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
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
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
--
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
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
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
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:
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
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
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
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
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
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
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
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
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)
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
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,
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
:
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
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
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
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.
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
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
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
.
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
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
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
/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
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
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
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
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
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:
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
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
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
/
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 sh
tom.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
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)
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
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
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
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
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
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
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
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
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
/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 h
/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
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_SWI
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 {
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
/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/b
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
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
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
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.Constr
. 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
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
, 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
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
, 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
t 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
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
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
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
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?
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.
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:
ppened 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 Dud
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
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
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 subdirecto
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).
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
Is there an easy way to ask whether a particular bond is rotatable?
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