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

2014-07-06 Thread 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

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

2014-07-06 Thread Tim Dudgeon
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

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

2014-07-07 Thread Tim Dudgeon
/formula.rb:556:in `block in system' BuildError: Failed executing: make 1. raise 2. ignore 3. backtrace 4. irb 5. shell Choose an action: Tim On 07/07/2014 08:23, Greg Landrum wrote: Hi Tim, On Sun, Jul 6, 2014 at 9:38 PM, Tim Dudgeon tdudgeon...@gmail.com mailto:tdudgeon...@gmail.com wrote

[Rdkit-discuss] java wrappers

2014-12-14 Thread 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 --

Re: [Rdkit-discuss] java wrappers

2014-12-18 Thread Tim Dudgeon
from the RDKit knime node package. I think it wouldn't be too much trouble to do java builds as part of the standard release. Let me investigate that. -greg On Sun, Dec 14, 2014 at 1:20 PM, Tim Dudgeon tdudgeon...@gmail.com mailto:tdudgeon...@gmail.com wrote: Is the only way to get

[Rdkit-discuss] install rdkit cartridge

2015-04-24 Thread 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

Re: [Rdkit-discuss] install rdkit cartridge

2015-04-24 Thread Tim Dudgeon
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

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

2015-05-12 Thread 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

[Rdkit-discuss] RDkit cartridge on Amazon RDS

2015-05-11 Thread 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:

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

2015-06-23 Thread Tim Dudgeon
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

[Rdkit-discuss] javadocs

2015-06-24 Thread 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

[Rdkit-discuss] failing to build java wrappers

2015-06-22 Thread 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

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

2015-05-25 Thread Tim Dudgeon
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

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

2015-05-25 Thread 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

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

2015-09-27 Thread Tim Dudgeon
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

[Rdkit-discuss] molecule standardization in cartridge search

2015-09-24 Thread 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

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

2015-09-25 Thread Tim Dudgeon
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 ChemAx

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

2016-06-22 Thread Tim Dudgeon
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)

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

2016-06-22 Thread 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

[Rdkit-discuss] Getting to grips with Open3DAlign

2016-06-21 Thread 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,

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

2016-03-07 Thread 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

[Rdkit-discuss] SDWriter from Java

2016-03-30 Thread 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

Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Tim Dudgeon
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

[Rdkit-discuss] strict parsing in java

2016-04-25 Thread 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

Re: [Rdkit-discuss] SDF reading in Java: from streams? iterating?

2016-04-26 Thread Tim Dudgeon
On 26/04/2016 10:57, Richard Sherhod wrote: Hi Greg, I’m having a few problems with reading SDFs using the Java bindings: First, is it possible for the SDMolSupplier or ForwardSDMolSupplier to run from an InputStream in Java? I’m working with some big SDFs (~8 million structures) and I

[Rdkit-discuss] cartridge search functions

2016-05-01 Thread 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

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

2016-04-19 Thread Tim Dudgeon
oot, 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/rd

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

2016-04-17 Thread 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

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

2016-04-17 Thread Tim Dudgeon
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

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

2016-04-21 Thread 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

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

2016-04-19 Thread Tim Dudgeon
e. 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/post

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

2016-04-18 Thread Tim Dudgeon
ian 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.

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

2016-06-30 Thread Tim Dudgeon
inimized to the closest minima. In other words, ETKDG relies on distance geometry for the sampling. Nevertheless, I will have a look at this particular pattern in the next version of ETKDG to see if we can improve it. Best, Sereina On 22 Jun 2016, at 10:41, Tim Dudgeon <tdudge

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

2016-09-15 Thread 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

Re: [Rdkit-discuss] junit version problems

2016-08-27 Thread 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 j

Re: [Rdkit-discuss] Hankering after faster builds

2016-12-04 Thread Tim Dudgeon
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 s

[Rdkit-discuss] Hankering after faster builds

2016-12-02 Thread 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

Re: [Rdkit-discuss] Fast similarity search

2017-05-19 Thread Tim Dudgeon
ions (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

[Rdkit-discuss] Fast similarity search

2017-05-18 Thread 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

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
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

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
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/gi

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
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 fo

Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread 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

Re: [Rdkit-discuss] RPM distros

2017-11-24 Thread Tim Dudgeon
e "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 in

Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread Tim Dudgeon
: 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

[Rdkit-discuss] Cartridge upgrades

2017-12-01 Thread 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

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Tim Dudgeon
ia 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 11/28/201

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread 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.

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

2017-11-21 Thread 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

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

2017-11-09 Thread 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-discuss] RPM distros

2017-11-08 Thread 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

Re: [Rdkit-discuss] RPM distros

2017-12-05 Thread Tim Dudgeon
. 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

Re: [Rdkit-discuss] Cartridge upgrades

2017-12-08 Thread Tim Dudgeon
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

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread 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

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Tim Dudgeon
/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

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

2018-06-10 Thread 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

Re: [Rdkit-discuss] Diversity picker

2018-01-04 Thread 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

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

2018-01-15 Thread 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

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

2018-01-15 Thread 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

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

2018-04-06 Thread Tim Dudgeon
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:

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

2018-04-05 Thread Tim Dudgeon
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: cma

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

2018-04-05 Thread 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

[Rdkit-discuss] Docker image for GSOC2018_MolVS_Integration

2018-09-25 Thread 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