[Rdkit-discuss] installing on mac with --with-java

[Tim Dudgeon]

I'm trying to install on Mac with the instructions here:
https://github.com/rdkit/homebrew-rdkit
The basic install:
brew install rdkit
works fine, but I want the Java wrappers so that I can run with Jython.
And I get this:

$ brew install --with-java rdkit
== Downloading 
https://github.com/rdkit/rdkit/archive/Release_2014_03_1.tar.gz

Already downloaded: /Library/Caches/Homebrew/rdkit-2014.03.1.tar.gz
== mkdir External/java_lib
== curl 
http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar 
-o External/java_lib/junit.jar
== cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' 
-DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev 
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON 
-DRDK_BUILD_CPP_TESTS=OFF



-- Configuring incomplete, errors occurred!
See also 
/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log.
See also 
/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log.


READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/rdkit/homebrew-rdkit/issues

$


The mentioned CMakeOutput.log and CMakeError.log files do not exist (not 
in the location mentioned and not anywhere).


Any ideas what's wrong?

Thanks
Tim


--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] installing on mac with --with-java

[Tim Dudgeon]

/Frameworks/JavaVM.framework/Versions/1.6/Home/bin/java 
(found version 1.6.0.65)
CMake Error at 
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:136 
(message):

  Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
  JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:343 
(_FPHSA_FAILURE_MESSAGE)
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindJNI.cmake:286 
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)

  Code/JavaWrappers/gmwrapper/CMakeLists.txt:6 (find_package)


-- Configuring incomplete, errors occurred!
See also 
/tmp/rdkit-ewWj/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log.
See also 
/tmp/rdkit-ewWj/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log.

/usr/local/Library/Homebrew/formula.rb:556:in `block in system'
BuildError: Failed executing: cmake 
-DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' 
-DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev 
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON 
-DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF 
-DPYTHON_LIBRARY='/System/Library/Frameworks/Python.framework/Versions/2.7/Python' 
-DPYTHON_INCLUDE_DIR='/System/Library/Frameworks/Python.framework/Versions/2.7/Headers' 
.

1. raise
2. ignore
3. backtrace
4. irb
5. shell
Choose an action:


Not obvious what action I should choose.

Tim


On 06/07/2014 17:43, Matthew Swain wrote:

Hi Tim,

Could you try running

brew install rdkit --with-java --verbose --debug

That should give more detailed error messages in the Terminal, and 
also holds off from deleting the log files right away.


Matt

On 6 Jul 2014, at 11:53, Tim Dudgeon tdudgeon...@gmail.com 
mailto:tdudgeon...@gmail.com wrote:



I'm trying to install on Mac with the instructions here:
https://github.com/rdkit/homebrew-rdkit
The basic install:
brew install rdkit
works fine, but I want the Java wrappers so that I can run with Jython.
And I get this:

$ brew install --with-java rdkit
== Downloading 
https://github.com/rdkit/rdkit/archive/Release_2014_03_1.tar.gz

Already downloaded: /Library/Caches/Homebrew/rdkit-2014.03.1.tar.gz
== mkdir External/java_lib
== curl 
http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar 
-o External/java_lib/junit.jar
== cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' 
-DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev 
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON 
-DRDK_BUILD_CPP_TESTS=OFF



-- Configuring incomplete, errors occurred!
See also 
/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log.
See also 
/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log.


READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

$


The mentioned CMakeOutput.log and CMakeError.log files do not exist 
(not in the location mentioned and not anywhere).


Any ideas what's wrong?

Thanks
Tim


--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community 
Edition

Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] java wrappers

[Tim Dudgeon]

Is the only way to get the java wrappers to build from source?
I'm currently using the Debian versions pulled from the Ubuntu 
repositories, but if I'm right this doesn't include the java wrappers 
for jython?

Tim

--
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration  more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] install rdkit cartridge

[Tim Dudgeon]

How to install RDKit cartridge?
The instructions here show how to use it, but not how to install it.
http://www.rdkit.org/docs/Cartridge.html

I have RDKit and PostgreSQL installed from the corresponding Debian 
packages, but alas no cartridge :-(

Tim

--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] install rdkit cartridge

[Tim Dudgeon]

Is it possible when using the packages?
I'm trying to get a reproducible build process so prefer not to have to 
build from sources.

Tim

On 24/04/2015 13:29, Axel Pahl wrote:
 The instructions below appliy to the RDKit installation from source 
 and are probably not applicable to the Debian package, sorry for 
 generating confusion.

 Kind regards,
 Axel

 On 04/24/2015 02:24 PM, Axel Pahl wrote:
 Dear Tim,

 please take a look at this README in your installation:
 your RDKit folder/Code/PgSQL/rdkit/README

 It essentially boils down to this:
 cd $RDBASE/Code/PgSQL/rdkit
 $ make
 $ sudo make install
 $ make installcheck

 (only the second step has to be performed as root)

 Kind regards,
 Axel

 On 04/24/2015 01:33 PM, Tim Dudgeon wrote:
 How to install RDKit cartridge?
 The instructions here show how to use it, but not how to install it.
 http://www.rdkit.org/docs/Cartridge.html

 I have RDKit and PostgreSQL installed from the corresponding Debian
 packages, but alas no cartridge :-(

 Tim

 --
  

 One dashboard for servers and applications across 
 Physical-Virtual-Cloud
 Widest out-of-the-box monitoring support with 50+ applications
 Performance metrics, stats and reports that give you Actionable 
 Insights
 Deep dive visibility with transaction tracing using APM Insight.
 http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


 --
  

 One dashboard for servers and applications across Physical-Virtual-Cloud
 Widest out-of-the-box monitoring support with 50+ applications
 Performance metrics, stats and reports that give you Actionable Insights
 Deep dive visibility with transaction tracing using APM Insight.
 http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDkit cartridge on Amazon RDS

[Tim Dudgeon]

It would indeed be cool, but it might be too specialised for them.
I will follow up and ask if you'd like, but I'd need a bit more 
information about what would be involved.


Tim

On 12/05/2015 02:53, Greg Landrum wrote:

Hi Tim,

On Mon, May 11, 2015 at 6:25 PM, Tim Dudgeon tdudgeon...@gmail.com 
mailto:tdudgeon...@gmail.com wrote:


I wondered if anyone has considered trying to get the RDkit cartridge
running on Amazon Relational Database Service (RDS)? When using
this you
don't get a shell on the underlying server and everything has to
be done
directly at the database level.
This seems to be the most relevant information:

http://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/CHAP_PostgreSQL.html#SQLServer.Concepts.General.FeatureSupport


It looks like you would need Amazon to add the rdkit to the list of 
supported extensions. This would be quite cool and, depending on what 
the underlying operating system is, may be very easy for them to do.


-greg



--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] RDkit cartridge on Amazon RDS

[Tim Dudgeon]

I wondered if anyone has considered trying to get the RDkit cartridge 
running on Amazon Relational Database Service (RDS)? When using this you 
don't get a shell on the underlying server and everything has to be done 
directly at the database level.
This seems to be the most relevant information:
http://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/CHAP_PostgreSQL.html#SQLServer.Concepts.General.FeatureSupport

Tim

--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] failing to build java wrappers

[Tim Dudgeon]

Hi Greg,

yes, that was the problem.
I updated the dockerfile and added a simple example.

Tim



On 23/06/2015 03:21, Greg Landrum wrote:

Hi Tim,

This error is due to a bad interaction between ubuntu (probably 
actually debian) and CMake.
The solution is to set the JAVA_HOME environment variable. Here's what 
I have:

declare -x JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64

-greg


On Mon, Jun 22, 2015 at 3:55 PM, Tim Dudgeon tdudgeon...@gmail.com 
mailto:tdudgeon...@gmail.com wrote:


Hi all,

I'm having problems building the java wrappers on Ubuntu with
OpenJDK7.
This is the error I have:

-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- regex
-- Found SWIG: /usr/bin/swig2.0 (found version 2.0.12)
-- Found Java: /usr/bin/java (found version 1.7.0.79)
CMake Error at
/usr/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136
(message):
Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
/usr/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:343
(_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-3.0/Modules/FindJNI.cmake:286
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)
Code/JavaWrappers/gmwrapper/CMakeLists.txt:6 (find_package)


-- Configuring incomplete, errors occurred!

A Dockerfile that illustrates this can be found here:
https://github.com/tdudgeon/dockerfiles/blob/master/rdkit_java/Dockerfile

Anyone got any ideas?
(p.s. it also fails using OpenJDK8 with an additional error).

Tim




--
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical  virtual servers, alerts via email  sms
for fault. Monitor 25 devices for free with no restriction.
Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
mailto:Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors 
network devices and physical  virtual servers, alerts via email  sms 
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] javadocs

[Tim Dudgeon]

Are javadocs for the java wrappers available anywhere?

Tim

--
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors 
network devices and physical  virtual servers, alerts via email  sms 
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] failing to build java wrappers

[Tim Dudgeon]

Hi all,

I'm having problems building the java wrappers on Ubuntu with OpenJDK7.
This is the error I have:

-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- regex
-- Found SWIG: /usr/bin/swig2.0 (found version 2.0.12)
-- Found Java: /usr/bin/java (found version 1.7.0.79)
CMake Error at 
/usr/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 
(message):

Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
/usr/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:343 
(_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-3.0/Modules/FindJNI.cmake:286 
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)

Code/JavaWrappers/gmwrapper/CMakeLists.txt:6 (find_package)


-- Configuring incomplete, errors occurred!

A Dockerfile that illustrates this can be found here:
https://github.com/tdudgeon/dockerfiles/blob/master/rdkit_java/Dockerfile

Anyone got any ideas?
(p.s. it also fails using OpenJDK8 with an additional error).

Tim


--
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors 
network devices and physical  virtual servers, alerts via email  sms 
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDkit cartridge on Amazon RDS

[Tim Dudgeon]

I followed up with AWS on this, and they they stated:


For the extension to be available we need to test it and white-list the 
extension. I have put in a feature request for the module to added in the 
future. Please note that this may take some time and there is no definite 
deadline at this point in time.


So, maybe this will happen sometime, but don't hold your breath.

Tim

On 12/05/2015 02:53, Greg Landrum wrote:

Hi Tim,

On Mon, May 11, 2015 at 6:25 PM, Tim Dudgeon tdudgeon...@gmail.com 
mailto:tdudgeon...@gmail.com wrote:


I wondered if anyone has considered trying to get the RDkit cartridge
running on Amazon Relational Database Service (RDS)? When using
this you
don't get a shell on the underlying server and everything has to
be done
directly at the database level.
This seems to be the most relevant information:

http://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/CHAP_PostgreSQL.html#SQLServer.Concepts.General.FeatureSupport


It looks like you would need Amazon to add the rdkit to the list of 
supported extensions. This would be quite cool and, depending on what 
the underlying operating system is, may be very easy for them to do.


-greg



--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Molecular dis / similarity using fingerprints

[Tim Dudgeon]

ECFP, like all fingerprints are notoriously sensitive to trivial 
structural changes so your example is no surprise (the extra carbonyl 
group also affects aromaticity depending on your view of aromaticity). 
But I don't think there is anything simple and fast that's better.
Maybe a clustering approach may work? Something like sphere exclusion 
clustering with counting the number of clusters at 0.9 - 0.8 
similarity)? With 30K structures it sounds computationally tractable?


Tim

On 25/05/2015 15:10, JP wrote:

RDKitters,

I have a partial RDKit / partial Methodology question.  I hope this 
email isn't much of the how long is a piece of string nature.


I have a set of molecules (~30,000) which I would like to get a 
structural diversity index for.  So I thought easy - generate some 
fingerprint I fancy (ECFP-like, rad 2), take a threshold I fancy 
(0.7), select a similarity metric I fancy (Tanimoto) and apply these 
to the set in a pairwise fashion (you can only do this for a small-ish 
number of molecules). The resulting distribution of Tanimoto scores 
defines the similarity (or dissimilarity) of the set.


First of all is there a better way to do this? Does anyone have a feel 
for the numbers to use (fingerprint type, radius, no of bits)?  Is 
there some 'Industry standard'?  Which method should I use 
GetMorganFingerprintAsBitVect or GetMorganFingerprint (considering I 
wanted ECFP like fingerprints) ?  What determines when to use one over 
the other?


All my scores are rather low even for relatively similar structures -- 
so I think one of my parameters must be off. Just adding (or removing) 
a carbonyl drops my score to 0.43.
I made this notebook example: 
http://nbviewer.ipython.org/gist/malteseunderdog/6af446c0dbb1ac9840e7


To the RDKit question: GetMorganFingerprintAsBitVect and 
GetMorganFingerprint give different tanimoto scores (with same radius: 
2).  This is of course because for the explicit bit vector we can set 
the length of the vector/fingerprint.  Is there an equivalence between 
the two? (say using n bits gives same results as 
GetMorganFingerprint).  How come the GetMorganFingerprint method has 
no user-defined length for the fingerprint?  What are the hashed 
equivalents of these fingerprints (e.g. GetHashedMorganFingerprint) ?


Take care,
JP

ps A small suggestion, if I am allowed.  The fingerprint classes could 
do with an informative toString (or non Java equivalent) - I know 
there is ToBitString, but you need to call that explicitly when printing




--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] molecule standardization in cartridge search

[Tim Dudgeon]

Jan and others
Thanks for all your suggestions. Just what I need.

Tim

On 26/09/2015 12:26, Jan Holst Jensen wrote:

Hi Tim,

Soren (cc:ed) wrote me and asked about molvs. Thanks to Soren for 
reminding that the original question was about standardization more 
than calling Python code from Postgres :-).

http://molvs.readthedocs.org/en/latest/

Take a look at molvs - it's got lots of functionality that you will 
need. We also use molvs as the backbone for much of our standardization.


Cheers
-- Jan


Hi Tim,

A simple getting-started example is:

CREATE FUNCTION smiles2molfile(smiles text) RETURNS text
  LANGUAGE plpythonu AS $$
import rdkit
from rdkit import Chem

mol = Chem.MolFromSmiles(smiles)
return Chem.MolToMolBlock(mol)
$$;


and you can then

select smiles2molfile('CC');

and get back a molfile.

For more advanced usage it is worth taking a look at the rdchord 
project that TJ has sent links to.


Cheers
-- Jan

On 2015-09-25 15:54, Tim Dudgeon wrote:

Jan,

thanks for that. I'll give it a try.
Are there any examples of writing RDKit functions and procedures for
postgres in python?
I see this general postgres docs:
http://www.postgresql.org/docs/9.4/static/plpython.html
but wondered if there are any RDKit specific examples anywhere?

Tim

On 25/09/2015 08:30, Jan Holst Jensen wrote:

On 2015-09-24 16:22, Tim Dudgeon wrote:

I'm trying to get to grips with using the RDKit cartridge, and so far
its going well.
One thing I'm concerned about is molecule standardization, along the
lines of the ChemAxon Standardizer that allows substructure searches to
be done is a way that is largely independent of the quirks of structure
representation. The classic example would be how nitro groups are
represented, so that it didn't matter which nitro representation was in
the query or target structures, because both were converted to a
canonical form.

My initial thoughts are that this would be done by:
1. loading the "raw" structures into a source column that would never be
changed
2. defining a function that performed the necessary transform to
generate the canonical form of a molecule.
3. generating a "canonical" structure column that was the result of
passing the raw structures through that function
4. building the SSS index on that canonical column
5. executing queries using that function to canonicalize the query
structure

The problem I'm finding is that there do not seem to be postgres
functions defined for doing molecular transforms (essentially a reaction
transform) and doing things like removing explicit hydrogens. At least
not in the functions listed on this page:
http://rdkit.org/docs/Cartridge.html#functions

Am I missing something here, or might I be barking up completely the
wrong tree?

Tim

Hi Tim,

We have about the same situation and we're adding standardization
(beyond what RDKit implicitly does when it sanitizes the molecule)
through Python stored procedures. You will need to build and maintain
a normal Python-enabled RDKit installation in parallel to the
cartridge. The Python stored procedures can access the normal RDKit
installation and then run whatever Python code is necessary to do
additional molecule cleanup.

You will need to tweak your Postgres environment so the Python stored
procedures can load RDKit. This is what I have defined in an
environment file on CentOS:

RDBASE=/opt/rdkit
LD_LIBRARY_PATH=/opt/rdkit/lib
PYTHONPATH=/opt/rdkit

On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in
a slightly different format where the values have to be single-quoted).

Cheers
-- Jan, Biochemfusion




--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] molecule standardization in cartridge search

[Tim Dudgeon]

I'm trying to get to grips with using the RDKit cartridge, and so far 
its going well.
One thing I'm concerned about is molecule standardization, along the 
lines of the ChemAxon Standardizer that allows substructure searches to 
be done is a way that is largely independent of the quirks of structure 
representation. The classic example would be how nitro groups are 
represented, so that it didn't matter which nitro representation was in 
the query or target structures, because both were converted to a 
canonical form.

My initial thoughts are that this would be done by:
1. loading the "raw" structures into a source column that would never be 
changed
2. defining a function that performed the necessary transform to 
generate the canonical form of a molecule.
3. generating a "canonical" structure column that was the result of 
passing the raw structures through that function
4. building the SSS index on that canonical column
5. executing queries using that function to canonicalize the query structure

The problem I'm finding is that there do not seem to be postgres 
functions defined for doing molecular transforms (essentially a reaction 
transform) and doing things like removing explicit hydrogens. At least 
not in the functions listed on this page: 
http://rdkit.org/docs/Cartridge.html#functions

Am I missing something here, or might I be barking up completely the 
wrong tree?

Tim




--
Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
Get real-time metrics from all of your servers, apps and tools
in one place.
SourceForge users - Click here to start your Free Trial of Datadog now!
http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] molecule standardization in cartridge search

[Tim Dudgeon]

Jan,

thanks for that. I'll give it a try.
Are there any examples of writing RDKit functions and procedures for 
postgres in python?
I see this general postgres docs: 
http://www.postgresql.org/docs/9.4/static/plpython.html
but wondered if there are any RDKit specific examples anywhere?

Tim

On 25/09/2015 08:30, Jan Holst Jensen wrote:
> On 2015-09-24 16:22, Tim Dudgeon wrote:
>> I'm trying to get to grips with using the RDKit cartridge, and so far
>> its going well.
>> One thing I'm concerned about is molecule standardization, along the
>> lines of the ChemAxon Standardizer that allows substructure searches to
>> be done is a way that is largely independent of the quirks of structure
>> representation. The classic example would be how nitro groups are
>> represented, so that it didn't matter which nitro representation was in
>> the query or target structures, because both were converted to a
>> canonical form.
>>
>> My initial thoughts are that this would be done by:
>> 1. loading the "raw" structures into a source column that would never be
>> changed
>> 2. defining a function that performed the necessary transform to
>> generate the canonical form of a molecule.
>> 3. generating a "canonical" structure column that was the result of
>> passing the raw structures through that function
>> 4. building the SSS index on that canonical column
>> 5. executing queries using that function to canonicalize the query 
>> structure
>>
>> The problem I'm finding is that there do not seem to be postgres
>> functions defined for doing molecular transforms (essentially a reaction
>> transform) and doing things like removing explicit hydrogens. At least
>> not in the functions listed on this page:
>> http://rdkit.org/docs/Cartridge.html#functions
>>
>> Am I missing something here, or might I be barking up completely the
>> wrong tree?
>>
>> Tim
>
> Hi Tim,
>
> We have about the same situation and we're adding standardization 
> (beyond what RDKit implicitly does when it sanitizes the molecule) 
> through Python stored procedures. You will need to build and maintain 
> a normal Python-enabled RDKit installation in parallel to the 
> cartridge. The Python stored procedures can access the normal RDKit 
> installation and then run whatever Python code is necessary to do 
> additional molecule cleanup.
>
> You will need to tweak your Postgres environment so the Python stored 
> procedures can load RDKit. This is what I have defined in an 
> environment file on CentOS:
>
> RDBASE=/opt/rdkit
> LD_LIBRARY_PATH=/opt/rdkit/lib
> PYTHONPATH=/opt/rdkit
>
> On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in 
> a slightly different format where the values have to be single-quoted).
>
> Cheers
> -- Jan, Biochemfusion


--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

[Tim Dudgeon]

re = pyO3A.Score()
print "Orig",score
Chem.MolToMolFile(mol1, "orig.mol")

cids = AllChem.EmbedMultipleConfs(mol1, numConfs=250,
maxAttempts=100,
pruneRmsThresh=0.5, useExpTorsionAnglePrefs=False,
useBasicKnowledge=False)
AllChem.MMFFOptimizeMoleculeConfs(mol1, mmffVariant='MMFF94s')
pyO3As = rdMolAlign.GetO3AForProbeConfs(mol1, mol2, numThreads=0)
i = 0
lowest = 9.9
highest = 0.0
for pyO3A in pyO3As:
rmsd = pyO3A.Align()
score = pyO3A.Score()
if score < lowest:
lowest = score
lowestConfId = i
if score > highest:
highest = score
highestConfId = i
i +=1

print "Lowest:", lowest, lowestConfId
print "Highest:", highest, highestConfId

Chem.MolToMolFile(mol1, "lowest.mol", confId=lowestConfId)
Chem.MolToMolFile(mol1, "highest.mol", confId=highestConfId)


On 06/21/16 15:41, Tim Dudgeon wrote:


Hi All,

I'm trying to get to grips with using Open3D Align in RDKit,
but hitting problems.

My approach is to generate random conformers of the probe
molecule and align it to the reference molecule.  My example is
cobbled together from the examples in the cookbook.



from rdkit import Chem, RDConfig
from rdkit.Chem import AllChem, rdMolAlign

ref =

Chem.MolFromSmiles('NC(=[NH2+])c1ccc(C[C@@H](NC(=O)CNS(=O)(=O)c2ccc3c3c2)C(=O)N2C2)cc1')
mol1 =

Chem.MolFromPDBFile(RDConfig.RDBaseDir+'/rdkit/Chem/test_data/1DWD_ligand.pdb')
mol1 = AllChem.AssignBondOrdersFromTemplate(ref, mol1)
mol2 =

Chem.MolFromPDBFile(RDConfig.RDBaseDir+'/rdkit/Chem/test_data/1PPC_ligand.pdb')
mol2 = AllChem.AssignBondOrdersFromTemplate(ref, mol2)

pyO3A = rdMolAlign.GetO3A(mol1, mol2)
score = pyO3A.Align()
print "Orig",score
Chem.MolToMolFile(mol1, "orig.mol")

cids = AllChem.EmbedMultipleConfs(mol1, numConfs=100,
maxAttempts=100, pruneRmsThresh=0.1,
useExpTorsionAnglePrefs=True, useBasicKnowledge=True)

pyO3As = rdMolAlign.GetO3AForProbeConfs(mol1, mol2, numThreads=0)
i = 0
lowest = 9.9
highest = 0.0
for pyO3A in pyO3As:
i +=1
score = pyO3A.Align()
if score < lowest:
lowest = score
lowestConfId = i
if score > highest:
highest = score
highestConfId = i

print "Lowest:", lowest, lowestConfId
print "Highest:", highest, highestConfId

Chem.MolToMolFile(mol1, "lowest.mol", confId=lowestConfId)
Chem.MolToMolFile(mol1, "highest.mol", confId=highestConfId)

What I'm finding is that the alignments with the lowest and
highest O3A scores are much worse alignments (visually) than
the original structure (the structure from 1DWD). Typical
scores are:

Original 1DWD structure: 0.38
Lowest scoring conformer: 0.186
Highest scoring conformer: 0.78

Now I'm assuming that lower O3A align scores are better (though
that's not specifically stated), so as my lowest score is lower
than the original alignment I would have expected it to be a
better alignment, but its clearly much worse. And if I'm wrong
and higher scores are better then the same applies.

Clearly I've not understood something correctly!

Tim




--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park
in San
Francisco, CA to explore cutting-edge tech and listen to tech
luminaries
present their vision of the future. This family event has
something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present t

[Rdkit-discuss] Conformer generation does not sample well?

[Tim Dudgeon]

This topic (https://sourceforge.net/p/rdkit/mailman/message/35173301/) 
discussed using conformer generation as input into Open3DAlign.

One thing I noticed is that the conformer generation (using the 
useExpTorsionAnglePrefs=True and
useBasicKnowledge=True options) does not generate conformers that align 
well for this example. The input is based on the 1DWD_ligand.pdb 
structure in the RDKit distro. What I find is the the rotation of the 
benzamidine ring is never in the right place for alignment (the other 
two ring systems align well). This is when generating up to 10,000 
conformers.

Does this suggest that the conformer generation does not sample 
conformational space very effectively? Are there options for improving this?

Thanks

Tim



--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Getting to grips with Open3DAlign

[Tim Dudgeon]

Hi All,

I'm trying to get to grips with using Open3D Align in RDKit, but hitting 
problems.


My approach is to generate random conformers of the probe molecule and 
align it to the reference molecule.  My example is cobbled together from 
the examples in the cookbook.


from rdkit import Chem, RDConfig
from rdkit.Chem import AllChem, rdMolAlign

ref = 
Chem.MolFromSmiles('NC(=[NH2+])c1ccc(C[C@@H](NC(=O)CNS(=O)(=O)c2ccc3c3c2)C(=O)N2C2)cc1')
mol1 = 
Chem.MolFromPDBFile(RDConfig.RDBaseDir+'/rdkit/Chem/test_data/1DWD_ligand.pdb')

mol1 = AllChem.AssignBondOrdersFromTemplate(ref, mol1)
mol2 = 
Chem.MolFromPDBFile(RDConfig.RDBaseDir+'/rdkit/Chem/test_data/1PPC_ligand.pdb')

mol2 = AllChem.AssignBondOrdersFromTemplate(ref, mol2)

pyO3A = rdMolAlign.GetO3A(mol1, mol2)
score = pyO3A.Align()
print "Orig",score
Chem.MolToMolFile(mol1, "orig.mol")

cids = AllChem.EmbedMultipleConfs(mol1, numConfs=100, maxAttempts=100, 
pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)


pyO3As = rdMolAlign.GetO3AForProbeConfs(mol1, mol2, numThreads=0)
i = 0
lowest = 9.9
highest = 0.0
for pyO3A in pyO3As:
i +=1
score = pyO3A.Align()
if score < lowest:
lowest = score
lowestConfId = i
if score > highest:
highest = score
highestConfId = i

print "Lowest:", lowest, lowestConfId
print "Highest:", highest, highestConfId

Chem.MolToMolFile(mol1, "lowest.mol", confId=lowestConfId)
Chem.MolToMolFile(mol1, "highest.mol", confId=highestConfId)

What I'm finding is that the alignments with the lowest and highest O3A 
scores are much worse alignments (visually) than the original structure 
(the structure from 1DWD). Typical scores are:


Original 1DWD structure: 0.38
Lowest scoring conformer: 0.186
Highest scoring conformer: 0.78

Now I'm assuming that lower O3A align scores are better (though that's 
not specifically stated), so as my lowest score is lower than the 
original alignment I would have expected it to be a better alignment, 
but its clearly much worse. And if I'm wrong and higher scores are 
better then the same applies.


Clearly I've not understood something correctly!

Tim

--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Using Java version of RDKit

[Tim Dudgeon]

Michaela

I have a Dockerfile that does this that should hopefully show what's needed:
https://github.com/InformaticsMatters/rdkit_java/blob/master/Dockerfile
Or you could even use the build Docker image:
https://hub.docker.com/r/informaticsmatters/rdkit_java/

Tim


On 25/02/2016 14:29, Michaela Hradilová wrote:

Hello,
I'm using Java version and I have some troubles. I've imported it to 
my project but UnsatisfiedLinkError appears when I'm compilling the 
project. Please could anybody helps me or does anyone has some manual 
for Java version?


Thank you in advance


--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] SDWriter from Java

[Tim Dudgeon]

Hi All,

this probably a pretty basic question, but I'm struggling to work out 
how to use the SDWriter from Java.
The class that SWIG has generated for SDWriter has a constructor of type:
SDWriter(SWIGTYPE_p_std__ostream outstream)
which looks like its the one I need (I need to write to a Java 
OutputStream, not a file).
But I can't would out how to generate an instance of 
SWIGTYPE_p_std__ostream from my Java OutputStream.
Any pointers?

(Also, what does the boolean takeownership param of the similar 
constructor do?)


Tim



--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] SDWriter from Java

[Tim Dudgeon]

And there's no other way to generate a SDF from Java?
e.g. can each ROMol be converted to text in SD format and then that text 
written to the Java OutputStream?


Tim

On 30/03/2016 13:31, Greg Landrum wrote:

Hi Tim,

That constructor is expecting a C++ stream pointer. The takeOwnership 
flag tells it to take assume ownership of the pointer (i.e. to free up 
the memory being used by the stream when the SDWriter itself is 
free'd). I am guessing that this will not be useable from Java (and 
should probably be disabled).


There is likely a way to set up the wrappers so that Java streams are 
properly handled, but it's difficult to assess how much work that 
would be.


-greg


On Wed, Mar 30, 2016 at 2:00 PM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


Hi All,

this probably a pretty basic question, but I'm struggling to work out
how to use the SDWriter from Java.
The class that SWIG has generated for SDWriter has a constructor
of type:
SDWriter(SWIGTYPE_p_std__ostream outstream)
which looks like its the one I need (I need to write to a Java
OutputStream, not a file).
But I can't would out how to generate an instance of
SWIGTYPE_p_std__ostream from my Java OutputStream.
Any pointers?

(Also, what does the boolean takeownership param of the similar
constructor do?)


Tim




--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] strict parsing in java

[Tim Dudgeon]

I've got molfiles that have element labels all in upper case (e.g. CL 
instead of Cl).
Parsing these fails (Element 'CL' not found).
I notice that in the C++ and Python APIs there is a 'strictParsing' 
option that I'm hoping makes RDKit tolerant of this, but this option 
does not seem to be present in the Java API, and guess, what, that's the 
one I'm using!
Is this possible from Java?

Tim

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] cartridge search functions

[Tim Dudgeon]

I'm slightly confused over the cartridge search functions.

The docs give examples like this:

select * from rdk.mols where m@>'c12c1CNCCN2'
select * from rdk.mols where m@>'c1[o,s]ncn1'::qmol

Q1: As SSS by definition uses a query mol, I'm not totally clear what's 
happening in the first of these.

Q2: Would the result be any different if if the smiles were cast to qmol?

Q3: using this form is only smiles or smarts supported or could the 
param be molfile (e.g. when using bind variables), or would the 
qmol_from_ctab() function need to be used.

There are functions mol_from_smiles(), mol_from_smarts() and 
mol_from_ctab().
There are also qmol_from_smiles(), and qmol_from_ctab().

Q4: why is there no qmol_from_smarts().

Thanks
Tim




--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

[Tim Dudgeon]

All,

Paolo helped me off-list to resolve this (many thanks Paolo!).
There were a number of things wrong, partly in what I was doing (cmake 
switches) and partly some problems in CMakeLists.txt that requires a 
patch until the PR that Paolo has submitted is merged.
I'll spare you of all the details, but here is what seem to be a working 
build:

https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile

The downside of this is that I needed to switch from building based on 
an image that has already built RDKit to one that does the complete 
RDkit build (which adds an hour or so to the build process) as the 
cartridge build is now part of the standard build, and so to build with 
cartridge support you must have postgres present.
So I ask if its still somehow possible to decouple the building of core 
RDKit from building (and installing) what's needed for postgres?


Tim


On 18/04/2016 19:43, Paolo Tosco wrote:

Dear Tim,

did you check that the Boost libraries you linked the RDKit against 
are in the postgres user LD_LIBRARY_PATH? You might need to login as 
root, then su postgres, and echo "export 
LD_LIBRARY_PATH=" > ~/.bashrc. Then, as root, 
restart the postgres service. That fixed the problem for me.


Kind regards,
p.

On 18/04/2016 09:18, Tim Dudgeon wrote:

I spoke too soon!
I'm still having problem with postgres cartridge.

psql -c 'create extension rdkit' rdkitdb
ERROR:  could not load library 
"/usr/lib/postgresql/9.4/lib/rdkit.so": 
/usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol: 
_ZTIN5boost6detail16thread_data_baseE


Is something else needed for cartridge?
The docker image is here:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
which is based on rdkit build that now works OK based on the earlier 
discussions in this thread.


Tim



On 17/04/2016 13:43, Brian Kelley wrote:
Now that we made thread safe the default, you also need boost-system 
( and boost-serialization for FilterCatalog serialization)

|Here is the apt get we use to configure docker files.|
|apt install -y wget flex bison build-essential python-numpy cmake 
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev 
libboost-thread-dev libboost-serialization-dev libboost-python-dev 
libboost-regex-dev; |

It looks like I should add a PR to detect this at build time?

I admit to being confused why this builds but doesn't run...

See here for more details:

https://github.com/rdkit/rdkit/issues/762

Brian Kelley

On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:

I've hit the same issue. Any thoughts on what the underlying issue 
is (without reverting to using anaconda)?

An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit

Tim

On 20/11/2015 16:02, Greg Landrum wrote:

Hi Huw,

This is not directly responsive to your question, but if you're 
working with anaconda, it is probably easier to just build and 
install the RDKit using the conda-rdkit recipes here:

https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.

-greg


On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones <huwdjo...@hotmail.com> 
wrote:


Hi there,

I’ve been building the Python RDKit modules direct from the
GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e. git
clone https://github.com/rdkit/rdkit.git).

*I use the following aptitude packages for the build process:*

flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1

*The build process is as follows:*

git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit

*I have recently been experiencing this error:*

Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> from rdkit import rdBase
Traceback (most recent call last):
  File "", line 1, in 
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv

*It looks like this error starts appearing from this commit
onwards:*


https://github.com/rdkit/rdkit/commit/996

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

[Tim Dudgeon]

I've hit the same issue. Any thoughts on what the underlying issue is 
(without reverting to using anaconda)?

An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit

Tim

On 20/11/2015 16:02, Greg Landrum wrote:

Hi Huw,

This is not directly responsive to your question, but if you're 
working with anaconda, it is probably easier to just build and install 
the RDKit using the conda-rdkit recipes here:

https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.

-greg


On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones > wrote:


Hi there,

I’ve been building the Python RDKit modules direct from the GitHub
repository recently on an Ubuntu 14.04 LTS VM (i.e. git clone
https://github.com/rdkit/rdkit.git).

*I use the following aptitude packages for the build process:*

flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1

*The build process is as follows:*

git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit

*I have recently been experiencing this error:*

Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import rdBase
Traceback (most recent call last):
  File "", line 1, in 
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv

*It looks like this error starts appearing from this commit onwards:*


https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331

Any ideas?

Many thanks as ever.

Huw Jones


--

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

[Tim Dudgeon]

Brian: thanks, adding libboost-system-dev libboost-thread-dev and 
libboost-serialization-dev solves the problem.


Greg: confirmed, flex and bison are not needed.

Many thanks.
Tim

On 17/04/2016 15:28, Greg Landrum wrote:



On Sun, Apr 17, 2016 at 2:43 PM, Brian Kelley <fustiga...@gmail.com 
<mailto:fustiga...@gmail.com>> wrote:


Now that we made thread safe the default, you also need
boost-system ( and boost-serialization for FilterCatalog
serialization)

|Here is the apt get we use to configure docker files.|

|apt install -y wget flex bison build-essential python-numpy cmake
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev
libboost-thread-dev libboost-serialization-dev libboost-python-dev
libboost-regex-dev; |


Flex and bison don't need to be on this list.

It looks like I should add a PR to detect this at build time?


We should probably add the explicit boost-system dependency to the 
appropriate CMakeLists.txt. It's technically not required for some 
older boost versions (I want to say pre 1.51, but that may not be 
correct), but it's not a heavy dependency. Serialization is a (very) 
nice to have, so don't think it should show up as an actual 
requirement in the CMakeLists.txt (i.e. I think the status quo is fine).


-greg


I admit to being confused why this builds but doesn't run...

See here for more details:

https://github.com/rdkit/rdkit/issues/762

Brian Kelley

On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:


I've hit the same issue. Any thoughts on what the underlying
issue is (without reverting to using anaconda)?
An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit

Tim

On 20/11/2015 16:02, Greg Landrum wrote:

Hi Huw,

This is not directly responsive to your question, but if you're
working with anaconda, it is probably easier to just build and
install the RDKit using the conda-rdkit recipes here:
https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.

-greg


On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones
<huwdjo...@hotmail.com <mailto:huwdjo...@hotmail.com>> wrote:

Hi there,

I’ve been building the Python RDKit modules direct from the
GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e.
git clone https://github.com/rdkit/rdkit.git).

*I use the following aptitude packages for the build process:*

flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1

*The build process is as follows:*

git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit

*I have recently been experiencing this error:*

Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> from rdkit import rdBase
Traceback (most recent call last):
  File "", line 1, in 
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv

*It looks like this error starts appearing from this commit
onwards:*


https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331

Any ideas?

Many thanks as ever.

Huw Jones


--

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss





--


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



--

[Rdkit-discuss] Build problems with Release_2016_03_1 with java + inchi

[Tim Dudgeon]

Hi

I'm having problems building the java wrappers for the 2016_03_1 release 
when inchi support is enabled (the -DRDK_BUILD_INCHI_SUPPORT=ON option).

If I turn inchi off or build from master it builds OK.
This is the error I get:

Scanning dependencies of target GraphMolWrap
[ 98%] Building CXX object 
Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o

Linking CXX shared module libGraphMolWrap.so
/usr/bin/ld: cannot find -lRDInchiLib_static
/usr/bin/ld: cannot find -lInchi_static
collect2: error: ld returned 1 exit status
make[2]: *** [Code/JavaWrappers/gmwrapper/libGraphMolWrap.so] Error 1
Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/build.make:194: 
recipe for target 'Code/JavaWrappers/gmwrapper/libGraphMolWrap.so' failed
make[1]: *** 
[Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2
CMakeFiles/Makefile2:8909: recipe for target 
'Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all' failed

make: *** [all] Error 2
Makefile:147: recipe for target 'all' failed
The command '/bin/sh -c make' returned a non-zero code: 2

Any idea what the problem is?
(building with inchi and without Java is fine)

Tim
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

[Tim Dudgeon]

No, afraid that doesn't seem to help.
The boost libs seem to be in /usr/lib/x86_64-linux-gnu but adding that 
directory to LD_LIBRARY_PATH  doesn't fix the problem.
In fact, for the plain rdkit image it works fine with just $RDBASE being 
on LD_LIBRARY_PATH.


Tim

On 18/04/2016 19:43, Paolo Tosco wrote:

Dear Tim,

did you check that the Boost libraries you linked the RDKit against 
are in the postgres user LD_LIBRARY_PATH? You might need to login as 
root, then su postgres, and echo "export 
LD_LIBRARY_PATH=" > ~/.bashrc. Then, as root, 
restart the postgres service. That fixed the problem for me.


Kind regards,
p.

On 18/04/2016 09:18, Tim Dudgeon wrote:

I spoke too soon!
I'm still having problem with postgres cartridge.

psql -c 'create extension rdkit' rdkitdb
ERROR:  could not load library 
"/usr/lib/postgresql/9.4/lib/rdkit.so": 
/usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol: 
_ZTIN5boost6detail16thread_data_baseE


Is something else needed for cartridge?
The docker image is here:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
which is based on rdkit build that now works OK based on the earlier 
discussions in this thread.


Tim



On 17/04/2016 13:43, Brian Kelley wrote:
Now that we made thread safe the default, you also need boost-system 
( and boost-serialization for FilterCatalog serialization)

|Here is the apt get we use to configure docker files.|
|apt install -y wget flex bison build-essential python-numpy cmake 
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev 
libboost-thread-dev libboost-serialization-dev libboost-python-dev 
libboost-regex-dev; |

It looks like I should add a PR to detect this at build time?

I admit to being confused why this builds but doesn't run...

See here for more details:

https://github.com/rdkit/rdkit/issues/762

Brian Kelley

On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:

I've hit the same issue. Any thoughts on what the underlying issue 
is (without reverting to using anaconda)?

An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit

Tim

On 20/11/2015 16:02, Greg Landrum wrote:

Hi Huw,

This is not directly responsive to your question, but if you're 
working with anaconda, it is probably easier to just build and 
install the RDKit using the conda-rdkit recipes here:

https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.

-greg


On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones <huwdjo...@hotmail.com> 
wrote:


Hi there,

I’ve been building the Python RDKit modules direct from the
GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e. git
clone https://github.com/rdkit/rdkit.git).

*I use the following aptitude packages for the build process:*

flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1

*The build process is as follows:*

git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit

*I have recently been experiencing this error:*

Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> from rdkit import rdBase
Traceback (most recent call last):
  File "", line 1, in 
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv

*It looks like this error starts appearing from this commit
onwards:*


https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331

Any ideas?

Many thanks as ever.

Huw Jones


--

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

[Tim Dudgeon]

I spoke too soon!
I'm still having problem with postgres cartridge.

psql -c 'create extension rdkit' rdkitdb
ERROR:  could not load library "/usr/lib/postgresql/9.4/lib/rdkit.so": 
/usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol: 
_ZTIN5boost6detail16thread_data_baseE


Is something else needed for cartridge?
The docker image is here:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
which is based on rdkit build that now works OK based on the earlier 
discussions in this thread.


Tim



On 17/04/2016 13:43, Brian Kelley wrote:
Now that we made thread safe the default, you also need boost-system ( 
and boost-serialization for FilterCatalog serialization)

|Here is the apt get we use to configure docker files.|
|apt install -y wget flex bison build-essential python-numpy cmake 
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev 
libboost-thread-dev libboost-serialization-dev libboost-python-dev 
libboost-regex-dev; |

It looks like I should add a PR to detect this at build time?

I admit to being confused why this builds but doesn't run...

See here for more details:

https://github.com/rdkit/rdkit/issues/762

Brian Kelley

On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


I've hit the same issue. Any thoughts on what the underlying issue is 
(without reverting to using anaconda)?

An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit

Tim

On 20/11/2015 16:02, Greg Landrum wrote:

Hi Huw,

This is not directly responsive to your question, but if you're 
working with anaconda, it is probably easier to just build and 
install the RDKit using the conda-rdkit recipes here:

https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.

-greg


On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones <huwdjo...@hotmail.com 
<mailto:huwdjo...@hotmail.com>> wrote:


Hi there,

I’ve been building the Python RDKit modules direct from the
GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e. git
clone https://github.com/rdkit/rdkit.git).

*I use the following aptitude packages for the build process:*

flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1

*The build process is as follows:*

git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit

*I have recently been experiencing this error:*

Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> from rdkit import rdBase
Traceback (most recent call last):
  File "", line 1, in 
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv

*It looks like this error starts appearing from this commit
onwards:*


https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331

Any ideas?

Many thanks as ever.

Huw Jones


--

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Find and fix application performance issues faster with Applications 
Manager
Applications Manager provides deep performance insights into multiple 
tiers of

your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net 
<mailto:Rdkit-discuss@lists.sourceforge.net>

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDKit Meetup in Cambridge October 19

[Tim Dudgeon]

Which Cambridge? Assume this is Cambridge MA not Cambridge UK?


On 15/09/2016 19:29, Brian Kelley wrote:
Novartis is kindly hosting an RDKit Meetup October 19th starting at 
4:30pm


The first 45 minutes or so will be devoted to introducing new features 
in the RDKit and also a Q and A or tutorial session.  From 5:30 - 7 or 
7:30 depending, we will be inviting speakers .  There are talking 
slots still free so please drop us a line if you want to give a short 
talk (20-30 minutes is what we are looking for.)


To attend or just join the community, please use the link below, we do 
have a maximum number of spots so please RSVP early.


http://www.meetup.com/Cambridge-RDKit-Meetup/events/234150101/?


Cheers,
 Brian Kelley


--


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] junit version problems

[Tim Dudgeon]

Hi Gianluca

Unfortunately that doesn't work. It's still picking up junit.jar not 
junit4.jar from /usr/share/java

Tim


On 26/08/2016 10:15, Gianluca Sforna wrote:
> On Thu, Aug 25, 2016 at 5:34 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>> It seems that RDKit looks for junit here: /usr/share/java/junit.jar
>>
>> But on my Ubuntu system that is a symlink to a JUnit3 jar file, and the
>> correct link for JUnit4 is /usr/share/java/junit4.jar, and the tests
>> require JUnit4 and so fail. Of course it may be different with other
>> Linux distros.
> In recent releases we are using the cmake "find_jar" function to
> determine the junit location; it seems you have installed both
> versions so it picks up the wrong one.
>
> Can you try the following and let us know if it works?
>
> Open up Code/JavaWrappers/gmwrapper/CMakelists.txt and change the line 13 
> from:
> find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir})
>
> to
>
> find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir} VERSIONS 4)
>
> According to cmake documentation, that should force a version match
> and use the correct one.
>
>


--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Hankering after faster builds

[Tim Dudgeon]

Hi Greg,

On 03/12/2016 13:16, Greg Landrum wrote:
Builds do take a while, but there is *no way* they should be taking 2 
hours unless they are running on extremely overloaded hardware. The 
travis builds, which include running all the tests, typically take 
less than 40 minutes.
yes on my normal machine a build takes about 45 mins. But on Docker hub 
it seems your only get pretty limited hardware (1 core for instance) and 
can't do anything about this.


If, for some reason, you do still need to deal with this, I would 
guess that it would help to start by building an image without the 
java (or python) wrappers and then build an image on top of that which 
adds just the java (or python) wrappers
Yes, I can try that. In fact I'm sort of doing this for the Java 
wrappers, but not quite in that way.


Still, I would hope that you don't need to run too many builds on 
docker. It seems like one of those "once per release" activities. 
Certainly not something you'd want to do after every commit.
Yes, that's the case. Typically I build when there is a new release 
(e.g. every 6 months) and from time to time check that the build on 
master is still OK.


Tim


-greg





On Fri, Dec 2, 2016 at 6:29 PM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


Of course builds from source are never fast enough, and the RDKit
one is
pretty big.
So far I've lived with this and made cups of coffee.
But since I've been working with the Release_2016_09_2 release my
Docker
image builds on Docker Hub [1] are timing out as they sometimes exceed
the 2 hour limit. If I try at a quiet time I can sometimes get them to
complete, but I suppose the situation is only going to get worse.

I've tried breaking the build into 2 steps, the first to prepare the
base image [2] and the second to build RDKit [3], and that's helped a
bit, but I don't think there's more mileage here as nearly all the
time
is spend in the 'make' command.

Anticipating things getting worse, does anyone have suggestions for
speeding this up. I hanker after a --fast mode, but I suppose if there
was one it would already be the default.

Any ideas?

In case anyone wonders I'm building from source as I need to also
create
a Java enabled version and one for the Postgres cartridge and want to
use the same approach to generating them all.

Tim

[1] https://hub.docker.com/r/informaticsmatters/rdkit/
<https://hub.docker.com/r/informaticsmatters/rdkit/>
[2] https://github.com/InformaticsMatters/rdkit_debian_base
<https://github.com/InformaticsMatters/rdkit_debian_base>
[3] https://github.com/InformaticsMatters/rdkit
<https://github.com/InformaticsMatters/rdkit>






--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>




--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Hankering after faster builds

[Tim Dudgeon]

Of course builds from source are never fast enough, and the RDKit one is 
pretty big.
So far I've lived with this and made cups of coffee.
But since I've been working with the Release_2016_09_2 release my Docker 
image builds on Docker Hub [1] are timing out as they sometimes exceed 
the 2 hour limit. If I try at a quiet time I can sometimes get them to 
complete, but I suppose the situation is only going to get worse.

I've tried breaking the build into 2 steps, the first to prepare the 
base image [2] and the second to build RDKit [3], and that's helped a 
bit, but I don't think there's more mileage here as nearly all the time 
is spend in the 'make' command.

Anticipating things getting worse, does anyone have suggestions for 
speeding this up. I hanker after a --fast mode, but I suppose if there 
was one it would already be the default.

Any ideas?

In case anyone wonders I'm building from source as I need to also create 
a Java enabled version and one for the Postgres cartridge and want to 
use the same approach to generating them all.

Tim

[1] https://hub.docker.com/r/informaticsmatters/rdkit/
[2] https://github.com/InformaticsMatters/rdkit_debian_base
[3] https://github.com/InformaticsMatters/rdkit





--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Fast similarity search

[Tim Dudgeon]

Greg, Nils, Andrew,

Thanks for all that info. Gives me plenty to work on!

Tim


On 19/05/2017 09:27, Andrew Dalke wrote:
> On May 19, 2017, at 08:33, Greg Landrum <greg.land...@gmail.com> wrote:
>> The best solution to this is to use chemfp. It's a remarkable piece of 
>> software.
> Thanks, Greg.
>
>> If you aren't willing to license that, the RDKit's search brute-force 
>> fingerprint search capabilities aren't too bad for in-memory fingerprints.
> To clarify, chemfp 1.1 is available for no cost from chemfp.com or PyPI, 
> while later versions (chemfp 3.0 now supports Python 3) costs money. Both are 
> distributed under the MIT license.
>
> Within a month or so I'll be making a new release of the no-cost version. 
> I'll update the fingerprint type names, to reflect a change in the recent 
> RDKit release.
>
> On Thu, May 18, 2017 at 11:15 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>> I think I recall Greg mentioning that RDKit can be used for very fast
>> similarity search (e.g. all vs. all comparisons or searches against
>> multi-million sized datasets).
> Greg's slides include a few timings numbers with single query searches. To 
> add some all vs. all numbers, chemfp takes about 40 minutes to cluster the 
> 1.58 million fingerprints from ChEMBL 21, at a threshold of 0.8 using 4 
> threads and 2048 bit RDKit fingerprints.
>
> This functionality is available in the no-cost version. Depending on the 
> fingerprint size and your CPU type the newest version (3.0) is between 5% and 
> 35% faster than chemfp 1.1.
>
> Feel free to contact me if you have questions about chemfp.
>
>
>
>   Andrew
>   da...@dalkescientific.com
>


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Fast similarity search

[Tim Dudgeon]

I think I recall Greg mentioning that RDKit can be used for very fast 
similarity search (e.g. all vs. all comparisons or searches against 
multi-million sized datasets).
If so, is this part the of the standard distro, or something extra 
(chemfp?).
And can it run inside the cartridge?
And any benchmarks?

Thanks
Tim


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

OK, makes sense, but I'm building on a Debian system. So neither 'yum 
install rpm-build' nor 'apt-get install rpm-build' doesn't work.


So (sorry for the stupid question) can DEBs only be built on a Debian 
based system and RPMs om a Red Hat based system?



On 15/11/2017 19:31, Paolo Tosco wrote:


Hi Tim,

It looks like you are missing the rpmbuild binary on the machine where 
you are trying to build the RPM.

Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:


So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY 
INCHI_INCLUDE_DIR)

CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR 
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb 
generated.



root@f083c3e3b6a1:/rdkit/build# cpack -G RPM
CPack: Create package using RPM
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CMake Error at /usr/share/cmake-3.7/Modules/CPackRPM.cmake:1573 
(message):

  RPM package requires rpmbuild executable
Call Stack (most recent call first):
  /usr/share/cmake-3.7/Modules/CPackRPM.cmake:2442 
(cpack_rpm_generate_package)



CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Problem compressing the directory
CPack Error: Error when generating package: RDKit


So it looks like the building the debs works OK (I didn't test them) 
but building rpms fails.


I'm probably doing something stupid here as I'm not that familiar 
with cmake and cpack.



On 10/11/2017 00:03, Francois BERENGER wrote:

On 11/08/2017 08:47 PM, Tim Dudgeon wrote:
There is mention of RPM distributions of RDKit 
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).


But on trying these:

1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.


In the bugtracker, there is an issue about the .deb:

https://github.com/rdkit/rdkit/issues/911

and there is a pull request by Patrick Avery
to fix them:

https://github.com/rdkit/rdkit/pull/1580

Maybe you can read the pull request, replace DEB by RPM and see
if that produces usable RPMs for your distro.


This is presumably no longer being maintained?
Anything that can be done to help with fixing this?

Tim


-- 


Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss





--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!http://sdm.lin

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY 
INCHI_INCLUDE_DIR)

CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR 
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb 
generated.



root@f083c3e3b6a1:/rdkit/build# cpack -G RPM
CPack: Create package using RPM
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CMake Error at /usr/share/cmake-3.7/Modules/CPackRPM.cmake:1573 (message):
  RPM package requires rpmbuild executable
Call Stack (most recent call first):
  /usr/share/cmake-3.7/Modules/CPackRPM.cmake:2442 
(cpack_rpm_generate_package)



CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Problem compressing the directory
CPack Error: Error when generating package: RDKit


So it looks like the building the debs works OK (I didn't test them) but 
building rpms fails.


I'm probably doing something stupid here as I'm not that familiar with 
cmake and cpack.



On 10/11/2017 00:03, Francois BERENGER wrote:

On 11/08/2017 08:47 PM, Tim Dudgeon wrote:
There is mention of RPM distributions of RDKit 
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).


But on trying these:

1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.


In the bugtracker, there is an issue about the .deb:

https://github.com/rdkit/rdkit/issues/911

and there is a pull request by Patrick Avery
to fix them:

https://github.com/rdkit/rdkit/pull/1580

Maybe you can read the pull request, replace DEB by RPM and see
if that produces usable RPMs for your distro.


This is presumably no longer being maintained?
Anything that can be done to help with fixing this?

Tim


-- 


Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

Thank you.
I now have RPMs built:

CPackRPM: Will use GENERATED spec file: 
/rdkit/build/_CPack_Packages/Linux/RPM/SPECS/rdkit-Runtime.spec
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.rpm generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.rpm 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.rpm 
generated.
CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.rpm 
generated.


Next, to check if they (and the DEBs) actually work!

Tim


On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


OK, makes sense, but I'm building on a Debian system. So neither 'yum 
install rpm-build' nor 'apt-get install rpm-build' doesn't work.


So (sorry for the stupid question) can DEBs only be built on a Debian 
based system and RPMs om a Red Hat based system?



On 15/11/2017 19:31, Paolo Tosco wrote:


Hi Tim,

It looks like you are missing the rpmbuild binary on the machine 
where you are trying to build the RPM.

Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:


So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:  
INCHI_LIBRARY INCHI_INCLUDE_DIR)

CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR 
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb generated.
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb generated.
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb generated.
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb generated.



root@f083c3e3b6a1:/rdkit/build# cpack -G RPM
CPack: Create package using RPM
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CMake Error at /usr/share/cmake-3.7/Modules/CPackRPM.cmake:1573 
(message):

  RPM package requires rpmbuild executable
Call Stack (most recent call first):
/usr/share/cmake-3.7/Modules/CPackRPM.cmake:2442 
(cpack_rpm_generate_package)



CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Error while execution CPackRPM.cmake
CPack Error: Problem compressing the directory
CPack Error: Error when generating package: RDKit


So it looks like the building the debs works OK (I didn't test 
them) but building rpms fails.


I'm probably doing something stupid here as I'm not that familiar 
with cmake and cpack.



On 10/11/2017 00:03, Francois BERENGER wrote:

On 11/08/2017 08:47 PM, Tim Dudgeon wrote:
There is mention of RPM distributions of RDKit 
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).


But on trying these:

1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.


In the bugtracker, there is an issue about the .deb:

https://github.com/rdkit/rdkit/issues/911

and there is a pull request by Patrick Avery
to fix them:

https://github.com/rdkit/rdkit/pull/1580

Maybe you can read the pull request, replace DEB by RPM and see
if that produces usabl

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

I see exactly the same when I build with those cmake args.


On 27/11/2017 09:11, Francois BERENGER wrote:

On 11/27/2017 06:01 PM, Tim Dudgeon wrote:

I did:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
-DCMAKE_INSTALL_PREFIX=/usr/ ..

Try this instead, just for the cmake part:

cmake -Wno-dev \
 -DRDK_INSTALL_INTREE=OFF \
 -DRDK_BUILD_INCHI_SUPPORT=ON \
 -DRDK_BUILD_AVALON_SUPPORT=ON \
 -DRDK_BUILD_PYTHON_WRAPPERS=ON \
 -DCMAKE_INSTALL_PREFIX=/usr \
 -DRDKit_VERSION=`date +%Y.%m` \
 ../

then do the rest (cpack ...) and test again
after an install of the freshly created package.

I advise to wipe out any prior rdkit install from your machine
before installing the new packages (so that we test what we intend to test).

On a Debian-like:
sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')


cpack -G DEB
cpack -G RPM


On 27/11/2017 00:05, Francois BERENGER wrote:

Hello,

What are the exact commands you used to configure and compile rdkit?

The script in there is my best attempt:

https://github.com/rdkit/rdkit/pull/1655

Regards,
F.

On 11/25/2017 12:50 AM, Tim Dudgeon wrote:

I got round to testing the debs and rpms but without success.

For the debs the following were built:

RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1.dev1-Linux-Python.deb
RDKit-2018.03.1.dev1-Linux-Runtime.deb

On a clean Ubuntu Xenial system, with just python added (apt-get -y
install python) the packages installed fine:

# dpkg -i *.deb
Selecting previously unselected package rdkit-development.
(Reading database ... 5666 files and directories currently installed.)
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
Unpacking rdkit-development (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-extras.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
Unpacking rdkit-extras (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-python.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
Unpacking rdkit-python (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-runtime.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
Unpacking rdkit-runtime (2018.03.1.dev1) ...
Setting up rdkit-development (2018.03.1.dev1) ...
Setting up rdkit-extras (2018.03.1.dev1) ...
Setting up rdkit-python (2018.03.1.dev1) ...
Setting up rdkit-runtime (2018.03.1.dev1) ...

There seem to be header files in /usr/include/rdkit and the RDKit
installation (.py and .so files) in
/usr/lib/python2.7/dist-packages/rdkit

But RDKit doesn't work from Python:

# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
    File "", line 1, in 
    File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in

  from .rdBase import rdkitVersion as __version__
ImportError: libpython2.7.so.1.0: cannot open shared object file: No
such file or directory

For the rpms the story is similar. The same 4 files are built as rpms.
Installing them on a clean centos7 machine went fine and the files seem
to get installed to the same places.
But RDKit again couldn't be used from Python, but with a different
error:

# python
Python 2.7.5 (default, Aug  4 2017, 00:39:18)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
    File "", line 1, in 
ImportError: No module named rdkit

On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:


OK, makes sense, but I'm building on a Debian system. So neither 'yum
install rpm-build' nor 'apt-get install rpm-build' doesn't work.

So (sorry for the stupid question) can DEBs only be built on a Debian
based system and RPMs om a Red Hat based system?


On 15/11/2017 19:31, Paolo Tosco wrote:

Hi Tim,

It looks like you are missing the rpmbuild binary on the machine
where you are trying to build the RPM.
Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:

So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:
INCHI_LIBRARY INCHI_INCLUDE_DIR)
CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find E

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

I got round to testing the debs and rpms but without success.

For the debs the following were built:

RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1.dev1-Linux-Python.deb
RDKit-2018.03.1.dev1-Linux-Runtime.deb

On a clean Ubuntu Xenial system, with just python added (apt-get -y 
install python) the packages installed fine:


# dpkg -i *.deb
Selecting previously unselected package rdkit-development.
(Reading database ... 5666 files and directories currently installed.)
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
Unpacking rdkit-development (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-extras.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
Unpacking rdkit-extras (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-python.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
Unpacking rdkit-python (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-runtime.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
Unpacking rdkit-runtime (2018.03.1.dev1) ...
Setting up rdkit-development (2018.03.1.dev1) ...
Setting up rdkit-extras (2018.03.1.dev1) ...
Setting up rdkit-python (2018.03.1.dev1) ...
Setting up rdkit-runtime (2018.03.1.dev1) ...

There seem to be header files in /usr/include/rdkit and the RDKit 
installation (.py and .so files) in /usr/lib/python2.7/dist-packages/rdkit


But RDKit doesn't work from Python:

# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in 


    from .rdBase import rdkitVersion as __version__
ImportError: libpython2.7.so.1.0: cannot open shared object file: No 
such file or directory

>>>


For the rpms the story is similar. The same 4 files are built as rpms.
Installing them on a clean centos7 machine went fine and the files seem 
to get installed to the same places.

But RDKit again couldn't be used from Python, but with a different error:

# python
Python 2.7.5 (default, Aug  4 2017, 00:39:18)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
  File "", line 1, in 
ImportError: No module named rdkit
>>>


On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


OK, makes sense, but I'm building on a Debian system. So neither 'yum 
install rpm-build' nor 'apt-get install rpm-build' doesn't work.


So (sorry for the stupid question) can DEBs only be built on a Debian 
based system and RPMs om a Red Hat based system?



On 15/11/2017 19:31, Paolo Tosco wrote:


Hi Tim,

It looks like you are missing the rpmbuild binary on the machine 
where you are trying to build the RPM.

Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:


So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:  
INCHI_LIBRARY INCHI_INCLUDE_DIR)

CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR 
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create packa

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

I did:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF 
-DCMAKE_INSTALL_PREFIX=/usr/ ..

cpack -G DEB
cpack -G RPM


On 27/11/2017 00:05, Francois BERENGER wrote:

Hello,

What are the exact commands you used to configure and compile rdkit?

The script in there is my best attempt:

https://github.com/rdkit/rdkit/pull/1655

Regards,
F.

On 11/25/2017 12:50 AM, Tim Dudgeon wrote:

I got round to testing the debs and rpms but without success.

For the debs the following were built:

RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1.dev1-Linux-Python.deb
RDKit-2018.03.1.dev1-Linux-Runtime.deb

On a clean Ubuntu Xenial system, with just python added (apt-get -y
install python) the packages installed fine:

# dpkg -i *.deb
Selecting previously unselected package rdkit-development.
(Reading database ... 5666 files and directories currently installed.)
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
Unpacking rdkit-development (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-extras.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
Unpacking rdkit-extras (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-python.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
Unpacking rdkit-python (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-runtime.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
Unpacking rdkit-runtime (2018.03.1.dev1) ...
Setting up rdkit-development (2018.03.1.dev1) ...
Setting up rdkit-extras (2018.03.1.dev1) ...
Setting up rdkit-python (2018.03.1.dev1) ...
Setting up rdkit-runtime (2018.03.1.dev1) ...

There seem to be header files in /usr/include/rdkit and the RDKit
installation (.py and .so files) in  /usr/lib/python2.7/dist-packages/rdkit

But RDKit doesn't work from Python:

# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
   File "", line 1, in 
   File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in

     from .rdBase import rdkitVersion as __version__
ImportError: libpython2.7.so.1.0: cannot open shared object file: No
such file or directory

For the rpms the story is similar. The same 4 files are built as rpms.
Installing them on a clean centos7 machine went fine and the files seem
to get installed to the same places.
But RDKit again couldn't be used from Python, but with a different error:

# python
Python 2.7.5 (default, Aug  4 2017, 00:39:18)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
   File "", line 1, in 
ImportError: No module named rdkit

On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:


OK, makes sense, but I'm building on a Debian system. So neither 'yum
install rpm-build' nor 'apt-get install rpm-build' doesn't work.

So (sorry for the stupid question) can DEBs only be built on a Debian
based system and RPMs om a Red Hat based system?


On 15/11/2017 19:31, Paolo Tosco wrote:

Hi Tim,

It looks like you are missing the rpmbuild binary on the machine
where you are trying to build the RPM.
Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:

So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:
INCHI_LIBRARY INCHI_INCLUDE_DIR)
CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")
Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinst

[Rdkit-discuss] Cartridge upgrades

[Tim Dudgeon]

If upgrading PostgreSQL to a new version of the RDKit cartridge is any 
maintenance needed?


Either rebuild the indexes or regenerate the fingerprints and rebuild 
the indexes?



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

Maciek

The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
The ones that are created are:

RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1-Linux-Extras.rpm
RDKit-2018.03.1.dev1-Linux-Python.rpm
RDKit-2018.03.1.dev1-Linux-Runtime.rpm

Tim


On 28/11/2017 08:48, Maciek Wójcikowski wrote:

Hi Tim and Francois,

To fix missing dependencies use "sudo apt install -f" and use "yum 
install rdkit_package_file.rpm" to install package to have all the 
dependencies.


On Debian (based systems) I prefer to install standalone packages via 
gdebi which does this automatically.



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>

2017-11-28 0:50 GMT+01:00 Francois BERENGER 
<beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>>:


    On 11/28/2017 12:42 AM, Tim Dudgeon wrote:
> I see exactly the same when I build with those cmake args.

Maybe you are missing some of the dependencies.
I don't think the packages we create have all the dependency
information:

fonts-freefont-ttf,
libboost-python1.58.0,
libboost-regex1.58.0,
libboost-system1.58.0,
libboost-thread1.58.0,
libc6 (>= 2.14),
libgcc1 (>= 1:4.1.1),
libpython2.7 (>= 2.7),
libstdc++6 (>= 5.2),
python (<< 2.8),
python (>= 2.7~)

You should install the ones you are missing and test again.

> On 27/11/2017 09:11, Francois BERENGER wrote:
>> On 11/27/2017 06:01 PM, Tim Dudgeon wrote:
>>> I did:
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
>>> -DCMAKE_INSTALL_PREFIX=/usr/ ..
>> Try this instead, just for the cmake part:
>>
>> cmake -Wno-dev \
>>  -DRDK_INSTALL_INTREE=OFF \
>>  -DRDK_BUILD_INCHI_SUPPORT=ON \
>>  -DRDK_BUILD_AVALON_SUPPORT=ON \
>>  -DRDK_BUILD_PYTHON_WRAPPERS=ON \
>>  -DCMAKE_INSTALL_PREFIX=/usr \
>>  -DRDKit_VERSION=`date +%Y.%m` \
>>  ../
>>
>> then do the rest (cpack ...) and test again
>> after an install of the freshly created package.
>>
>> I advise to wipe out any prior rdkit install from your machine
>> before installing the new packages (so that we test what we
intend to
>> test).
>>
>> On a Debian-like:
>> sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')
>>
>>> cpack -G DEB
>>> cpack -G RPM
>>>
>>>
>>> On 27/11/2017 00:05, Francois BERENGER wrote:
>>>> Hello,
>>>>
>>>> What are the exact commands you used to configure and compile
rdkit?
>>>>
>>>> The script in there is my best attempt:
>>>>
>>>> https://github.com/rdkit/rdkit/pull/1655
<https://github.com/rdkit/rdkit/pull/1655>
>>>>
>>>> Regards,
>>>> F.
>>>>
>>>> On 11/25/2017 12:50 AM, Tim Dudgeon wrote:
>>>>> I got round to testing the debs and rpms but without success.
>>>>>
>>>>> For the debs the following were built:
>>>>>
>>>>> RDKit-2018.03.1.dev1-Linux-Development.deb
>>>>> RDKit-2018.03.1.dev1-Linux-Extras.deb
>>>>> RDKit-2018.03.1.dev1-Linux-Python.deb
>>>>> RDKit-2018.03.1.dev1-Linux-Runtime.deb
>>>>>
>>>>> On a clean Ubuntu Xenial system, with just python added
(apt-get -y
>>>>> install python) the packages installed fine:
>>>>>
>>>>> # dpkg -i *.deb
>>>>> Selecting previously unselected package rdkit-development.
>>>>> (Reading database ... 5666 files and directories currently
installed.)
>>>>> Preparing to unpack
RDKit-2018.03.1.dev1-Linux-Development.deb ...
>>>>> Unpacking rdkit-development (2018.03.1.dev1) ...
>>>>> Selecting previously unselected package rdkit-extras.
>>>>> Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
>>>>> Unpacking rdkit-extras (2018.03.1.dev1) ...
>>>>> Selecting previously unselected package rdkit-python.
>>>>> Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
>>>>> Unpacking rdkit-python (2018.03.1.dev1) ...
>>>>> Selecting previously unselected package rdkit-runtime.
>>>>> Preparing to unpack

Re: [Rdkit-discuss] RDkit and Pubchem

[Tim Dudgeon]

In what way? Given a single PubChem compound or substance ID you just 
want to pull the smiles or molfile into RDKit?


Tim

On 01/12/17 17:26, Sundar wrote:

Hi RDkit users,

I was wondering if RDkit has a means of downloading compounds from 
Pubchem.

Also let me other ways that helps here.

Thanks,
Jubi


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

[Tim Dudgeon]

I've got some dockerfiles that might be worth a look.
https://github.com/InformaticsMatters/docker_jupyter

Not sure if they will help.

Tim



On 21/11/2017 15:25, JP wrote:

Yo RDKitters,

I am running a CADD workshop for a group of MSc students and would 
like to show them some some RDKit awesomeness.


I thought the best way to do this is to use an rdkit enabled docker 
image + jupyter notebooks (they are comfortable with python).


In preparation, I tried building the docker image from the docker file 
at 
https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3 
but this fails on Ubuntu 16.04.3 LTS with the following error:


$ docker build -t run_rdkit_conda 
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
Downloading build context from remote url: 
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile 
   357B

Sending build context to Docker daemon  2.048kB
Step 1/7 : FROM continuumio/miniconda3
latest: Pulling from continuumio/miniconda3
85b1f47fba49: Pull complete
6b3cb0c49789: Pull complete
fecb432dacf0: Pull complete
f461f7e3890d: Pull complete
Digest: 
sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc

Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> f700f7f570c7
Step 2/7 : MAINTAINER Greg Landrum >

 ---> Running in ad6a648c18ba
 ---> 18e6d6093d5b
Removing intermediate container ad6a648c18ba
Step 3/7 : ENV PATH /opt/conda/bin:$PATH
 ---> Running in e21cf8e5332f
 ---> ddef65292068
Removing intermediate container e21cf8e5332f
Step 4/7 : ENV LANG C
 ---> Running in efa12ef17f37
 ---> 137d7e20350d
Removing intermediate container efa12ef17f37
Step 5/7 : RUN conda config --add channels 
https://conda.anaconda.org/rdkit

 ---> Running in 79566bf4b6e9
 ---> 032965875391
Removing intermediate container 79566bf4b6e9
Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
 ---> Running in c5aa6417a63a
Fetching package metadata .
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in 
conflict:

  - cairocffi -> python 3.5* -> xz 5.0.5
  - python 3.6*
Use "conda info " to see the dependencies for each package.

The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo 
cairocffi jupyter' returned a non-zero code: 1


Any ideas?
JP


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Error when installing cartridge on postgres DB 95

[Tim Dudgeon]

I just hit the same problem.

Setup:

- Centos7 with postgres already present.
- Install miniconda
- conda install -y -c rdkit rdkit-postgres95

The install ran OK with no errors. However I notice that it states that 
these packages are installed:


  rdkit: 2017.09.1-py27_1 rdkit
  rdkit-postgresql95: 2016.09.4-py27_1 rdkit

Note that the versions are different. Is this expected?

Then when I run:
psql -c 'create extension rdkit' mydatabase
I get:
ERROR: could not open extension control file 
"/opt/rh/rh-postgresql95/root/usr/share/pgsql/extension/rdkit.control": 
No such file or directory


And indeed there is no such file. A search of the filesystem shows that 
file is only present within the miniconda2 directory, so it seems that 
the cartridge extensions were not deployed correctly.


The same happens if I try to use the rdkit-postgresql RPM packages.

Tim


On 28/10/2017 16:06, Drew Gibson via Rdkit-discuss wrote:

Hello,

I have installed anaconda3 on Ubuntu 16.04.3 LTS, and have installed 
the |rdkit-postgresql95 |

conda environment.

When trying to install the cartridge on a new db, I get the message -

ERROR:  could not open extension control file 
"/home/drew/anaconda3/envs/rdkit/share/postgresql/extension/rdkit.control": 
No such file or directory


Sequence of commands to install and set-up (error occurs after the 
last command)...
NB, when I do the following with the standard rdkit-postgresql 
package, I don't get the error.


// having installed anaconda3, install the rdkit-postgresql95 conda 
environment

//    rdkit:  2017.09.1-py35_1   rdkit
//    rdkit-postgresql95: 2016.09.4-py35_1   rdkit
conda create -c rdkit -n rdkit rdkit-postgresql95


// create the directory for postgres data
mkdir ~/anaconda3/envs/rdkit/pgdata


// activate the environment
source activate rdkit


// navigate to the /bin directory
cd ~/anaconda3/envs/rdkit/bin


// run initdb
./initdb ~/anaconda3/envs/rdkit/pgdata


// initdb creates postgres.conf in the /pgdata folder -
// we can now edit to rdkit recommended settings.

    "To improve performance while loading the database and building 
the index, I changed a

    couple of postgres configuration settings in postgresql.conf :"
        synchronous_commit = off    # immediate fsync at commit
        full_page_writes = off        # recover from partial page writes

    "And to improve search performance, I allowed postgresql to use 
more memory than the

    extremely conservative default settings:"
        shared_buffers = 2048MB        # min 128kB (change requires 
restart)

        work_mem = 128MB        # min 64kB


// reboot (to new config), activate the environment then start the DB 
server from /bin

./pg_ctl -D /home/drew/anaconda3/envs/rdkit/pgdata -l logfile start


// navigate to the /bin directory and create chembl DB
./createdb chembl_23


// back out to command line and setup rdkit cartridge on db
./psql -c 'create extension rdkit' chembl_23


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] RPM distros

[Tim Dudgeon]

There is mention of RPM distributions of RDKit 
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).


But on trying these:

1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.

This is presumably no longer being maintained?
Anything that can be done to help with fixing this?

Tim


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

Not sure how best to do this.
This issue (https://github.com/rdkit/rdkit/issues/911) is closed, and 
only partly relevant.


I'm happy to open a new issue to handle the CMake/CPack stuff for both 
deb and rpm, but not sure is that is really the way to go, considering 
Gianluca's comments.


What I would like to see is a standard way to build debs and rpms from 
source, including packages for cartridge and binding for Python and 
Java. I'm happy to help with this, but low level build stuff is not my 
expertise. My prime motivation for this is in generating lighter weight 
Docker images.


Tim


On 04/12/17 00:16, Francois BERENGER wrote:

Please report your problems in the rdkit bugtracker.

What you do exactly to test, on which distro, etc.

If you don't, this issue will be forgotten.

Regards,
F.

On 12/02/2017 02:53 AM, Tim Dudgeon wrote:

Read back to the top of this thread for all the details, but the key bit
is this:


In the bugtracker, there is an issue about the .deb:

https://github.com/rdkit/rdkit/issues/911

and there is a pull request by Patrick Avery
to fix them:

https://github.com/rdkit/rdkit/pull/1580

Tim



On 01/12/17 17:51, Gianluca Sforna wrote:

On Fri, Dec 1, 2017 at 6:04 PM, Tim Dudgeon <tdudgeon...@gmail.com>
wrote:

Maciek

The 'cpack -G RPM' command does not seem to create a
rdkit_package_file.rpm.
The ones that are created are:

RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1-Linux-Extras.rpm
RDKit-2018.03.1.dev1-Linux-Python.rpm
RDKit-2018.03.1.dev1-Linux-Runtime.rpm

Sorry guys, I got back on the list mid-thread so I really need to ask:
is there a reason why you are trying to use cpack to build RPMs,
instead of the standard rpmbuild tools?






--

Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Cartridge upgrades

[Tim Dudgeon]

Thanks Greg.
I hit some strange problems with similarity search not working after an 
upgrade (SSS seemed OK). I never really got to the bottom of this as I 
managed to solve it by deleting the RDKit artifacts from the database 
and dropping and reinstalling the cartridge and after that all works fine.



On 05/12/17 07:18, Greg Landrum wrote:


On Fri, Dec 1, 2017 at 7:24 PM, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


If upgrading PostgreSQL to a new version of the RDKit cartridge is
any maintenance needed?

Either rebuild the indexes or regenerate the fingerprints and
rebuild the indexes?


It depend on the release. Usually you don't need to, but there are 
cases where it's required.

I normally try to capture this in the release notes.
For example, this was in the *important* section of the 2017.03.1 
release notes:


- The fix for bug #879 changes the definition of the layered
fingerprint.
  This means that all database columns using layered fingerprints
as well as
  all substructure search indices should be rebuilt.


Having said that, bug fixes that affect things like aromaticity 
perception could change some fingerprints and I don't always think to 
capture a specific note about changing fingerprints in these cases.


It's generally a good idea to go through the release notes before an 
upgrade in any case.


If the database isn't too big, regenerating fingerprints and indices 
isn't a terrible idea... just to be safe. :-)


-greg




--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

Francois,

I'm assuming you are meaning to install those packages on the debian 
system prior to installing the RDKit-2018.03.1.dev1-Linux-*.deb files.


Unfortunately that didn't help.

Tim

On 27/11/2017 23:50, Francois BERENGER wrote:

On 11/28/2017 12:42 AM, Tim Dudgeon wrote:

I see exactly the same when I build with those cmake args.

Maybe you are missing some of the dependencies.
I don't think the packages we create have all the dependency information:

fonts-freefont-ttf,
libboost-python1.58.0,
libboost-regex1.58.0,
libboost-system1.58.0,
libboost-thread1.58.0,
libc6 (>= 2.14),
libgcc1 (>= 1:4.1.1),
libpython2.7 (>= 2.7),
libstdc++6 (>= 5.2),
python (<< 2.8),
python (>= 2.7~)

You should install the ones you are missing and test again.


On 27/11/2017 09:11, Francois BERENGER wrote:

On 11/27/2017 06:01 PM, Tim Dudgeon wrote:

I did:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
-DCMAKE_INSTALL_PREFIX=/usr/ ..

Try this instead, just for the cmake part:

cmake -Wno-dev \
  -DRDK_INSTALL_INTREE=OFF \
  -DRDK_BUILD_INCHI_SUPPORT=ON \
  -DRDK_BUILD_AVALON_SUPPORT=ON \
  -DRDK_BUILD_PYTHON_WRAPPERS=ON \
  -DCMAKE_INSTALL_PREFIX=/usr \
  -DRDKit_VERSION=`date +%Y.%m` \
  ../

then do the rest (cpack ...) and test again
after an install of the freshly created package.

I advise to wipe out any prior rdkit install from your machine
before installing the new packages (so that we test what we intend to
test).

On a Debian-like:
sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')


cpack -G DEB
cpack -G RPM


On 27/11/2017 00:05, Francois BERENGER wrote:

Hello,

What are the exact commands you used to configure and compile rdkit?

The script in there is my best attempt:

https://github.com/rdkit/rdkit/pull/1655

Regards,
F.

On 11/25/2017 12:50 AM, Tim Dudgeon wrote:

I got round to testing the debs and rpms but without success.

For the debs the following were built:

RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1.dev1-Linux-Python.deb
RDKit-2018.03.1.dev1-Linux-Runtime.deb

On a clean Ubuntu Xenial system, with just python added (apt-get -y
install python) the packages installed fine:

# dpkg -i *.deb
Selecting previously unselected package rdkit-development.
(Reading database ... 5666 files and directories currently installed.)
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
Unpacking rdkit-development (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-extras.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
Unpacking rdkit-extras (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-python.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
Unpacking rdkit-python (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-runtime.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
Unpacking rdkit-runtime (2018.03.1.dev1) ...
Setting up rdkit-development (2018.03.1.dev1) ...
Setting up rdkit-extras (2018.03.1.dev1) ...
Setting up rdkit-python (2018.03.1.dev1) ...
Setting up rdkit-runtime (2018.03.1.dev1) ...

There seem to be header files in /usr/include/rdkit and the RDKit
installation (.py and .so files) in
/usr/lib/python2.7/dist-packages/rdkit

But RDKit doesn't work from Python:

# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
     File "", line 1, in 
     File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line
2, in

   from .rdBase import rdkitVersion as __version__
ImportError: libpython2.7.so.1.0: cannot open shared object file: No
such file or directory

For the rpms the story is similar. The same 4 files are built as rpms.
Installing them on a clean centos7 machine went fine and the files
seem
to get installed to the same places.
But RDKit again couldn't be used from Python, but with a different
error:

# python
Python 2.7.5 (default, Aug  4 2017, 00:39:18)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import rdkit

Traceback (most recent call last):
     File "", line 1, in 
ImportError: No module named rdkit

On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:


OK, makes sense, but I'm building on a Debian system. So neither
'yum
install rpm-build' nor 'apt-get install rpm-build' doesn't work.

So (sorry for the stupid question) can DEBs only be built on a
Debian
based system and RPMs om a Red Hat based system?


On 15/11/2017 19:31, Paolo Tosco wrote:

Hi Tim,

It looks 

Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

Read back to the top of this thread for all the details, but the key bit 
is this:



In the bugtracker, there is an issue about the .deb:

https://github.com/rdkit/rdkit/issues/911

and there is a pull request by Patrick Avery
to fix them:

https://github.com/rdkit/rdkit/pull/1580


Tim



On 01/12/17 17:51, Gianluca Sforna wrote:

On Fri, Dec 1, 2017 at 6:04 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:

Maciek

The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
The ones that are created are:

RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1-Linux-Extras.rpm
RDKit-2018.03.1.dev1-Linux-Python.rpm
RDKit-2018.03.1.dev1-Linux-Runtime.rpm


Sorry guys, I got back on the list mid-thread so I really need to ask:
is there a reason why you are trying to use cpack to build RPMs,
instead of the standard rpmbuild tools?







--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Building DEB and RPM packages for cartridge

[Tim Dudgeon]

As some of you will know I am creating various Docker images for RDKit. 
See [1] and [2] if you want to know more.


The key to these is building RPM and DEB packages using `cpack`.
This is mostly working pretty well as you will see in those links.

Now I'm wanting to extend this to building images for the postgres 
cartridge and I'm at a point where I'm stuck and would welcome some advice.


I just modified the build process on Debian [3] to include the postgres 
packages and the add the options to cmake for building the cartridge. 
That all went OK and I end up with a functioning cartridge.


The key part of the Dockerfile looks like this:

RUN cmake -Wno-dev\
  -DRDK_INSTALL_INTREE=OFF\
  -DRDK_BUILD_INCHI_SUPPORT=ON\
  -DRDK_BUILD_AVALON_SUPPORT=ON\
  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
  -DRDK_BUILD_SWIG_WRAPPERS=ON\
  -DRDK_BUILD_PGSQL=ON\
  -DPostgreSQL_ROOT=/usr/lib/postgresql/10\
-DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/10/server\
  -DCMAKE_INSTALL_PREFIX=/usr\
  ..

RUN nproc=$(getconf _NPROCESSORS_ONLN)\
  && make -j $(( nproc > 2 ? nproc - 2 : 1 ))\
  && make install\
  && sh Code/PgSQL/rdkit/pgsql_install.sh\
  && cpack -G DEB\
  && cpack -G RPM

But what I was hoping is that cpack would magically create DEB and RPM 
packages for postgres for me, but that does not seem to be the case. If 
only life were so simple:-)


I know there are processes in place that can build these packages for 
cartridge (certainly for Centos) but it's not obvious to me how these 
work and whether this is in any way related to the way that cpack is 
being used here.


Can anyone shed any light on this?

Thanks
Tim

[1] https://github.com/InformaticsMatters/docker-rdkit
[2] https://www.informaticsmatters.com/category/containers/index.html
[3] 
https://github.com/InformaticsMatters/docker-rdkit/blob/master/Dockerfile-build-debian



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Diversity picker

[Tim Dudgeon]

I think the MaxMinPicker can do what you want.
A blog on using this can be found here: 
https://rdkit.blogspot.co.uk/2017/11/revisting-maxminpicker.html



On 03/01/18 19:53, Sundar wrote:

Hi RDKit users,

Is it possible to pick a subset of (diverse) compounds that have less 
than a particular Tanimoto coefficient (for eg. 0.7) from a larger set 
using RDKit.
The current version of the Diverse Picker picks a diverse set based on 
a "number of compounds" instead of Tanimoto score.


Thanks
Jubilant


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[Tim Dudgeon]

Incorporating and "industrialising" Matt's MolVS tautomer and 
standardizer code?

http://molvs.readthedocs.io/en/latest/index.html


On 15/01/18 07:09, Greg Landrum wrote:

Dear all,

We've been invited again to participate in the OpenChemistry 
application for Google Summer of Code.


In order to participate we need ideas for projects and mentors to go 
along with them.


The current list of RDKit ideas is being maintained here:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of 
last year's project ideas).


If you're willing to be a mentor (please ask me about the ~5 
hours/week required here) or have ideas, please reply to this thread.


Best,
-greg


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[Tim Dudgeon]

Agreed. Good support for reading and writing mol2 format would indeed be 
useful.

But not convinced this alone is sexy enough for GSoC.
Could there be something in a more general project to bridge the 
compound (mol/smiles), sequence (protein/nucleotide seq + alignments) 
and structure (pdb/mmcif/mmtf) worlds?
OK, so that's far too much to ask for, but is there something that could 
be plucked out from there that is useful and achievable?


Tim


On 15/01/18 09:19, Greg Landrum wrote:



On Mon, Jan 15, 2018 at 9:50 AM, Francois BERENGER 
> wrote:


Supporting mol2 files as input would be nice.


Do you mean as output? You can already (in a limited way) read them.
-greg


There is already some code out there, people have worked on it and
several people would like to have the feature...

On 01/15/2018 04:09 PM, Greg Landrum wrote:
> Dear all,
>
> We've been invited again to participate in the OpenChemistry
application
> for Google Summer of Code.
>
> In order to participate we need ideas for projects and mentors to go
> along with them.
>
> The current list of RDKit ideas is being maintained here:
>
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

>
> (Note: at the point that I'm pressing "send", that's still a copy of
> last year's project ideas).
>
> If you're willing to be a mentor (please ask me about the ~5
hours/week
> required here) or have ideas, please reply to this thread.
>
> Best,
> -greg
>
>
>

--
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net

> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

>


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss





--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

[Tim Dudgeon]

Yes, I was referring to the online docs.


On 06/04/18 05:19, Greg Landrum wrote:

Tim: where did you see the mention of cmake 2.6?
The docs that are part of the source tree have already been updated to 
mention that cmake 3.1 or newer is required:

https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md
maybe you're looking at the online docs? I don't update those for the 
beta releases, so those still correspond to the previous version.



I'd like to be sure I didn't miss anything else.

-greg



On Thu, Apr 5, 2018 at 5:52 PM, Greg Landrum <greg.land...@gmail.com 
<mailto:greg.land...@gmail.com>> wrote:


Yeah, thats another change that has been made. I will update the docs.

Thanks for pointing out the oversight

-greg

On Thu, 5 Apr 2018 at 17:30, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:

Greg,

Does this explain problems I'm seeing with building on Centos:

From the current docs:
cmake. You need version 2.6 (or more recent)

With a current centos7 distro after a `yum install cmake`

# cmake --version
cmake version 2.8.12.2

When you build from current master branch you get this error:

CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1 or higher is required.  You are running version
2.8.12.2

This is not seen when you build from the Release_2017_09_2 branch.

Tim




On 04/04/18 04:23, Greg Landrum wrote:


NOTE: If you don't work with the RDKit at the C++ level or
build the code yourself from source, you probably don't need
to read this email.

TL;DR: When we do the beta for the 2018.03.1 release we're
going to switch the C++ backend to use modern C++ (=C++11).
For people who can't switch to use that code, we will
continue to provide bug fixes for the 2017.09 release for at
least another 6 months.

--
# What's happening?

As part of the upcoming 2018.03 release, we will start using
modern C++ for the RDKit - this means C++11 at the moment,
the goal is that you should be able to build the code with
g++ v4.8. I've been talking about this for a while, blogged
about it
(https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218

<https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218>),
and posted to the rdkit-devel list
(https://sourceforge.net/p/rdkit/mailman/message/35811216/
<https://sourceforge.net/p/rdkit/mailman/message/35811216/>),
now it's finally happening.

Concretely what this means in github is that the current
master branch will be renamed to legacy and the modern_cxx
branch will be renamed to master.

# Who does this affect?

This should only affect people who need to build the RDKit
C++ code themselves. If you use a binary version of the RDKit
like the ones available inside of Anaconda Python or KNIME,
this change should have no impact upon you.

# What about people who can't use up-to-date compilers?

We realize that some people on older operating systems will
not be able to switch to start using a compiler that supports
C++11. In order to continue to support this subset of
developers, we will continue to apply bug fixes to the
current Release_2017_09 branch and do occasional patch
releases. Since this is intended for people who need to build
the code themselves anyway, we won't do builds of these
releases any more.

We will keep doing these patch release at least until the
2018.09 release. Whether or not we continue past that date
will depend on demand, so if you are using these releases
please let us know.

# Why are you doing this?

There's a long, rambling answer to this, but I'm not going to
give it here. :-)
The simplest explanation is that we think that the core of
the RDKit should be using a modern and (reasonably)
up-to-date version of the language that it's written in. The
developer experience is better and, happily, the code ends up
being faster.






--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<https://lists

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

[Tim Dudgeon]

So that means its not easy to build on a up to date centos (and maybe 
most other Red Hat based) distros?
You would need to install a newer version of cmake from some other 
source e.g https://cmake.org/ ?



On 05/04/18 16:52, Greg Landrum wrote:

Yeah, thats another change that has been made. I will update the docs.

Thanks for pointing out the oversight

-greg

On Thu, 5 Apr 2018 at 17:30, Tim Dudgeon <tdudgeon...@gmail.com 
<mailto:tdudgeon...@gmail.com>> wrote:


Greg,

Does this explain problems I'm seeing with building on Centos:

From the current docs:
cmake. You need version 2.6 (or more recent)

With a current centos7 distro after a `yum install cmake`

# cmake --version
cmake version 2.8.12.2

When you build from current master branch you get this error:

CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1 or higher is required.  You are running version 2.8.12.2

This is not seen when you build from the Release_2017_09_2 branch.

Tim




On 04/04/18 04:23, Greg Landrum wrote:


NOTE: If you don't work with the RDKit at the C++ level or build
the code yourself from source, you probably don't need to read
this email.

TL;DR: When we do the beta for the 2018.03.1 release we're going
to switch the C++ backend to use modern C++ (=C++11). For people
who can't switch to use that code, we will continue to provide
bug fixes for the 2017.09 release for at least another 6 months.

--
# What's happening?

As part of the upcoming 2018.03 release, we will start using
modern C++ for the RDKit - this means C++11 at the moment, the
goal is that you should be able to build the code with g++ v4.8.
I've been talking about this for a while, blogged about it
(https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218),
and posted to the rdkit-devel list
(https://sourceforge.net/p/rdkit/mailman/message/35811216/), now
it's finally happening.

Concretely what this means in github is that the current master
branch will be renamed to legacy and the modern_cxx branch will
be renamed to master.

# Who does this affect?

This should only affect people who need to build the RDKit C++
code themselves. If you use a binary version of the RDKit like
the ones available inside of Anaconda Python or KNIME, this
change should have no impact upon you.

# What about people who can't use up-to-date compilers?

We realize that some people on older operating systems will not
be able to switch to start using a compiler that supports C++11.
In order to continue to support this subset of developers, we
will continue to apply bug fixes to the current Release_2017_09
branch and do occasional patch releases. Since this is intended
for people who need to build the code themselves anyway, we won't
do builds of these releases any more.

We will keep doing these patch release at least until the 2018.09
release. Whether or not we continue past that date will depend on
demand, so if you are using these releases please let us know.

# Why are you doing this?

There's a long, rambling answer to this, but I'm not going to
give it here. :-)
The simplest explanation is that we think that the core of the
RDKit should be using a modern and (reasonably) up-to-date
version of the language that it's written in. The developer
experience is better and, happily, the code ends up being faster.






--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!
http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

[Tim Dudgeon]

Greg,

Does this explain problems I'm seeing with building on Centos:

From the current docs:
cmake. You need version 2.6 (or more recent)

With a current centos7 distro after a `yum install cmake`

# cmake --version
cmake version 2.8.12.2

When you build from current master branch you get this error:

CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1 or higher is required.  You are running version 2.8.12.2

This is not seen when you build from the Release_2017_09_2 branch.

Tim




On 04/04/18 04:23, Greg Landrum wrote:


NOTE: If you don't work with the RDKit at the C++ level or build the 
code yourself from source, you probably don't need to read this email.


TL;DR: When we do the beta for the 2018.03.1 release we're going to 
switch the C++ backend to use modern C++ (=C++11). For people who 
can't switch to use that code, we will continue to provide bug fixes 
for the 2017.09 release for at least another 6 months.


--
# What's happening?

As part of the upcoming 2018.03 release, we will start using modern 
C++ for the RDKit - this means C++11 at the moment, the goal is that 
you should be able to build the code with g++ v4.8. I've been talking 
about this for a while, blogged about it 
(https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218 
), 
and posted to the rdkit-devel list 
(https://sourceforge.net/p/rdkit/mailman/message/35811216/ 
), now it's 
finally happening.


Concretely what this means in github is that the current master branch 
will be renamed to legacy and the modern_cxx branch will be renamed to 
master.


# Who does this affect?

This should only affect people who need to build the RDKit C++ code 
themselves. If you use a binary version of the RDKit like the ones 
available inside of Anaconda Python or KNIME, this change should have 
no impact upon you.


# What about people who can't use up-to-date compilers?

We realize that some people on older operating systems will not be 
able to switch to start using a compiler that supports C++11. In order 
to continue to support this subset of developers, we will continue to 
apply bug fixes to the current Release_2017_09 branch and do 
occasional patch releases. Since this is intended for people who need 
to build the code themselves anyway, we won't do builds of these 
releases any more.


We will keep doing these patch release at least until the 2018.09 
release. Whether or not we continue past that date will depend on 
demand, so if you are using these releases please let us know.


# Why are you doing this?

There's a long, rambling answer to this, but I'm not going to give it 
here. :-)
The simplest explanation is that we think that the core of the RDKit 
should be using a modern and (reasonably) up-to-date version of the 
language that it's written in. The developer experience is better and, 
happily, the code ends up being faster.






--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Docker image for GSOC2018_MolVS_Integration

[Tim Dudgeon]

I was very happy to hear about the integration of MolVS into RDKit core 
in the talk by Susan Leung at the recent UGM.


https://github.com/rdkit/UGM_2018/blob/master/Presentations/Leung_GSoC_RDKit-MolVS_Integration.pdf
This is going to be incredibly useful once it gets released.

To help with testing of this I have created a Docker image based on the 
code on Susan's fork 
(https://github.com/susanhleung/rdkit/tree/dev/GSOC2018_MolVS_Integration) 
which I believe is what is used for the PR on the RDKit repo 
(https://github.com/rdkit/rdkit/pull/2002).


I will try to keep this updated at suitable intervals until the code is 
merged into the main RDKit repo.


To run the Docker image try something like this:

$ docker run -it --rm 
informaticsmatters/rdkit-python-debian:standardizer python

Python 2.7.15+ (default, Aug 31 2018, 11:56:52)
[GCC 8.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
>>> from rdkit.Chem.MolStandardize import rdMolStandardize
>>> m = 
rdMolStandardize.StandardizeSmiles('[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1')

[09:18:41] Initializing MetalDisconnector
[09:18:41] Running MetalDisconnector
[09:18:41] Removed covalent bond between Na and O
[09:18:41] Initializing Normalizer
[09:18:41] Running Normalizer
[09:18:41] Rule applied: SulfonetoS(=O)(=O)
>>> m
'O=C([O-])c1ccc(C[S](=O)=O)cc1.[Na+]'
>>>



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] 答复: Generating R-group representation

[Tim Dudgeon]

Hi Hongbin,

Thanks for that. It helped me track down part of the solution using 
rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition


See https://gist.github.com/tdudgeon/d29dea62540b4eb017d68250bca5d38f

But I'm still not quite there. I have a SMARTS but I want a real SMILES 
(see bottom of the notebook).
I think I sort of know how this could be done longhand, but suspect 
there's a real simple way!


Tim

On 27/08/2019 03:56, Hongbin Yang wrote:


Hi Tim,

Greg posted a gist on how to generate R-group matrices shortly before.

https://sourceforge.net/p/rdkit/mailman/message/36744886/

Does it help?

Hongbin Yang

*发件人: *Tim Dudgeon <mailto:tdudgeon...@gmail.com>
*发送时间: *2019年8月26日21:08
*收件人: *rdkit-discuss@lists.sourceforge.net 
<mailto:rdkit-discuss@lists.sourceforge.net>

*主题: *[Rdkit-discuss] Generating R-group representation

I have a set of molecules that share a common scaffold and differ by

substitution at a small number of sites (typically one or two).

I'd like to generate a generic R-group molecule that summarises the

molecules (e.g. showing the scaffold with the sites of substitution as

R1, R2 etc.).

Finding the MCS of such a set of molecules with RDKit seems straight

forward, but the output of that is a SMARTS expression for the MCS.

Does anyone have any examples (or hints) of using this to generate a

R-group representation?

Tim

___

Rdkit-discuss mailing list

Rdkit-discuss@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Xenon atoms have hydrogen added

[Tim Dudgeon]

Rocco,

Great. You nailed it!

Many thanks.

Tim

On 04/09/2019 17:41, Rocco Moretti wrote:
I think the issue is that you're making an explicit bond to a Xenon 
atom, and Xenon's valence model in the RDKit says that it has either 
zero bond or it has two bonds. (Don't worry - it's not really 
something you should have known /a priori /- valence models are funky. 
<https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/>) 



list( Chem.GetPeriodicTable().GetValenceList("Xe") ) # Returns [0, 2]

Since you have at least one bond to Xenon (to the carbon), you can't 
have zero bonds, so you must have two bonds, so RDKit fills in the 
missing valence with an implicit hydrogen:


atom.GetTotalValence() # returns 2
atom.GetNumImplicitHs() # returns 1

The hydrogen is implicit, so removing the hydrogens with 
Chem.RemoveHs() won't do anything.


This then interacts with the Smiles code. The Smiles model says that 
if you have an atom in brackets (which Xenon always is), you need to 
explicitly record the hydrogens it has. (See here 
<https://baoilleach.blogspot.com/2017/01/counting-hydrogens-in-smiles-string.html 
> for more.)


Ways around it: The easiest would be if you could change your element 
to something which takes a single valence, or something that doesn't 
have valences for implicit hydrogen purposes. (Astatine is a decent 
choice for the former, many of the the actinides work well for the 
latter.) If you really do want to use Xenon, you can always manually 
flag the atom to not have any implicit hydrogens.*

*
*
*
*...*
xe = Chem.Atom(54) # 54 is Xenon
*xe.SetNoImplicit(True)*
idx = mw.AddAtom(xe)
mw.AddBond(0,6,Chem.BondType.SINGLE)
Chem.SanitizeMol(mw)
atom = mw.GetAtomWithIdx(idx)
atom.GetExplicitValence() # returns 1
atom.GetTotalValence() *# returns 1*
atom.GetNumImplicitHs() *# returns 0***
Chem.MolToSmiles(mw) *# returns '[Xe]c1c1'*

On Wed, Sep 4, 2019 at 9:35 AM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:


I'm finding that if I add a Xenon atom to a molecule it seems to
get an
unwanted hydrogen added to it.
Example notebook here:
https://gist.github.com/tdudgeon/ba3497341d9de95b4d78f3e5ed9fc0f7

Basic code is like this:

from rdkit import Chem
m = Chem.MolFromSmiles("c1c1")
mw = Chem.RWMol(m)
xe = Chem.Atom(54) # 54 is Xenon
idx = mw.AddAtom(xe)
mw.AddBond(0,6,Chem.BondType.SINGLE)
Chem.SanitizeMol(mw)
atom = mw.GetAtomWithIdx(idx)
atom.GetExplicitValence() # returns 1
Chem.MolToSmiles(mw) # returns [XeH]c1c1, expecting [Xe]c1c1

Even if I do a Chem.RemoveHs() the H remains.

Any ideas why and how to fix?





___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Xenon atoms have hydrogen added

[Tim Dudgeon]

I'm finding that if I add a Xenon atom to a molecule it seems to get an 
unwanted hydrogen added to it.
Example notebook here: 
https://gist.github.com/tdudgeon/ba3497341d9de95b4d78f3e5ed9fc0f7


Basic code is like this:

from rdkit import Chem
m = Chem.MolFromSmiles("c1c1")
mw = Chem.RWMol(m)
xe = Chem.Atom(54) # 54 is Xenon
idx = mw.AddAtom(xe)
mw.AddBond(0,6,Chem.BondType.SINGLE)
Chem.SanitizeMol(mw)
atom = mw.GetAtomWithIdx(idx)
atom.GetExplicitValence() # returns 1
Chem.MolToSmiles(mw) # returns [XeH]c1c1, expecting [Xe]c1c1

Even if I do a Chem.RemoveHs() the H remains.

Any ideas why and how to fix?





___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] The "maxAttempts" option in "EmbedMultipleConfs"

[Tim Dudgeon]

This is in regard to the pruneRmsThresh option which removes very 
similar conformers.
If let's say numConfs is set to 10 and maxAttempts is set to 20 then it 
will use UP TO 20 attempts to generate 10 conformers.
If too many conformers get rejected due to pruneRmsThresh then you will 
end up with less than 10 conformers.


Or to put it another way, maxAttempts avoids you trying for ever to 
generate conformers that are all the same and getting rejected!


Tim

On 17/12/2019 16:24, topgunhaides . wrote:

Hi guys,

Can anyone tell me more about the "maxAttempts" option in 
"EmbedMultipleConfs"?


In the documentation, it says " maxAttempts: the maximum number of 
attempts to try embedding".
Dose it mean the "maximum number of attempts" to generate each 
conformer or to generate the total number of conformers specified by 
"numConfs"? Or something else?
I need to generate a huge amount of conformers for each molecule, so I 
want to know what is the proper "maxAttempts" to reach a balance 
between accuracy and cost.

Thank you!

Best,
Leon




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] The "maxAttempts" option in "EmbedMultipleConfs"

[Tim Dudgeon]

AFAIK the only correlation is the molecule(s) you are "conformering" (is 
that a verb?).


And no number of numConfs can be considered enough, let alone a number 
of maxAttempts.
It  depends on the problem you are wanting to solve, the molecules you 
are looking at, and the amount of CPU you have to crack that particular nut.


I tend to use 1.5x - 2.0x but for a set of (fairly small) molecules.
If your molecules are more flexible then you maybe you need to go 10x.

Tim

On 17/12/2019 19:57, topgunhaides . wrote:

Hi Tim,

Many thanks for your help! One further question:
Is there any correlation between the maxAttempts and numConfs?
For instance, do I need to set a higher maxAttempts value if I request 
a higher numConfs value?


Or to put it another way, what maxAttempts value can be considered as 
"enough"?

Best,
Leon





On Tue, Dec 17, 2019 at 12:22 PM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:


This is in regard to the pruneRmsThresh option which removes very
similar conformers.
If let's say numConfs is set to 10 and maxAttempts is set to 20
then it will use UP TO 20 attempts to generate 10 conformers.
If too many conformers get rejected due to pruneRmsThresh then you
will end up with less than 10 conformers.

Or to put it another way, maxAttempts avoids you trying for ever
to generate conformers that are all the same and getting rejected!

Tim

On 17/12/2019 16:24, topgunhaides . wrote:

Hi guys,

Can anyone tell me more about the "maxAttempts" option in
"EmbedMultipleConfs"?

In the documentation, it says " maxAttempts: the maximum number
of attempts to try embedding".
Dose it mean the "maximum number of attempts" to generate each
conformer or to generate the total number of conformers
specified by "numConfs"? Or something else?
I need to generate a huge amount of conformers for each molecule,
so I want to know what is the proper "maxAttempts" to reach a
balance between accuracy and cost.
Thank you!

Best,
Leon




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net  
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Clearing isotope info

[Tim Dudgeon]

I'm wanting to write isomeric smiles that does not include isotope 
information.
The standard Chem.MolToSmiles(m, isomericSmiles=True) includes isotope 
information which is what I'm wanting to exclude.


I note that there is a Atom.SetIsotope(int) method and after a bit of 
hacking around I found that doing a Atom.SetIsotope(0) seems to do the 
trick, but does look a bit strange. Is this really a surrogate for the 
non-existent Atom.ClearIsotope() method?


Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Clearing isotope info

[Tim Dudgeon]

Well, the there is already the isomericSmiles option in 
Chem.MolToSmiles() that handles stereo.

But it's true that there isn't one for isotopes.

An alternative might be to use the standardizer (rdMolStandardize 
package) as my process is already using part of this and does seem to 
have some stuff there for isotopes, but I couldn't figure out how to use 
this.


On 12/12/2019 16:39, Rafal Roszak wrote:

On Wed, 11 Dec 2019 10:53:47 +
Tim Dudgeon  wrote:


I'm wanting to write isomeric smiles that does not include isotope
information.

I also had sytuation when I need to generate smiles with either
isotopes or stereochemistry but not both. Maybe it is worth to add two
options to ChemMolToSmiles function:

dontIncludeStereochemistry=True/False
dontIncludeIsotopes=True/False

Right now it is not straightforward to generate smiles w/o isotopes
(but with stereochemistry) - one need to remove isotope, export to
smiles and restore isotopes.

Best,

Rafał


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RD Kit PostgreSQL in a container

[Tim Dudgeon]

you might want to look at these that we're been using for several years:
https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian/tags

This the GitHub repo for this and several other flavours of RDKit 
container images:

https://github.com/InformaticsMatters/docker-rdkit

Tim

On 04/12/2019 18:36, Webster Homer wrote:


I’m looking at running  RD Kit Postgresql cartridge in a docker 
container. Has anyone done this? There are PostgreSQL containers 
available on line at https://hub.docker.com/_/postgres if there is an 
existing dockerfile with the RDKit extension, that would be great.


If not has anyone built one? Ideally I’d start from one of the 
existing dockerfiles.


RDKit Postgresql in the current distribution is version 11.2, the 
dockerfiles on the hub include an 11 and an 11.6 version. Any idea as 
to which one to use?


I’m new to dockerfiles, I’d appreciate any suggestions

Regards,

Webster Homer

This message and any attachment are confidential and may be privileged 
or otherwise protected from disclosure. If you are not the intended 
recipient, you must not copy this message or attachment or disclose 
the contents to any other person. If you have received this 
transmission in error, please notify the sender immediately and delete 
the message and any attachment from your system. Merck KGaA, 
Darmstadt, Germany and any of its subsidiaries do not accept liability 
for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any 
unauthorized changes of the content of this message and any attachment 
thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do 
not guarantee that this message is free of viruses and does not accept 
liability for any damages caused by any virus transmitted therewith. 
Click http://www.merckgroup.com/disclaimer to access the German, 
French, Spanish and Portuguese versions of this disclaimer.



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDkit in Python vs. on PostgreSQL?

[Tim Dudgeon]

I think you need to explain what benchmarks you are running and what is 
really meant by "faster".
And what hardware (for Spark how many nodes, how big; for PostgreSQL 
what size server, what settings esp. the shared_buffers setting).


A very obvious critique of what you reported is that what you describe 
as "running in Python" includes generating the fingerprints for each 
molecule on the fly, whereas for "the cartridge" these are already 
calculated, so will obviously be much faster (as the fingerprint 
generation dominates the compute).


Tim

On 25/02/2020 11:14, Deepti Gupta via Rdkit-discuss wrote:

Hi Gurus,

I'm absolutely new to Chem-informatics domain. I've been assigned a 
PoC where I've to compare RDKit in Python and RDKit on PostgreSQL. 
I've installed both and am trying some hands-on exercises to 
understand the differences. What I've understood that the structure 
searches are slower in Python (Spark Cluster) than in PostgreSQL 
database. Please correct me if I'm wrong as I'm a newbie in this and 
maybe talking silly.


The similarity search using the below functions (example) -
Python methods -

fps = 
FingerprintMols.FingerprintMol(Chem.MolFromSmiles(smile_structure, 
sanitize=False))

similarity = DataStructs.TanimotoSimilarity(fps1,fps2)

takes too long (45 minutes) for a 2 million file while the same thing 
is very quick (in seconds) on PostgreSQL

Database functions -

select count(*) from (select 
modality_id,m,tanimoto_sml(morganbv_fp(mol_from_smiles('CCOC(=O)c1cc2cc(ccc2[nH]1)C(=O)O'::cstring)),mfp2) 
as similarity from fingerprints join mols using (modality_id)) as fps 
where similarity between 0.45 and 0.50;


Does this conclude that for production workloads one must always use 
database cartridge only? Like RDKit, BINGO, etc.?


Regards,
DA


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDkit in Python vs. on PostgreSQL?

[Tim Dudgeon]

Well, as I mentioned previously the big difference is because from 
Python you are iterating through the molecules, calculating the 
fingerprints and then doing a comparison on the fingerprints. Whereas in 
the PostgreSQL cartridge the fingerprints are already generated and 
indexed so the search is mostly about querying the index which will be 
very fast.


If you are repeatedly running queries against the same set of molecules 
then the cartridge will e the way to go. Doing ti procedurally from 
Python only really makes sense if you have a relatively small dataset 
and/or if the molecules you are searching are different every time.


In principle you should be able to cache the fingerprints in Python to 
avoid needing to recalculate them, but effectively you're implementing 
logic that is already present in the cartridge, and will be much more 
effective.


Tim

On 26/02/2020 08:46, Deepti Gupta wrote:

Hi Tim,

Thank you!

I'll be more detailed in my post, sorry about that. As this was a PoC, 
I had a spark cluster with 2 worker nodes with 4 vCPUs with disk size 
500GB and memory 15GB on Google Cloud. I timed the response against 2 
million data points consisting of Chembl id, Smile structures.


Substructure search - 2 mins
Similarity search - 43 mins

PostgreSQL DB was installed on VM having 4 vCPUs and disk size of 500 
GB and 15GB memory. The value of shared_buffers = 2048MB  was edited 
in the  postgresql.conf file.


Substructure search - within 5 secs
Similarity search - within 3 secs

I tried to store the converted molecules and fingerprints in a file to 
get better performance while trying the pyspark program but was not 
able to do so.


Regards,
DA

On Wednesday, February 26, 2020, 12:57:43 AM GMT+5:30, Tim Dudgeon 
 wrote:



I think you need to explain what benchmarks you are running and what 
is really meant by "faster".
And what hardware (for Spark how many nodes, how big; for PostgreSQL 
what size server, what settings esp. the shared_buffers setting).


A very obvious critique of what you reported is that what you describe 
as "running in Python" includes generating the fingerprints for each 
molecule on the fly, whereas for "the cartridge" these are already 
calculated, so will obviously be much faster (as the fingerprint 
generation dominates the compute).


Tim

On 25/02/2020 11:14, Deepti Gupta via Rdkit-discuss wrote:
Hi Gurus,

I'm absolutely new to Chem-informatics domain. I've been assigned a 
PoC where I've to compare RDKit in Python and RDKit on PostgreSQL. 
I've installed both and am trying some hands-on exercises to 
understand the differences. What I've understood that the structure 
searches are slower in Python (Spark Cluster) than in PostgreSQL 
database. Please correct me if I'm wrong as I'm a newbie in this and 
maybe talking silly.


The similarity search using the below functions (example) -
Python methods -

fps = 
FingerprintMols.FingerprintMol(Chem.MolFromSmiles(smile_structure, 
sanitize=False))

similarity = DataStructs.TanimotoSimilarity(fps1,fps2)

takes too long (45 minutes) for a 2 million file while the same thing 
is very quick (in seconds) on PostgreSQL

Database functions -

select count(*) from (select 
modality_id,m,tanimoto_sml(morganbv_fp(mol_from_smiles('CCOC(=O)c1cc2cc(ccc2[nH]1)C(=O)O'::cstring)),mfp2) 
as similarity from fingerprints join mols using (modality_id)) as fps 
where similarity between 0.45 and 0.50;


Does this conclude that for production workloads one must always use 
database cartridge only? Like RDKit, BINGO, etc.?


Regards,
DA


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net  
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net 
<mailto:Rdkit-discuss@lists.sourceforge.net>

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] How does rdkit cartridge work?

[Tim Dudgeon]

Greg is too modest to mention it, but he recently blogged on performance 
aspects of the cartridge which covers many aspects of how it works:

http://rdkit.blogspot.com/2020/01/some-thoughts-on-performance-of-rdkit.html

On 25/01/2020 05:11, Greg Landrum wrote:

Hi Changge,

On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji > wrote:



I find that rdkit cartridge is quite efficient in substructure
searching.


Glad to hear that! :-)

Is there any paper or similar paper that describes things behind
rdkit cartridge?


No, just the documentation.

For example, what kind of substructures were indexed?


The Pattern fingerprint is what's used to build the index for 
substructure searching. That fingerprint is described in the RDKit 
documentation here: 
https://www.rdkit.org/docs/RDKit_Book.html#pattern-fingerprints


Is there a way that the users can add custom defined fingerprints
and substructures?


I'm not sure what you mean by substructures, but you can, from Python, 
use custom fingerprints in the cartridge. That's explained here: 
http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html


Best,
-greg

Many thanks for your help!

Best,
Changge


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Getting Started with the RDKit in Java

[Tim Dudgeon]

Yes, not a typo!

RDKit has excellent docs for Python, but the Java side of things have 
received less love ;-)


Would there be interest from the community in helping put together a 
guide that is similar in principle to the "Getting Started with the 
RDKit in Python" page [1]. I'd be happy to contribute to this, but feel 
it needs a broader contribution.


Also, to publish an up to date set of JavaDocs on the site, and maybe 
improve the JavaDocs?


Tim

[1] http://rdkit.org/docs/GettingStartedInPython.html



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Standardizer code from Java

[Tim Dudgeon]

Hi Greg,

Did you get a chance to add any more tests or docs here?
I'm happy to help to improve the docs (see my recent message about RDKit 
from Java), but not sure where to start.


More specifically I'm wanting to run the equivalent to this Python code 
from Java. Any hints would be appreciated.


uncharger = rdMolStandardize.Uncharger()

def remove_isotopes(mol):
    for atom in mol.GetAtoms():
    atom.SetIsotope(0)

def standardize(mol):
    mol = rdMolStandardize.Cleanup(mol)
    mol = uncharger.uncharge(mol)
    remove_isotopes(mol)
    return mol

Thanks
Tim


On 27/12/2019 14:20, Greg Landrum wrote:

Hi Tim,

Unfortunately I don't have decent example code for using the 
standardizer from Java. Normally I reference the tests, but in this 
case they are extremely minimal:
https://github.com/rdkit/rdkit/blob/master/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/MolStandardizeTest.java 



I will try to make some time to improve the situation here with the 
goal of

a) have better tests
b) making it more obvious how to use the code from Java

-greg


On Thu, Dec 26, 2019 at 4:55 PM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:


I'm trying to get my head round using the new standardizer code
from Java.
Looks like this should be accessible from the RDKFuncs class, but
I'm failing at stage 1.

Simple example is:

package org.exmple;

import org.RDKit.RDKFuncs;
import org.RDKit.RWMol;

public class Simple {

 static {
 System.loadLibrary("GraphMolWrap");
 }

 public static void main(String[] args) {
 RWMol mol1 = RWMol.MolFromSmiles("CC");
 try {
 RWMol mol2 = RDKFuncs.cleanup(mol1);
 System.out.println(mol2.MolToSmiles());
 }catch (Exception ex) {
 System.out.println("Exception! " + ex.getMessage());
 ex.printStackTrace();
 }
 }
}

Result is:

Exception! null
org.RDKit.GenericRDKitException
at org.RDKit.RDKFuncsJNI.cleanup__SWIG_1(Native Method)
at org.RDKit.RDKFuncs.cleanup(RDKFuncs.java:5173)
at org.squonk.fragnet.Simple.main(Simple.java:15)

Exception doesn't give much to go on!

This is running against code on RDKit Release_2019_09 branch and using Java 
11.

Has anyone got this working?

Tim

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RD Kit Cartridge Postgresql upgrade

[Tim Dudgeon]

The latest cartridge containers for 
informaticsmatters/rdkit-cartridge-debian are based on PostgreSQL 
version 11.


This can/will change with different RDKit major version builds as the 
base Debian packages change and I have little control over this.
I'd like to do this better but building all combinations of Debian * 
RDKit * PostgreSQL is not practical so what I go for is based on the 
version of Debian that is needed to build the particular version of 
RDKit, and use whatever version of PostgreSQL that comes with that 
version of Debian.


Normally I use the latest stable version of Debian unless something in 
RDKit requires going cutting edge, which is sometimes needed, for 
instance because of the cpp and boost changes that happened a couple of 
years ago.


Here are more gory details if you suffer from insomnia: 
https://github.com/InformaticsMatters/docker-rdkit/blob/master/README.md


Tim


On 16/01/2020 16:34, dmaziuk via Rdkit-discuss wrote:

On 1/16/2020 10:20 AM, Greg Landrum wrote:


It does look like Tim Dudgeon is creating docker images for the RDKit +
cartridge:
https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian

Have you looked at those?


In a postgres-only container, changing from postgres 12 to 11 should 
be as simple as editing the pgdg repository url -- edit the Dockerfile 
and rebuild the container.


Dima


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] passing options to javac when building from source

[Tim Dudgeon]

Hi Paolo,

I'm afraid that's not working for me. Still getting Java11 class files.
My cmake command is:

cmake -Wno-dev\
  -DPYTHON_EXECUTABLE=/usr/bin/python3\
  -DRDK_BUILD_INCHI_SUPPORT=ON\
  -DRDK_BUILD_AVALON_SUPPORT=ON\
  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
  -DRDK_BUILD_SWIG_WRAPPERS=ON\
  -DJAVA_COMPILE="/usr/bin/javac -source 8"\
  ..


When it's built I run:

javap -cp ./Code/JavaWrappers/gmwrapper/org.RDKit.jar -verbose 
org.RDKit.RDKFuncs | grep major


and get:

  major version: 55

55 is the class version for Java11.

In fact if I set JAVA_COMPILE to complete nonsense everything still 
builds OK!


Tim

On 26/12/2019 15:39, Paolo Tosco wrote:

Hi Tim,

Try adding this to your CMake command:

-DJAVA_COMPILE="/usr/bin/javac -source 8"

Cheers,
p.

On 26/12/2019 15:22, Tim Dudgeon wrote:
When building the Java wrappers from source (the 
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options 
to pass on to javac.


Specifically I'm wanting to use the '-source 8' option as most 
distros now come with java11 (and make it difficult to install an 
earlier one) but I want to build a version of org.RDKit.jar that is 
compatible with older Java versions.


Thanks

Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Standardizer code from Java

[Tim Dudgeon]

I'm trying to get my head round using the new standardizer code from Java.
Looks like this should be accessible from the RDKFuncs class, but I'm 
failing at stage 1.


Simple example is:

package org.exmple;

import org.RDKit.RDKFuncs;
import org.RDKit.RWMol;

public class Simple {

static {
System.loadLibrary("GraphMolWrap");
}

public static void main(String[] args) {
RWMol mol1 = RWMol.MolFromSmiles("CC");
try {
RWMol mol2 = RDKFuncs.cleanup(mol1);
System.out.println(mol2.MolToSmiles());
}catch (Exception ex) {
System.out.println("Exception! " + ex.getMessage());
ex.printStackTrace();
}
}
}

Result is:

Exception! null
org.RDKit.GenericRDKitException
at org.RDKit.RDKFuncsJNI.cleanup__SWIG_1(Native Method)
at org.RDKit.RDKFuncs.cleanup(RDKFuncs.java:5173)
at org.squonk.fragnet.Simple.main(Simple.java:15)

Exception doesn't give much to go on!

This is running against code on RDKit Release_2019_09 branch and using Java 11.

Has anyone got this working?

Tim

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] passing options to javac when building from source

[Tim Dudgeon]

When building the Java wrappers from source (the 
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options to 
pass on to javac.


Specifically I'm wanting to use the '-source 8' option as most distros 
now come with java11 (and make it difficult to install an earlier one) 
but I want to build a version of org.RDKit.jar that is compatible with 
older Java versions.


Thanks

Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] passing options to javac when building from source

[Tim Dudgeon]

Still no joy.
I tried adding this to the CMakeLists.txt files in the top level dir and 
in Code/JavaWrappers/ but it seem to have no effect.

I'm no cmake expert so I might not be doing this right.

Tim

On 03/01/2020 21:15, Paolo Tosco wrote:


Hi Tim,

based on

https://cmake.org/cmake/help/latest/module/UseJava.html

set(CMAKE_JAVA_COMPILE_FLAGS"-source 8")
might do the trick.

Cheers,
p.

On 03/01/2020 17:41, Tim Dudgeon wrote:

Hi Paolo,

I'm afraid that's not working for me. Still getting Java11 class files.
My cmake command is:

cmake -Wno-dev\
  -DPYTHON_EXECUTABLE=/usr/bin/python3\
  -DRDK_BUILD_INCHI_SUPPORT=ON\
  -DRDK_BUILD_AVALON_SUPPORT=ON\
  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
  -DRDK_BUILD_SWIG_WRAPPERS=ON\
  -DJAVA_COMPILE="/usr/bin/javac -source 8"\
  ..


When it's built I run:

javap -cp ./Code/JavaWrappers/gmwrapper/org.RDKit.jar -verbose 
org.RDKit.RDKFuncs | grep major


and get:

  major version: 55

55 is the class version for Java11.

In fact if I set JAVA_COMPILE to complete nonsense everything still 
builds OK!


Tim

On 26/12/2019 15:39, Paolo Tosco wrote:

Hi Tim,

Try adding this to your CMake command:

-DJAVA_COMPILE="/usr/bin/javac -source 8"

Cheers,
p.

On 26/12/2019 15:22, Tim Dudgeon wrote:
When building the Java wrappers from source (the 
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options 
to pass on to javac.


Specifically I'm wanting to use the '-source 8' option as most 
distros now come with java11 (and make it difficult to install an 
earlier one) but I want to build a version of org.RDKit.jar that is 
compatible with older Java versions.


Thanks

Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] passing options to javac when building from source

[Tim Dudgeon]

I've only built on Linux so can't comment on what works on Mac.
Here is an example Dockerfile that builds pretty well everything:

https://github.com/InformaticsMatters/docker-rdkit/blob/master/Dockerfile-build-debian#L70-L81

On 06/01/2020 06:17, Francois Berenger wrote:

Hi Tim,

How do you compile rdkit for Java?

Last time I tried on a Mac, it did not work:
https://github.com/rdkit/homebrew-rdkit/issues/38

Thanks a lot,
F.

On 26/12/2019 23:22, Tim Dudgeon wrote:

When building the Java wrappers from source (the
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options to
pass on to javac.

Specifically I'm wanting to use the '-source 8' option as most distros
now come with java11 (and make it difficult to install an earlier one)
but I want to build a version of org.RDKit.jar that is compatible with
older Java versions.

Thanks

Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Complications with ConstrainedEmbed

[Tim Dudgeon]

I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of 
a molecule tethered to a molecule that should always have some MCS. I 
found some code on the internet that mostly works, but I don't fully 
understand.


It generally works as planned, but for a small number of examples it fails.

Can someone guide me to what is wrong. Here is an example (good and bad):

https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Complications with ConstrainedEmbed

[Tim Dudgeon]

I think I tracked it down.

If I use 'bondCompare=rdFMCS.BondCompare.CompareOrderExact' for the 
FindMCS() function then it seem to find the right MCS.


Seems like by default it matches aromatic and aliphatic rings, and by 
doing so in my example it finds a bigger MCS so uses it.


On 17/04/2020 19:02, Paolo Tosco wrote:

Hi Tim,

I’ll take a look later and get back to you.

Cheers,
p.


On 17 Apr 2020, at 18:55, Tim Dudgeon  wrote:

I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of a 
molecule tethered to a molecule that should always have some MCS. I found some 
code on the internet that mostly works, but I don't fully understand.

It generally works as planned, but for a small number of examples it fails.

Can someone guide me to what is wrong. Here is an example (good and bad):

https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Complications with ConstrainedEmbed

[Tim Dudgeon]

I also updated the Jupyter notebook with the solution.

Out of interest, I now need to get the atom indices of the part of the 
molecule that matched.
As Jupyter is nicely highlighting this that must already be present in 
the molecule somehow, but I can't find out how.


I look at molecule and atom properties but can't find anything that 
suggests "highlight me".


How is this encoded?

Tim

On 17/04/2020 19:02, Paolo Tosco wrote:

Hi Tim,

I’ll take a look later and get back to you.

Cheers,
p.


On 17 Apr 2020, at 18:55, Tim Dudgeon  wrote:

I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of a 
molecule tethered to a molecule that should always have some MCS. I found some 
code on the internet that mostly works, but I don't fully understand.

It generally works as planned, but for a small number of examples it fails.

Can someone guide me to what is wrong. Here is an example (good and bad):

https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Complications with ConstrainedEmbed

[Tim Dudgeon]

On 18/04/2020 11:56, Paolo Tosco wrote:


Hi Tim,

mol.GetSubstructMatch(query) will give you indices in mol that match 
query.


Yes, I can re-calculate it, but the fact that it's getting highlighted 
in Jupyter suggests that the mol already has that info so it shouldn't 
need recalculating. But I can't find it.


Also note that |rdFMCS.||MCSResult| has a |queryMol |property that 
encode the MCS query, so you don't need to rebuild the query molecule 
out of the SMARTS pattern.



Good. I'll use that.


p.

On 18/04/2020 10:27, Tim Dudgeon wrote:

I also updated the Jupyter notebook with the solution.

Out of interest, I now need to get the atom indices of the part of 
the molecule that matched.
As Jupyter is nicely highlighting this that must already be present 
in the molecule somehow, but I can't find out how.


I look at molecule and atom properties but can't find anything that 
suggests "highlight me".


How is this encoded?

Tim

On 17/04/2020 19:02, Paolo Tosco wrote:

Hi Tim,

I’ll take a look later and get back to you.

Cheers,
p.


On 17 Apr 2020, at 18:55, Tim Dudgeon  wrote:

I'm wanting to use AllChem.ConstrainedEmbed() to generate a 
conformer of a molecule tethered to a molecule that should always 
have some MCS. I found some code on the internet that mostly works, 
but I don't fully understand.


It generally works as planned, but for a small number of examples 
it fails.


Can someone guide me to what is wrong. Here is an example (good and 
bad):


https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

[Tim Dudgeon]

Thanks Paolo, that fixed it.

On 30/03/2020 15:05, Paolo Tosco wrote:

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if 
(prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) == 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] 
Error 2

make: *** [Makefile:163: all] Error 2




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

[Tim Dudgeon]

Yes, that did the trick. Thanks.

On 30/03/2020 15:05, Paolo Tosco wrote:

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if 
(prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) == 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] 
Error 2

make: *** [Makefile:163: all] Error 2




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

[Tim Dudgeon]

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON  ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if (prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) 
== 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] Error 2

make: *** [Makefile:163: all] Error 2




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] In a pickle with pandas

[Tim Dudgeon]

Strange. It's just started working now.

I can't explain it.


On 30/03/2020 08:30, Markus Heller wrote:


Probably not the reason, but there was an older version of pandas, 
0.24 IIRC, that dinner render the molecules correctly.


Can you perform calculations on the mol objects?


On Mar 29, 2020, at 4:07 AM, Tim Dudgeon  wrote:



I'm finding that if I create a pandas dataframe using 
PandasTools.LoadSDF() and then write the dataframe out using 
df.to_pickle() then I can read that pickle back in as a dataframe, 
but the RDKit molecules don't get handled correctly.


Is there a way to fix this?




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

[Tim Dudgeon]

It's availalbe from the org.RDKit.RDKFuncs class. e.g:

String RDKFuncs.standardizeSmiles(String smiles)​

RWMol cleanup​(RWMol mol)

TIm

On 28/04/2020 15:09, Thomas Eckert wrote:
That helped, thanks! Didn't realize 'make install' was needed after 
building the wrappers - I had built without the wrappers first, trying 
to detect problems iteratively.


So now I'm able to use the wrappers in Java but noticed not all "core 
functionality" is covered by the wrappers. Specifically, I'm looking 
for a way to access

    rdkit.Chem.MolStandardize.rdMolStandardize
from Java. I could not find any matching Java class nor function. Is 
this functionality supported via the Java wrappers ?


Thanks & Regards,
  Thomas

On Wed, Apr 22, 2020 at 11:55 AM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:


Have a look in 'Code/JavaWrappers/gmwrapper/' not
'build/Code/JavaWrappers/gmwrapper/' ?

Tim

On 22/04/2020 10:36, Thomas Eckert wrote:

Hi folks,

Trying to build RDKit + JavaWrappers from scratch but, in the
end, the JAR files are missing.

Working on a freshly installed Ubuntu 19.10 and followed the
steps described at [1]. All dependencies installed via Ubuntu's
apt, no manually installed libs.

Cloned the RDKit sources to
    /home/thomas/git/rdkit
and set env variables
    RDBASE=/home/thomas/git/rdkit
LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/

Using this 'cmake' command
  cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF
-DRDK_BUILD_SWIG_WRAPPERS=ON ..
I get OK looking output except for
    CMake Warning (dev) at
/usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message):
      Policy CMP0078 is not set.  Run "cmake --help-policy
CMP0078" for policy
      details.  Use the cmake_policy command to set the policy
and suppress this
      warning.
    Call Stack (most recent call first):
Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
    This warning is for project developers.  Use -Wno-dev to
suppress it.
but as the warning states, this seems to be fine for
non-rdkit-dev users, so I just carry on.

'make' then runs happily with a few warnings on the first build
but no errors are reported. It even states
    (...)
    [ 99%] Built target GraphMolWrap_swig_compilation
    [ 99%] Built target GraphMolWrap
    [100%] building jar
    [100%] Built target GraphMolWrapJar
    [100%] building test classes
    [100%] Built target BuildJavaWrapperTests
which seems to mean the JavaWrappers were built. However this is
then the case
    ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
    total 16M
    drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
    drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
    drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
    -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
    -rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
so no JAR files to be found even though the shared library
mentioned in "Building the Java wrappers" at [1] is there.

Thus I ran the tests
   /git/rdkit/build$ ctest
Test project /home/thomas/git/rdkit/build
(...)
73% tests passed, 39 tests failed out of 143

Total Test time (real) =  98.60 sec

The following tests FAILED:
        105 - JavaAromaticTests (Failed)
        106 - JavaAtomPairsTests (Failed)
        107 - JavaBasicMoleculeTests (Failed)
        108 - JavaBasicMolecule2Tests (Failed)
        109 - JavaChemAtomTests (Failed)
        110 - JavaChemBondTests (Failed)
        111 - JavaChemReactionTests (Failed)
        112 - JavaChemSmartsTests (Failed)
        113 - JavaChemTests (Failed)
        114 - JavaChemv2Tests (Failed)
        115 - JavaConformerTests (Failed)
        116 - JavaDescriptorTests (Failed)
        117 - JavaDistanceGeometryTests (Failed)
        118 - JavaErrorHandlingTests (Failed)
        119 - JavaFingerprintsTests (Failed)
        120 - JavaForceFieldsTests (Failed)
        121 - JavaHManipulationsTests (Failed)
        122 - JavaLipinskiTests (Failed)
        123 - JavaPicklingTests (Failed)
        124 - JavaSmilesCreationTests (Failed)
        125 - JavaSmilesDetailsTests (Failed)
        126 - JavaSmilesTests (Failed)
        127 - JavaSuppliersTests (Failed)
        128 - JavaTrajectoryTests (Failed)
        129 - JavaWrapperTests (Failed)
        130 - JavaChemTransformsTests (Failed)
        131 - JavaFMCSTests (Failed)
        132 - JavaPDBTests (Failed)
        133 - JavaSequenceTests (Failed)
        134 - JavaAlignTests (Failed)

Re: [Rdkit-discuss] Complications with ConstrainedEmbed

[Tim Dudgeon]

I have a follow up question on ConstrainedEmbed.

You pass the molecule to embed and the substructure core into this 
function and get back the embedded and aligned molecule.


In rare cases there will be multiple substructure matches (e.g. in the 
case of symmetry). How would one go about generating alignment for all 
of these matches rather than (presumably) just the first?


Tim

On 18/04/2020 11:56, Paolo Tosco wrote:


Hi Tim,

mol.GetSubstructMatch(query) will give you indices in mol that match 
query.


Also note that |rdFMCS.||MCSResult| has a |queryMol |property that 
encode the MCS query, so you don't need to rebuild the query molecule 
out of the SMARTS pattern.


p.

On 18/04/2020 10:27, Tim Dudgeon wrote:

I also updated the Jupyter notebook with the solution.

Out of interest, I now need to get the atom indices of the part of 
the molecule that matched.
As Jupyter is nicely highlighting this that must already be present 
in the molecule somehow, but I can't find out how.


I look at molecule and atom properties but can't find anything that 
suggests "highlight me".


How is this encoded?

Tim

On 17/04/2020 19:02, Paolo Tosco wrote:

Hi Tim,

I’ll take a look later and get back to you.

Cheers,
p.


On 17 Apr 2020, at 18:55, Tim Dudgeon  wrote:

I'm wanting to use AllChem.ConstrainedEmbed() to generate a 
conformer of a molecule tethered to a molecule that should always 
have some MCS. I found some code on the internet that mostly works, 
but I don't fully understand.


It generally works as planned, but for a small number of examples 
it fails.


Can someone guide me to what is wrong. Here is an example (good and 
bad):


https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb




___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

[Tim Dudgeon]

Have a look in 'Code/JavaWrappers/gmwrapper/' not 
'build/Code/JavaWrappers/gmwrapper/' ?


Tim

On 22/04/2020 10:36, Thomas Eckert wrote:

Hi folks,

Trying to build RDKit + JavaWrappers from scratch but, in the end, the 
JAR files are missing.


Working on a freshly installed Ubuntu 19.10 and followed the steps 
described at [1]. All dependencies installed via Ubuntu's apt, no 
manually installed libs.


Cloned the RDKit sources to
    /home/thomas/git/rdkit
and set env variables
    RDBASE=/home/thomas/git/rdkit
LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/

Using this 'cmake' command
  cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON ..
I get OK looking output except for
    CMake Warning (dev) at 
/usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message):
      Policy CMP0078 is not set.  Run "cmake --help-policy CMP0078" 
for policy
      details.  Use the cmake_policy command to set the policy and 
suppress this

      warning.
    Call Stack (most recent call first):
      Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
    This warning is for project developers.  Use -Wno-dev to suppress it.
but as the warning states, this seems to be fine for non-rdkit-dev 
users, so I just carry on.


'make' then runs happily with a few warnings on the first build but no 
errors are reported. It even states

    (...)
    [ 99%] Built target GraphMolWrap_swig_compilation
    [ 99%] Built target GraphMolWrap
    [100%] building jar
    [100%] Built target GraphMolWrapJar
    [100%] building test classes
    [100%] Built target BuildJavaWrapperTests
which seems to mean the JavaWrappers were built. However this is then 
the case

    ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
    total 16M
    drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
    drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
    drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
    -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
    -rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
so no JAR files to be found even though the shared library mentioned 
in "Building the Java wrappers" at [1] is there.


Thus I ran the tests
   /git/rdkit/build$ ctest
Test project /home/thomas/git/rdkit/build
(...)
73% tests passed, 39 tests failed out of 143

Total Test time (real) =  98.60 sec

The following tests FAILED:
        105 - JavaAromaticTests (Failed)
        106 - JavaAtomPairsTests (Failed)
        107 - JavaBasicMoleculeTests (Failed)
        108 - JavaBasicMolecule2Tests (Failed)
        109 - JavaChemAtomTests (Failed)
        110 - JavaChemBondTests (Failed)
        111 - JavaChemReactionTests (Failed)
        112 - JavaChemSmartsTests (Failed)
        113 - JavaChemTests (Failed)
        114 - JavaChemv2Tests (Failed)
        115 - JavaConformerTests (Failed)
        116 - JavaDescriptorTests (Failed)
        117 - JavaDistanceGeometryTests (Failed)
        118 - JavaErrorHandlingTests (Failed)
        119 - JavaFingerprintsTests (Failed)
        120 - JavaForceFieldsTests (Failed)
        121 - JavaHManipulationsTests (Failed)
        122 - JavaLipinskiTests (Failed)
        123 - JavaPicklingTests (Failed)
        124 - JavaSmilesCreationTests (Failed)
        125 - JavaSmilesDetailsTests (Failed)
        126 - JavaSmilesTests (Failed)
        127 - JavaSuppliersTests (Failed)
        128 - JavaTrajectoryTests (Failed)
        129 - JavaWrapperTests (Failed)
        130 - JavaChemTransformsTests (Failed)
        131 - JavaFMCSTests (Failed)
        132 - JavaPDBTests (Failed)
        133 - JavaSequenceTests (Failed)
        134 - JavaAlignTests (Failed)
        135 - JavaMolQueryTests (Failed)
        136 - JavaFilterCatalogTests (Failed)
        137 - JavaSubstructLibraryTests (Failed)
        138 - JavaRGroupDecompositionTests (Failed)
        139 - JavaScaffoldNetworkTests (Failed)
        140 - JavaMolHashTest (Failed)
        141 - JavaDiversityPickerTests (Failed)
        142 - JavaBitOpsTests (Failed)
        143 - MolStandardizeTest (Failed)
Errors while running CTest

At this point I cannot find anything in the documentation to proceed 
further. I'm not familiar with most of the stack used with/for RDKit 
either, so I don't know where to look. Any hints on where to look or 
what to check ?


Regards,
  Thomas

[1] https://www.rdkit.org/docs/Install.html#building-from-source


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] RDKit Application for Google Season of the Docs

[Tim Dudgeon]

Would it be possible to add improving the docs for Java to the list?

e.g. https://sourceforge.net/p/rdkit/mailman/message/36929992/


Tim


On 23/04/2020 16:17, Scalfani, Vincent wrote:


Dear RDKit Community,


Greg and I are putting together an application for the Google Season 
of the Docs program:



https://developers.google.com/season-of-docs


The program connects open source organizations with technical writers. 
A technical writer would work with several RDKit community mentors to 
advance the documentation over a 3 month period (starting in August).



We have a few project ideas already including expansion of the RDKit 
Book to include additional undocumented methods, creating a beginner 
friendly guide to making the most of the Python API Docs, and creating 
an official RDKit with Pandas Book. Detailed project descriptions will 
be available on the RDKit blog soon, and I'm also happy to share 
directly with you.



We are seeking mentors to help us advance the RDKit documentation and 
participate in Google Season of the Docs. Here are the mentor 
responsibilities:



https://developers.google.com/season-of-docs/docs/admin-mentor-responsibilities


We'll need to submit our application by May 4, so please do get in 
touch if you are interested.



Thanks,


Vin Scalfani







___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Atom contributions for rdShapeHelpers.ShapeProtrudeDist

[Tim Dudgeon]

I'm using the rdShapeHelpers.ShapeProtrudeDist() method to generate a 
protrude distance score like this:


protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, 
query_mol,allowReordering=False)

Is it possible to determine the contributions that each atom of a 
molecule makes to the score?


Thanks
Tim

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Usage of CombineFeatMaps

[Tim Dudgeon]

Hi Greg, yes that mostly makes sense and is a great help.

What's not clear is the usage of mergeMethod as this does not seem to be 
specifiable in CombineFeatMaps(), but you say that that method uses it 
when calling MergeFeatPoints(). Why isn't it in the signature of the former?


Tim

On 06/05/2020 16:55, Greg Landrum wrote:

We're deep in the underdocumented space now. Sorry about that.

Here's an attempt to provide some at least sense of what these things 
mean. This is going from (old) memory and a quick skim of the code... 
hopefully I don't make any egregious errors.


mergeMetric is the metric used to determine whether or not two feature 
points will be combined into a single point. These use the the mergeTol

- NoMerge means don't merge points at all
- Distance means combine points that are less than mergeTol apart
- Overlap means combine points that have an overlap more than 
mergeTol (the feature map itself computes this with GetFeatFeatScore())


dirMergeMode is not used (thankfully)

mergeMethod is a parameter to MergeFeatPoints, which CombineFeatMaps 
calls.
The default value is to use the weighted average of the features to 
determine the location and weight of the replacement feature.
The other two possibilities are Average (does a non-weighted average) 
and UseLarger which just keeps the location and weight of the feature 
point with the larger weight.


does that help?

-greg




On Wed, May 6, 2020 at 5:27 PM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:


I'm trying to use the FeatureMaps functionality in RDKit
(described here
http://rdkit.blogspot.com/2017/11/using-feature-maps.html) and have a
question on the parameters for CombineFeatMaps.

See here:

http://rdkit.org/docs/source/rdkit.Chem.FeatMaps.FeatMapUtils.html?highlight=combinefeatmaps#rdkit.Chem.FeatMaps.FeatMapUtils.CombineFeatMaps

In particular what is the meaning of the 'mergeMetric' param
(Distance
vs. Overlap) and the 'dirMergeMode' param (NoMerge vs. Sum). And
there
is a class for MergeMethod that seems relevant but that is not
part of
the parameters for CombineFeatMaps.

Thanks
Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Usage of CombineFeatMaps

[Tim Dudgeon]

I'm trying to use the FeatureMaps functionality in RDKit (described here 
http://rdkit.blogspot.com/2017/11/using-feature-maps.html) and have a 
question on the parameters for CombineFeatMaps.


See here: 
http://rdkit.org/docs/source/rdkit.Chem.FeatMaps.FeatMapUtils.html?highlight=combinefeatmaps#rdkit.Chem.FeatMaps.FeatMapUtils.CombineFeatMaps


In particular what is the meaning of the 'mergeMetric' param (Distance 
vs. Overlap) and the 'dirMergeMode' param (NoMerge vs. Sum). And there 
is a class for MergeMethod that seems relevant but that is not part of 
the parameters for CombineFeatMaps.


Thanks
Tim



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] h-bond geometry

[Tim Dudgeon]

Hi All,
thanks for the suggestions.

Greg, that's part of what's needed but there's also some more complex logic
needed. For instance, if the atom the H is attached to is rotatable e.g. an
OH group) then it is more complex than if it is fixed (e.g a N in a ring).
I was wondering whether anyone had already encoded these types of rules.

BTW I also found https://oddt.readthedocs.io/en/latest/ which seems to
handle a whole range of interaction types nicely, and can use RDKit as its
underlying toolkit (as well as OBabel).

Tim

On Tue, Sep 8, 2020 at 1:24 PM Greg Landrum  wrote:

> Hi Tim,
>
> Assuming that you already have the indices of the atoms that you're
> interested in looking at, it's pretty easy to calculate the angle between
> three arbitrary atoms. Here's an example:
>
> In [3]: m = Chem.AddHs(Chem.MolFromSmiles('COCO'))
>
> In [4]: AllChem.EmbedMolecule(m)
> Out[4]: 0
>
> In [5]: conf = m.GetConformer()
>
> In [6]: ps = [conf.GetAtomPosition(x) for x in range(conf.GetNumAtoms())]
>
> The atom0 - atom1 - atom2 angle:
> In [7]: (ps[1]-ps[0]).AngleTo(ps[1]-ps[2])
> Out[7]: 1.8295300825582068
>
>
> Those happened to be bonded, but that's not necessary, here's the atom1 -
> atom6 - atom3 angle:
> In [15]: (ps[6]-ps[1]).AngleTo(ps[6]-ps[3])
> Out[15]: 0.4862648980647286
>
> Is that what you're looking for?
>
> -greg
>
>
>
> On Mon, Sep 7, 2020 at 3:06 PM Tim Dudgeon  wrote:
>
>> Hi RDKitters,
>> I was wondering whether anyone has any RDKit code that checks on the
>> geometry of a H-bond.
>> e.g. once a donor and acceptor are located within a reasonable
>> distance of each other to check on the angles involved to establish if that
>> is a reasonable H-bond.
>> Tim
>>
>>
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] h-bond geometry

[Tim Dudgeon]

Hi RDKitters,
I was wondering whether anyone has any RDKit code that checks on the
geometry of a H-bond.
e.g. once a donor and acceptor are located within a reasonable distance of
each other to check on the angles involved to establish if that is a
reasonable H-bond.
Tim
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] EmbedMolecule and chirality

[Tim Dudgeon]

I've encountered a strange problem when doing constrained embedding that
seems to be related to chirality.
The example is here:
https://gist.github.com/tdudgeon/c4604f3ee9124eeec60668b5eefe465e

The molecule being embedded has a single chiral carbon, and while that atom
is tethered, only one of it's attached atoms is also tethered, so if I
understand correctly, there should be no reason why the chiral atom cannot
be embedded correctly.

But when I use the enforceChirality=True option the embedding usually
fails, and takes several seconds to do so. Very occasionally it succeeds
and the chirality is preserved as expected.

If however I use the enforceChirality=False option the embedding
succeeds and is very quick. In all cases I've run so far the
stereochemistry is preserved.

Can someone explain this behaviour?

Tim
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"

[Tim Dudgeon]

Thanks Paulo. Deleting CMakeCache.txt seems to have fixed the problem.
I then hit a problem being unable to build against boost 1.71 but when I
switched back to 1.67 it was OK.
Seems to be building fine now.
Tim

On Thu, May 28, 2020 at 5:09 PM Paolo Tosco 
wrote:

> Hi Tim,
>
> could you please run a pwd in your build directory? Also, could you try
> deleting CMakeCache.txt and re-running cmake?
>
> With "subdirectory" I was asking whether your build directory was a
> subdirectory of the RDKit root dir or a subdirectory of gmwrapper,
> because I get that error if I try to run your command from
> rdkit/Code/JavaWrappers/gmwrapper/build rather than from rdkit/build, as
> in that case the main CMakeLists.txt file is not sourced.
>
> Cheers,
> p.
> On 28/05/2020 17:01, Tim Dudgeon wrote:
>
> well, I am running it from a subdirectory - the build subdirectory which
> is where it has always been run from.
> e.g.
>
> mkdir build
> cd build
> cmake -DPYTHON_EXECUTABLE=/usr/bin/python3  -DRDK_BUILD_INCHI_SUPPORT=ON
>  -DRDK_BUILD_AVALON_SUPPORT=ON  -DRDK_BUILD_PYTHON_WRAPPERS=ON
>  -DRDK_BUILD_SWIG_WRAPPERS=ON ..
>
>
>
> Tim
>
> On Thu, May 28, 2020 at 4:46 PM Paolo Tosco 
> wrote:
>
>> Hi Tim,
>>
>> downloadAndCheckMD5 is a function defined in
>> Code/cmake/Modules/RDKitUtils.cmake, which is included by the main
>> CMakeLists.txt file and then is available to all children CMakeLists.txt
>> files.
>>
>> From the line number where the error occurs
>>
>> $ grep -n downloadAndCheckMD5 `find . -name CMakeLists.txt`
>> ./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
>> downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
>> ${JUNIT_MD5SUM})
>> it looks like you might be running cmake in a subdirectory rather than
>> in the RDKit root directory.
>>
>> HTH, cheers
>> p.
>>
>> On 28/05/2020 16:28, Tim Dudgeon wrote:
>>
>> I'm not able to build form source (master branch) from a new machine I've
>> recently set up (Ubuntu 20.04).
>>
>> $ cmake  -DPYTHON_EXECUTABLE=/usr/bin/python3
>>  -DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON
>>  -DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON  ..
>> CMake Error at CMakeLists.txt:21 (downloadAndCheckMD5):
>>   Unknown CMake command "downloadAndCheckMD5".
>>
>>
>> -- Configuring incomplete, errors occurred!
>> See also
>> "/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
>>
>> $ cmake --version
>> cmake version 3.16.3
>>
>> Has anything changed with cmake recently?
>>
>> Tim
>>
>>
>> ___
>> Rdkit-discuss mailing 
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"

[Tim Dudgeon]

well, I am running it from a subdirectory - the build subdirectory which is
where it has always been run from.
e.g.

mkdir build
cd build
cmake -DPYTHON_EXECUTABLE=/usr/bin/python3  -DRDK_BUILD_INCHI_SUPPORT=ON
 -DRDK_BUILD_AVALON_SUPPORT=ON  -DRDK_BUILD_PYTHON_WRAPPERS=ON
 -DRDK_BUILD_SWIG_WRAPPERS=ON ..



Tim

On Thu, May 28, 2020 at 4:46 PM Paolo Tosco 
wrote:

> Hi Tim,
>
> downloadAndCheckMD5 is a function defined in
> Code/cmake/Modules/RDKitUtils.cmake, which is included by the main
> CMakeLists.txt file and then is available to all children CMakeLists.txt
> files.
>
> From the line number where the error occurs
>
> $ grep -n downloadAndCheckMD5 `find . -name CMakeLists.txt`
> ./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
> downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
> ${JUNIT_MD5SUM})
> it looks like you might be running cmake in a subdirectory rather than in
> the RDKit root directory.
>
> HTH, cheers
> p.
>
> On 28/05/2020 16:28, Tim Dudgeon wrote:
>
> I'm not able to build form source (master branch) from a new machine I've
> recently set up (Ubuntu 20.04).
>
> $ cmake  -DPYTHON_EXECUTABLE=/usr/bin/python3
>  -DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON
>  -DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON  ..
> CMake Error at CMakeLists.txt:21 (downloadAndCheckMD5):
>   Unknown CMake command "downloadAndCheckMD5".
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
>
> $ cmake --version
> cmake version 3.16.3
>
> Has anything changed with cmake recently?
>
> Tim
>
>
> ___
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"

[Tim Dudgeon]

I'm not able to build form source (master branch) from a new machine I've
recently set up (Ubuntu 20.04).

$ cmake  -DPYTHON_EXECUTABLE=/usr/bin/python3  -DRDK_BUILD_INCHI_SUPPORT=ON
 -DRDK_BUILD_AVALON_SUPPORT=ON  -DRDK_BUILD_PYTHON_WRAPPERS=ON
 -DRDK_BUILD_SWIG_WRAPPERS=ON  ..
CMake Error at CMakeLists.txt:21 (downloadAndCheckMD5):
  Unknown CMake command "downloadAndCheckMD5".


-- Configuring incomplete, errors occurred!
See also
"/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".

$ cmake --version
cmake version 3.16.3

Has anything changed with cmake recently?

Tim
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] IsBondRotatable() ?

[Tim Dudgeon]

Is there an easy way to ask whether a particular bond is rotatable?
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss