToImage
canvas = Canvas(img)
  File "/home/ric/ric/RDKit/rdkit-trunk/rdkit/Chem/Draw/cairoCanvas.py",
line 36, in __init__
imgd = image.tostring("raw","BGRA")
  File "/usr/lib64/python2.6/site-packages/PIL/Image.py", line 516, in tostring
e = _getencoder(self.mode, encoder_name, args)
  File "/usr/lib64/python2.6/site-packages/PIL/Image.py", line 389, in
_getencoder
return apply(encoder, (mode,) + args + extra)
SystemError: unknown raw mode

The problem disappears when reverting rdkit/Chem/Draw/cairoCanvas.py
to the earlier repository revision.

My understanding of image formats, encodings and the graphics
subsystem is extremely limited so I don't know exactly which other
information could be useful to tracking the problem.. the installed
python imaging library is PIL 1.1.6. Are there other library revisions
I could check or dependencies I should verify are correctly solved?

Thanks in advance,

Best regards,
Riccardo

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Re: [Rdkit-discuss] RDKit packaging issues

[Riccardo Vianello]

Hello,

On Tue, Jul 6, 2010 at 10:16 AM, Noel O'Boyle  wrote:
> On 5 July 2010 21:33, Gianluca Sforna  wrote:
>[...]
>> Installation - files installed by the "make install" step should
>> honour the "DESTDIR" environment variable; this is becasue packagers
>> need to put files under a certain build directory to be picked up
>> later by the packaging script; this is usually accomplished by setting
>> the env variable DESTDIR or running "make install DESTDIR=xxx". I also
>> need to mention this buildroot (xxx in the example) usually translates
>> to "/" when the package is installed, so default installation
>> subdirectories should be picked according to common standard naming.
>
> AFAIK, with CMAKE you set -DCMAKE_INSTALL_PREFIX for a local install.

yes, but I think prefix and destdir are used in slightly different
ways. Prefix informs the build systems about the filesystem location
where the software will be installed (in order, for example, to
configure the application and/or hardcoding paths), and destdir is
used when packaging to perform a staged installation that reproduces
the final layout under a temporary filesystem location (so that it is
possible to keep track of which files are produced by the installation
process in a reliable way).

If I'm not wrong, cmake supports both mechanisms, but I've got the
impression that the basic issue here is that RDKit is usually
installed inside its own "source" tree, which is fine for personal use
and custom builds, but doesn't integrate very well with a linux
distribution.

Riccardo

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Re: [Rdkit-discuss] something new

[Riccardo Vianello]

That's wonderful news. Congratulations and thank you and your
colleagues for all this work.

Regards,
Riccardo

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Re: [Rdkit-discuss] help

[Riccardo Vianello]

Hi,

2009/10/7 Christian de Bouillé :
> [...]
>> Using Fedora 10 64 bytes and now Fedora 11 32 bytes
>> using boost-jam to create bjam and paste bjam when to be used
>> I see many messages about failed or skipped targets
>> for compiling boost and after $RDBASE/Code
>> rdbase is not created.
>>
>> Probably Fedora is a bad distribution to be used for RDKIT
>> there is some message about gcc not compiling some files

I checked my Fedora 11 (32 bits) at home and here are a few additional
details I missed yesterday. RDKit_Q22009_1 should build fine with
Boost 1.37.0 from boost.org and boost-numeric-bindings-20081116 from
mathema.tician.de; iirc, all of the other dependencies should be
resolved by the distribution. I don't remember why I used boost 1.37
when 1.39 was already available, maybe it was just because 1.37 is
also shipped with the distribution.

HTH,
Riccardo

Re: [Rdkit-discuss] help

[Riccardo Vianello]

Hello,

On Wed, Oct 7, 2009 at 12:15 PM, Greg Landrum  wrote:
> Hi,
>
> 2009/10/7 Christian de Bouillé :
>>> Using Fedora 10 64 bytes and now Fedora 11 32 bytes
>>> using boost-jam to create bjam and paste bjam when to be used
>>> I see many messages about failed or skipped targets
>>> for compiling boost and after $RDBASE/Code
>>> rdbase is not created.
>>>
>>> Probably Fedora is a bad distribution to be used for RDKIT
>>> there is some message about gcc not compiling some files
>>>
>
> More on this below, but I think some of the problems you may be having
> at the moment are due to the use of gcc 4.4.x; I haven't compiled the
> RDKit with the gcc 4.4 series butI have had some reports that there
> are problems.

I shut down my computer at home this morning, so I can't access it
from here and check the exact versions, but I'm using a 32bits
Fedora11 there and I've now built rdkit a few times on that machine
without noticing any distribution-specific problem. I'm likely to have
used a more recent version of the boost libraries though (from the
reported diagnostics I would say boost 1.36.0 was being compiled in
the present case) and this may eventually make a difference with
regard to the available version of gcc, but in my experience problems
were most often due to accidental mistakes in managing the build
procedure (from this point of view I've found running bjam with the
additional -q option - so that it stopped as soon as any target failed
- quite useful).

Since the successful builds listed on the google code wiki are also
based on more recent versions of Boost, I would consider trying one of
those prior to reinstalling the system.

Regards,
Riccardo

Re: [Rdkit-discuss] cmake based build

[Riccardo Vianello]

Hi Greg,

thanks for integrating those files so quickly.

>> * boost-numeric-bindings: [...].
>
> For now I've put the most recent version of the numeric bindings in
> External, as you suggest, and checked this into svn. For the actual
> release we could either keep things this way or require the user to
> download the numeric bindings and extract them in the External
> directory themselves. There are arguments for and against both of
> these approaches, but I basically agree that the current (on trunk)
> requirement that the user extract the numeric bindings over the system
> (usually) boost is not really idea.

Yes, I undestand your concerns. If the boost-numeric-bindings had a
binary library file to link against or if they were needed in any
other phase  than at build time I would have considered redistributing
an additional third-party package a sub-optimal choice. On the other
hand, since these bindings are not yet part of the official Boost
Libraries their development cycle, versioning, packaging seemed a bit
confusing to me. Redistribution simplifies some operations, but maybe
one could also ask on the  boost-ublas mailing list for advice on this
subject.

>> * re-engineering of the test-suite: together with building "out of the
>> source tree" I would like to be able to install files to more standard
>> locations (eventually under a user-provided prefix). Unfortunately, if
>> I understood it correctly, several tests expect build and
>> installation to occur inside the source tree. This way, a
>> build-install-test sequence is enforced, while I would usually expect
>> to perform tests prior to the installation step (and avoid
>> installation altogether, in case tests failed). Moreover, some tests
>> currently rely on $RDBASE and make this environment variable necessary
>> again.
>
> The tests that expected build and test to happen in the source tree
> were incorrect. These should have been using $RDBASE to find their
> test data. I fixed those in svn, so a pure out-of-source build works
> now. Installation of the shared libraries and python modules to a
> user-specified location should also work, but we will need to figure
> out how to copy data files with that install. This is part of cmake I
> haven't figured out yet.

I think I've seen something about the management of installation
details while searching the cmake docs, but at the moment I preferred
to postpone the problem. I'm really glad you reviewed this part, I
verified that most tests ran successfully, but my environment seemed
quite untidy (some tests worked from the build directory, some others
if executed the "old" way :-) Now that a reference configuration is
available from a dedicated svn branch I will try to understand the
test suite and installation process a bit better.

> This is a good place for an explanation of what $RDBASE is used for:
>
> Uses of $RDBASE:
> 1) By the build system to locate include files and decide where to
> install things to.
> 2) By the test code to find input and output data.
> 3) By some runtime components to find default parameter files.
>
> Use 1) could (and should) be handled within the build system (i.e. via
> CMAKE_SOURCE_DIR), but I think 2) and particularly 3) are best done
> using the environment variable.

Ahhh... I see.. I think a clean, acceptable alternative might
eventually be available for 2) but I was totally unaware about 3) .. I
must go fix the runtime environment of my rdkit installation then..
More exactly, what components depend on $RDBASE at runtime?

>> Finally, with regard to the cmake port.. I'm very new both to rdkit
>> and cmake, there are risks that reviewing my attempt to the port might
>> cost more than doing the work from scratch..  but since it took some
>> hours, I've got it here, and since it seems to produce a mostly
>> complete (and mostly sane) build, it might even provide a
>> better-than-nothing starting point, I don't know.. and I'm therefore
>> attaching a tarball [*]. Please, feel free to have a quick look at it,
>> and reuse it or discard it at your best convenience.
>
> Using your files directly worked almost perfectly; I only had to make
> small changes to get things working for me. You saved me a lot of time
> by doing this! I cannot thank you enough.

No need to. I'm just glad to know it worked smoothly and was useful.
Thank you to you for this toolkit, I'm still discovering
subdirectories with features and/or components I didn't know about.

Best regards,
Riccardo